From heikki at nildram.co.uk Thu Jan 1 08:43:53 2004 From: heikki at nildram.co.uk (Heikki Lehvaslaiho) Date: Thu Jan 1 08:51:07 2004 Subject: [Bioperl-l] my bioperl-db hacks In-Reply-To: <1072853565.5303.3.camel@rattus.Localdomain> References: <5830A5B0-3AFC-11D8-A5FA-000A959EB4C4@gmx.net> <1072853565.5303.3.camel@rattus.Localdomain> Message-ID: <200401011343.53225.heikki@nildram.co.uk> Hilmar, I'd be happy to create the tar balls and put them up if you tell me when the files are in a good state. An other option is to remove the 0.1 version from the web site and replace it with a 0.2 snapshot and put it into the developer section. Let me know, -Heikki On Wednesday 31 Dec 2003 6:52 am, William Kenworthy wrote: > Would it not be a good idea to release a current, matched pair? Seems > like a lot of this stuff is never in sync, making it hard on new users. > BillK > > On Wed, 2003-12-31 at 03:14, Hilmar Lapp wrote: > > Note that bioperl-db 0.1 has been outdated since about a year now. It > > won't work with the present biosql schema either. In order to use 0.1 > > you will also need to use a pre-Singapore version of biosql. > > > > The current and interoperating versions of bioperl-db and biosql are > > the respective cvs HEADs. > > > > -hilmar > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. 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From chenn at cshl.edu Thu Jan 1 17:53:27 2004 From: chenn at cshl.edu (Jack Chen) Date: Thu Jan 1 18:00:38 2004 Subject: [Bioperl-l] a minor correction Message-ID: Hi, In the Bio::Tools::Run::Genewise SYNOPSIS, the line: my $genes = $factory->run($protein_seq, $genomic_seq); should be written as: my ($genes) = $factory->run($protein_seq, $genomic_seq); Jack ++++++++++++++++++++++++++++++++++++++++++++ o-o Jack Chen, Stein Laboratory o---o Cold Spring Harbor Laboratory o----o #5 Williams, 1 Bungtown Road O----O Cold Spring Harbor, NY, 11724 0--o Tel: 1 516 367 8394 O e-mail: chenn@cshl.org o-o Website: http://www.wormbase.org +++++++++++++++++++++++++++++++++++++++++++++ From wes.barris at csiro.au Thu Jan 1 18:46:34 2004 From: wes.barris at csiro.au (Wes Barris) Date: Thu Jan 1 18:53:58 2004 Subject: [Bioperl-l] Bug in SeqIO genbank output In-Reply-To: <200312171330.32205.heikki@nildram.co.uk> References: <200312171330.32205.heikki@nildram.co.uk> Message-ID: <3FF4B15A.4070204@csiro.au> Heikki Lehvaslaiho wrote: > Wes, > > You didnot say which versionof bioperl you are using. For some reason I am using bioperl-1.2.3 > which I > can not quite understand, the current code: > $self->_print(sprintf("%-6s%s\n",'ORIGIN',$o ? $o->value : '')); > > does print out the requred six spaces after the word ORIGIN. This was > recently Really? How? In the above line "%-6s" left justifies 'ORIGIN' (which is already 6 characters). The '6' needs to be changed to '12' to get six extra spaces. See below. > fixed. Now, why doesn't it work for you? Could you check that you do not > have > multiple copies of bioperl in your computer and the older one gets > accidently > executed? > > Sorry, I can not comeupwith any better explanation, > > -Heikki > > On Tuesday 16 Dec 2003 4:38 am, Wes Barris wrote: > > Hi, > > > > I have just succeeded in tracking down a bug that prevents genbank files > > written from bioperl from being properly imported into StackPack > > (clustering software). The problem is due to a subtle difference in > > a genbank entry downloaded from NCBI and a genbank entry produced using > > genbank.pm. If you use "od -c" to look at a genbank record from NCBI, > > you will notice that the word "ORIGIN" is followed by six space > characters. > > > > ORIGIN > > 1 cggccgcgtc gacttttttt ttaggtattt ttctcttatt atttctaaaa > > tataaatttt 61 ggacattcaa aagtgcaaca ngttaatgtg cctgtgggga atatcacagt > > taaaaaaata > > > > If I process this file using bioperl and then write out a new genbank > > format file, the word "ORIGIN" is followed immediately by a carriage > return > > (newline) character. > > > > It seems silly to me that spaces should be required after the word > > "ORIGIN", but they do exist in files downloaded from NCBI and StackPack > > seems to require these space characters in order to import a genbank > file. > > Is there an official specification for the genbank format? I have > sent a > > bug report to the makers of StackPack too. > > > > In the meantime, I have modified my installed copy of > Bio/SeqIO/genbank.pm > > changing this line: > > > > $self->_print(sprintf("%-6s%s\n",'ORIGIN',$o ? $o->value : > '')); > > > > to this: > > > > $self->_print(sprintf("%-12s%s\n",'ORIGIN ',$o ? > $o->value : > > '')); > > -- > ______ _/ _/_____________________________________________________ > _/ _/ http://www.ebi.ac.uk/mutations/ > _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk > _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute > _/ _/ _/ Wellcome Trust Genome Campus, Hinxton > _/ _/ _/ Cambs. CB10 1SD, United Kingdom > _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 > ___ _/_/_/_/_/________________________________________________________ > -- Wes Barris E-Mail: Wes.Barris@csiro.au From wes.barris at csiro.au Thu Jan 1 18:46:34 2004 From: wes.barris at csiro.au (Wes Barris) Date: Thu Jan 1 18:54:02 2004 Subject: [Bioperl-l] Bug in SeqIO genbank output In-Reply-To: <200312171330.32205.heikki@nildram.co.uk> References: <200312171330.32205.heikki@nildram.co.uk> Message-ID: <3FF4B15A.4070204@csiro.au> Heikki Lehvaslaiho wrote: > Wes, > > You didnot say which versionof bioperl you are using. For some reason I am using bioperl-1.2.3 > which I > can not quite understand, the current code: > $self->_print(sprintf("%-6s%s\n",'ORIGIN',$o ? $o->value : '')); > > does print out the requred six spaces after the word ORIGIN. This was > recently Really? How? In the above line "%-6s" left justifies 'ORIGIN' (which is already 6 characters). The '6' needs to be changed to '12' to get six extra spaces. See below. > fixed. Now, why doesn't it work for you? Could you check that you do not > have > multiple copies of bioperl in your computer and the older one gets > accidently > executed? > > Sorry, I can not comeupwith any better explanation, > > -Heikki > > On Tuesday 16 Dec 2003 4:38 am, Wes Barris wrote: > > Hi, > > > > I have just succeeded in tracking down a bug that prevents genbank files > > written from bioperl from being properly imported into StackPack > > (clustering software). The problem is due to a subtle difference in > > a genbank entry downloaded from NCBI and a genbank entry produced using > > genbank.pm. If you use "od -c" to look at a genbank record from NCBI, > > you will notice that the word "ORIGIN" is followed by six space > characters. > > > > ORIGIN > > 1 cggccgcgtc gacttttttt ttaggtattt ttctcttatt atttctaaaa > > tataaatttt 61 ggacattcaa aagtgcaaca ngttaatgtg cctgtgggga atatcacagt > > taaaaaaata > > > > If I process this file using bioperl and then write out a new genbank > > format file, the word "ORIGIN" is followed immediately by a carriage > return > > (newline) character. > > > > It seems silly to me that spaces should be required after the word > > "ORIGIN", but they do exist in files downloaded from NCBI and StackPack > > seems to require these space characters in order to import a genbank > file. > > Is there an official specification for the genbank format? I have > sent a > > bug report to the makers of StackPack too. > > > > In the meantime, I have modified my installed copy of > Bio/SeqIO/genbank.pm > > changing this line: > > > > $self->_print(sprintf("%-6s%s\n",'ORIGIN',$o ? $o->value : > '')); > > > > to this: > > > > $self->_print(sprintf("%-12s%s\n",'ORIGIN ',$o ? > $o->value : > > '')); > > -- > ______ _/ _/_____________________________________________________ > _/ _/ http://www.ebi.ac.uk/mutations/ > _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk > _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute > _/ _/ _/ Wellcome Trust Genome Campus, Hinxton > _/ _/ _/ Cambs. CB10 1SD, United Kingdom > _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 > ___ _/_/_/_/_/________________________________________________________ > -- Wes Barris E-Mail: Wes.Barris@csiro.au From jason at cgt.duhs.duke.edu Thu Jan 1 20:16:17 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Thu Jan 1 20:23:36 2004 Subject: [Bioperl-l] Bug in SeqIO genbank output In-Reply-To: <3FF4B15A.4070204@csiro.au> References: <200312171330.32205.heikki@nildram.co.uk> <3FF4B15A.4070204@csiro.au> Message-ID: The reason Heikki was not seeing the problems is probably because he was doing roundtripping with a genbank file - if you start with embl or fasta you see that the trailing 6 spaces aren't coming in. This is because of this code (parsing of genbank) ! if(defined($_) && s/^ORIGIN//) { chomp; if( $annotation && length($_) > 0 ) { $annotation->add_Annotation('origin', Bio::Annotation::SimpleValue->new(-value => $_)); } changing this to ! if(defined($_) && s/^ORIGIN\s+//) { So the $o value in the ORIGIN writer was getting set with the 6 spaces when inputting the genbank file. This is a silly thing to store as an annotation. So fixing the ORIGIN problem Index: Bio/SeqIO/genbank.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/SeqIO/genbank.pm,v retrieving revision 1.99 diff -r1.99 genbank.pm 543c543 < if(defined($_) && s/^ORIGIN//) { --- > if(defined($_) && s/^ORIGIN\s+//) { 819c819,820 < $self->_print(sprintf("%-6s%s\n",'ORIGIN',$o ? $o->value : '')); --- > $self->_print(sprintf("%-12s%s\n", > 'ORIGIN', $o ? $o->value : '')); I also exposed an embl parsing bugs when there is no feature table that I fixed on main trunk and also merged onto the branch. Happy New Year. --jason On Fri, 2 Jan 2004, Wes Barris wrote: > Heikki Lehvaslaiho wrote: > > > Wes, > > > > You didnot say which versionof bioperl you are using. For some reason > > I am using bioperl-1.2.3 > > > which I > > can not quite understand, the current code: > > $self->_print(sprintf("%-6s%s\n",'ORIGIN',$o ? $o->value : '')); > > > > does print out the requred six spaces after the word ORIGIN. This was > > recently > > Really? How? In the above line "%-6s" left justifies 'ORIGIN' (which is > already 6 characters). The '6' needs to be changed to '12' to get six > extra spaces. See below. > > > > fixed. Now, why doesn't it work for you? Could you check that you do not > > have > > multiple copies of bioperl in your computer and the older one gets > > accidently > > executed? > > > > Sorry, I can not comeupwith any better explanation, > > > > -Heikki > > > > On Tuesday 16 Dec 2003 4:38 am, Wes Barris wrote: > > > Hi, > > > > > > I have just succeeded in tracking down a bug that prevents genbank files > > > written from bioperl from being properly imported into StackPack > > > (clustering software). The problem is due to a subtle difference in > > > a genbank entry downloaded from NCBI and a genbank entry produced using > > > genbank.pm. If you use "od -c" to look at a genbank record from NCBI, > > > you will notice that the word "ORIGIN" is followed by six space > > characters. > > > > > > ORIGIN > > > 1 cggccgcgtc gacttttttt ttaggtattt ttctcttatt atttctaaaa > > > tataaatttt 61 ggacattcaa aagtgcaaca ngttaatgtg cctgtgggga atatcacagt > > > taaaaaaata > > > > > > If I process this file using bioperl and then write out a new genbank > > > format file, the word "ORIGIN" is followed immediately by a carriage > > return > > > (newline) character. > > > > > > It seems silly to me that spaces should be required after the word > > > "ORIGIN", but they do exist in files downloaded from NCBI and StackPack > > > seems to require these space characters in order to import a genbank > > file. > > > Is there an official specification for the genbank format? I have > > sent a > > > bug report to the makers of StackPack too. > > > > > > In the meantime, I have modified my installed copy of > > Bio/SeqIO/genbank.pm > > > changing this line: > > > > > > $self->_print(sprintf("%-6s%s\n",'ORIGIN',$o ? $o->value : > > '')); > > > > > > to this: > > > > > > $self->_print(sprintf("%-12s%s\n",'ORIGIN ',$o ? > > $o->value : > > > '')); > > > > -- > > ______ _/ _/_____________________________________________________ > > _/ _/ http://www.ebi.ac.uk/mutations/ > > _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk > > _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute > > _/ _/ _/ Wellcome Trust Genome Campus, Hinxton > > _/ _/ _/ Cambs. CB10 1SD, United Kingdom > > _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 > > ___ _/_/_/_/_/________________________________________________________ > > > > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From donald.jackson at bms.com Fri Jan 2 11:23:11 2004 From: donald.jackson at bms.com (Donald Jackson) Date: Fri Jan 2 11:30:21 2004 Subject: [Bioperl-l] Controlling glyph position with Bio::Graphics::Panel Message-ID: <5cb0c5f689.5f6895cb0c@bms.com> Hi Lincoln, I have a question about controlling the vertical position of glyphs using Bio::Graphics::Panel. I'm drawing out hits and hsps from a blast search (as lists of Bio::Search::HSP objects) using the segments glyph. I've run into a problem when I have two non-overlapping hits. I'd like to force these to appear at distinct y-coordinates in the image, but can't figure out how to do this. I tried 'bump', but that only affects _overlapping_ hits. I'd appreciate any suggestions you or others on the list might have. Thanks, Don Jackson BMS Bioinformatics From heikki at nildram.co.uk Fri Jan 2 13:13:00 2004 From: heikki at nildram.co.uk (Heikki Lehvaslaiho) Date: Fri Jan 2 13:23:29 2004 Subject: [Bioperl-l] Bug in SeqIO genbank output In-Reply-To: References: <200312171330.32205.heikki@nildram.co.uk> <3FF4B15A.4070204@csiro.au> Message-ID: <200401021813.00997.heikki@nildram.co.uk> On Friday 02 Jan 2004 1:16 am, Jason Stajich wrote: > The reason Heikki was not seeing the problems is probably because he was > doing roundtripping with a genbank file - if you start with embl or fasta > you see that the trailing 6 spaces aren't coming in. This is because of So that's what it was! I was using a genbank file. Thanks, Jason, -Heikki > this code > (parsing of genbank) > ! if(defined($_) && s/^ORIGIN//) { > chomp; > if( $annotation && length($_) > 0 ) { > $annotation->add_Annotation('origin', > Bio::Annotation::SimpleValue->new(-value => $_)); > } > changing this to > ! if(defined($_) && s/^ORIGIN\s+//) { > > So the $o value in the ORIGIN writer was getting set with the 6 spaces > when inputting the genbank file. This is a silly thing to store as an > annotation. > > So fixing the ORIGIN problem > Index: Bio/SeqIO/genbank.pm > =================================================================== > RCS file: /home/repository/bioperl/bioperl-live/Bio/SeqIO/genbank.pm,v > retrieving revision 1.99 > diff -r1.99 genbank.pm > 543c543 > < if(defined($_) && s/^ORIGIN//) { > --- > > > if(defined($_) && s/^ORIGIN\s+//) { > > 819c819,820 > < $self->_print(sprintf("%-6s%s\n",'ORIGIN',$o ? $o->value : '')); > --- > > > $self->_print(sprintf("%-12s%s\n", > > 'ORIGIN', $o ? $o->value : '')); > > I also exposed an embl parsing bugs when there is no feature table that > I fixed on main trunk and also merged onto the branch. > > > Happy New Year. > --jason > > On Fri, 2 Jan 2004, Wes Barris wrote: > > Heikki Lehvaslaiho wrote: > > > Wes, > > > > > > You didnot say which versionof bioperl you are using. For some reason > > > > I am using bioperl-1.2.3 > > > > > which I > > > can not quite understand, the current code: > > > $self->_print(sprintf("%-6s%s\n",'ORIGIN',$o ? $o->value : > > > '')); > > > > > > does print out the requred six spaces after the word ORIGIN. This was > > > recently > > > > Really? How? In the above line "%-6s" left justifies 'ORIGIN' (which is > > already 6 characters). The '6' needs to be changed to '12' to get six > > extra spaces. See below. > > > > > fixed. Now, why doesn't it work for you? Could you check that you do > > > not have > > > multiple copies of bioperl in your computer and the older one gets > > > accidently > > > executed? > > > > > > Sorry, I can not comeupwith any better explanation, > > > > > > -Heikki > > > > > > On Tuesday 16 Dec 2003 4:38 am, Wes Barris wrote: > > > > Hi, > > > > > > > > I have just succeeded in tracking down a bug that prevents genbank > > > > files written from bioperl from being properly imported into > > > > StackPack (clustering software). The problem is due to a subtle > > > > difference in a genbank entry downloaded from NCBI and a genbank > > > > entry produced using genbank.pm. If you use "od -c" to look at a > > > > genbank record from NCBI, you will notice that the word "ORIGIN" is > > > > followed by six space > > > > > > characters. > > > > > > > ORIGIN > > > > 1 cggccgcgtc gacttttttt ttaggtattt ttctcttatt atttctaaaa > > > > tataaatttt 61 ggacattcaa aagtgcaaca ngttaatgtg cctgtgggga atatcacagt > > > > taaaaaaata > > > > > > > > If I process this file using bioperl and then write out a new > > > > genbank format file, the word "ORIGIN" is followed immediately by a > > > > carriage > > > > > > return > > > > > > > (newline) character. > > > > > > > > It seems silly to me that spaces should be required after the word > > > > "ORIGIN", but they do exist in files downloaded from NCBI and > > > > StackPack seems to require these space characters in order to import > > > > a genbank > > > > > > file. > > > > > > > Is there an official specification for the genbank format? I have > > > > > > sent a > > > > > > > bug report to the makers of StackPack too. > > > > > > > > In the meantime, I have modified my installed copy of > > > > > > Bio/SeqIO/genbank.pm > > > > > > > changing this line: > > > > > > > > $self->_print(sprintf("%-6s%s\n",'ORIGIN',$o ? $o->value : > > > > > > '')); > > > > > > > to this: > > > > > > > > $self->_print(sprintf("%-12s%s\n",'ORIGIN ',$o ? > > > > > > $o->value : > > > > '')); > > > > > > -- > > > ______ _/ _/_____________________________________________________ > > > _/ _/ http://www.ebi.ac.uk/mutations/ > > > _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk > > > _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute > > > _/ _/ _/ Wellcome Trust Genome Campus, Hinxton > > > _/ _/ _/ Cambs. CB10 1SD, United Kingdom > > > _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 > > > ___ _/_/_/_/_/________________________________________________________ > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From junhu54 at hotmail.com Fri Jan 2 18:30:06 2004 From: junhu54 at hotmail.com (jun hu) Date: Fri Jan 2 18:37:18 2004 Subject: [Bioperl-l] bioperl graphic question Message-ID: Sorry for the previous email. I just find the way to solve my problem ... I have to "export LANG=en_US" before I do the bundle::BioPerl installation... after I did that, bundle installable worked, and so does the png images.... now I am going to try it on my linux 7.3 mahcine, hope anything is work well too... Best regards, Jun Hu >From: Jason Stajich >To: Lincoln Stein >CC: Todd Harris , bioperl-l@bioperl.org, jun hu > >Subject: Re: [Bioperl-l] bioperl graphic question >Date: Wed, 31 Dec 2003 16:24:05 -0500 (EST) > >I built gd2 from the fedora SRPMs and had no problem (save other RPMs >dependancy on libgd 1.8 (gnuplot,php,webalizer on RHL 7.3)) > >SRPM is here >http://download.fedora.redhat.com/pub/fedora/linux/core/1/i386/os/SRPMS/gd-2.0.15-1.src.rpm > >I can put the compiled RPMs for 7.3 and 9.0 on the bioperl site if it >would help. > >-jason >On Wed, 31 Dec 2003, Lincoln Stein wrote: > > > Does anyone know where the gd2 RPMs can be found? I know almost > > nothing about RPMs. > > > > Lincoln > > > > On Tuesday 30 December 2003 10:24 am, Jason Stajich wrote: > > > We might want to post pointers to gd2 rpms for the redhat crowd... > > > as RH 9 still ships with libgd 1.8.x > > > > > > > > > -jason > > > > > > On Mon, 29 Dec 2003, Todd Harris wrote: > > > > Hi Jun Hu - > > > > > > > > As noted in the install guide, you will need to upgrade your > > > > libgd. Although using libgd 1.8.4 may not necessarily result in > > > > runtime errors, graphical elements may not appear as intended. > > > > Some glyphs will not render at all with 1.8.4. > > > > > > > > We needed to move to libgd2 in order to support the generation of > > > > both raster (png) and vector (svg) images from the same codebase. > > > > > > > > todd > > > > > > -- > > > Jason Stajich > > > Duke University > > > jason at cgt.mc.duke.edu > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l@portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > >-- >Jason Stajich >Duke University >jason at cgt.mc.duke.edu >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l _________________________________________________________________ Enjoy a special introductory offer for dial-up Internet access limited time only! http://join.msn.com/?page=dept/dialup From junhu54 at hotmail.com Fri Jan 2 18:19:21 2004 From: junhu54 at hotmail.com (jun hu) Date: Sat Jan 3 12:19:52 2004 Subject: [Bioperl-l] bioperl graphic question Message-ID: Hi, Happy new Year, everyone! Thanks for the info about graphic packages, I download the rpm Jason provided and install it on another linux 9 machine, I also download the latest bioperl-live using cvs on the same machine. However, when install Bundle::bioperl using `perl -MCPAN -e "install Bundle::BioPerl"` ,one error happen... Bundle summary: The following items in bundle Bundle::LWP had installation problems: Digest::MD5 This problem did not happen when I install on previous linux 7.3 machine. Since it is related to LWP, I assue that I might be able to get away with it... so I continue... the other installation steps seem all right, and I have libgd2 now, so I hope everything will be fine... But I am not so lucky..., when I use the bioperl test program, like before, no error message, I can get one png file (2217 bytes, which is much larger than previous 838 bytes), however, the new png file is not viewable, at least not on windows ... and the previous png file(when I use libgd1.8.4 on linux 7.3), although no labels /feature, is still viewable... I was wondering what else can go wrong ... , I also attach the png files I generated although it is binary... Jun Hu UMDNJ >From: Jason Stajich >To: Lincoln Stein >CC: Todd Harris , bioperl-l@bioperl.org, jun hu > >Subject: Re: [Bioperl-l] bioperl graphic question >Date: Wed, 31 Dec 2003 16:24:05 -0500 (EST) > >I built gd2 from the fedora SRPMs and had no problem (save other RPMs >dependancy on libgd 1.8 (gnuplot,php,webalizer on RHL 7.3)) > >SRPM is here >http://download.fedora.redhat.com/pub/fedora/linux/core/1/i386/os/SRPMS/gd-2.0.15-1.src.rpm > >I can put the compiled RPMs for 7.3 and 9.0 on the bioperl site if it >would help. > >-jason >On Wed, 31 Dec 2003, Lincoln Stein wrote: > > > Does anyone know where the gd2 RPMs can be found? I know almost > > nothing about RPMs. > > > > Lincoln > > > > On Tuesday 30 December 2003 10:24 am, Jason Stajich wrote: > > > We might want to post pointers to gd2 rpms for the redhat crowd... > > > as RH 9 still ships with libgd 1.8.x > > > > > > > > > -jason > > > > > > On Mon, 29 Dec 2003, Todd Harris wrote: > > > > Hi Jun Hu - > > > > > > > > As noted in the install guide, you will need to upgrade your > > > > libgd. Although using libgd 1.8.4 may not necessarily result in > > > > runtime errors, graphical elements may not appear as intended. > > > > Some glyphs will not render at all with 1.8.4. > > > > > > > > We needed to move to libgd2 in order to support the generation of > > > > both raster (png) and vector (svg) images from the same codebase. > > > > > > > > todd > > > > > > -- > > > Jason Stajich > > > Duke University > > > jason at cgt.mc.duke.edu > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l@portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > >-- >Jason Stajich >Duke University >jason at cgt.mc.duke.edu >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l _________________________________________________________________ Get reliable dial-up Internet access now with our limited-time introductory offer. http://join.msn.com/?page=dept/dialup -------------- next part -------------- A non-text attachment was scrubbed... Name: junk2.png Type: application/octet-stream Size: 2217 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040102/61b11350/junk2.obj From tdhoufek at unity.ncsu.edu Sat Jan 3 13:21:57 2004 From: tdhoufek at unity.ncsu.edu (T.D. Houfek) Date: Sat Jan 3 13:29:38 2004 Subject: [Bioperl-l] my bioperl-db hacks Message-ID: <1073154082.31800.12.camel@aether> It would definitely be helpful to me if there were coordinated releases of bioperl-db and biosql. I'm willing to pitch in and help. Has anyone adapted GMOD's GBROWSE browser to expose views of a biosql database? Someone I know thought maybe they had heard something to that effect, but was not sure. TD -- ------------------------------- T.D. Houfek (email sound-alike: tdhoufek-AT-unity-DOT-ncsu-DOT-edu bioinformatics development lead Tobacco Genome Initiative North Carolina State University ------------------------------- From kvddrift at earthlink.net Sat Jan 3 14:04:22 2004 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat Jan 3 14:12:33 2004 Subject: [Bioperl-l] where is "sw.h" ? Message-ID: Hi, I am trying to compile the bioperl-ext pckage, and Align.xs fails because it cannot find the file 'sw.h'. I checked my system, but there is no sw.h. Is this part of a third party package? thanks, - Koen. From kvddrift at earthlink.net Sat Jan 3 14:26:00 2004 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat Jan 3 14:34:12 2004 Subject: Out of Office AutoReply: [Bioperl-l] where is "sw.h" ? In-Reply-To: <73FC8D4DCAD8D41190B300508B6980C207CE5997@rarusraexs13.prius.jnj.com> References: <73FC8D4DCAD8D41190B300508B6980C207CE5997@rarusraexs13.prius.jnj.com> Message-ID: On Jan 3, 2004, at 2:14 PM, Li, Qingqin [PRDUS] wrote: > will be out of office between Jan 5-12 for PSB meeting. Please > contact Dr. Nadine Cohen (7510) for urgent issues. I will repond to > your messages after returning. I doubt if Dr. Cohen can answer my question :-) Anyway, I found it, it's in bioperl-ext itself (duh). Not sure why it cannot find it. Maybe because I changed the include and lib directory to use with fink on Mac OS X. - Koen. From lstein at cshl.edu Sat Jan 3 16:00:18 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Sat Jan 3 16:07:33 2004 Subject: [Bioperl-l] my bioperl-db hacks In-Reply-To: <1073154082.31800.12.camel@aether> References: <1073154082.31800.12.camel@aether> Message-ID: <200401031600.18381.lstein@cshl.edu> Hi, We have had gbrowse running on top of the old (Singapore) biosql API for some time, and Vsevolod Iyuschenko at CSHL is close to being finished with a port to the new (post-Hackathon) API. He and Hilmar are coordinating. I imagine it will be ready for release soon, and probably for preview immediately. Lincoln On Saturday 03 January 2004 01:21 pm, T.D. Houfek wrote: > It would definitely be helpful to me if there were coordinated > releases of bioperl-db and biosql. I'm willing to pitch in and > help. Has anyone adapted GMOD's GBROWSE browser to expose views of > a biosql database? Someone I know thought maybe they had heard > something to that effect, but was not sure. > > TD From lstein at cshl.edu Sat Jan 3 16:32:27 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Sat Jan 3 16:39:42 2004 Subject: [Bioperl-l] Controlling glyph position with Bio::Graphics::Panel In-Reply-To: <5cb0c5f689.5f6895cb0c@bms.com> References: <5cb0c5f689.5f6895cb0c@bms.com> Message-ID: <200401031632.27760.lstein@cshl.edu> Hi Don, There used to be a -bump=>2 option, which turned on the kind of bumping that (I think) you want. No two glyphs are allowed to occupy the same Y position in the track. This option was removed when I found a way to speed up the regular bumping; I never really liked it. I can go back in CVS time and try to resurrect -bump=>2, but please confirm that this is what you're looking for. Lincoln On Friday 02 January 2004 11:23 am, Donald Jackson wrote: > Hi Lincoln, > > I have a question about controlling the vertical position of glyphs > using Bio::Graphics::Panel. > > I'm drawing out hits and hsps from a blast search (as lists of > Bio::Search::HSP objects) using the segments glyph. I've run into > a problem when I have two non-overlapping hits. I'd like to force > these to appear at distinct y-coordinates in the image, but can't > figure out how to do this. I tried 'bump', but that only affects > _overlapping_ hits. > > I'd appreciate any suggestions you or others on the list might > have. > > Thanks, > > Don Jackson > BMS Bioinformatics > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From Richard.Holland at agresearch.co.nz Sun Jan 4 15:13:10 2004 From: Richard.Holland at agresearch.co.nz (Holland, Richard) Date: Sun Jan 4 15:29:05 2004 Subject: [Bioperl-l] Errors loading RefSeqs Message-ID: Hi, I'm loading the vertebrate mammalian refseqs using load_seqdatabase.pl, having just downloaded them over the holidays. bioperl-db throws a wobbly on a few of them, an example follows: DBD::Oracle::st execute failed: ORA-01438: value larger than specified precision allows for this column (DBD ERROR: OCIStmtExecute) [for Statement "INSERT INTO bioentry_reference (ent_oid, ref_oid, rank, end_pos, start_pos) VALUES (?, ?, ?, ?, ?)" with ParamValues: :p5='1', :p3=129, :p1='26993', :p4='156', :p2='27237'] at /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAda ptor.pm line 418, line 44098. -------------------- WARNING --------------------- MSG: ReferenceAdaptor::add_assoc: unexpected failure of statement execution: ORA-01438: value larger than specified precision allows for this column (DBD ERROR: OCIStmtExecute) name: INSERT ASSOC [3] Bio::Seq::RichSeq;Bio::Annotation::Reference values: FK[Bio::Seq::RichSeq]:26993, FK[Bio::Annotation::Reference]:27237, rank:"129", end:"156", start:"1" --------------------------------------------------- The first error of this kind always refers to rank 100. I'm assuming that the BioSQL schema (in Oracle anyway) only allows ranks of 1-99 (ie. two digits), as this error occurs for all ranks of 100+. Is this an error with the RefSeqs or with bioperl-db, or the Oracle BioSQL schema? cheers, Richard --- Richard Holland Bioinformatics Database Developer ITS, Agresearch Invermay x3279 ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From hlapp at gmx.net Sun Jan 4 16:46:31 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Sun Jan 4 16:53:40 2004 Subject: [Bioperl-l] Errors loading RefSeqs In-Reply-To: Message-ID: <756E5BC0-3EFF-11D8-92C6-000A959EB4C4@gmx.net> This is a problem with the Oracle version of biosql. Sorry you had to be the first one to be hit by this. The rank as you suspected correctly is a NUMBER(2). Do the following in sqlplus (or any other sql-shell you're using for Oracle) to relax the restriction. SQL> ALTER TABLE sg_bioentry_ref_assoc MODIFY (rank NUMBER(4)); You'll need to issue this command as the schema owner, and be aware that it will implicitly commit an open transaction if there is any (b/c it is a DDL statement). Of course, there are lots of GUI-based tools that will let you do the same. I'll fix this in the repository. -hilmar On Sunday, January 4, 2004, at 12:13 PM, Holland, Richard wrote: > Hi, > > I'm loading the vertebrate mammalian refseqs using load_seqdatabase.pl, > having just downloaded them over the holidays. bioperl-db throws a > wobbly on a few of them, an example follows: > > DBD::Oracle::st execute failed: ORA-01438: value larger than specified > precision allows for this column (DBD ERROR: OCIStmtExecute) [for > Statement "INSERT INTO bioentry_reference (ent_oid, ref_oid, rank, > end_pos, start_pos) VALUES (?, ?, ?, ?, ?)" with ParamValues: :p5='1', > :p3=129, :p1='26993', :p4='156', :p2='27237'] at > /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/DB/BioSQL/ > BasePersistenceAda > ptor.pm line 418, line 44098. > > -------------------- WARNING --------------------- > MSG: ReferenceAdaptor::add_assoc: unexpected failure of statement > execution: ORA-01438: value larger than specified precision allows for > this column (DBD ERROR: OCIStmtExecute) > name: INSERT ASSOC [3] > Bio::Seq::RichSeq;Bio::Annotation::Reference > values: FK[Bio::Seq::RichSeq]:26993, > FK[Bio::Annotation::Reference]:27237, rank:"129", end:"156", start:"1" > --------------------------------------------------- > > The first error of this kind always refers to rank 100. I'm assuming > that the BioSQL schema (in Oracle anyway) only allows ranks of 1-99 > (ie. > two digits), as this error occurs for all ranks of 100+. Is this an > error with the RefSeqs or with bioperl-db, or the Oracle BioSQL schema? > > cheers, > Richard > > --- > Richard Holland > Bioinformatics Database Developer > ITS, Agresearch Invermay x3279 > > > > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From Richard.Holland at agresearch.co.nz Sun Jan 4 16:09:43 2004 From: Richard.Holland at agresearch.co.nz (Holland, Richard) Date: Sun Jan 4 17:18:45 2004 Subject: [Bioperl-l] Could not load GO terms to BioSQL Message-ID: On attempting to load the current GO definitions I get this: bifo6.agresearch.co.nz> /usr/users/oracle/bioperl-db/scripts/biosql/load_ontology.pl --host bifo6 --dbname seqstore --dbuser zzzz --dbpass zzzz --driver Oracle --namespace "Gene Ontology" --lookup --remove --format goflat --fmtargs "-defs_file,/raidset/tmp/goterms/GO.defs.txt" /raidset/tmp/goterms/function.ontology.txt Parsing input ... Loading ontology Gene Ontology: ... terms DBD::Oracle::st execute failed: ORA-01401: inserted value too large for column (DBD ERROR: OCIStmtExecute) [for Statement "INSERT INTO dbxref (dbname, accession, version) VALUES (?, ?, ?)" with ParamValues: :p3=0, :p1='MetaCyc', :p2='TRANS-HEXAPRENYLTRANSTRANSFERASE-RXN'] at /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/DB/BioSQL/BaseDriver.pm line 1001, line 10575. -------------------- WARNING --------------------- MSG: insert in Bio::DB::BioSQL::DBLinkAdaptor (driver) failed, values were ("MetaCyc","TRANS-HEXAPRENYLTRANSTRANSFERASE-RXN","0") FKs () ORA-01401: inserted value too large for column (DBD ERROR: OCIStmtExecute) --------------------------------------------------- Could not store GO:0000010 (trans-hexaprenyltranstransferase activity): ------------- EXCEPTION ------------- MSG: create: object (Bio::Annotation::DBLink) failed to insert or to be found by unique key STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAda ptor.pm:207 STACK Bio::DB::BioSQL::TermAdaptor::store_children /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/DB/BioSQL/TermAdaptor.pm:291 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAda ptor.pm:215 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAda ptor.pm:253 STACK Bio::DB::Persistent::PersistentObject::store /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/DB/Persistent/PersistentObje ct.pm:270 STACK (eval) /usr/users/oracle/bioperl-db/scripts/biosql/load_ontology.pl:506 STACK toplevel /usr/users/oracle/bioperl-db/scripts/biosql/load_ontology.pl:488 -------------------------------------- bifo6.agresearch.co.nz> Simple fix is to adjust the size of the accession column in dbxref. I have doubled it to 64 characters. Could someone verify this is sensible and see if the schema could be updated to match? I don't have access to CVS to do it myself. PS. Whilst you're at it could you also modify the rank column of bioentry_reference to allow numbers up to 3 digits long, not 2, as per my previous email. cheers, Richard --- Richard Holland Bioinformatics Database Developer ITS, Agresearch Invermay x3279 ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From hlapp at gmx.net Sun Jan 4 17:26:15 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Sun Jan 4 17:33:24 2004 Subject: [Bioperl-l] Could not load GO terms to BioSQL In-Reply-To: Message-ID: <02379A84-3F05-11D8-92C6-000A959EB4C4@gmx.net> On Sunday, January 4, 2004, at 01:09 PM, Holland, Richard wrote: > Simple fix is to adjust the size of the accession column in dbxref. I > have doubled it to 64 characters. Could someone verify this is sensible > and see if the schema could be updated to match? I encountered the same problem a while ago and applied the exact same fix, although I wasn't extremely happy with this solution, as it is caused by GO references in a way hijacking dbxref and not necessary for any other reason. The real fix requires substantial code changes though across the bioperl and bioperl-db board, as the object model has the real flaws here. Juguangs fixes to Bio::Ontology::Term may have actually brought us closer to that goal. The reason why the fix isn't in cvs is that we maintain a local version of the biosql-schema repository for our Symgene project. This has caused synchronization issues a number of times and generally annoys me; I'll remedy this situation as soon as biosql is released the first time. Another aspect that's driving me to really make this happen now. -hilmar -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From felipew at users.sourceforge.net Mon Jan 5 08:21:27 2004 From: felipew at users.sourceforge.net (Felipe Wettstein) Date: Mon Jan 5 08:28:34 2004 Subject: [Bioperl-l] new sourforge project using bioperl: RFLP planner Message-ID: <11675112-3F82-11D8-82FA-000393484DF2@users.sourceforge.net> Hi, I wrote a program that helps to plan RFLP experiments: It finds restriction enzymes that cut a set of homologue DNA sequences in different ways and simulates the resulting gel- electrophoresis image. The program helps you to find the crucial restriction enzymes that characterize the population. With the electrophoresis simulation it is easy to chose the restriction enzymes that show the best polymorphism on the gel. The program is written in perl, uses some modules of bioperl and the GD-Library. The program should be platform independet, but is tested only on Mac OS X, perl 5.8.0, bioperl 1.2.3. Any comments are welcome, even those telling me where I should have anounced this project. project web site: http://restrifind.sourceforge.net/ sourceforge web site: http://sourceforge.net/projects/restrifind/ Used modules Alignement and restriction Bio::SeqIO Bio::AlignIO Bio::Align::AlignI Bio::Tools::Run::Alignment::Clustalw Bio::Tools::RestrictionEnzyme Gel drawing GD Bio::Seq Bio::Tools::Gel Colored printout Term::ANSIColor #only for output a red nucleotide in cli, obsolete:) felipe wettstein From DBSMITH at OhioHealth.com Mon Jan 5 12:09:47 2004 From: DBSMITH at OhioHealth.com (DBSMITH@OhioHealth.com) Date: Mon Jan 5 12:18:53 2004 Subject: [Bioperl-l] biometrics Message-ID: I have a broad but quick question.... is the bio* modules within Perl capable of giving users the ability to authenticate themselves from their fingerprints as in a touch screen? The platforms are intel based workstations running a thin client and a HPUX server running a pharmacy application. thank you! Derek B. Smith OhioHealth IT UNIX systems programming / Backup, RestoreTeam From donald.jackson at bms.com Mon Jan 5 08:45:26 2004 From: donald.jackson at bms.com (Donald G. Jackson) Date: Mon Jan 5 12:19:35 2004 Subject: [Bioperl-l] Controlling glyph position with Bio::Graphics::Panel In-Reply-To: <200401031632.27760.lstein@cshl.edu> References: <5cb0c5f689.5f6895cb0c@bms.com> <200401031632.27760.lstein@cshl.edu> Message-ID: <3FF96A76.4050201@bms.com> Hi Lincoln, I'm not sure if that's what I want or not, because I'm not exactly sure what a glyph is ;). I give Bio::Graphics::Glyph::segments a listref of all the HSPs for a BLAST hit and have it draw out the individual HSPs with a connector (I've attached an example image from my current script). Multiple HSPs for the same hit are connected by dashed lines; in other cases there are hsps from different hits close to each other - most users would think these were also from the same hit. If the set of connected HSPs is a single glyph, then it sounds like your old code would do the trick. If each individual HSP is a glyph then that wouldn't work. If it's easy to dig out an older version of the code with the -bump=>2 option I'd like to give it a try and see what happens. I agree that most of the time the bump=>1 behavior makes the most sense, but for search results I think it's confusing - the 1 track = 1 hit is easier for people to keep straight. Thanks very much for your help! Don Jackson Lincoln Stein wrote: >Hi Don, > >There used to be a -bump=>2 option, which turned on the kind of >bumping that (I think) you want. No two glyphs are allowed to occupy >the same Y position in the track. This option was removed when I >found a way to speed up the regular bumping; I never really liked it. > >I can go back in CVS time and try to resurrect -bump=>2, but please >confirm that this is what you're looking for. > >Lincoln > > >On Friday 02 January 2004 11:23 am, Donald Jackson wrote: > > >>Hi Lincoln, >> >>I have a question about controlling the vertical position of glyphs >>using Bio::Graphics::Panel. >> >>I'm drawing out hits and hsps from a blast search (as lists of >>Bio::Search::HSP objects) using the segments glyph. I've run into >>a problem when I have two non-overlapping hits. I'd like to force >>these to appear at distinct y-coordinates in the image, but can't >>figure out how to do this. I tried 'bump', but that only affects >>_overlapping_ hits. >> >>I'd appreciate any suggestions you or others on the list might >>have. >> >>Thanks, >> >>Don Jackson >>BMS Bioinformatics >> >>_______________________________________________ >>Bioperl-l mailing list >>Bioperl-l@portal.open-bio.org >>http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> > > > -------------- next part -------------- A non-text attachment was scrubbed... Name: blast_hits_example.png Type: image/png Size: 5243 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040105/275f1de0/blast_hits_example.png From Richard.Holland at agresearch.co.nz Mon Jan 5 16:05:31 2004 From: Richard.Holland at agresearch.co.nz (Holland, Richard) Date: Mon Jan 5 16:14:07 2004 Subject: [Bioperl-l] Gaps in sequences Message-ID: Hi, Some RefSeq sequences I downloaded in GenBank format from the NCBI have interesting location descriptors which cause BioPerl to fail with the following error: -------------------- WARNING --------------------- MSG: exception while parsing location line [join(AC145223.1:1..25742,gap(646),AC145223.1:26389..31181)] in reading EMBL/GenBank/SwissProt, ignoring feature CONTIG (seqid=NT_079570): ------------- EXCEPTION ------------- MSG: operator "gap" unrecognized by parser STACK Bio::Factory::FTLocationFactory::from_string /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/Factory/FTLocationFactory.pm :160 STACK Bio::Factory::FTLocationFactory::from_string /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/Factory/FTLocationFactory.pm :157 STACK (eval) /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/SeqIO/FTHelper.pm:124 STACK Bio::SeqIO::FTHelper::_generic_seqfeature /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/SeqIO/FTHelper.pm:123 STACK Bio::SeqIO::genbank::next_seq /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/SeqIO/genbank.pm:421 STACK toplevel /usr/users/oracle/bioperl-db/scripts/biosql/load_seqdatabase.pl:457 -------------------------------------- --------------------------------------------------- Any ideas anyone? Is this a broken location descriptor, or a broken parser? (So far the only ones I have found all occur in vertebrate_mammalian3.genomic.gbff) cheers, Richard --- Richard Holland Bioinformatics Database Developer ITS, Agresearch Invermay x3279 ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From jason at cgt.duhs.duke.edu Mon Jan 5 16:19:11 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Mon Jan 5 16:26:17 2004 Subject: [Bioperl-l] Gaps in sequences In-Reply-To: References: Message-ID: http://bugzilla.open-bio.org/show_bug.cgi?id=1319 No one has fixed this yet AFAIK. -jason On Tue, 6 Jan 2004, Holland, Richard wrote: > Hi, > > Some RefSeq sequences I downloaded in GenBank format from the NCBI have > interesting location descriptors which cause BioPerl to fail with the > following error: > > -------------------- WARNING --------------------- > MSG: exception while parsing location line > [join(AC145223.1:1..25742,gap(646),AC145223.1:26389..31181)] in reading > EMBL/GenBank/SwissProt, ignoring feature CONTIG (seqid=NT_079570): > ------------- EXCEPTION ------------- > MSG: operator "gap" unrecognized by parser > STACK Bio::Factory::FTLocationFactory::from_string > /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/Factory/FTLocationFactory.pm > :160 > STACK Bio::Factory::FTLocationFactory::from_string > /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/Factory/FTLocationFactory.pm > :157 > STACK (eval) > /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/SeqIO/FTHelper.pm:124 > STACK Bio::SeqIO::FTHelper::_generic_seqfeature > /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/SeqIO/FTHelper.pm:123 > STACK Bio::SeqIO::genbank::next_seq > /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/SeqIO/genbank.pm:421 > STACK toplevel > /usr/users/oracle/bioperl-db/scripts/biosql/load_seqdatabase.pl:457 > > -------------------------------------- > > --------------------------------------------------- > > Any ideas anyone? Is this a broken location descriptor, or a broken > parser? (So far the only ones I have found all occur in > vertebrate_mammalian3.genomic.gbff) > > cheers, > Richard > > --- > Richard Holland > Bioinformatics Database Developer > ITS, Agresearch Invermay x3279 > > > > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From Richard.Holland at agresearch.co.nz Mon Jan 5 17:03:59 2004 From: Richard.Holland at agresearch.co.nz (Holland, Richard) Date: Mon Jan 5 17:11:15 2004 Subject: [Bioperl-l] Gaps in sequences Message-ID: I read the bug report and had a thought - the problem seems to be that there is no way of representing a gap as a reproducable feature (ie. you could either not bother annotating it because it is empty space, or you are stuck because you can only annotate actual alignments in contigs with actual sequences). My (somewhat off-the-wall) idea is that you could introduce the concept of the Empty Sequence to BioPerl, as a global static sequence of infinite length and no content, which is used whenever gaps appear in alignments. The parser would translate gap(400) to be EMPTY:1...400 or something like that before processing it, and could translate EMPTY:1...400 back to gap(400) on output. In BioSQL the Empty Sequence would be represented as a simple bioentry being the sole member of a special Empty biodatabase with a corresponding biosequence with null SEQ and MAX_INT length. Do you think that might work? I haven't thought it through in any detail or looked at the code to see if it is even possible, but I thought I'd mention it anyway. cheers, Richard --- Richard Holland Bioinformatics Database Developer ITS, Agresearch Invermay x3279 -----Original Message----- From: Jason Stajich [mailto:jason@cgt.duhs.duke.edu] Sent: Tuesday, 6 January 2004 10:19 a.m. To: Holland, Richard Cc: bioperl-l@bioperl.org Subject: Re: [Bioperl-l] Gaps in sequences http://bugzilla.open-bio.org/show_bug.cgi?id=1319 No one has fixed this yet AFAIK. -jason On Tue, 6 Jan 2004, Holland, Richard wrote: > Hi, > > Some RefSeq sequences I downloaded in GenBank format from the NCBI > have interesting location descriptors which cause BioPerl to fail with > the following error: > > -------------------- WARNING --------------------- > MSG: exception while parsing location line > [join(AC145223.1:1..25742,gap(646),AC145223.1:26389..31181)] in > reading EMBL/GenBank/SwissProt, ignoring feature CONTIG > (seqid=NT_079570): > ------------- EXCEPTION ------------- > MSG: operator "gap" unrecognized by parser > STACK Bio::Factory::FTLocationFactory::from_string > /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/Factory/FTLocationFactory.pm > :160 > STACK Bio::Factory::FTLocationFactory::from_string > /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/Factory/FTLocationFactory.pm > :157 > STACK (eval) > /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/SeqIO/FTHelper.pm:124 > STACK Bio::SeqIO::FTHelper::_generic_seqfeature > /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/SeqIO/FTHelper.pm:123 > STACK Bio::SeqIO::genbank::next_seq > /usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/SeqIO/genbank.pm:421 > STACK toplevel > /usr/users/oracle/bioperl-db/scripts/biosql/load_seqdatabase.pl:457 > > -------------------------------------- > > --------------------------------------------------- > > Any ideas anyone? Is this a broken location descriptor, or a broken > parser? (So far the only ones I have found all occur in > vertebrate_mammalian3.genomic.gbff) > > cheers, > Richard > > --- > Richard Holland > Bioinformatics Database Developer > ITS, Agresearch Invermay x3279 > > > > ====================================================================== > = > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > -- Jason Stajich Duke University jason at cgt.mc.duke.edu ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From heikki at nildram.co.uk Mon Jan 5 18:03:36 2004 From: heikki at nildram.co.uk (Heikki Lehvaslaiho) Date: Mon Jan 5 18:10:43 2004 Subject: [Bioperl-l] biometrics In-Reply-To: References: Message-ID: <200401052303.37875.heikki@nildram.co.uk> Derek, We definitely do not have anything in bioperl. I queried CPAN with key words 'fingerprint' and 'touch' and could not find anyting relevant, either. Yours, -Heikki On Monday 05 Jan 2004 5:09 pm, DBSMITH@OhioHealth.com wrote: > I have a broad but quick question.... > > is the bio* modules within Perl capable of giving users the ability to > authenticate themselves from their fingerprints as in a touch screen? > The platforms are intel based workstations running a thin client and a > HPUX server running a pharmacy application. > > thank you! > Derek B. Smith > OhioHealth IT > UNIX systems programming / Backup, RestoreTeam -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From Richard.Holland at agresearch.co.nz Mon Jan 5 18:58:20 2004 From: Richard.Holland at agresearch.co.nz (Holland, Richard) Date: Mon Jan 5 19:05:28 2004 Subject: [Bioperl-l] Interpro parsing problems - and solutions Message-ID: Hi all. A long one this but I hope it's worth the read. I found a possible bug in Bio/OntologyIO/InterProParser.pm. The default behaviour for OntologyEngineI implementors is supposed to be a 'simple' OntologyEngine. However, the code in InterProParser does not default to anything if no engine is specified - it tries to set up an 'undef' engine, which fails with a not-yet-implemented message. The other parsers based on dagflat.pm do exhibit the default behaviour, so to make InterProParser.pm do the same I added the following line at line 130 (just before "if(lc($eng_type) eq 'simple')"): $eng_type = 'simple' unless $eng_type; Another possible bug in the same module - InterProParser.pm assumes that it has been passed a filename not a filehandle. As OntologyIO allows for both cases, I have adapted InterProParser.pm to suit: sub parse{ my $self = shift; my $ret; if ($self->file()) { $ret = $self->{_parser}->parse( Source => { SystemId => $self->file() } ); } elsif ($self->_fh()) { $ret = $self->{_parser}->parse( Source => { ByteStream => $self->_fh() } ); } else { $ret = undef; $self->throw("You have not provided any InterPro XML to parse.\n"); } $self->_is_parsed(1); return $ret; } Also, in Bio/OntologyIO/Handlers/InterProHandler.pm (note different module!), a definite bug this time, it does not know about two of the interpro types - Active_site and Binding_site. Adding lines to start_element as follows seems to work: sub start_element { my ($self, $element) = @_; my $ont = $self->ontology(); my $fact = $self->term_factory(); if ($element->{Name} eq 'interprodb') { # TWO NEW LINES FOLLOW $ont->add_term($fact->create_object(-identifier => "Active_site", -name => "Active Site") ); $ont->add_term($fact->create_object(-identifier => "Binding_site", -name => "Binding Site") ); # CONTINUE WITH ORIGINAL CODE $ont->add_term($fact->create_object(-identifier => "Family", -name => "Family") ); $ont->add_term($fact->create_object(-identifier => "Domain", -name => "Domain") ); $ont->add_term($fact->create_object(-identifier => "Repeat", -name => "Repeat") ); $ont->add_term($fact->create_object(-identifier => "PTM", -name => "post-translational modification")); There is a problem with the relation loader in Bio/Ontology/SimpleOntologyEngine.pm as well - get_term_by_identifier returns an array of @terms, but the get_relationships subroutine calls it twice and both times expects it to only return a single term. Other calls to get_term_by_identifier in this module are correct. I have adapted the two incorrect references in get_relationships to loop through all terms returned by get_term_by_identifier instead, as follows: # if a term is supplied, add a relationship for the parent to the term # except if the parent is the term itself (we added that one before) if($term && ($parent_id ne $term->identifier())) { my @parent_terms = $self->get_term_by_identifier($parent_id); foreach my $parent_term (@parent_terms) { push(@rels, $relfact->create_object(-object_term => $parent_term, -subject_term => $term, -predicate_term => $parent_entry->{$term->identifier}, -ontology => $term->ontology() ) ); } } else { # otherwise, i.e., no term supplied, or the parent equals the # supplied term my @parent_terms = $term ? ($term) : $self->get_term_by_identifier($parent_id); foreach my $child_id (keys %$parent_entry) { my $rel_info = $parent_entry->{$child_id}; foreach my $parent_term (@parent_terms) { push(@rels, $relfact->create_object(-object_term => $parent_term, -subject_term => $self->get_term_by_identifier( $child_id), -predicate_term => $rel_info, -ontology =>$parent_term->ontology ) ); } } } There is also a bug in Bio/OntologyIO/Handlers/InterProHandler.pm which does not set the current ontology of new temporary terms when used in relationships. This causes "cannot call method 'name' on an undefined value" errors later on when get_relationships tries to find out the name of the ontology of each relationship. It also does not set the 'name' values for these terms, so that you get 'cannot insert null into SG_TERM.NAME' errors when the terms are later committed to the database, because the name column of sg_term has a 'not null' constraint, at least in the Oracle implementation of BioSQL. These problems can both be fixed by altering the call to the create_object function, in sub _create_relationship, to include the -ontology and -name parameters: $term_temp = $ont->engine->add_term( $fact->create_object( -InterPro_id => $ref_id, -name => $ref_id, -ontology => $ont ) ); And in sub start_element in the same module the same fix needs applying (no need for -ontology here as the existing code following this statement does this for us explicitly using a term->ontology() call): $self->_term( (!defined $term_temp) ? $ont->add_term( $fact->create_object(-InterPro_id => $id, -name => $id ) ) : $term_temp ); Note that this call defaults the name to be the same as the InterPro ID. Most temporary terms will be overridden with permanent data later in the process, but for those that slip through without permanent definitions (possibly a bug in the InterPro XML datafile?) the above change is necessary to allow them to be inserted into the database and their relations to other terms kept valid. Lastly, the definition field of the term table is too short to take, for example, IPR001967 - I have extended it to the Oracle varchar2 maximum of 4000 chars (up from 2000) in my BioSQL instance, but found it still to be too short, so I added a quick fix to Bio/Ontology/Term.pm to truncate definitions to be no more than this length, but would like to know if this is a more general problem: sub definition { my $self = shift; return $self->{'definition'} = substr(shift,0,4000) if @_; return $self->{'definition'}; } # definition Finally, Bio/OntologyIO/Handlers/InterProHandler.pm fails to set the ontology for the base IS_A, CONTAINS and FOUND_IN relationship types. This causes a null foreign key error on SG_TERM.ONT_OID when it tries to insert them into the database. After checking Bio/Ontology/SimpleGOEngine.pm and finding that it does set the ontology names for these relationships, I modified InterProHandler to do the same by adding the following three lines in the constructor (new) method directly after the instantiation of the three relationship types: $is_a_rel->ontology($self->ontology()); $contains_rel->ontology($self->ontology()); $found_in_rel->ontology($self->ontology()); With all these changes in place, "bioperl-db/scripts/biosql/load_ontology.pl --format interpro interpro.xml" works correctly for the current release of interpro.xml. It _does_ give many "unique constraint violated" errors on TERM_RELATIONSHIP while inserting the relationships into BioSQL, but I suspect this is because the get_relationships function in InterProHandler.pm does not check to see if a relation has already been pushed before pushing it onto the array of relations it returns. To fix this would slow down the code considerably so it's probably best to just live with the messages. Are these acceptable modifications or is there a better way to fix these problems? I admit my Perl may not be the best but hopefully you get the idea of how my fixes work and may be able to code them in a better way. If any of these changes are acceptable could someone implement them for me? I do not have access to CVS. Finally, if you think that I have been spending too much time trying to fix these bugs when in fact there is an alternative and fully functional way to load InterPro XML data into BioPerl/BioSQL, please feel free to slap me around a bit with a wet haddock. This is my first ever contribution to an open source project so I could do with some advice on how to do things better next time. cheers, Richard PS. Totally unrelated but also a database field length problem - the description field in bioentry is too short to hold SwissProt P05067 - in my case I have lengthened the field to 1024 chars which does the trick. PPS. Certain annotations in RefSeqs cause a similar overflow in seqfeature_qualifier_value.value. I'm guessing that without using CLOBs for all cases where free text is allowed, we'll never see the end of these kinds of problems in the Oracle version of BioSQL? --- Richard Holland Bioinformatics Database Developer ITS, Agresearch Invermay x3279 ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From Richard.Holland at agresearch.co.nz Mon Jan 5 19:15:52 2004 From: Richard.Holland at agresearch.co.nz (Holland, Richard) Date: Mon Jan 5 19:22:59 2004 Subject: [Bioperl-l] Relations Message-ID: Me again! Sorry about this heap of messages from me today, I'm having a couple of BioPerl days to hammer out all the things my boss wants done before the end of the month... Has anyone got a script to load GO term associations into BioSQL bioentry_qualifier_value with? If not I'll put one together and post it when it's done, but I don't want to write one if one already exists. I'm interested in linking GO terms to RefSeqs (not sure where to get the associations from there though), GO to InterPro, and GO to SwissProt. Also InterPro to SwissProt if possible. cheers, Richard --- Richard Holland Bioinformatics Database Developer ITS, Agresearch Invermay x3279 ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From donald.jackson at bms.com Tue Jan 6 10:05:43 2004 From: donald.jackson at bms.com (Donald Jackson) Date: Tue Jan 6 10:13:13 2004 Subject: [Bioperl-l] Alternate hit sorting for Bio::Search::Result objects In-Reply-To: References: Message-ID: <3FFACEC7.6050701@bms.com> Chris and Jason, I've coded up a sort_hits method for Bio::Search::ResultI.pm (attached) which does what I was hoping. I realized my last email was contradictory - one must either modify the hits list in the result object or modify the writers; I decided to go for the former. I've held off on committing this because I'm still not sure we want to do this in ResultI instead of ResultWriter. What are peoples' thoughts? Thanks, Don Jackson BMS Bioinformatics ############################################################# # # POD and code for proposed sort_hits() method in Bio::Search::ResultI.pm follow # ######################################################################## =head2 sort_hits Title : sort_hits Usage : $result->sort_hits(\&sort_function) Function : Sorts the available hit objects by a user-supplied function Returns : n/a Args : A coderef for the sort function. See the documentation on the Perl sort() function for guidelines on writing sort functions. Note : To access the special variables $a and $b used by the Perl sort() function the user function must access Bio::Search::Result::ResultI namespace. For example, use : $result->sort_hits( sub{$Bio::Search::Result::ResultI::a->length <=> $Bio::Search::Result::ResultI::b->length}); NOT $result->sort_hits($a->length <=>$b->length); =cut sub sort_hits { my ($self, $coderef) = @_; my @sorted_hits; unless ($coderef and ref($coderef) eq 'CODE') { $self->throw('next_hit requires a sort function passed as a subroutine reference'); } my @hits = $self->hits(); eval {@sorted_hits = sort $coderef @hits }; if ($@) { $self->throw("Unable to sort hits: $@"); } else { $self->{'_hits'} = \@sorted_hits; $self->{'_no_iterations'} = 1; # to bypass iteration checking in hits() method 1; } } > > From Laurence.Amilhat at clermont.inra.fr Tue Jan 6 11:30:04 2004 From: Laurence.Amilhat at clermont.inra.fr (Laurence Amilhat) Date: Tue Jan 6 11:36:30 2004 Subject: [Bioperl-l] GCG and Perl Message-ID: <5.1.1.6.0.20040106172024.00b6f388@valmont> Hi everyone, I would like to run GCG programs in a Perl script (such as bestfit), but I cannot make it work. I know that there are BioPerl modules to run EMBOSS program, but I don't have Emboos installed in my system. Does anyone have an idea? Thank you, Sincerely, Laurence ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ INRA, UMR INRA/UBP Am?lioration et Sant? des Plantes 234 avenue du Br?zet 63039 Clermont-Ferrand Cedex 2 Tel 04 73 62 40 87 Fax 04 73 62 44 53 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From hlapp at gmx.net Tue Jan 6 11:50:57 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue Jan 6 11:58:04 2004 Subject: [Bioperl-l] Relations In-Reply-To: Message-ID: <8034A572-4068-11D8-942D-000A959EB4C4@gmx.net> I've heard someone wanted to code this up half a year ago, but AFAIK the script never made it into the repository. I think this would be very useful to have. The GO associations for RefSeq are present in RefSeq most of the time but obfuscated in the feature table. I wrote a SeqProcessor that promotes them to annotations, but RefSeq keeps changing the format of that on me, so even though possible it's not an approach that warms your heart. Note that LL also comes with GO links in the records, which are extracted fairly well by the parser. -hilmar On Monday, January 5, 2004, at 04:15 PM, Holland, Richard wrote: > Me again! Sorry about this heap of messages from me today, I'm having a > couple of BioPerl days to hammer out all the things my boss wants done > before the end of the month... > > Has anyone got a script to load GO term associations into BioSQL > bioentry_qualifier_value with? If not I'll put one together and post it > when it's done, but I don't want to write one if one already exists. > I'm > interested in linking GO terms to RefSeqs (not sure where to get the > associations from there though), GO to InterPro, and GO to SwissProt. > Also InterPro to SwissProt if possible. > > cheers, > Richard > > --- > Richard Holland > Bioinformatics Database Developer > ITS, Agresearch Invermay x3279 > > > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From brian_osborne at cognia.com Tue Jan 6 11:53:11 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Tue Jan 6 12:00:42 2004 Subject: [Bioperl-l] GCG and Perl In-Reply-To: <5.1.1.6.0.20040106172024.00b6f388@valmont> Message-ID: Laurence, If there's a program in the EMBOSS suite that can functionally replace bestfit then you could install EMBOSS and use it. Is there any reason you can't do this? What kind of computer are you using? Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Laurence Amilhat Sent: Tuesday, January 06, 2004 11:30 AM To: bioperl-l@bioperl.org Subject: [Bioperl-l] GCG and Perl Hi everyone, I would like to run GCG programs in a Perl script (such as bestfit), but I cannot make it work. I know that there are BioPerl modules to run EMBOSS program, but I don't have Emboos installed in my system. Does anyone have an idea? Thank you, Sincerely, Laurence ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ INRA, UMR INRA/UBP Am?lioration et Sant? des Plantes 234 avenue du Br?zet 63039 Clermont-Ferrand Cedex 2 Tel 04 73 62 40 87 Fax 04 73 62 44 53 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From jason at cgt.duhs.duke.edu Tue Jan 6 12:25:26 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Jan 6 12:32:34 2004 Subject: [Bioperl-l] GCG and Perl In-Reply-To: References: Message-ID: Here is a list of substitutes for GCG programs. http://www.no.embnet.org/Programs/SAL/EMBOSS/fromGCG.php3 On Tue, 6 Jan 2004, Brian Osborne wrote: > Laurence, > > If there's a program in the EMBOSS suite that can functionally replace > bestfit then you could install EMBOSS and use it. Is there any reason you > can't do this? What kind of computer are you using? > > Brian O. > > > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org > [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Laurence Amilhat > Sent: Tuesday, January 06, 2004 11:30 AM > To: bioperl-l@bioperl.org > Subject: [Bioperl-l] GCG and Perl > > > Hi everyone, > > I would like to run GCG programs in a Perl script (such as bestfit), but I > cannot make it work. > I know that there are BioPerl modules to run EMBOSS program, but I don't > have Emboos installed in my system. > Does anyone have an idea? > > Thank you, > > Sincerely, > > Laurence > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > INRA, UMR INRA/UBP Am?lioration et Sant? des Plantes > 234 avenue du Br?zet > 63039 Clermont-Ferrand Cedex 2 > > Tel 04 73 62 40 87 > Fax 04 73 62 44 53 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From rfreimut at im.wustl.edu Tue Jan 6 12:33:51 2004 From: rfreimut at im.wustl.edu (Freimuth,Robert) Date: Tue Jan 6 12:52:12 2004 Subject: [Bioperl-l] GCG and Perl Message-ID: <94625DAE73CA7C4286529B2D0911A584289194@imex3.im.wustl.edu> > Date: Tue, 06 Jan 2004 17:30:04 +0100 > From: Laurence Amilhat > Subject: [Bioperl-l] GCG and Perl > > I would like to run GCG programs in a Perl script (such as > bestfit), but I cannot make it work. > I know that there are BioPerl modules to run EMBOSS program, > but I don't have Emboos installed in my system. > Does anyone have an idea? >> Date: Tue, 6 Jan 2004 11:53:11 -0500 >> From: "Brian Osborne" >> Subject: RE: [Bioperl-l] GCG and Perl >> >> If there's a program in the EMBOSS suite that can functionally replace >> bestfit then you could install EMBOSS and use it. Is there >> any reason you >> can't do this? What kind of computer are you using? >> >> Brian O. Hi Laurence, A few years ago (during my pre-perl years) I wrote some unix shell scripts to call bestfit and/or gap, so I know it's possible to call GCG programs from the command line. What have you tried? That said, I agree with Brian: EMBOSS has a lot of great tools, so you may want to look into installing it (the two alignment programs you'd probably be most interested in are 'needle' and 'water'). The one catch is that it requires a *nix OS, so if you're running Windows you'll need to look into Cygwin. Finally, take a look at the pSW module in Bio::Tools, if you want to call a local alignment algorithm from perl. There isn't a global alignment module yet, AFAIK, but if you need one you could try to tweek pSW. Alternatively, I wrote a needleman-wunsch module that I would be happy to share, but it's far from optimized and (since I'm still quite the beginner) probably fairly ugly code. Bob Robert Freimuth, PhD Post-Doctoral Fellow Washington University School of Medicine Department of Internal Medicine Division of Molecular Oncology From letondal at pasteur.fr Tue Jan 6 13:06:03 2004 From: letondal at pasteur.fr (Catherine Letondal) Date: Tue Jan 6 13:13:06 2004 Subject: [Bioperl-l] GCG and Perl In-Reply-To: <5.1.1.6.0.20040106172024.00b6f388@valmont>; from Laurence.Amilhat@clermont.inra.fr on Tue, Jan 06, 2004 at 05:30:04PM +0100 References: <5.1.1.6.0.20040106172024.00b6f388@valmont> Message-ID: <20040106190603.B519450@electre.pasteur.fr> On Tue, Jan 06, 2004 at 05:30:04PM +0100, Laurence Amilhat wrote: > > > Hi everyone, > > I would like to run GCG programs in a Perl script (such as bestfit), but I > cannot make it work. > I know that there are BioPerl modules to run EMBOSS program, but I don't > have Emboos installed in my system. > Does anyone have an idea? > > Thank you, > > Sincerely, > > Laurence > If you don't want to - or cannot - install EMBOSS locally, you can use the Bio::Tools::Run Pise modules. See: http://www.pasteur.fr/recherche/unites/sis/Pise/#pisebioperl (there is an example with needle, another EMBOSS program). Do not hesitate to ask for additional information. -- Catherine Letondal -- Pasteur Institute Computing Center From barry.moore at genetics.utah.edu Tue Jan 6 16:29:50 2004 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Tue Jan 6 16:36:56 2004 Subject: [Bioperl-l] Trouble installing bioperl-ext-1.4 Message-ID: <3FFB28CE.8020706@genetics.utah.edu> I'm installing bioperl 1.4 on my linux machine (RedHat 9.0, Perl 5.8). Bioperl-1.4 (the core) and bioperl-run-1.4 installed fine. I get the following errors when trying to install bioperl-ext-1.4: [root@Tatshenshini bioperl-ext-1.4]# perl Makefile.PL Checking if your kit is complete... Looks good Writing Makefile for Bio::Ext::Align ERROR from evaluation of /home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/Makefile.PL: Can't locate Inline/MakeMaker.pm in @INC (@INC contains: /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 /home/bmoore/bioperl-ext-1.4 .) at ./Makefile.PL line 1. BEGIN failed--compilation aborted at ./Makefile.PL line 1. [root@Tatshenshini bioperl-ext-1.4]# I'm a bit linux challenged so any pointers, no matter how remedial, will be greatly appreciated. Barry Moore Dept. Human Genetics University of Utah From jason at cgt.duhs.duke.edu Tue Jan 6 16:36:08 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Jan 6 16:43:12 2004 Subject: [Bioperl-l] Trouble installing bioperl-ext-1.4 In-Reply-To: <3FFB28CE.8020706@genetics.utah.edu> References: <3FFB28CE.8020706@genetics.utah.edu> Message-ID: Hey Barry! You need to have installed Inline::C first. You don't need bioperl-ext unless you want the specialized stuff in there (a smith-waterman implementation and access to the staden io library for reading in trace files directly through perl). -jason On Tue, 6 Jan 2004, Barry Moore wrote: > > I'm installing bioperl 1.4 on my linux machine (RedHat 9.0, Perl 5.8). > Bioperl-1.4 (the core) and bioperl-run-1.4 installed fine. I get the > following errors when trying to install bioperl-ext-1.4: > > [root@Tatshenshini bioperl-ext-1.4]# perl Makefile.PL > Checking if your kit is complete... > Looks good > Writing Makefile for Bio::Ext::Align > ERROR from evaluation of > /home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/Makefile.PL: Can't locate > Inline/MakeMaker.pm in @INC > (@INC contains: /usr/lib/perl5/5.8.0/i386-linux-thread-multi > /usr/lib/perl5/5.8.0 > /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl > /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl > /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 > /home/bmoore/bioperl-ext-1.4 .) at ./Makefile.PL line 1. > BEGIN failed--compilation aborted at ./Makefile.PL line 1. > [root@Tatshenshini bioperl-ext-1.4]# > > I'm a bit linux challenged so any pointers, no matter how remedial, will > be greatly appreciated. > > Barry Moore > Dept. Human Genetics > University of Utah > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From barry.moore at genetics.utah.edu Tue Jan 6 18:15:19 2004 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Tue Jan 6 19:59:08 2004 Subject: [Bioperl-l] Trouble installing bioperl-ext-1.4 In-Reply-To: References: <3FFB28CE.8020706@genetics.utah.edu> Message-ID: <3FFB4187.3050102@genetics.utah.edu> Jason et al- ...while trying to install bioperl-ext-1.4 your suggestion for installing Inline::C first seems to have worked. Makefile.PL ran fine (highlighted below in green - if your reading HTML mail). However, now I get errors on running make. I've copied the entire output from the make command below (with some masking of low complexity regions). Sorry it's so long, but I'm having trouble spotting the problem, so I didn't want to leave out any of the important parts. The part indicating errors is at the end (highlighted in red). Barry [root@Tatshenshini bioperl-ext-1.4]# perl Makefile.PL Checking if your kit is complete... Looks good Writing Makefile for Bio::Ext::Align Please tell us where your Staden io_lib "read" library is installed: [/usr/local/lib] Please tell us where your Staden io_lib "Read.h" header is installed: [/usr/local/include/io_lib] Writing Makefile for Bio::SeqIO::staden::read Writing Makefile for Bio One or more DATA sections were not processed by Inline. [root@Tatshenshini bioperl-ext-1.4]# make cp Bio/Ext/Align/libs/hscore.h blib/lib/Bio/Ext/Align/libs/hscore.h ###Removed alot of cp commands to shorten e-mail post### cp Bio/Ext/Align/libs/wisefile.h blib/lib/Bio/Ext/Align/libs/wisefile.h make[1]: Entering directory `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align' cp Align.pm ../blib/lib/Bio/Ext/Align.pm DEFINE='-DPOSIX -DNOERROR'; CC='gcc'; export DEFINE INC CC; \ cd libs && make CC=gcc libsw.a -e make[2]: Entering directory `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align/libs' gcc -c -O -c -o aln.o aln.c ###Removed alot of gcc commands to shorten e-mail post### gcc -c -O -c -o linspc.o linspc.c ar ru libsw.a aln.o alnconvert.o alnrange.o asciibtcanvas.o basematrix.o btcanvas.o commandline.o complexconsensi.o complexevalset.o complexsequence.o compmat.o codon.o dna.o dnamatrix.o dpenvelope.o dynlibcross.o histogram.o hscore.o linesubs.o packaln.o probability.o protein.o proteindb.o proteinsw.o seqaligndisplay.o sequence.o sequencedb.o sw_wrap.o wiseerror.o wisefile.o wisememman.o wiseoverlay.o wiserandom.o wisestring.o wisetime.o dpalign.o linspc.o make[2]: Leaving directory `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align/libs' /usr/bin/perl /usr/lib/perl5/5.8.0/ExtUtils/xsubpp -typemap /usr/lib/perl5/5.8.0/ExtUtils/typemap -typemap typemap Align.xs > Align.xsc && mv Align.xsc Align.c gcc -c -I./libs -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS -DDEBUGGING -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -march=i386 -mcpu=i686 -g -DVERSION=\"0.1\" -DXS_VERSION=\"0.1\" -fPIC "-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE" -DPOSIX -DNOERROR Align.c Running Mkbootstrap for Bio::Ext::Align () chmod 644 Align.bs rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so LD_RUN_PATH="" gcc -shared -L/usr/local/lib Align.o -o ../blib/arch/auto/Bio/Ext/Align/Align.so libs/libsw.a -lm chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so cp Align.bs ../blib/arch/auto/Bio/Ext/Align/Align.bs chmod 644 ../blib/arch/auto/Bio/Ext/Align/Align.bs make[1]: Leaving directory `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align' make[1]: Entering directory `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden' cp read.pm ../blib/lib/Bio/SeqIO/staden/read.pm /usr/bin/perl -Mblib -MInline=NOISY,_INSTALL_ -MBio::SeqIO::staden::read -e1 0.01 ../blib/arch Starting Build Prepocess Stage Finished Build Prepocess Stage Starting Build Parse Stage Finished Build Parse Stage Starting Build Glue 1 Stage Finished Build Glue 1 Stage Starting Build Glue 2 Stage Finished Build Glue 2 Stage Starting Build Glue 3 Stage Finished Build Glue 3 Stage Starting Build Compile Stage Starting "perl Makefile.PL" Stage Note (probably harmless): No library found for -lread Writing Makefile for Bio::SeqIO::staden::read Finished "perl Makefile.PL" Stage Starting "make" Stage make[2]: Entering directory `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/read' /usr/bin/perl /usr/lib/perl5/5.8.0/ExtUtils/xsubpp -typemap /usr/lib/perl5/5.8.0/ExtUtils/typemap read.xs > read.xsc && mv read.xsc read.c gcc -c -I/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden -I/usr/local/include/io_lib -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS -DDEBUGGING -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -march=i386 -mcpu=i686 -g -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC "-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE" read.c read.xs:5:18: Read.h: No such file or directory read.xs: In function `staden_write_trace': read.xs:9: `Read' undeclared (first use in this function) read.xs:9: (Each undeclared identifier is reported only once read.xs:9: for each function it appears in.) read.xs:15: invalid lvalue in assignment read.xs:16: request for member `base' in something not a structure or union read.xs:18: request for member `ident' in something not a structure or union read.xs:21: request for member `ident' in something not a structure or union read.xs:23: request for member `info' in something not a structure or union read.xs:26: request for member `info' in something not a structure or union read.xs:28: request for member `format' in something not a structure or union read.xs:29: request for member `leftCutoff' in something not a structure or union read.xs:30: request for member `rightCutoff' in something not a structure or union read.xs:32: warning: assignment from incompatible pointer type read.xs:38: request for member `base' in something not a structure or union read.xs:41: request for member `prob_A' in something not a structure or union read.xs:45: request for member `prob_C' in something not a structure or union read.xs:49: request for member `prob_G' in something not a structure or union read.xs:53: request for member `prob_T' in something not a structure or union read.xs:58: request for member `prob_A' in something not a structure or union read.xs:58: request for member `prob_C' in something not a structure or union read.xs:59: request for member `prob_G' in something not a structure or union read.xs:59: request for member `prob_T' in something not a structure or union read.xs:62: request for member `prob_A' in something not a structure or union read.xs:62: request for member `prob_C' in something not a structure or union read.xs:63: request for member `prob_G' in something not a structure or union read.xs:63: request for member `prob_T' in something not a structure or union read.xs: In function `staden_read_trace': read.xs:76: `Read' undeclared (first use in this function) read.xs:81: invalid lvalue in assignment read.xs:83: `NULLRead' undeclared (first use in this function) read.xs:88: request for member `leftCutoff' in something not a structure or union read.xs:90: request for member `rightCutoff' in something not a structure or union read.xs:91: request for member `NBases' in something not a structure or union read.xs:91: request for member `NBases' in something not a structure or union read.xs:93: request for member `base' in something not a structure or union read.xs:94: request for member `prob_A' in something not a structure or union read.xs:94: request for member `prob_C' in something not a structure or union read.xs:95: request for member `prob_G' in something not a structure or union read.xs:95: request for member `prob_T' in something not a structure or union read.xs:144: request for member `ident' in something not a structure or union read.xs:145: request for member `info' in something not a structure or union make[2]: *** [read.o] Error 1 make[2]: Leaving directory `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/read' A problem was encountered while attempting to compile and install your Inline C code. The command that failed was: make The build directory was: /home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/read To debug the problem, cd to the build directory, and inspect the output files. at -e line 0 INIT failed--call queue aborted. make[1]: *** [read.inl] Error 2 make[1]: Leaving directory `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden' make: *** [subdirs] Error 2 Jason Stajich wrote: >Hey Barry! > You need to have installed Inline::C first. > > You don't need bioperl-ext unless you want the specialized stuff in there >(a smith-waterman implementation and access to the staden io library for > reading in trace files directly through perl). > >-jason >On Tue, 6 Jan 2004, Barry Moore wrote: > > > >>I'm installing bioperl 1.4 on my linux machine (RedHat 9.0, Perl 5.8). >>Bioperl-1.4 (the core) and bioperl-run-1.4 installed fine. I get the >>following errors when trying to install bioperl-ext-1.4: >> >>[root@Tatshenshini bioperl-ext-1.4]# perl Makefile.PL >>Checking if your kit is complete... >>Looks good >>Writing Makefile for Bio::Ext::Align >>ERROR from evaluation of >>/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/Makefile.PL: Can't locate >>Inline/MakeMaker.pm in @INC >>(@INC contains: /usr/lib/perl5/5.8.0/i386-linux-thread-multi >>/usr/lib/perl5/5.8.0 >>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi >>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl >>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi >>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl >>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 >>/home/bmoore/bioperl-ext-1.4 .) at ./Makefile.PL line 1. >>BEGIN failed--compilation aborted at ./Makefile.PL line 1. >>[root@Tatshenshini bioperl-ext-1.4]# >> >>I'm a bit linux challenged so any pointers, no matter how remedial, will >>be greatly appreciated. >> >>Barry Moore >>Dept. Human Genetics >>University of Utah >> >>_______________________________________________ >>Bioperl-l mailing list >>Bioperl-l@portal.open-bio.org >>http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> >> > >-- >Jason Stajich >Duke University >jason at cgt.mc.duke.edu >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > From Richard.Holland at agresearch.co.nz Tue Jan 6 20:30:15 2004 From: Richard.Holland at agresearch.co.nz (Holland, Richard) Date: Tue Jan 6 20:37:38 2004 Subject: [Bioperl-l] Relations Message-ID: Hi, I have written a script for loading term-term or sequence-term relations which comes in three parts - all now loaded and committed in CVS under bioperl-live/scripts/terms. The main script (importrelation.pl) is the core script which does not need to be touched to work (or should not!) - just run it and it will read all it's options from the configuration file, conf.xml. There are also a number of helper scripts of which I have so far written just one - these scripts expect data on STDIN, and output comma-separated pairs of terms and sequences on output. For instance, the interpro2go.pl parser supplied (which parses InterPro->GO relations from the interpro2go files) outputs pairs like IPR002291,GO:0008606. All helper scripts should output in this format - source term or sequence accession.version, comma, target term. The relations are stored as term_relationship entries for TERM2TERM relations, and bioentry_qualifier_value entries for SEQ2TERM relations, the former being Bio::Ontology::TermRelationship objects and the latter Bio::Annotation::OntologyTerm objects. Sample output from a config file using the existing interpro2go.pl helper script: ---START OUTPUT--- [hollandr@bifo1 biosql-go]$ ./importrelation.pl Running parsers... Parser interpro2go (type TERM2TERM) lives at ./interpro2go.pl (links InterPro to Gene Ontology) Downloading data from: http://www.geneontology.org/external2go/interpro2go ...downloaded to /tmp/LRbPjjDpYs. Parser starting... ...1000 records processed... ...2000 records processed... ...3000 records processed... ...4000 records processed... ...could not find target object GO:0008606 (for source IPR002291) - skipping... ...5000 records processed... ...6000 records processed... ...7000 records processed... ...could not find target object GO:0008567 (for source IPR004273) - skipping... ...8000 records processed... ...9000 records processed... ...10000 records processed... ...11000 records processed... ...parser finished with 11395 records. All parsers run. ---END OUTPUT--- The config file is a simple XML format - the parsers section defines all the parsers and where they get their datafiles from (scriptdir is where the helper scripts live). The httpproxy section defines your proxy server if you need one (optional), and the database section is the database config to connect to your BioSQL database with. Each parser in the parsers section has a name and a type (TERM2TERM for relations such as InterPro to GO, or SEQ2TERM for relations such as SwissProt to GO). The sourcenamespace is either the ontology name of the source terms, or the biodatabase name of the source accessions. The targetnamespace should be the ontology name of the target terms. Script is the name of the script to run, and the server section defines where to get the datafile from to parse with the script. TERM2TERM helper scripts output the first term name, comma, second term name. SEQ2TERM helper scripts output the accession and version separated by a fullstop, comma, term name. So... now all I need is some more helper scripts and the appropriate datasources to feed them with! It would be very easy to write some more once the datasources have been tracked down. Any volunteers? I'll keep working on my own ones for the time being until I hear some more. cheers, Richard PS. The code is not very well commented nor has any bug-checking in it, but it works if you're sensible. I might tidy it up one day... --- Richard Holland Bioinformatics Database Developer ITS, Agresearch Invermay x3279 -----Original Message----- From: Hilmar Lapp [mailto:hlapp@gmx.net] Sent: Wednesday, 7 January 2004 5:51 a.m. To: Holland, Richard Cc: bioperl-l@bioperl.org Subject: Re: [Bioperl-l] Relations I've heard someone wanted to code this up half a year ago, but AFAIK the script never made it into the repository. I think this would be very useful to have. The GO associations for RefSeq are present in RefSeq most of the time but obfuscated in the feature table. I wrote a SeqProcessor that promotes them to annotations, but RefSeq keeps changing the format of that on me, so even though possible it's not an approach that warms your heart. Note that LL also comes with GO links in the records, which are extracted fairly well by the parser. -hilmar On Monday, January 5, 2004, at 04:15 PM, Holland, Richard wrote: > Me again! Sorry about this heap of messages from me today, I'm having > a couple of BioPerl days to hammer out all the things my boss wants > done before the end of the month... > > Has anyone got a script to load GO term associations into BioSQL > bioentry_qualifier_value with? If not I'll put one together and post > it when it's done, but I don't want to write one if one already > exists. I'm interested in linking GO terms to RefSeqs (not sure where > to get the associations from there though), GO to InterPro, and GO to > SwissProt. Also InterPro to SwissProt if possible. > > cheers, > Richard > > --- > Richard Holland > Bioinformatics Database Developer > ITS, Agresearch Invermay x3279 > > > ====================================================================== > = > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From amackey at pcbi.upenn.edu Tue Jan 6 20:37:02 2004 From: amackey at pcbi.upenn.edu (Aaron J Mackey) Date: Tue Jan 6 20:44:03 2004 Subject: [Bioperl-l] Trouble installing bioperl-ext-1.4 In-Reply-To: <3FFB4187.3050102@genetics.utah.edu> Message-ID: This was the bit that you should have paid attention to: > Note (probably harmless): No library found for -lread Did you actually read the README, where it tells you that: This extension needs the rest of the main bioperl distribution to function properly. It is only useful as a helper module for the SeqIO system to read sequence trace files handled by the Staden package's io_lib "read" library. You should have this library installed prior to installing Bio::SeqIO::staden::read, it's currently available at: ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/io_lib/ -Aaron From Richard.Holland at agresearch.co.nz Tue Jan 6 21:17:12 2004 From: Richard.Holland at agresearch.co.nz (Holland, Richard) Date: Tue Jan 6 21:24:24 2004 Subject: [Bioperl-l] Interpro parsing problems - and solutions Message-ID: InterProParser.t has the following line: my $ipp = Bio::OntologyIO->new( -format => 'interpro', -file => $io->catfile('t','data','interpro_short.xml'), -ontology_engine => 'simple' ); As you can see it is specifying 'simple' for the ontology_engine - even if it did not, we should get a simple engine anyway, but until yesterday's fix we got an exception instead if this option was not specified. However I have left the test untouched as I'm not sure whether we should be testing default behaviour or not. I have tested all my changes from yesterday with this script, they passed, and I have committed them to the bioperl-live repository. cheers, Richard --- Richard Holland Bioinformatics Database Developer ITS, Agresearch Invermay x3279 -----Original Message----- From: Hilmar Lapp [mailto:hlapp@gmx.net] Sent: Wednesday, 7 January 2004 5:56 a.m. To: Holland, Richard Subject: Re: [Bioperl-l] Interpro parsing problems - and solutions Thanks for the fixes Richard. It is tremendously helpful if people submit patches. Do you have a cvs account? Would you be interested in applying those fixes (and possibly more :) yourself? As for the engine default, I thought the test would run without the type set. Maybe I'm mistaken on this one. Have you already tested all your changes against the InterProParser.t test script? -hilmar On Monday, January 5, 2004, at 03:58 PM, Holland, Richard wrote: > Hi all. A long one this but I hope it's worth the read. > > I found a possible bug in Bio/OntologyIO/InterProParser.pm. The > default behaviour for OntologyEngineI implementors is supposed to be a > 'simple' OntologyEngine. However, the code in InterProParser does not > default to anything if no engine is specified - it tries to set up an > 'undef' engine, which fails with a not-yet-implemented message. The > other parsers based on dagflat.pm do exhibit the default behaviour, so > to make InterProParser.pm do the same I added the following line at > line 130 (just before "if(lc($eng_type) eq 'simple')"): > > $eng_type = 'simple' unless $eng_type; > > Another possible bug in the same module - InterProParser.pm assumes > that > it has been passed a filename not a filehandle. As OntologyIO allows > for > both cases, I have adapted InterProParser.pm to suit: > > sub parse{ > my $self = shift; > > my $ret; > if ($self->file()) { > $ret = $self->{_parser}->parse( Source => { > SystemId => $self->file() } ); > } elsif ($self->_fh()) { > $ret = $self->{_parser}->parse( Source => { > ByteStream => $self->_fh() } ); > } else { > $ret = undef; > $self->throw("You have not provided any InterPro XML to > parse.\n"); > } > $self->_is_parsed(1); > return $ret; > } > > Also, in Bio/OntologyIO/Handlers/InterProHandler.pm (note different > module!), a definite bug this time, it does not know about two of the > interpro types - Active_site and Binding_site. Adding lines to > start_element as follows seems to work: > > sub start_element { > my ($self, $element) = @_; > my $ont = $self->ontology(); > my $fact = $self->term_factory(); > > if ($element->{Name} eq 'interprodb') { > # TWO NEW LINES FOLLOW > $ont->add_term($fact->create_object(-identifier => "Active_site", > -name => "Active Site") > ); > $ont->add_term($fact->create_object(-identifier => > "Binding_site", > -name => "Binding Site") > ); > # CONTINUE WITH ORIGINAL CODE > $ont->add_term($fact->create_object(-identifier => "Family", > -name => "Family") ); > $ont->add_term($fact->create_object(-identifier => "Domain", > -name => "Domain") ); > $ont->add_term($fact->create_object(-identifier => "Repeat", > -name => "Repeat") ); > $ont->add_term($fact->create_object(-identifier => "PTM", > -name => "post-translational > modification")); > > There is a problem with the relation loader in > Bio/Ontology/SimpleOntologyEngine.pm as well - get_term_by_identifier > returns an array of @terms, but the get_relationships subroutine calls > it twice and both times expects it to only return a single term. Other > calls to get_term_by_identifier in this module are correct. I have > adapted the two incorrect references in get_relationships to loop > through all terms returned by get_term_by_identifier instead, as > follows: > > # if a term is supplied, add a relationship for the parent to > the term > # except if the parent is the term itself (we added that one > before) > if($term && ($parent_id ne $term->identifier())) { > my @parent_terms = > $self->get_term_by_identifier($parent_id); > foreach my $parent_term (@parent_terms) { > push(@rels, > $relfact->create_object(-object_term => > $parent_term, > -subject_term => $term, > -predicate_term => > > $parent_entry->{$term->identifier}, > -ontology => > $term->ontology() > ) > ); > } > > } else { > # otherwise, i.e., no term supplied, or the parent equals > the > # supplied term > my @parent_terms = $term ? > ($term) : $self->get_term_by_identifier($parent_id); > foreach my $child_id (keys %$parent_entry) { > my $rel_info = $parent_entry->{$child_id}; > > foreach my $parent_term (@parent_terms) { > push(@rels, > $relfact->create_object(-object_term => > $parent_term, > -subject_term => > > $self->get_term_by_identifier( > > $child_id), > -predicate_term => > $rel_info, > -ontology > =>$parent_term->ontology > ) > ); > } > } > } > > There is also a bug in Bio/OntologyIO/Handlers/InterProHandler.pm > which does not set the current ontology of new temporary terms when > used in relationships. This causes "cannot call method 'name' on an > undefined value" errors later on when get_relationships tries to find > out the name of the ontology of each relationship. It also does not > set the 'name' values for these terms, so that you get 'cannot insert > null into SG_TERM.NAME' errors when the terms are later committed to > the database, > because the name column of sg_term has a 'not null' constraint, at > least > in the Oracle implementation of BioSQL. These problems can both be > fixed > by altering the call to the create_object function, in sub > _create_relationship, to include the -ontology and -name parameters: > > $term_temp = $ont->engine->add_term( $fact->create_object( > -InterPro_id => $ref_id, > -name > => $ref_id, > > -ontology => $ont ) ); > > And in sub start_element in the same module the same fix needs > applying (no need for -ontology here as the existing code following > this statement does this for us explicitly using a term->ontology() > call): > > $self->_term( > (!defined $term_temp) > ? $ont->add_term( $fact->create_object(-InterPro_id > => $id, > > -name => $id ) ) > : $term_temp > ); > > Note that this call defaults the name to be the same as the InterPro > ID. > Most temporary terms will be overridden with permanent data later in > the > process, but for those that slip through without permanent definitions > (possibly a bug in the InterPro XML datafile?) the above change is > necessary to allow them to be inserted into the database and their > relations to other terms kept valid. > > Lastly, the definition field of the term table is too short to take, > for > example, IPR001967 - I have extended it to the Oracle varchar2 maximum > of 4000 chars (up from 2000) in my BioSQL instance, but found it still > to be too short, so I added a quick fix to Bio/Ontology/Term.pm to > truncate definitions to be no more than this length, but would like to > know if this is a more general problem: > > sub definition { > my $self = shift; > > return $self->{'definition'} = substr(shift,0,4000) if @_; > return $self->{'definition'}; > } # definition > > Finally, Bio/OntologyIO/Handlers/InterProHandler.pm fails to set the > ontology for the base IS_A, CONTAINS and FOUND_IN relationship types. > This causes a null foreign key error on SG_TERM.ONT_OID when it tries > to insert them into the database. After checking > Bio/Ontology/SimpleGOEngine.pm and finding that it does set the > ontology > names for these relationships, I modified InterProHandler to do the > same > by adding the following three lines in the constructor (new) method > directly after the instantiation of the three relationship types: > > $is_a_rel->ontology($self->ontology()); > $contains_rel->ontology($self->ontology()); > $found_in_rel->ontology($self->ontology()); > > With all these changes in place, > "bioperl-db/scripts/biosql/load_ontology.pl --format interpro > interpro.xml" works correctly for the current release of interpro.xml. > It _does_ give many "unique constraint violated" errors on > TERM_RELATIONSHIP while inserting the relationships into BioSQL, but I > suspect this is because the get_relationships function in > InterProHandler.pm does not check to see if a relation has already > been pushed before pushing it onto the array of relations it returns. > To fix this would slow down the code considerably so it's probably > best to just live with the messages. > > Are these acceptable modifications or is there a better way to fix > these > problems? I admit my Perl may not be the best but hopefully you get the > idea of how my fixes work and may be able to code them in a better way. > > If any of these changes are acceptable could someone implement them > for me? I do not have access to CVS. > > Finally, if you think that I have been spending too much time trying > to fix these bugs when in fact there is an alternative and fully > functional way to load InterPro XML data into BioPerl/BioSQL, please > feel free to slap me around a bit with a wet haddock. This is my first > ever contribution to an open source project so I could do with some > advice on > how to do things better next time. > > cheers, > Richard > > PS. Totally unrelated but also a database field length problem - the > description field in bioentry is too short to hold SwissProt P05067 - > in my case I have lengthened the field to 1024 chars which does the > trick. > > PPS. Certain annotations in RefSeqs cause a similar overflow in > seqfeature_qualifier_value.value. I'm guessing that without using > CLOBs for all cases where free text is allowed, we'll never see the > end of these kinds of problems in the Oracle version of BioSQL? > > --- > Richard Holland > Bioinformatics Database Developer > ITS, Agresearch Invermay x3279 > > > ====================================================================== > = > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From juguang at tll.org.sg Tue Jan 6 22:11:19 2004 From: juguang at tll.org.sg (Juguang Xiao) Date: Tue Jan 6 22:17:48 2004 Subject: [Bioperl-l] Interpro parsing problems - and solutions In-Reply-To: Message-ID: <2A348A5B-40BF-11D8-B785-000A957702FE@tll.org.sg> Hi Richard, I have found the similar problem before, and my solution is to write the Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm for loading the InterPro into BioSQL database, since the serious user of InterPro will load the whole db, rather than the small piece in the test. When you load the InterPro into memory, you will found 1) your 1 GB virtual memory will be occupied in with Mac OSX, so that you cannot even do any further operation, and 2) nearly 10% of records are missing with current parser. I am trying to improve biosql a bit, with Hilmar's guidance, to adapt InterPro record ,and will complete the InterPro-BioSQL parser after that. The work is going to finish later and you will be noticed in this list. A bit further, my point is, for the huge biological file-based database, it is wise to load the complete set into RDBMS, rather than parsing them in memory, for the sake of the speed for the complicated queries, and the reliability of your script (due to the out-of-memory). Juguang On Tuesday, January 6, 2004, at 07:58 am, Holland, Richard wrote: > Hi all. A long one this but I hope it's worth the read. > > I found a possible bug in Bio/OntologyIO/InterProParser.pm. From xtordoir at ulg.ac.be Wed Jan 7 08:15:57 2004 From: xtordoir at ulg.ac.be (Tordoir Xavier) Date: Wed Jan 7 08:22:58 2004 Subject: [Bioperl-l] rendering features on global alignments Message-ID: <63607.139.165.180.188.1073481357.squirrel@mail2.ulg.ac.be> Hi, I am currently working on a system to interactively display features on multispecies global alignments. The purpose is to use the alignment as reference instead of choosing arbitrarily one of the original sequences as reference. So far I have been able to display a global alignment (ins, dels or dna at high magnification) on the Generic Genome Browser, but I had to use a few tricks to make it work (e.g. 'segments' Glyph is designed for local alignments). Before going further, I would like to know if someone is aware of a customizable browser for global alignments (preferably based on Bioperl) or if someone described a way to use the GGB for multiple global alignments. Thank you in advance, Xavier Tordoir From Annie.Law at nrc-cnrc.gc.ca Wed Jan 7 16:30:03 2004 From: Annie.Law at nrc-cnrc.gc.ca (Law, Annie) Date: Wed Jan 7 16:37:15 2004 Subject: [Bioperl-l] Clones and Unigene annotation Message-ID: <10C94843061E094A98C02EB77CFC328722FDF0@nrcmrdex1d.imsb.nrc.ca> Hi, I have started to look at the resources available on the bioperl website. It looks like there are are some tools available that will help me accomplish my task. I have a list of clone IDs and I would like to do some annotation. For starters I have gone to the I.M.A.G.E. site and I have found the Genbank accession numbers corresponding to the clone IDs. I would like to find the corresponding unigene IDs for these accession numbers. My goal is to have a database with clone IDs, accession number, and unigene ID, and allow a user to add his own personal annotation as well. Later on, I would like to annotate with other information as well. I would like to know if bioperl is the way to go or if there is already something available. One of the advantages with bioperl is that I will be able to control how often the database gets updated. This is a problem with some of the tools I have seen that are available on the web. Basically, I think that there are two tools that are available from bioperl that are of use to me. There is a file called load_seqdatabase.pl that will allow me to load a unigene file into a biosql db. Aside from the resource link listed below is there any more documentation or examples available for the use of this script? http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-db/scripts/Attic/ load_seqdatabase.pl?logsort=date&annotate=1.31&sortby=log&hideattic=1&search =None&hidecvsroot=1&diff_format=h There are also Unigene objects and a parsing tool Bio::Cluster::UniGene, and Bio::ClusterIO respectively. I saw in a March 2003 post that someone was trying to do something along the same lines without the database idea using the unigene objects. http://bioperl.org/pipermail/bioperl-l/2003-March/011733.html However, the major complaint was that it was too slow (I will be dealing with 20 000 clone IDs at a time). I was wondering if anything has changed since then. Even if the process was fast. My next question would be if I used the parser to find a matching accession number and the corresponding unigene ID would the next natural step be to insert this data in some database I created. I am not sure whether the load_seqdatabase.pl tool or the unigene objects is best suited for my needs. Since I am new to bioperl I am not to sure what the intention was for the creation of the Unigene objects and what most people use them for. I would appreciate any tips on the most appropriate way to use bioperl to accomplish my task. thanks very much, Annie. From brian_osborne at cognia.com Wed Jan 7 16:55:30 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Wed Jan 7 17:03:25 2004 Subject: [Bioperl-l] Clones and Unigene annotation In-Reply-To: <10C94843061E094A98C02EB77CFC328722FDF0@nrcmrdex1d.imsb.nrc.ca> Message-ID: Annie, It sounds like part of your project may involve retrieving id's from Genbank entries. Take a look at the Feature-Annotation HOWTO, perhaps it will answer some of your questions on this particular topic. However this doesn't sound like the tricky part of your project... Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Law, Annie Sent: Wednesday, January 07, 2004 4:30 PM To: 'bioperl-l@portal.open-bio.org' Subject: [Bioperl-l] Clones and Unigene annotation Hi, I have started to look at the resources available on the bioperl website. It looks like there are are some tools available that will help me accomplish my task. I have a list of clone IDs and I would like to do some annotation. For starters I have gone to the I.M.A.G.E. site and I have found the Genbank accession numbers corresponding to the clone IDs. I would like to find the corresponding unigene IDs for these accession numbers. My goal is to have a database with clone IDs, accession number, and unigene ID, and allow a user to add his own personal annotation as well. Later on, I would like to annotate with other information as well. I would like to know if bioperl is the way to go or if there is already something available. One of the advantages with bioperl is that I will be able to control how often the database gets updated. This is a problem with some of the tools I have seen that are available on the web. Basically, I think that there are two tools that are available from bioperl that are of use to me. There is a file called load_seqdatabase.pl that will allow me to load a unigene file into a biosql db. Aside from the resource link listed below is there any more documentation or examples available for the use of this script? http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-db/scripts/Attic/ load_seqdatabase.pl?logsort=date&annotate=1.31&sortby=log&hideattic=1&search =None&hidecvsroot=1&diff_format=h There are also Unigene objects and a parsing tool Bio::Cluster::UniGene, and Bio::ClusterIO respectively. I saw in a March 2003 post that someone was trying to do something along the same lines without the database idea using the unigene objects. http://bioperl.org/pipermail/bioperl-l/2003-March/011733.html However, the major complaint was that it was too slow (I will be dealing with 20 000 clone IDs at a time). I was wondering if anything has changed since then. Even if the process was fast. My next question would be if I used the parser to find a matching accession number and the corresponding unigene ID would the next natural step be to insert this data in some database I created. I am not sure whether the load_seqdatabase.pl tool or the unigene objects is best suited for my needs. Since I am new to bioperl I am not to sure what the intention was for the creation of the Unigene objects and what most people use them for. I would appreciate any tips on the most appropriate way to use bioperl to accomplish my task. thanks very much, Annie. _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From natg at shore.net Wed Jan 7 20:46:22 2004 From: natg at shore.net (Nathan (Nat) Goodman) Date: Wed Jan 7 20:54:57 2004 Subject: [Bioperl-l] RE: Clones and Unigene annotation Message-ID: <001e01c3d589$37feff00$3300a8c0@goodmandesktop> Hi Annie > My goal is to have a database with clone IDs, accession number, > and unigene ID,... We have a system called Connect-the-Dots that does exactly this. You can check out a web demo at http://jdrf.systemsbiology.org/software/website/cgi-bin/dotHome.cgi. (Although I just tried it and see that it?s broken, so please let us know if it?s still broken when you try.) The system probably does exactly what you want in terms of copnnecting IDs. If not, it?s easy to extend. If you have more IDs than the web demo allows, contact us and we can do a "private" run for you. The person working on this is Yang Wang, cc?ed above. I?ve also cc?ed Erin Helton who handles general web issues (among many other things). Good luck, Nat Goodman ---------------------------------------------------------------------- Nathan (Nat) Goodman Senior Research Scientist Institute for Systems Biology 1441 North 34th Street Seattle, WA 98103-8904 206-331-0077 206-363-0431 (fax) natg@shore.net http://home.comcast.net/~natgoodman/ From bhurwitz at twt.com Wed Jan 7 22:17:48 2004 From: bhurwitz at twt.com (bhurwitz@twt.com) Date: Wed Jan 7 22:26:47 2004 Subject: [Bioperl-l] Trouble installing bioperl-1.4 due to RestrictionIO Message-ID: Hello, I am installing BioPerl 1.4 on a virtual machine through vmware that previously did not have bioperl (RedHat 7.3, perl 5.6.1). I am getting the following error from CPAN. Does anyone know what this could mean? I have installed the BioPerl Bundle prior to this successfully (C/CR/CRAFFI/Bundle-BioPerl-2.1.0.tar.gz) -Bonnie Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/RestrictionIO.t 14 1 7.14% 10 121 subtests skipped. Failed 1/179 test scripts, 99.44% okay. 1/8268 subtests failed, 99.99% okay. make: *** [test_dynamic] Error 11 /usr/bin/make test -- NOT OK Running make install make test had returned bad status, won't install without force Barry Moore .edu> cc: bioperl-l@bioperl.org Sent by: Subject: Re: [Bioperl-l] Trouble installing bioperl-ext-1.4 bioperl-l-bounces@portal.o pen-bio.org 01/06/2004 05:15 PM Jason et al- ...while trying to install bioperl-ext-1.4 your suggestion for installing Inline::C first seems to have worked. Makefile.PL ran fine (highlighted below in green - if your reading HTML mail). However, now I get errors on running make. I've copied the entire output from the make command below (with some masking of low complexity regions). Sorry it's so long, but I'm having trouble spotting the problem, so I didn't want to leave out any of the important parts. The part indicating errors is at the end (highlighted in red). Barry [root@Tatshenshini bioperl-ext-1.4]# perl Makefile.PL Checking if your kit is complete... Looks good Writing Makefile for Bio::Ext::Align Please tell us where your Staden io_lib "read" library is installed: [/usr/local/lib] Please tell us where your Staden io_lib "Read.h" header is installed: [/usr/local/include/io_lib] Writing Makefile for Bio::SeqIO::staden::read Writing Makefile for Bio One or more DATA sections were not processed by Inline. [root@Tatshenshini bioperl-ext-1.4]# make cp Bio/Ext/Align/libs/hscore.h blib/lib/Bio/Ext/Align/libs/hscore.h ###Removed alot of cp commands to shorten e-mail post### cp Bio/Ext/Align/libs/wisefile.h blib/lib/Bio/Ext/Align/libs/wisefile.h make[1]: Entering directory `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align' cp Align.pm ../blib/lib/Bio/Ext/Align.pm DEFINE='-DPOSIX -DNOERROR'; CC='gcc'; export DEFINE INC CC; \ cd libs && make CC=gcc libsw.a -e make[2]: Entering directory `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align/libs' gcc -c -O -c -o aln.o aln.c ###Removed alot of gcc commands to shorten e-mail post### gcc -c -O -c -o linspc.o linspc.c ar ru libsw.a aln.o alnconvert.o alnrange.o asciibtcanvas.o basematrix.o btcanvas.o commandline.o complexconsensi.o complexevalset.o complexsequence.o compmat.o codon.o dna.o dnamatrix.o dpenvelope.o dynlibcross.o histogram.o hscore.o linesubs.o packaln.o probability.o protein.o proteindb.o proteinsw.o seqaligndisplay.o sequence.o sequencedb.o sw_wrap.o wiseerror.o wisefile.o wisememman.o wiseoverlay.o wiserandom.o wisestring.o wisetime.o dpalign.o linspc.o make[2]: Leaving directory `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align/libs' /usr/bin/perl /usr/lib/perl5/5.8.0/ExtUtils/xsubpp -typemap /usr/lib/perl5/5.8.0/ExtUtils/typemap -typemap typemap Align.xs > Align.xsc && mv Align.xsc Align.c gcc -c -I./libs -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS -DDEBUGGING -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -march=i386 -mcpu=i686 -g -DVERSION=\"0.1\" -DXS_VERSION=\"0.1\" -fPIC "-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE" -DPOSIX -DNOERROR Align.c Running Mkbootstrap for Bio::Ext::Align () chmod 644 Align.bs rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so LD_RUN_PATH="" gcc -shared -L/usr/local/lib Align.o -o ../blib/arch/auto/Bio/Ext/Align/Align.so libs/libsw.a -lm chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so cp Align.bs ../blib/arch/auto/Bio/Ext/Align/Align.bs chmod 644 ../blib/arch/auto/Bio/Ext/Align/Align.bs make[1]: Leaving directory `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align' make[1]: Entering directory `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden' cp read.pm ../blib/lib/Bio/SeqIO/staden/read.pm /usr/bin/perl -Mblib -MInline=NOISY,_INSTALL_ -MBio::SeqIO::staden::read -e1 0.01 ../blib/arch Starting Build Prepocess Stage Finished Build Prepocess Stage Starting Build Parse Stage Finished Build Parse Stage Starting Build Glue 1 Stage Finished Build Glue 1 Stage Starting Build Glue 2 Stage Finished Build Glue 2 Stage Starting Build Glue 3 Stage Finished Build Glue 3 Stage Starting Build Compile Stage Starting "perl Makefile.PL" Stage Note (probably harmless): No library found for -lread Writing Makefile for Bio::SeqIO::staden::read Finished "perl Makefile.PL" Stage Starting "make" Stage make[2]: Entering directory `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/read' /usr/bin/perl /usr/lib/perl5/5.8.0/ExtUtils/xsubpp -typemap /usr/lib/perl5/5.8.0/ExtUtils/typemap read.xs > read.xsc && mv read.xsc read.c gcc -c -I/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden -I/usr/local/include/io_lib -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS -DDEBUGGING -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -march=i386 -mcpu=i686 -g -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC "-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE" read.c read.xs:5:18: Read.h: No such file or directory read.xs: In function `staden_write_trace': read.xs:9: `Read' undeclared (first use in this function) read.xs:9: (Each undeclared identifier is reported only once read.xs:9: for each function it appears in.) read.xs:15: invalid lvalue in assignment read.xs:16: request for member `base' in something not a structure or union read.xs:18: request for member `ident' in something not a structure or union read.xs:21: request for member `ident' in something not a structure or union read.xs:23: request for member `info' in something not a structure or union read.xs:26: request for member `info' in something not a structure or union read.xs:28: request for member `format' in something not a structure or union read.xs:29: request for member `leftCutoff' in something not a structure or union read.xs:30: request for member `rightCutoff' in something not a structure or union read.xs:32: warning: assignment from incompatible pointer type read.xs:38: request for member `base' in something not a structure or union read.xs:41: request for member `prob_A' in something not a structure or union read.xs:45: request for member `prob_C' in something not a structure or union read.xs:49: request for member `prob_G' in something not a structure or union read.xs:53: request for member `prob_T' in something not a structure or union read.xs:58: request for member `prob_A' in something not a structure or union read.xs:58: request for member `prob_C' in something not a structure or union read.xs:59: request for member `prob_G' in something not a structure or union read.xs:59: request for member `prob_T' in something not a structure or union read.xs:62: request for member `prob_A' in something not a structure or union read.xs:62: request for member `prob_C' in something not a structure or union read.xs:63: request for member `prob_G' in something not a structure or union read.xs:63: request for member `prob_T' in something not a structure or union read.xs: In function `staden_read_trace': read.xs:76: `Read' undeclared (first use in this function) read.xs:81: invalid lvalue in assignment read.xs:83: `NULLRead' undeclared (first use in this function) read.xs:88: request for member `leftCutoff' in something not a structure or union read.xs:90: request for member `rightCutoff' in something not a structure or union read.xs:91: request for member `NBases' in something not a structure or union read.xs:91: request for member `NBases' in something not a structure or union read.xs:93: request for member `base' in something not a structure or union read.xs:94: request for member `prob_A' in something not a structure or union read.xs:94: request for member `prob_C' in something not a structure or union read.xs:95: request for member `prob_G' in something not a structure or union read.xs:95: request for member `prob_T' in something not a structure or union read.xs:144: request for member `ident' in something not a structure or union read.xs:145: request for member `info' in something not a structure or union make[2]: *** [read.o] Error 1 make[2]: Leaving directory `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/read' A problem was encountered while attempting to compile and install your Inline C code. The command that failed was: make The build directory was: /home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/read To debug the problem, cd to the build directory, and inspect the output files. at -e line 0 INIT failed--call queue aborted. make[1]: *** [read.inl] Error 2 make[1]: Leaving directory `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden' make: *** [subdirs] Error 2 Jason Stajich wrote: >Hey Barry! > You need to have installed Inline::C first. > > You don't need bioperl-ext unless you want the specialized stuff in there >(a smith-waterman implementation and access to the staden io library for > reading in trace files directly through perl). > >-jason >On Tue, 6 Jan 2004, Barry Moore wrote: > > > >>I'm installing bioperl 1.4 on my linux machine (RedHat 9.0, Perl 5.8). >>Bioperl-1.4 (the core) and bioperl-run-1.4 installed fine. I get the >>following errors when trying to install bioperl-ext-1.4: >> >>[root@Tatshenshini bioperl-ext-1.4]# perl Makefile.PL >>Checking if your kit is complete... >>Looks good >>Writing Makefile for Bio::Ext::Align >>ERROR from evaluation of >>/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/Makefile.PL: Can't locate >>Inline/MakeMaker.pm in @INC >>(@INC contains: /usr/lib/perl5/5.8.0/i386-linux-thread-multi >>/usr/lib/perl5/5.8.0 >>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi >>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl >>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi >>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl >>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 >>/home/bmoore/bioperl-ext-1.4 .) at ./Makefile.PL line 1. >>BEGIN failed--compilation aborted at ./Makefile.PL line 1. >>[root@Tatshenshini bioperl-ext-1.4]#>> >>I'm a bit linux challenged so any pointers, no matter how remedial, will >>be greatly appreciated. >> >>Barry Moore >>Dept. Human Genetics >>University of Utah >> >>_______________________________________________ >>Bioperl-l mailing list >>Bioperl-l@portal.open-bio.org >>http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> >> > >-- >Jason Stajich >Duke University >jason at cgt.mc.duke.edu >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From iain.wallace at ucd.ie Thu Jan 8 07:18:23 2004 From: iain.wallace at ucd.ie (Iain Wallace) Date: Thu Jan 8 07:25:23 2004 Subject: [Bioperl-l] Mid point rooting of a tree Message-ID: <1073564303.3969.3.camel@bioinf10> Hi all, I was wondering if anyone knows of a command line program that can root an unrooted tree. I know of a graphical program , NJPlot, but I want to root lots of trees output from clustalw. Thanks Iain From amackey at virginia.edu Thu Jan 8 09:09:47 2004 From: amackey at virginia.edu (Aaron J.Mackey) Date: Thu Jan 8 09:16:47 2004 Subject: [Bioperl-l] Fwd: mistake in documentation Message-ID: <50D9D0DC-41E4-11D8-AD9C-000A958C5008@virginia.edu> Begin forwarded message: > From: heiko@mwgdna.com > Date: January 8, 2004 8:52:09 AM EST > To: amackey@virginia.edu > Subject: mistake in documentation > > Hi there is a mistake in the documentation: > > http://doc.bioperl.org/releases/bioperl-1.4/Bio/DB/GenBank.html#POD2 > > this function throws a warning not an exception > since version 1.4 > From peter.robinson at charite.de Thu Jan 8 10:18:22 2004 From: peter.robinson at charite.de (Robinson, Peter) Date: Thu Jan 8 10:26:17 2004 Subject: [Bioperl-l] loading sprot.dat Message-ID: <5F7CE35370B6CF429AA3CA960ECC27805389E3@EXCHANGE2.charite.de> Hi all, I would like to load the contents of the Swiss-Prot file sprot.dat into a mysql database. Since I have a relatively specific question, I would like to use a databse of my own design and just extract portions of the relevant entries from sprot.dat rather than the whole thing. I would appreciate it if someone could point me to an example script for this kind of thing. I did not see anything like this in my perusals of the archives or google, please forgive me if this question has been asked before! Thanks Peter From jason at cgt.duhs.duke.edu Thu Jan 8 10:45:31 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Thu Jan 8 10:52:32 2004 Subject: [Bioperl-l] Trouble installing bioperl-1.4 due to RestrictionIO In-Reply-To: References: Message-ID: Just ignore it. cpan> force install Bio::Perl if you like. On Wed, 7 Jan 2004 bhurwitz@twt.com wrote: > > Hello, > > I am installing BioPerl 1.4 on a virtual machine through vmware that > previously did not have bioperl (RedHat 7.3, perl 5.6.1). I am getting the > following error from CPAN. Does anyone know what this could mean? I have > installed the BioPerl Bundle prior to this successfully > (C/CR/CRAFFI/Bundle-BioPerl-2.1.0.tar.gz) > > -Bonnie > > > Failed Test Stat Wstat Total Fail Failed List of Failed > ------------------------------------------------------------------------------- > t/RestrictionIO.t 14 1 7.14% 10 > 121 subtests skipped. > Failed 1/179 test scripts, 99.44% okay. 1/8268 subtests failed, 99.99% > okay. > make: *** [test_dynamic] Error 11 > /usr/bin/make test -- NOT OK > Running make install > make test had returned bad status, won't install without force > > > > > > Barry Moore > > .edu> cc: bioperl-l@bioperl.org > Sent by: Subject: Re: [Bioperl-l] Trouble installing bioperl-ext-1.4 > bioperl-l-bounces@portal.o > pen-bio.org > > > 01/06/2004 05:15 PM > > > > > > > Jason et al- > > ...while trying to install bioperl-ext-1.4 your suggestion for > installing Inline::C first seems to have worked. Makefile.PL ran fine > (highlighted below in green - if your reading HTML mail). However, now > I get errors on running make. I've copied the entire output from the > make command below (with some masking of low complexity regions). Sorry > it's so long, but I'm having trouble spotting the problem, so I didn't > want to leave out any of the important parts. The part indicating > errors is at the end (highlighted in red). > > Barry > > [root@Tatshenshini bioperl-ext-1.4]# perl Makefile.PL > Checking if your kit is complete... > Looks good > Writing Makefile for Bio::Ext::Align > Please tell us where your Staden io_lib "read" library is installed: > [/usr/local/lib] > Please tell us where your Staden io_lib "Read.h" header is installed: > [/usr/local/include/io_lib] > Writing Makefile for Bio::SeqIO::staden::read > Writing Makefile for Bio > One or more DATA sections were not processed by Inline. > > [root@Tatshenshini bioperl-ext-1.4]# make > cp Bio/Ext/Align/libs/hscore.h blib/lib/Bio/Ext/Align/libs/hscore.h > ###Removed alot of cp commands to shorten e-mail post### > cp Bio/Ext/Align/libs/wisefile.h blib/lib/Bio/Ext/Align/libs/wisefile.h > make[1]: Entering directory `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align' > cp Align.pm ../blib/lib/Bio/Ext/Align.pm > DEFINE='-DPOSIX -DNOERROR'; CC='gcc'; export DEFINE INC CC; \ > cd libs && make CC=gcc libsw.a -e > make[2]: Entering directory > `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align/libs' > gcc -c -O -c -o aln.o aln.c > ###Removed alot of gcc commands to shorten e-mail post### > gcc -c -O -c -o linspc.o linspc.c > ar ru libsw.a aln.o alnconvert.o alnrange.o asciibtcanvas.o basematrix.o > btcanvas.o commandline.o complexconsensi.o > complexevalset.o complexsequence.o compmat.o codon.o dna.o dnamatrix.o > dpenvelope.o dynlibcross.o histogram.o hscore.o linesubs.o packaln.o > probability.o protein.o proteindb.o proteinsw.o seqaligndisplay.o > sequence.o sequencedb.o sw_wrap.o wiseerror.o wisefile.o wisememman.o > wiseoverlay.o wiserandom.o wisestring.o wisetime.o dpalign.o linspc.o > make[2]: Leaving directory > `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align/libs' > /usr/bin/perl /usr/lib/perl5/5.8.0/ExtUtils/xsubpp -typemap > /usr/lib/perl5/5.8.0/ExtUtils/typemap -typemap typemap > Align.xs > Align.xsc && mv Align.xsc Align.c > gcc -c -I./libs -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS > -DDEBUGGING -fno-strict-aliasing -I/usr/local/include > -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 > -march=i386 -mcpu=i686 -g -DVERSION=\"0.1\" -DXS_VERSION=\"0.1\" -fPIC > "-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE" -DPOSIX -DNOERROR > Align.c > Running Mkbootstrap for Bio::Ext::Align () > chmod 644 Align.bs > rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so > LD_RUN_PATH="" gcc -shared -L/usr/local/lib Align.o -o > ../blib/arch/auto/Bio/Ext/Align/Align.so libs/libsw.a -lm > > chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so > cp Align.bs ../blib/arch/auto/Bio/Ext/Align/Align.bs > chmod 644 ../blib/arch/auto/Bio/Ext/Align/Align.bs > make[1]: Leaving directory `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align' > make[1]: Entering directory `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden' > cp read.pm ../blib/lib/Bio/SeqIO/staden/read.pm > /usr/bin/perl -Mblib -MInline=NOISY,_INSTALL_ -MBio::SeqIO::staden::read > -e1 0.01 ../blib/arch > Starting Build Prepocess Stage > Finished Build Prepocess Stage > > Starting Build Parse Stage > Finished Build Parse Stage > > Starting Build Glue 1 Stage > Finished Build Glue 1 Stage > > Starting Build Glue 2 Stage > Finished Build Glue 2 Stage > > Starting Build Glue 3 Stage > Finished Build Glue 3 Stage > > Starting Build Compile Stage > Starting "perl Makefile.PL" Stage > Note (probably harmless): No library found for -lread > Writing Makefile for Bio::SeqIO::staden::read > Finished "perl Makefile.PL" Stage > > Starting "make" Stage > make[2]: Entering directory > `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/read' > > /usr/bin/perl /usr/lib/perl5/5.8.0/ExtUtils/xsubpp -typemap > /usr/lib/perl5/5.8.0/ExtUtils/typemap read.xs > read.xsc && mv > read.xsc read.c > gcc -c -I/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden > -I/usr/local/include/io_lib -D_REENTRANT -D_GNU_SOURCE > -DTHREADS_HAVE_PIDS -DDEBUGGING -fno-strict-aliasing > -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 > -I/usr/include/gdbm -O2 -march=i386 -mcpu=i686 -g -DVERSION=\"0.01\" > -DXS_VERSION=\"0.01\" -fPIC > "-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE" read.c > read.xs:5:18: Read.h: No such file or directory > read.xs: In function `staden_write_trace': > read.xs:9: `Read' undeclared (first use in this function) > read.xs:9: (Each undeclared identifier is reported only once > read.xs:9: for each function it appears in.) > read.xs:15: invalid lvalue in assignment > read.xs:16: request for member `base' in something not a structure or union > read.xs:18: request for member `ident' in something not a structure or > union > read.xs:21: request for member `ident' in something not a structure or > union > read.xs:23: request for member `info' in something not a structure or union > read.xs:26: request for member `info' in something not a structure or union > read.xs:28: request for member `format' in something not a structure or > union > read.xs:29: request for member `leftCutoff' in something not a structure > or union > read.xs:30: request for member `rightCutoff' in something not a > structure or union > read.xs:32: warning: assignment from incompatible pointer type > read.xs:38: request for member `base' in something not a structure or union > read.xs:41: request for member `prob_A' in something not a structure or > union > read.xs:45: request for member `prob_C' in something not a structure or > union > read.xs:49: request for member `prob_G' in something not a structure or > union > read.xs:53: request for member `prob_T' in something not a structure or > union > read.xs:58: request for member `prob_A' in something not a structure or > union > read.xs:58: request for member `prob_C' in something not a structure or > union > read.xs:59: request for member `prob_G' in something not a structure or > union > read.xs:59: request for member `prob_T' in something not a structure or > union > read.xs:62: request for member `prob_A' in something not a structure or > union > read.xs:62: request for member `prob_C' in something not a structure or > union > read.xs:63: request for member `prob_G' in something not a structure or > union > read.xs:63: request for member `prob_T' in something not a structure or > union > read.xs: In function `staden_read_trace': > read.xs:76: `Read' undeclared (first use in this function) > read.xs:81: invalid lvalue in assignment > read.xs:83: `NULLRead' undeclared (first use in this function) > read.xs:88: request for member `leftCutoff' in something not a structure > or union > read.xs:90: request for member `rightCutoff' in something not a > structure or union > read.xs:91: request for member `NBases' in something not a structure or > union > read.xs:91: request for member `NBases' in something not a structure or > union > read.xs:93: request for member `base' in something not a structure or union > read.xs:94: request for member `prob_A' in something not a structure or > union > read.xs:94: request for member `prob_C' in something not a structure or > union > read.xs:95: request for member `prob_G' in something not a structure or > union > read.xs:95: request for member `prob_T' in something not a structure or > union > read.xs:144: request for member `ident' in something not a structure or > union > read.xs:145: request for member `info' in something not a structure or > union > make[2]: *** [read.o] Error 1 > make[2]: Leaving directory > `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/read' > > > A problem was encountered while attempting to compile and install your > Inline > C code. The command that failed was: > make > > The build directory was: > /home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/read > > > To debug the problem, cd to the build directory, and inspect the output > files. > > at -e line 0 > INIT failed--call queue aborted. > make[1]: *** [read.inl] Error 2 > make[1]: Leaving directory `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden' > make: *** [subdirs] Error 2 > > > Jason Stajich wrote: > > >Hey Barry! > > You need to have installed Inline::C first. > > > > You don't need bioperl-ext unless you want the specialized stuff in there > >(a smith-waterman implementation and access to the staden io library for > > reading in trace files directly through perl). > > > >-jason > >On Tue, 6 Jan 2004, Barry Moore wrote: > > > > > > > >>I'm installing bioperl 1.4 on my linux machine (RedHat 9.0, Perl 5.8). > >>Bioperl-1.4 (the core) and bioperl-run-1.4 installed fine. I get the > >>following errors when trying to install bioperl-ext-1.4: > >> > >>[root@Tatshenshini bioperl-ext-1.4]# perl Makefile.PL > >>Checking if your kit is complete... > >>Looks good > >>Writing Makefile for Bio::Ext::Align > >>ERROR from evaluation of > >>/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/Makefile.PL: Can't locate > >>Inline/MakeMaker.pm in @INC > >>(@INC contains: /usr/lib/perl5/5.8.0/i386-linux-thread-multi > >>/usr/lib/perl5/5.8.0 > >>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi > >>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl > >>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi > >>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl > >>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 > >>/home/bmoore/bioperl-ext-1.4 .) at ./Makefile.PL line 1. > >>BEGIN failed--compilation aborted at ./Makefile.PL line 1. > >>[root@Tatshenshini bioperl-ext-1.4]# >> > >>I'm a bit linux challenged so any pointers, no matter how remedial, will > >>be greatly appreciated. > >> > >>Barry Moore > >>Dept. Human Genetics > >>University of Utah > >> > >>_______________________________________________ > >>Bioperl-l mailing list > >>Bioperl-l@portal.open-bio.org > >>http://portal.open-bio.org/mailman/listinfo/bioperl-l > >> > >> > >> > > > >-- > >Jason Stajich > >Duke University > >jason at cgt.mc.duke.edu > >_______________________________________________ > >Bioperl-l mailing list > >Bioperl-l@portal.open-bio.org > >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From brian_osborne at cognia.com Thu Jan 8 10:55:43 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Thu Jan 8 11:03:04 2004 Subject: [Bioperl-l] loading sprot.dat In-Reply-To: <5F7CE35370B6CF429AA3CA960ECC27805389E3@EXCHANGE2.charite.de> Message-ID: Peter, Some of the data in a SwissProt file is parsed into Features, some of it into Annotations (Swissprot entries are RichSeq objects, like Genbank and EMBL entries). So probably you'll want to look at the Feature-Annotation HOWTO. Unfortunately there are no Swissprot examples there but the logic will be the same, open the file with SeqIO and print out specific entries, or portions of entries, with the desired characteristics. Perhaps the SeqIO HOWTO would be useful as well... Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Robinson, Peter Sent: Thursday, January 08, 2004 10:18 AM To: bioperl-l@bioperl.org Subject: [Bioperl-l] loading sprot.dat Hi all, I would like to load the contents of the Swiss-Prot file sprot.dat into a mysql database. Since I have a relatively specific question, I would like to use a databse of my own design and just extract portions of the relevant entries from sprot.dat rather than the whole thing. I would appreciate it if someone could point me to an example script for this kind of thing. I did not see anything like this in my perusals of the archives or google, please forgive me if this question has been asked before! Thanks Peter _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From redwards at utmem.edu Thu Jan 8 12:03:19 2004 From: redwards at utmem.edu (Rob Edwards) Date: Thu Jan 8 12:10:27 2004 Subject: [Bioperl-l] Trouble installing bioperl-1.4 due to RestrictionIO In-Reply-To: ; from jason@cgt.duhs.duke.edu on Thu, Jan 08, 2004 at 10:45:31AM -0500 References: Message-ID: <20040108110319.X22435@redwards2.utmem.edu> I am curious as to why this test is failing. Has anyone else had this fail? It passes for me (on Mac OS10.3) Rob On Thu, Jan 08, 2004 at 10:45:31AM -0500, Jason Stajich wrote: > Just ignore it. > > cpan> force install Bio::Perl > > if you like. > > On Wed, 7 Jan 2004 bhurwitz@twt.com wrote: > > > > > Hello, > > > > I am installing BioPerl 1.4 on a virtual machine through vmware that > > previously did not have bioperl (RedHat 7.3, perl 5.6.1). I am getting the > > following error from CPAN. Does anyone know what this could mean? I have > > installed the BioPerl Bundle prior to this successfully > > (C/CR/CRAFFI/Bundle-BioPerl-2.1.0.tar.gz) > > > > -Bonnie > > > > > > Failed Test Stat Wstat Total Fail Failed List of Failed > > ------------------------------------------------------------------------------- > > t/RestrictionIO.t 14 1 7.14% 10 > > 121 subtests skipped. > > Failed 1/179 test scripts, 99.44% okay. 1/8268 subtests failed, 99.99% > > okay. > > make: *** [test_dynamic] Error 11 > > /usr/bin/make test -- NOT OK > > Running make install > > make test had returned bad status, won't install without force > > > > > > > > > > > > Barry Moore > > > > .edu> cc: bioperl-l@bioperl.org > > Sent by: Subject: Re: [Bioperl-l] Trouble installing bioperl-ext-1.4 > > bioperl-l-bounces@portal.o > > pen-bio.org > > > > > > 01/06/2004 05:15 PM > > > > > > > > > > > > > > Jason et al- > > > > ...while trying to install bioperl-ext-1.4 your suggestion for > > installing Inline::C first seems to have worked. Makefile.PL ran fine > > (highlighted below in green - if your reading HTML mail). However, now > > I get errors on running make. I've copied the entire output from the > > make command below (with some masking of low complexity regions). Sorry > > it's so long, but I'm having trouble spotting the problem, so I didn't > > want to leave out any of the important parts. The part indicating > > errors is at the end (highlighted in red). > > > > Barry > > > > [root@Tatshenshini bioperl-ext-1.4]# perl Makefile.PL > > Checking if your kit is complete... > > Looks good > > Writing Makefile for Bio::Ext::Align > > Please tell us where your Staden io_lib "read" library is installed: > > [/usr/local/lib] > > Please tell us where your Staden io_lib "Read.h" header is installed: > > [/usr/local/include/io_lib] > > Writing Makefile for Bio::SeqIO::staden::read > > Writing Makefile for Bio > > One or more DATA sections were not processed by Inline. > > > > [root@Tatshenshini bioperl-ext-1.4]# make > > cp Bio/Ext/Align/libs/hscore.h blib/lib/Bio/Ext/Align/libs/hscore.h > > ###Removed alot of cp commands to shorten e-mail post### > > cp Bio/Ext/Align/libs/wisefile.h blib/lib/Bio/Ext/Align/libs/wisefile.h > > make[1]: Entering directory `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align' > > cp Align.pm ../blib/lib/Bio/Ext/Align.pm > > DEFINE='-DPOSIX -DNOERROR'; CC='gcc'; export DEFINE INC CC; \ > > cd libs && make CC=gcc libsw.a -e > > make[2]: Entering directory > > `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align/libs' > > gcc -c -O -c -o aln.o aln.c > > ###Removed alot of gcc commands to shorten e-mail post### > > gcc -c -O -c -o linspc.o linspc.c > > ar ru libsw.a aln.o alnconvert.o alnrange.o asciibtcanvas.o basematrix.o > > btcanvas.o commandline.o complexconsensi.o > > complexevalset.o complexsequence.o compmat.o codon.o dna.o dnamatrix.o > > dpenvelope.o dynlibcross.o histogram.o hscore.o linesubs.o packaln.o > > probability.o protein.o proteindb.o proteinsw.o seqaligndisplay.o > > sequence.o sequencedb.o sw_wrap.o wiseerror.o wisefile.o wisememman.o > > wiseoverlay.o wiserandom.o wisestring.o wisetime.o dpalign.o linspc.o > > make[2]: Leaving directory > > `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align/libs' > > /usr/bin/perl /usr/lib/perl5/5.8.0/ExtUtils/xsubpp -typemap > > /usr/lib/perl5/5.8.0/ExtUtils/typemap -typemap typemap > > Align.xs > Align.xsc && mv Align.xsc Align.c > > gcc -c -I./libs -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS > > -DDEBUGGING -fno-strict-aliasing -I/usr/local/include > > -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 > > -march=i386 -mcpu=i686 -g -DVERSION=\"0.1\" -DXS_VERSION=\"0.1\" -fPIC > > "-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE" -DPOSIX -DNOERROR > > Align.c > > Running Mkbootstrap for Bio::Ext::Align () > > chmod 644 Align.bs > > rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so > > LD_RUN_PATH="" gcc -shared -L/usr/local/lib Align.o -o > > ../blib/arch/auto/Bio/Ext/Align/Align.so libs/libsw.a -lm > > > > chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so > > cp Align.bs ../blib/arch/auto/Bio/Ext/Align/Align.bs > > chmod 644 ../blib/arch/auto/Bio/Ext/Align/Align.bs > > make[1]: Leaving directory `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align' > > make[1]: Entering directory `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden' > > cp read.pm ../blib/lib/Bio/SeqIO/staden/read.pm > > /usr/bin/perl -Mblib -MInline=NOISY,_INSTALL_ -MBio::SeqIO::staden::read > > -e1 0.01 ../blib/arch > > Starting Build Prepocess Stage > > Finished Build Prepocess Stage > > > > Starting Build Parse Stage > > Finished Build Parse Stage > > > > Starting Build Glue 1 Stage > > Finished Build Glue 1 Stage > > > > Starting Build Glue 2 Stage > > Finished Build Glue 2 Stage > > > > Starting Build Glue 3 Stage > > Finished Build Glue 3 Stage > > > > Starting Build Compile Stage > > Starting "perl Makefile.PL" Stage > > Note (probably harmless): No library found for -lread > > Writing Makefile for Bio::SeqIO::staden::read > > Finished "perl Makefile.PL" Stage > > > > Starting "make" Stage > > make[2]: Entering directory > > `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/read' > > > > /usr/bin/perl /usr/lib/perl5/5.8.0/ExtUtils/xsubpp -typemap > > /usr/lib/perl5/5.8.0/ExtUtils/typemap read.xs > read.xsc && mv > > read.xsc read.c > > gcc -c -I/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden > > -I/usr/local/include/io_lib -D_REENTRANT -D_GNU_SOURCE > > -DTHREADS_HAVE_PIDS -DDEBUGGING -fno-strict-aliasing > > -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 > > -I/usr/include/gdbm -O2 -march=i386 -mcpu=i686 -g -DVERSION=\"0.01\" > > -DXS_VERSION=\"0.01\" -fPIC > > "-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE" read.c > > read.xs:5:18: Read.h: No such file or directory > > read.xs: In function `staden_write_trace': > > read.xs:9: `Read' undeclared (first use in this function) > > read.xs:9: (Each undeclared identifier is reported only once > > read.xs:9: for each function it appears in.) > > read.xs:15: invalid lvalue in assignment > > read.xs:16: request for member `base' in something not a structure or union > > read.xs:18: request for member `ident' in something not a structure or > > union > > read.xs:21: request for member `ident' in something not a structure or > > union > > read.xs:23: request for member `info' in something not a structure or union > > read.xs:26: request for member `info' in something not a structure or union > > read.xs:28: request for member `format' in something not a structure or > > union > > read.xs:29: request for member `leftCutoff' in something not a structure > > or union > > read.xs:30: request for member `rightCutoff' in something not a > > structure or union > > read.xs:32: warning: assignment from incompatible pointer type > > read.xs:38: request for member `base' in something not a structure or union > > read.xs:41: request for member `prob_A' in something not a structure or > > union > > read.xs:45: request for member `prob_C' in something not a structure or > > union > > read.xs:49: request for member `prob_G' in something not a structure or > > union > > read.xs:53: request for member `prob_T' in something not a structure or > > union > > read.xs:58: request for member `prob_A' in something not a structure or > > union > > read.xs:58: request for member `prob_C' in something not a structure or > > union > > read.xs:59: request for member `prob_G' in something not a structure or > > union > > read.xs:59: request for member `prob_T' in something not a structure or > > union > > read.xs:62: request for member `prob_A' in something not a structure or > > union > > read.xs:62: request for member `prob_C' in something not a structure or > > union > > read.xs:63: request for member `prob_G' in something not a structure or > > union > > read.xs:63: request for member `prob_T' in something not a structure or > > union > > read.xs: In function `staden_read_trace': > > read.xs:76: `Read' undeclared (first use in this function) > > read.xs:81: invalid lvalue in assignment > > read.xs:83: `NULLRead' undeclared (first use in this function) > > read.xs:88: request for member `leftCutoff' in something not a structure > > or union > > read.xs:90: request for member `rightCutoff' in something not a > > structure or union > > read.xs:91: request for member `NBases' in something not a structure or > > union > > read.xs:91: request for member `NBases' in something not a structure or > > union > > read.xs:93: request for member `base' in something not a structure or union > > read.xs:94: request for member `prob_A' in something not a structure or > > union > > read.xs:94: request for member `prob_C' in something not a structure or > > union > > read.xs:95: request for member `prob_G' in something not a structure or > > union > > read.xs:95: request for member `prob_T' in something not a structure or > > union > > read.xs:144: request for member `ident' in something not a structure or > > union > > read.xs:145: request for member `info' in something not a structure or > > union > > make[2]: *** [read.o] Error 1 > > make[2]: Leaving directory > > `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/read' > > > > > > A problem was encountered while attempting to compile and install your > > Inline > > C code. The command that failed was: > > make > > > > The build directory was: > > /home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/read > > > > > > To debug the problem, cd to the build directory, and inspect the output > > files. > > > > at -e line 0 > > INIT failed--call queue aborted. > > make[1]: *** [read.inl] Error 2 > > make[1]: Leaving directory `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden' > > make: *** [subdirs] Error 2 > > > > > > Jason Stajich wrote: > > > > >Hey Barry! > > > You need to have installed Inline::C first. > > > > > > You don't need bioperl-ext unless you want the specialized stuff in there > > >(a smith-waterman implementation and access to the staden io library for > > > reading in trace files directly through perl). > > > > > >-jason > > >On Tue, 6 Jan 2004, Barry Moore wrote: > > > > > > > > > > > >>I'm installing bioperl 1.4 on my linux machine (RedHat 9.0, Perl 5.8). > > >>Bioperl-1.4 (the core) and bioperl-run-1.4 installed fine. I get the > > >>following errors when trying to install bioperl-ext-1.4: > > >> > > >>[root@Tatshenshini bioperl-ext-1.4]# perl Makefile.PL > > >>Checking if your kit is complete... > > >>Looks good > > >>Writing Makefile for Bio::Ext::Align > > >>ERROR from evaluation of > > >>/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/Makefile.PL: Can't locate > > >>Inline/MakeMaker.pm in @INC > > >>(@INC contains: /usr/lib/perl5/5.8.0/i386-linux-thread-multi > > >>/usr/lib/perl5/5.8.0 > > >>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi > > >>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl > > >>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi > > >>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl > > >>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 > > >>/home/bmoore/bioperl-ext-1.4 .) at ./Makefile.PL line 1. > > >>BEGIN failed--compilation aborted at ./Makefile.PL line 1. > > >>[root@Tatshenshini bioperl-ext-1.4]# >> > > >>I'm a bit linux challenged so any pointers, no matter how remedial, will > > >>be greatly appreciated. > > >> > > >>Barry Moore > > >>Dept. Human Genetics > > >>University of Utah > > >> > > >>_______________________________________________ > > >>Bioperl-l mailing list > > >>Bioperl-l@portal.open-bio.org > > >>http://portal.open-bio.org/mailman/listinfo/bioperl-l > > >> > > >> > > >> > > > > > >-- > > >Jason Stajich > > >Duke University > > >jason at cgt.mc.duke.edu > > >_______________________________________________ > > >Bioperl-l mailing list > > >Bioperl-l@portal.open-bio.org > > >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From brian_osborne at cognia.com Thu Jan 8 12:58:00 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Thu Jan 8 13:05:57 2004 Subject: [Bioperl-l] Trouble installing bioperl-1.4 due to RestrictionIO In-Reply-To: <20040108110319.X22435@redwards2.utmem.edu> Message-ID: Rob, Partially fails for me as well, on Cygwin: ~/bioperl-live>perl t/RestrictionIO.t 1..14 ok 1 ok 2 ok 3 not ok 4 # Test 4 got: '530' (t/RestrictionIO.t at line 43) # Expected: '532' ok 5 ok 6 ok 7 ok 8 ok 9 not ok 10 # Test 10 got: '17' (t/RestrictionIO.t at line 63) # Expected: '11' ok 11 ok 12 not ok 13 # Test 13 got: '19' (t/RestrictionIO.t at line 78) # Expected: '16' ok 14 The 3 failing tests are $renzs->each_enzyme, where $renz is a RestrictionIO object, 3 different files. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Rob Edwards Sent: Thursday, January 08, 2004 12:03 PM To: Jason Stajich Cc: bhurwitz@twt.com; bioperl-l@bioperl.org Subject: Re: [Bioperl-l] Trouble installing bioperl-1.4 due to RestrictionIO I am curious as to why this test is failing. Has anyone else had this fail? It passes for me (on Mac OS10.3) Rob On Thu, Jan 08, 2004 at 10:45:31AM -0500, Jason Stajich wrote: > Just ignore it. > > cpan> force install Bio::Perl > > if you like. > > On Wed, 7 Jan 2004 bhurwitz@twt.com wrote: > > > > > Hello, > > > > I am installing BioPerl 1.4 on a virtual machine through vmware that > > previously did not have bioperl (RedHat 7.3, perl 5.6.1). I am getting the > > following error from CPAN. Does anyone know what this could mean? I have > > installed the BioPerl Bundle prior to this successfully > > (C/CR/CRAFFI/Bundle-BioPerl-2.1.0.tar.gz) > > > > -Bonnie > > > > > > Failed Test Stat Wstat Total Fail Failed List of Failed > > -------------------------------------------------------------------------- ----- > > t/RestrictionIO.t 14 1 7.14% 10 > > 121 subtests skipped. > > Failed 1/179 test scripts, 99.44% okay. 1/8268 subtests failed, 99.99% > > okay. > > make: *** [test_dynamic] Error 11 > > /usr/bin/make test -- NOT OK > > Running make install > > make test had returned bad status, won't install without force > > > > > > > > > > > > Barry Moore > > > > .edu> cc: bioperl-l@bioperl.org > > Sent by: Subject: Re: [Bioperl-l] Trouble installing bioperl-ext-1.4 > > bioperl-l-bounces@portal.o > > pen-bio.org > > > > > > 01/06/2004 05:15 PM > > > > > > > > > > > > > > Jason et al- > > > > ...while trying to install bioperl-ext-1.4 your suggestion for > > installing Inline::C first seems to have worked. Makefile.PL ran fine > > (highlighted below in green - if your reading HTML mail). However, now > > I get errors on running make. I've copied the entire output from the > > make command below (with some masking of low complexity regions). Sorry > > it's so long, but I'm having trouble spotting the problem, so I didn't > > want to leave out any of the important parts. The part indicating > > errors is at the end (highlighted in red). > > > > Barry > > > > [root@Tatshenshini bioperl-ext-1.4]# perl Makefile.PL > > Checking if your kit is complete... > > Looks good > > Writing Makefile for Bio::Ext::Align > > Please tell us where your Staden io_lib "read" library is installed: > > [/usr/local/lib] > > Please tell us where your Staden io_lib "Read.h" header is installed: > > [/usr/local/include/io_lib] > > Writing Makefile for Bio::SeqIO::staden::read > > Writing Makefile for Bio > > One or more DATA sections were not processed by Inline. > > > > [root@Tatshenshini bioperl-ext-1.4]# make > > cp Bio/Ext/Align/libs/hscore.h blib/lib/Bio/Ext/Align/libs/hscore.h > > ###Removed alot of cp commands to shorten e-mail post### > > cp Bio/Ext/Align/libs/wisefile.h blib/lib/Bio/Ext/Align/libs/wisefile.h > > make[1]: Entering directory `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align' > > cp Align.pm ../blib/lib/Bio/Ext/Align.pm > > DEFINE='-DPOSIX -DNOERROR'; CC='gcc'; export DEFINE INC CC; \ > > cd libs && make CC=gcc libsw.a -e > > make[2]: Entering directory > > `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align/libs' > > gcc -c -O -c -o aln.o aln.c > > ###Removed alot of gcc commands to shorten e-mail post### > > gcc -c -O -c -o linspc.o linspc.c > > ar ru libsw.a aln.o alnconvert.o alnrange.o asciibtcanvas.o basematrix.o > > btcanvas.o commandline.o complexconsensi.o > > complexevalset.o complexsequence.o compmat.o codon.o dna.o dnamatrix.o > > dpenvelope.o dynlibcross.o histogram.o hscore.o linesubs.o packaln.o > > probability.o protein.o proteindb.o proteinsw.o seqaligndisplay.o > > sequence.o sequencedb.o sw_wrap.o wiseerror.o wisefile.o wisememman.o > > wiseoverlay.o wiserandom.o wisestring.o wisetime.o dpalign.o linspc.o > > make[2]: Leaving directory > > `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align/libs' > > /usr/bin/perl /usr/lib/perl5/5.8.0/ExtUtils/xsubpp -typemap > > /usr/lib/perl5/5.8.0/ExtUtils/typemap -typemap typemap > > Align.xs > Align.xsc && mv Align.xsc Align.c > > gcc -c -I./libs -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS > > -DDEBUGGING -fno-strict-aliasing -I/usr/local/include > > -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 > > -march=i386 -mcpu=i686 -g -DVERSION=\"0.1\" -DXS_VERSION=\"0.1\" -fPIC > > "-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE" -DPOSIX -DNOERROR > > Align.c > > Running Mkbootstrap for Bio::Ext::Align () > > chmod 644 Align.bs > > rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so > > LD_RUN_PATH="" gcc -shared -L/usr/local/lib Align.o -o > > ../blib/arch/auto/Bio/Ext/Align/Align.so libs/libsw.a -lm > > > > chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so > > cp Align.bs ../blib/arch/auto/Bio/Ext/Align/Align.bs > > chmod 644 ../blib/arch/auto/Bio/Ext/Align/Align.bs > > make[1]: Leaving directory `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align' > > make[1]: Entering directory `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden' > > cp read.pm ../blib/lib/Bio/SeqIO/staden/read.pm > > /usr/bin/perl -Mblib -MInline=NOISY,_INSTALL_ -MBio::SeqIO::staden::read > > -e1 0.01 ../blib/arch > > Starting Build Prepocess Stage > > Finished Build Prepocess Stage > > > > Starting Build Parse Stage > > Finished Build Parse Stage > > > > Starting Build Glue 1 Stage > > Finished Build Glue 1 Stage > > > > Starting Build Glue 2 Stage > > Finished Build Glue 2 Stage > > > > Starting Build Glue 3 Stage > > Finished Build Glue 3 Stage > > > > Starting Build Compile Stage > > Starting "perl Makefile.PL" Stage > > Note (probably harmless): No library found for -lread > > Writing Makefile for Bio::SeqIO::staden::read > > Finished "perl Makefile.PL" Stage > > > > Starting "make" Stage > > make[2]: Entering directory > > `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/stade n/read' > > > > /usr/bin/perl /usr/lib/perl5/5.8.0/ExtUtils/xsubpp -typemap > > /usr/lib/perl5/5.8.0/ExtUtils/typemap read.xs > read.xsc && mv > > read.xsc read.c > > gcc -c -I/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden > > -I/usr/local/include/io_lib -D_REENTRANT -D_GNU_SOURCE > > -DTHREADS_HAVE_PIDS -DDEBUGGING -fno-strict-aliasing > > -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 > > -I/usr/include/gdbm -O2 -march=i386 -mcpu=i686 -g -DVERSION=\"0.01\" > > -DXS_VERSION=\"0.01\" -fPIC > > "-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE" read.c > > read.xs:5:18: Read.h: No such file or directory > > read.xs: In function `staden_write_trace': > > read.xs:9: `Read' undeclared (first use in this function) > > read.xs:9: (Each undeclared identifier is reported only once > > read.xs:9: for each function it appears in.) > > read.xs:15: invalid lvalue in assignment > > read.xs:16: request for member `base' in something not a structure or union > > read.xs:18: request for member `ident' in something not a structure or > > union > > read.xs:21: request for member `ident' in something not a structure or > > union > > read.xs:23: request for member `info' in something not a structure or union > > read.xs:26: request for member `info' in something not a structure or union > > read.xs:28: request for member `format' in something not a structure or > > union > > read.xs:29: request for member `leftCutoff' in something not a structure > > or union > > read.xs:30: request for member `rightCutoff' in something not a > > structure or union > > read.xs:32: warning: assignment from incompatible pointer type > > read.xs:38: request for member `base' in something not a structure or union > > read.xs:41: request for member `prob_A' in something not a structure or > > union > > read.xs:45: request for member `prob_C' in something not a structure or > > union > > read.xs:49: request for member `prob_G' in something not a structure or > > union > > read.xs:53: request for member `prob_T' in something not a structure or > > union > > read.xs:58: request for member `prob_A' in something not a structure or > > union > > read.xs:58: request for member `prob_C' in something not a structure or > > union > > read.xs:59: request for member `prob_G' in something not a structure or > > union > > read.xs:59: request for member `prob_T' in something not a structure or > > union > > read.xs:62: request for member `prob_A' in something not a structure or > > union > > read.xs:62: request for member `prob_C' in something not a structure or > > union > > read.xs:63: request for member `prob_G' in something not a structure or > > union > > read.xs:63: request for member `prob_T' in something not a structure or > > union > > read.xs: In function `staden_read_trace': > > read.xs:76: `Read' undeclared (first use in this function) > > read.xs:81: invalid lvalue in assignment > > read.xs:83: `NULLRead' undeclared (first use in this function) > > read.xs:88: request for member `leftCutoff' in something not a structure > > or union > > read.xs:90: request for member `rightCutoff' in something not a > > structure or union > > read.xs:91: request for member `NBases' in something not a structure or > > union > > read.xs:91: request for member `NBases' in something not a structure or > > union > > read.xs:93: request for member `base' in something not a structure or union > > read.xs:94: request for member `prob_A' in something not a structure or > > union > > read.xs:94: request for member `prob_C' in something not a structure or > > union > > read.xs:95: request for member `prob_G' in something not a structure or > > union > > read.xs:95: request for member `prob_T' in something not a structure or > > union > > read.xs:144: request for member `ident' in something not a structure or > > union > > read.xs:145: request for member `info' in something not a structure or > > union > > make[2]: *** [read.o] Error 1 > > make[2]: Leaving directory > > `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/stade n/read' > > > > > > A problem was encountered while attempting to compile and install your > > Inline > > C code. The command that failed was: > > make > > > > The build directory was: > > /home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden /read > > > > > > To debug the problem, cd to the build directory, and inspect the output > > files. > > > > at -e line 0 > > INIT failed--call queue aborted. > > make[1]: *** [read.inl] Error 2 > > make[1]: Leaving directory `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden' > > make: *** [subdirs] Error 2 > > > > > > Jason Stajich wrote: > > > > >Hey Barry! > > > You need to have installed Inline::C first. > > > > > > You don't need bioperl-ext unless you want the specialized stuff in there > > >(a smith-waterman implementation and access to the staden io library for > > > reading in trace files directly through perl). > > > > > >-jason > > >On Tue, 6 Jan 2004, Barry Moore wrote: > > > > > > > > > > > >>I'm installing bioperl 1.4 on my linux machine (RedHat 9.0, Perl 5.8). > > >>Bioperl-1.4 (the core) and bioperl-run-1.4 installed fine. I get the > > >>following errors when trying to install bioperl-ext-1.4: > > >> > > >>[root@Tatshenshini bioperl-ext-1.4]# perl Makefile.PL > > >>Checking if your kit is complete... > > >>Looks good > > >>Writing Makefile for Bio::Ext::Align > > >>ERROR from evaluation of > > >>/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/Makefile.PL: Can't locate > > >>Inline/MakeMaker.pm in @INC > > >>(@INC contains: /usr/lib/perl5/5.8.0/i386-linux-thread-multi > > >>/usr/lib/perl5/5.8.0 > > >>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi > > >>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl > > >>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi > > >>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl > > >>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 > > >>/home/bmoore/bioperl-ext-1.4 .) at ./Makefile.PL line 1. > > >>BEGIN failed--compilation aborted at ./Makefile.PL line 1. > > >>[root@Tatshenshini bioperl-ext-1.4]# >> > > >>I'm a bit linux challenged so any pointers, no matter how remedial, will > > >>be greatly appreciated. > > >> > > >>Barry Moore > > >>Dept. Human Genetics > > >>University of Utah > > >> > > >>_______________________________________________ > > >>Bioperl-l mailing list > > >>Bioperl-l@portal.open-bio.org > > >>http://portal.open-bio.org/mailman/listinfo/bioperl-l > > >> > > >> > > >> > > > > > >-- > > >Jason Stajich > > >Duke University > > >jason at cgt.mc.duke.edu > > >_______________________________________________ > > >Bioperl-l mailing list > > >Bioperl-l@portal.open-bio.org > > >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From czmasek at gnf.org Thu Jan 8 13:14:03 2004 From: czmasek at gnf.org (Chris Zmasek) Date: Thu Jan 8 13:21:09 2004 Subject: [Bioperl-l] Mid point rooting of a tree Message-ID: <7BA50F61CB491B4692B8BCFBB656B5F91305C2@EXCHCLUSTER01.lj.gnf.org> Hi, Iain: You could use my rio/forester package (available at: http://www.genetics.wustl.edu/eddy/forester/). It contains a Java program called "SDIdirectory" which can root (by various, user selectable methods) all trees in a given directory. Option "-h" allows to root by minimizing the tree height. If you have any questions, please feel free to email me. Hope this helps, Christian [czmasek@gnf.org] > -----Original Message----- > From: Iain Wallace [mailto:iain.wallace@ucd.ie] > Sent: Thursday, January 08, 2004 4:18 AM > To: bioperl-l@portal.open-bio.org > Subject: [Bioperl-l] Mid point rooting of a tree > > > Hi all, > > I was wondering if anyone knows of a command line program > that can root > an unrooted tree. I know of a graphical program , NJPlot, but > I want to > root lots of trees output from clustalw. > > Thanks > > Iain > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From jason at cgt.duhs.duke.edu Thu Jan 8 14:22:00 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Thu Jan 8 14:29:10 2004 Subject: [Bioperl-l] Trouble installing bioperl-1.4 due to RestrictionIO In-Reply-To: References: Message-ID: Hey Brian - what version of perl? What about you Bonnie? I get no errors with perl 5.8.0 on rh 9 or on OSX with perl 5.8.1-RC3 but I do see this on perl 5.6.1 (rh 7.3) with the main-trunk live and 1.4 code (released and 1.4 branch) 1..14 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 Use of uninitialized value in string eq at Bio/Restriction/IO/withrefm.pm line 130, line 13. Use of uninitialized value in string eq at Bio/Restriction/IO/withrefm.pm line 130, line 24. ok 9 not ok 10 # Test 10 got: '9' (t/RestrictionIO.t at line 63) # Expected: '11' ok 11 ok 12 ok 13 ok 14 -jason On Thu, 8 Jan 2004, Brian Osborne wrote: > Rob, > > Partially fails for me as well, on Cygwin: > > ~/bioperl-live>perl t/RestrictionIO.t > 1..14 > ok 1 > ok 2 > ok 3 > not ok 4 > # Test 4 got: '530' (t/RestrictionIO.t at line 43) > # Expected: '532' > ok 5 > ok 6 > ok 7 > ok 8 > ok 9 > not ok 10 > # Test 10 got: '17' (t/RestrictionIO.t at line 63) > # Expected: '11' > ok 11 > ok 12 > not ok 13 > # Test 13 got: '19' (t/RestrictionIO.t at line 78) > # Expected: '16' > ok 14 > > The 3 failing tests are $renzs->each_enzyme, where $renz is a RestrictionIO > object, 3 different files. > > Brian O. > > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org > [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Rob Edwards > Sent: Thursday, January 08, 2004 12:03 PM > To: Jason Stajich > Cc: bhurwitz@twt.com; bioperl-l@bioperl.org > Subject: Re: [Bioperl-l] Trouble installing bioperl-1.4 due to RestrictionIO > > I am curious as to why this test is failing. Has anyone else had this fail? > > It passes for me (on Mac OS10.3) > > Rob > > On Thu, Jan 08, 2004 at 10:45:31AM -0500, Jason Stajich wrote: > > Just ignore it. > > > > cpan> force install Bio::Perl > > > > if you like. > > > > On Wed, 7 Jan 2004 bhurwitz@twt.com wrote: > > > > > > > > Hello, > > > > > > I am installing BioPerl 1.4 on a virtual machine through vmware that > > > previously did not have bioperl (RedHat 7.3, perl 5.6.1). I am getting > the > > > following error from CPAN. Does anyone know what this could mean? I > have > > > installed the BioPerl Bundle prior to this successfully > > > (C/CR/CRAFFI/Bundle-BioPerl-2.1.0.tar.gz) > > > > > > -Bonnie > > > > > > > > > Failed Test Stat Wstat Total Fail Failed List of Failed > > > > -------------------------------------------------------------------------- > ----- > > > t/RestrictionIO.t 14 1 7.14% 10 > > > 121 subtests skipped. > > > Failed 1/179 test scripts, 99.44% okay. 1/8268 subtests failed, 99.99% > > > okay. > > > make: *** [test_dynamic] Error 11 > > > /usr/bin/make test -- NOT OK > > > Running make install > > > make test had returned bad status, won't install without force > > > > > > > > > > > > > > > > > > Barry Moore > > > Stajich > > > .edu> cc: > bioperl-l@bioperl.org > > > Sent by: Subject: Re: > [Bioperl-l] Trouble installing bioperl-ext-1.4 > > > bioperl-l-bounces@portal.o > > > pen-bio.org > > > > > > > > > 01/06/2004 05:15 PM > > > > > > > > > > > > > > > > > > > > > Jason et al- > > > > > > ...while trying to install bioperl-ext-1.4 your suggestion for > > > installing Inline::C first seems to have worked. Makefile.PL ran fine > > > (highlighted below in green - if your reading HTML mail). However, now > > > I get errors on running make. I've copied the entire output from the > > > make command below (with some masking of low complexity regions). Sorry > > > it's so long, but I'm having trouble spotting the problem, so I didn't > > > want to leave out any of the important parts. The part indicating > > > errors is at the end (highlighted in red). > > > > > > Barry > > > > > > [root@Tatshenshini bioperl-ext-1.4]# perl Makefile.PL > > > Checking if your kit is complete... > > > Looks good > > > Writing Makefile for Bio::Ext::Align > > > Please tell us where your Staden io_lib "read" library is installed: > > > [/usr/local/lib] > > > Please tell us where your Staden io_lib "Read.h" header is installed: > > > [/usr/local/include/io_lib] > > > Writing Makefile for Bio::SeqIO::staden::read > > > Writing Makefile for Bio > > > One or more DATA sections were not processed by Inline. > > > > > > [root@Tatshenshini bioperl-ext-1.4]# make > > > cp Bio/Ext/Align/libs/hscore.h blib/lib/Bio/Ext/Align/libs/hscore.h > > > ###Removed alot of cp commands to shorten e-mail post### > > > cp Bio/Ext/Align/libs/wisefile.h blib/lib/Bio/Ext/Align/libs/wisefile.h > > > make[1]: Entering directory `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align' > > > cp Align.pm ../blib/lib/Bio/Ext/Align.pm > > > DEFINE='-DPOSIX -DNOERROR'; CC='gcc'; export DEFINE INC CC; \ > > > cd libs && make CC=gcc libsw.a -e > > > make[2]: Entering directory > > > `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align/libs' > > > gcc -c -O -c -o aln.o aln.c > > > ###Removed alot of gcc commands to shorten e-mail post### > > > gcc -c -O -c -o linspc.o linspc.c > > > ar ru libsw.a aln.o alnconvert.o alnrange.o asciibtcanvas.o basematrix.o > > > btcanvas.o commandline.o complexconsensi.o > > > complexevalset.o complexsequence.o compmat.o codon.o dna.o dnamatrix.o > > > dpenvelope.o dynlibcross.o histogram.o hscore.o linesubs.o packaln.o > > > probability.o protein.o proteindb.o proteinsw.o seqaligndisplay.o > > > sequence.o sequencedb.o sw_wrap.o wiseerror.o wisefile.o wisememman.o > > > wiseoverlay.o wiserandom.o wisestring.o wisetime.o dpalign.o linspc.o > > > make[2]: Leaving directory > > > `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align/libs' > > > /usr/bin/perl /usr/lib/perl5/5.8.0/ExtUtils/xsubpp -typemap > > > /usr/lib/perl5/5.8.0/ExtUtils/typemap -typemap typemap > > > Align.xs > Align.xsc && mv Align.xsc Align.c > > > gcc -c -I./libs -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS > > > -DDEBUGGING -fno-strict-aliasing -I/usr/local/include > > > -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 > > > -march=i386 -mcpu=i686 -g -DVERSION=\"0.1\" -DXS_VERSION=\"0.1\" -fPIC > > > "-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE" -DPOSIX -DNOERROR > > > Align.c > > > Running Mkbootstrap for Bio::Ext::Align () > > > chmod 644 Align.bs > > > rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so > > > LD_RUN_PATH="" gcc -shared -L/usr/local/lib Align.o -o > > > ../blib/arch/auto/Bio/Ext/Align/Align.so libs/libsw.a -lm > > > > > > chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so > > > cp Align.bs ../blib/arch/auto/Bio/Ext/Align/Align.bs > > > chmod 644 ../blib/arch/auto/Bio/Ext/Align/Align.bs > > > make[1]: Leaving directory `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align' > > > make[1]: Entering directory > `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden' > > > cp read.pm ../blib/lib/Bio/SeqIO/staden/read.pm > > > /usr/bin/perl -Mblib -MInline=NOISY,_INSTALL_ -MBio::SeqIO::staden::read > > > -e1 0.01 ../blib/arch > > > Starting Build Prepocess Stage > > > Finished Build Prepocess Stage > > > > > > Starting Build Parse Stage > > > Finished Build Parse Stage > > > > > > Starting Build Glue 1 Stage > > > Finished Build Glue 1 Stage > > > > > > Starting Build Glue 2 Stage > > > Finished Build Glue 2 Stage > > > > > > Starting Build Glue 3 Stage > > > Finished Build Glue 3 Stage > > > > > > Starting Build Compile Stage > > > Starting "perl Makefile.PL" Stage > > > Note (probably harmless): No library found for -lread > > > Writing Makefile for Bio::SeqIO::staden::read > > > Finished "perl Makefile.PL" Stage > > > > > > Starting "make" Stage > > > make[2]: Entering directory > > > > `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/stade > n/read' > > > > > > /usr/bin/perl /usr/lib/perl5/5.8.0/ExtUtils/xsubpp -typemap > > > /usr/lib/perl5/5.8.0/ExtUtils/typemap read.xs > read.xsc && mv > > > read.xsc read.c > > > gcc -c -I/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden > > > -I/usr/local/include/io_lib -D_REENTRANT -D_GNU_SOURCE > > > -DTHREADS_HAVE_PIDS -DDEBUGGING -fno-strict-aliasing > > > -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 > > > -I/usr/include/gdbm -O2 -march=i386 -mcpu=i686 -g -DVERSION=\"0.01\" > > > -DXS_VERSION=\"0.01\" -fPIC > > > "-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE" read.c > > > read.xs:5:18: Read.h: No such file or directory > > > read.xs: In function `staden_write_trace': > > > read.xs:9: `Read' undeclared (first use in this function) > > > read.xs:9: (Each undeclared identifier is reported only once > > > read.xs:9: for each function it appears in.) > > > read.xs:15: invalid lvalue in assignment > > > read.xs:16: request for member `base' in something not a structure or > union > > > read.xs:18: request for member `ident' in something not a structure or > > > union > > > read.xs:21: request for member `ident' in something not a structure or > > > union > > > read.xs:23: request for member `info' in something not a structure or > union > > > read.xs:26: request for member `info' in something not a structure or > union > > > read.xs:28: request for member `format' in something not a structure or > > > union > > > read.xs:29: request for member `leftCutoff' in something not a structure > > > or union > > > read.xs:30: request for member `rightCutoff' in something not a > > > structure or union > > > read.xs:32: warning: assignment from incompatible pointer type > > > read.xs:38: request for member `base' in something not a structure or > union > > > read.xs:41: request for member `prob_A' in something not a structure or > > > union > > > read.xs:45: request for member `prob_C' in something not a structure or > > > union > > > read.xs:49: request for member `prob_G' in something not a structure or > > > union > > > read.xs:53: request for member `prob_T' in something not a structure or > > > union > > > read.xs:58: request for member `prob_A' in something not a structure or > > > union > > > read.xs:58: request for member `prob_C' in something not a structure or > > > union > > > read.xs:59: request for member `prob_G' in something not a structure or > > > union > > > read.xs:59: request for member `prob_T' in something not a structure or > > > union > > > read.xs:62: request for member `prob_A' in something not a structure or > > > union > > > read.xs:62: request for member `prob_C' in something not a structure or > > > union > > > read.xs:63: request for member `prob_G' in something not a structure or > > > union > > > read.xs:63: request for member `prob_T' in something not a structure or > > > union > > > read.xs: In function `staden_read_trace': > > > read.xs:76: `Read' undeclared (first use in this function) > > > read.xs:81: invalid lvalue in assignment > > > read.xs:83: `NULLRead' undeclared (first use in this function) > > > read.xs:88: request for member `leftCutoff' in something not a structure > > > or union > > > read.xs:90: request for member `rightCutoff' in something not a > > > structure or union > > > read.xs:91: request for member `NBases' in something not a structure or > > > union > > > read.xs:91: request for member `NBases' in something not a structure or > > > union > > > read.xs:93: request for member `base' in something not a structure or > union > > > read.xs:94: request for member `prob_A' in something not a structure or > > > union > > > read.xs:94: request for member `prob_C' in something not a structure or > > > union > > > read.xs:95: request for member `prob_G' in something not a structure or > > > union > > > read.xs:95: request for member `prob_T' in something not a structure or > > > union > > > read.xs:144: request for member `ident' in something not a structure or > > > union > > > read.xs:145: request for member `info' in something not a structure or > > > union > > > make[2]: *** [read.o] Error 1 > > > make[2]: Leaving directory > > > > `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/stade > n/read' > > > > > > > > > A problem was encountered while attempting to compile and install your > > > Inline > > > C code. The command that failed was: > > > make > > > > > > The build directory was: > > > > /home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden > /read > > > > > > > > > To debug the problem, cd to the build directory, and inspect the output > > > files. > > > > > > at -e line 0 > > > INIT failed--call queue aborted. > > > make[1]: *** [read.inl] Error 2 > > > make[1]: Leaving directory > `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden' > > > make: *** [subdirs] Error 2 > > > > > > > > > Jason Stajich wrote: > > > > > > >Hey Barry! > > > > You need to have installed Inline::C first. > > > > > > > > You don't need bioperl-ext unless you want the specialized stuff in > there > > > >(a smith-waterman implementation and access to the staden io library > for > > > > reading in trace files directly through perl). > > > > > > > >-jason > > > >On Tue, 6 Jan 2004, Barry Moore wrote: > > > > > > > > > > > > > > > >>I'm installing bioperl 1.4 on my linux machine (RedHat 9.0, Perl 5.8). > > > >>Bioperl-1.4 (the core) and bioperl-run-1.4 installed fine. I get the > > > >>following errors when trying to install bioperl-ext-1.4: > > > >> > > > >>[root@Tatshenshini bioperl-ext-1.4]# perl Makefile.PL > > > >>Checking if your kit is complete... > > > >>Looks good > > > >>Writing Makefile for Bio::Ext::Align > > > >>ERROR from evaluation of > > > >>/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/Makefile.PL: Can't > locate > > > >>Inline/MakeMaker.pm in @INC > > > >>(@INC contains: /usr/lib/perl5/5.8.0/i386-linux-thread-multi > > > >>/usr/lib/perl5/5.8.0 > > > >>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi > > > >>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl > > > >>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi > > > >>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl > > > >>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 > > > >>/home/bmoore/bioperl-ext-1.4 .) at ./Makefile.PL line 1. > > > >>BEGIN failed--compilation aborted at ./Makefile.PL line 1. > > > >>[root@Tatshenshini bioperl-ext-1.4]# >> > > > >>I'm a bit linux challenged so any pointers, no matter how remedial, > will > > > >>be greatly appreciated. > > > >> > > > >>Barry Moore > > > >>Dept. Human Genetics > > > >>University of Utah > > > >> > > > >>_______________________________________________ > > > >>Bioperl-l mailing list > > > >>Bioperl-l@portal.open-bio.org > > > >>http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > >> > > > >> > > > >> > > > > > > > >-- > > > >Jason Stajich > > > >Duke University > > > >jason at cgt.mc.duke.edu > > > >_______________________________________________ > > > >Bioperl-l mailing list > > > >Bioperl-l@portal.open-bio.org > > > >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l@portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l@portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > -- > > Jason Stajich > > Duke University > > jason at cgt.mc.duke.edu > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From jason at cgt.duhs.duke.edu Thu Jan 8 14:47:25 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Thu Jan 8 14:54:54 2004 Subject: [Bioperl-l] TIGR xml parser(s) Message-ID: Josh - I have a Bio::SeqIO parser for what I think to be the newer TIGR XML. Like you see in (which doesn't have a DTD last time checked): ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/p_yoelii/annotation_dbs/PYA1.coordset ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/p_falciparum/annotation_dbs/PFA1_chromo_1.coordset Which is different from ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_1.0/chr01.dir/chr01.xml which is what your parser reads. I don't have any insight if this is an in-progress format, something to do manatee or what, will have to try and get clarification from someone at TIGR. At any rate, I'm not sure what to call it in comparison to your parser (Bio::SeqIO::tigr) for now it is called SeqIO::tigrxml. I've been using it for a little tigrxml2gff script for loading data into Gbrowse. It also calculates and adds 5' and 3' UTR features based on the CDS and mRNA annotations. I wrote it with XML::SAX and found that to be quite easy to use and has a nice way of using different parsers underneath so a slow pure-perl implementation by default but XML::LibXML and others can be plugged in the back automagically for speed. Anyways - I'll commit it soon - if you have suggestions about naming or if we want to try and find a way to combine the two modules into one where you can just switch by a 'version number' could try and work that as well. -jason -- Jason Stajich Duke University jason at cgt.mc.duke.edu From laurichj at bioinfo.ucr.edu Thu Jan 8 15:37:01 2004 From: laurichj at bioinfo.ucr.edu (Josh Lauricha) Date: Thu Jan 8 15:44:01 2004 Subject: [Bioperl-l] TIGR xml parser(s) In-Reply-To: References: Message-ID: <20040108203701.GD29545@bioinfo.ucr.edu> I asked TIGR about that awhile ago and those are in-progress files, whereas the one tigr.pm parser handles what those will become when they are released. O. stativa is a good example of this, avilible in both [1] which is parsable with tigr.pm and in [2] which has the coordset files. How is the memory usage in XML::SAX? If its not bad maybe I'll redo tigr.pm with that. I'd love not to be using regex to parse the thing. [1] ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/ [2] ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/BAC_PAC_clnes/ On Thu 01/08/04 14:47, Jason Stajich wrote: > Josh - > > I have a Bio::SeqIO parser for what I think to be the newer TIGR XML. > > Like you see in (which doesn't have a DTD last time checked): > ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/p_yoelii/annotation_dbs/PYA1.coordset > ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/p_falciparum/annotation_dbs/PFA1_chromo_1.coordset > > Which is different from > ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_1.0/chr01.dir/chr01.xml > which is what your parser reads. > > I don't have any insight if this is an in-progress format, something to do > manatee or what, will have to try and get clarification from someone at > TIGR. > > At any rate, I'm not sure what to call it in comparison to your parser > (Bio::SeqIO::tigr) for now it is called SeqIO::tigrxml. > > I've been using it for a little tigrxml2gff script for loading data into > Gbrowse. It also calculates and adds 5' and 3' UTR features based on the > CDS and mRNA annotations. > > I wrote it with XML::SAX and found that to be quite easy to use and has a > nice way of using different parsers underneath so a slow pure-perl > implementation by default but XML::LibXML and others can be plugged in the > back automagically for speed. > > Anyways - I'll commit it soon - if you have suggestions about naming or if > we want to try and find a way to combine the two modules into one where > you can just switch by a 'version number' could try and work that as well. > > > -jason > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- ---------------------------- | Josh Lauricha | | laurichj@bioinfo.ucr.edu | | Bioinformatics, UCR | |--------------------------| From junhu54 at hotmail.com Thu Jan 8 15:42:28 2004 From: junhu54 at hotmail.com (jun hu) Date: Thu Jan 8 15:49:30 2004 Subject: [Bioperl-l] Trouble installing bioperl-1.4 due to RestrictionIO Message-ID: I saw similar problems when I was in intall bioperl-live on both RH9 (with perl 5.8) and RH7.3 (with perl 5.6). Some problems can be fixed after you track download the exact package that gives you problem =>then download and install tarball instead of using "perl -MCPAN -e shell". However, sometimes you just have to force install some packages ... which might lead to those failed tests... Jun Hu >From: Jason Stajich >To: Brian Osborne >CC: Rob Edwards , bhurwitz@twt.com, >bioperl-l@bioperl.org >Subject: RE: [Bioperl-l] Trouble installing bioperl-1.4 due to >RestrictionIO >Date: Thu, 8 Jan 2004 14:22:00 -0500 (EST) > >Hey Brian - what version of perl? What about you Bonnie? > >I get no errors with perl 5.8.0 on rh 9 or on OSX with perl 5.8.1-RC3 but >I do see this on perl 5.6.1 (rh 7.3) with the main-trunk live and 1.4 code >(released and 1.4 branch) > >1..14 >ok 1 >ok 2 >ok 3 >ok 4 >ok 5 >ok 6 >ok 7 >ok 8 >Use of uninitialized value in string eq at Bio/Restriction/IO/withrefm.pm >line 130, line 13. >Use of uninitialized value in string eq at Bio/Restriction/IO/withrefm.pm >line 130, line 24. >ok 9 >not ok 10 ># Test 10 got: '9' (t/RestrictionIO.t at line 63) ># Expected: '11' >ok 11 >ok 12 >ok 13 >ok 14 > >-jason > >On Thu, 8 Jan 2004, Brian Osborne wrote: > > > Rob, > > > > Partially fails for me as well, on Cygwin: > > > > ~/bioperl-live>perl t/RestrictionIO.t > > 1..14 > > ok 1 > > ok 2 > > ok 3 > > not ok 4 > > # Test 4 got: '530' (t/RestrictionIO.t at line 43) > > # Expected: '532' > > ok 5 > > ok 6 > > ok 7 > > ok 8 > > ok 9 > > not ok 10 > > # Test 10 got: '17' (t/RestrictionIO.t at line 63) > > # Expected: '11' > > ok 11 > > ok 12 > > not ok 13 > > # Test 13 got: '19' (t/RestrictionIO.t at line 78) > > # Expected: '16' > > ok 14 > > > > The 3 failing tests are $renzs->each_enzyme, where $renz is a >RestrictionIO > > object, 3 different files. > > > > Brian O. > > > > -----Original Message----- > > From: bioperl-l-bounces@portal.open-bio.org > > [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Rob Edwards > > Sent: Thursday, January 08, 2004 12:03 PM > > To: Jason Stajich > > Cc: bhurwitz@twt.com; bioperl-l@bioperl.org > > Subject: Re: [Bioperl-l] Trouble installing bioperl-1.4 due to >RestrictionIO > > > > I am curious as to why this test is failing. Has anyone else had this >fail? > > > > It passes for me (on Mac OS10.3) > > > > Rob > > > > On Thu, Jan 08, 2004 at 10:45:31AM -0500, Jason Stajich wrote: > > > Just ignore it. > > > > > > cpan> force install Bio::Perl > > > > > > if you like. > > > > > > On Wed, 7 Jan 2004 bhurwitz@twt.com wrote: > > > > > > > > > > > Hello, > > > > > > > > I am installing BioPerl 1.4 on a virtual machine through vmware >that > > > > previously did not have bioperl (RedHat 7.3, perl 5.6.1). I am >getting > > the > > > > following error from CPAN. Does anyone know what this could mean? >I > > have > > > > installed the BioPerl Bundle prior to this successfully > > > > (C/CR/CRAFFI/Bundle-BioPerl-2.1.0.tar.gz) > > > > > > > > -Bonnie > > > > > > > > > > > > Failed Test Stat Wstat Total Fail Failed List of Failed > > > > > > >-------------------------------------------------------------------------- > > ----- > > > > t/RestrictionIO.t 14 1 7.14% 10 > > > > 121 subtests skipped. > > > > Failed 1/179 test scripts, 99.44% okay. 1/8268 subtests failed, >99.99% > > > > okay. > > > > make: *** [test_dynamic] Error 11 > > > > /usr/bin/make test -- NOT OK > > > > Running make install > > > > make test had returned bad status, won't install without force > > > > > > > > > > > > > > > > > > > > > > > > Barry Moore > > > > Jason > > Stajich > > > > .edu> cc: > > bioperl-l@bioperl.org > > > > Sent by: Subject: >Re: > > [Bioperl-l] Trouble installing bioperl-ext-1.4 > > > > bioperl-l-bounces@portal.o > > > > pen-bio.org > > > > > > > > > > > > 01/06/2004 05:15 PM > > > > > > > > > > > > > > > > > > > > > > > > > > > > Jason et al- > > > > > > > > ...while trying to install bioperl-ext-1.4 your suggestion for > > > > installing Inline::C first seems to have worked. Makefile.PL ran >fine > > > > (highlighted below in green - if your reading HTML mail). However, >now > > > > I get errors on running make. I've copied the entire output from >the > > > > make command below (with some masking of low complexity regions). >Sorry > > > > it's so long, but I'm having trouble spotting the problem, so I >didn't > > > > want to leave out any of the important parts. The part indicating > > > > errors is at the end (highlighted in red). > > > > > > > > Barry > > > > > > > > [root@Tatshenshini bioperl-ext-1.4]# perl Makefile.PL > > > > Checking if your kit is complete... > > > > Looks good > > > > Writing Makefile for Bio::Ext::Align > > > > Please tell us where your Staden io_lib "read" library is installed: > > > > [/usr/local/lib] > > > > Please tell us where your Staden io_lib "Read.h" header is >installed: > > > > [/usr/local/include/io_lib] > > > > Writing Makefile for Bio::SeqIO::staden::read > > > > Writing Makefile for Bio > > > > One or more DATA sections were not processed by Inline. > > > > > > > > [root@Tatshenshini bioperl-ext-1.4]# make > > > > cp Bio/Ext/Align/libs/hscore.h blib/lib/Bio/Ext/Align/libs/hscore.h > > > > ###Removed alot of cp commands to shorten e-mail post### > > > > cp Bio/Ext/Align/libs/wisefile.h >blib/lib/Bio/Ext/Align/libs/wisefile.h > > > > make[1]: Entering directory >`/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align' > > > > cp Align.pm ../blib/lib/Bio/Ext/Align.pm > > > > DEFINE='-DPOSIX -DNOERROR'; CC='gcc'; export DEFINE INC CC; \ > > > > cd libs && make CC=gcc libsw.a -e > > > > make[2]: Entering directory > > > > `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align/libs' > > > > gcc -c -O -c -o aln.o aln.c > > > > ###Removed alot of gcc commands to shorten e-mail post### > > > > gcc -c -O -c -o linspc.o linspc.c > > > > ar ru libsw.a aln.o alnconvert.o alnrange.o asciibtcanvas.o >basematrix.o > > > > btcanvas.o commandline.o complexconsensi.o > > > > complexevalset.o complexsequence.o compmat.o codon.o dna.o >dnamatrix.o > > > > dpenvelope.o dynlibcross.o histogram.o hscore.o linesubs.o packaln.o > > > > probability.o protein.o proteindb.o proteinsw.o seqaligndisplay.o > > > > sequence.o sequencedb.o sw_wrap.o wiseerror.o wisefile.o >wisememman.o > > > > wiseoverlay.o wiserandom.o wisestring.o wisetime.o dpalign.o >linspc.o > > > > make[2]: Leaving directory > > > > `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align/libs' > > > > /usr/bin/perl /usr/lib/perl5/5.8.0/ExtUtils/xsubpp -typemap > > > > /usr/lib/perl5/5.8.0/ExtUtils/typemap -typemap typemap > > > > Align.xs > Align.xsc && mv Align.xsc Align.c > > > > gcc -c -I./libs -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS > > > > -DDEBUGGING -fno-strict-aliasing -I/usr/local/include > > > > -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 > > > > -march=i386 -mcpu=i686 -g -DVERSION=\"0.1\" -DXS_VERSION=\"0.1\" >-fPIC > > > > "-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE" -DPOSIX >-DNOERROR > > > > Align.c > > > > Running Mkbootstrap for Bio::Ext::Align () > > > > chmod 644 Align.bs > > > > rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so > > > > LD_RUN_PATH="" gcc -shared -L/usr/local/lib Align.o -o > > > > ../blib/arch/auto/Bio/Ext/Align/Align.so libs/libsw.a -lm > > > > > > > > chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so > > > > cp Align.bs ../blib/arch/auto/Bio/Ext/Align/Align.bs > > > > chmod 644 ../blib/arch/auto/Bio/Ext/Align/Align.bs > > > > make[1]: Leaving directory >`/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align' > > > > make[1]: Entering directory > > `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden' > > > > cp read.pm ../blib/lib/Bio/SeqIO/staden/read.pm > > > > /usr/bin/perl -Mblib -MInline=NOISY,_INSTALL_ >-MBio::SeqIO::staden::read > > > > -e1 0.01 ../blib/arch > > > > Starting Build Prepocess Stage > > > > Finished Build Prepocess Stage > > > > > > > > Starting Build Parse Stage > > > > Finished Build Parse Stage > > > > > > > > Starting Build Glue 1 Stage > > > > Finished Build Glue 1 Stage > > > > > > > > Starting Build Glue 2 Stage > > > > Finished Build Glue 2 Stage > > > > > > > > Starting Build Glue 3 Stage > > > > Finished Build Glue 3 Stage > > > > > > > > Starting Build Compile Stage > > > > Starting "perl Makefile.PL" Stage > > > > Note (probably harmless): No library found for -lread > > > > Writing Makefile for Bio::SeqIO::staden::read > > > > Finished "perl Makefile.PL" Stage > > > > > > > > Starting "make" Stage > > > > make[2]: Entering directory > > > > > > >`/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/stade > > n/read' > > > > > > > > /usr/bin/perl /usr/lib/perl5/5.8.0/ExtUtils/xsubpp -typemap > > > > /usr/lib/perl5/5.8.0/ExtUtils/typemap read.xs > read.xsc && mv > > > > read.xsc read.c > > > > gcc -c -I/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden > > > > -I/usr/local/include/io_lib -D_REENTRANT -D_GNU_SOURCE > > > > -DTHREADS_HAVE_PIDS -DDEBUGGING -fno-strict-aliasing > > > > -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 > > > > -I/usr/include/gdbm -O2 -march=i386 -mcpu=i686 -g >-DVERSION=\"0.01\" > > > > -DXS_VERSION=\"0.01\" -fPIC > > > > "-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE" read.c > > > > read.xs:5:18: Read.h: No such file or directory > > > > read.xs: In function `staden_write_trace': > > > > read.xs:9: `Read' undeclared (first use in this function) > > > > read.xs:9: (Each undeclared identifier is reported only once > > > > read.xs:9: for each function it appears in.) > > > > read.xs:15: invalid lvalue in assignment > > > > read.xs:16: request for member `base' in something not a structure >or > > union > > > > read.xs:18: request for member `ident' in something not a structure >or > > > > union > > > > read.xs:21: request for member `ident' in something not a structure >or > > > > union > > > > read.xs:23: request for member `info' in something not a structure >or > > union > > > > read.xs:26: request for member `info' in something not a structure >or > > union > > > > read.xs:28: request for member `format' in something not a structure >or > > > > union > > > > read.xs:29: request for member `leftCutoff' in something not a >structure > > > > or union > > > > read.xs:30: request for member `rightCutoff' in something not a > > > > structure or union > > > > read.xs:32: warning: assignment from incompatible pointer type > > > > read.xs:38: request for member `base' in something not a structure >or > > union > > > > read.xs:41: request for member `prob_A' in something not a structure >or > > > > union > > > > read.xs:45: request for member `prob_C' in something not a structure >or > > > > union > > > > read.xs:49: request for member `prob_G' in something not a structure >or > > > > union > > > > read.xs:53: request for member `prob_T' in something not a structure >or > > > > union > > > > read.xs:58: request for member `prob_A' in something not a structure >or > > > > union > > > > read.xs:58: request for member `prob_C' in something not a structure >or > > > > union > > > > read.xs:59: request for member `prob_G' in something not a structure >or > > > > union > > > > read.xs:59: request for member `prob_T' in something not a structure >or > > > > union > > > > read.xs:62: request for member `prob_A' in something not a structure >or > > > > union > > > > read.xs:62: request for member `prob_C' in something not a structure >or > > > > union > > > > read.xs:63: request for member `prob_G' in something not a structure >or > > > > union > > > > read.xs:63: request for member `prob_T' in something not a structure >or > > > > union > > > > read.xs: In function `staden_read_trace': > > > > read.xs:76: `Read' undeclared (first use in this function) > > > > read.xs:81: invalid lvalue in assignment > > > > read.xs:83: `NULLRead' undeclared (first use in this function) > > > > read.xs:88: request for member `leftCutoff' in something not a >structure > > > > or union > > > > read.xs:90: request for member `rightCutoff' in something not a > > > > structure or union > > > > read.xs:91: request for member `NBases' in something not a structure >or > > > > union > > > > read.xs:91: request for member `NBases' in something not a structure >or > > > > union > > > > read.xs:93: request for member `base' in something not a structure >or > > union > > > > read.xs:94: request for member `prob_A' in something not a structure >or > > > > union > > > > read.xs:94: request for member `prob_C' in something not a structure >or > > > > union > > > > read.xs:95: request for member `prob_G' in something not a structure >or > > > > union > > > > read.xs:95: request for member `prob_T' in something not a structure >or > > > > union > > > > read.xs:144: request for member `ident' in something not a structure >or > > > > union > > > > read.xs:145: request for member `info' in something not a structure >or > > > > union > > > > make[2]: *** [read.o] Error 1 > > > > make[2]: Leaving directory > > > > > > >`/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/stade > > n/read' > > > > > > > > > > > > A problem was encountered while attempting to compile and install >your > > > > Inline > > > > C code. The command that failed was: > > > > make > > > > > > > > The build directory was: > > > > > > >/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden > > /read > > > > > > > > > > > > To debug the problem, cd to the build directory, and inspect the >output > > > > files. > > > > > > > > at -e line 0 > > > > INIT failed--call queue aborted. > > > > make[1]: *** [read.inl] Error 2 > > > > make[1]: Leaving directory > > `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden' > > > > make: *** [subdirs] Error 2 > > > > > > > > > > > > Jason Stajich wrote: > > > > > > > > >Hey Barry! > > > > > You need to have installed Inline::C first. > > > > > > > > > > You don't need bioperl-ext unless you want the specialized stuff >in > > there > > > > >(a smith-waterman implementation and access to the staden io >library > > for > > > > > reading in trace files directly through perl). > > > > > > > > > >-jason > > > > >On Tue, 6 Jan 2004, Barry Moore wrote: > > > > > > > > > > > > > > > > > > > >>I'm installing bioperl 1.4 on my linux machine (RedHat 9.0, Perl >5.8). > > > > >>Bioperl-1.4 (the core) and bioperl-run-1.4 installed fine. I get >the > > > > >>following errors when trying to install bioperl-ext-1.4: > > > > >> > > > > >>[root@Tatshenshini bioperl-ext-1.4]# perl Makefile.PL > > > > >>Checking if your kit is complete... > > > > >>Looks good > > > > >>Writing Makefile for Bio::Ext::Align > > > > >>ERROR from evaluation of > > > > >>/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/Makefile.PL: Can't > > locate > > > > >>Inline/MakeMaker.pm in @INC > > > > >>(@INC contains: /usr/lib/perl5/5.8.0/i386-linux-thread-multi > > > > >>/usr/lib/perl5/5.8.0 > > > > >>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi > > > > >>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl > > > > >>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi > > > > >>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl > > > > >>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 > > > > >>/home/bmoore/bioperl-ext-1.4 .) at ./Makefile.PL line 1. > > > > >>BEGIN failed--compilation aborted at ./Makefile.PL line 1. > > > > >>[root@Tatshenshini bioperl-ext-1.4]# >> > > > > >>I'm a bit linux challenged so any pointers, no matter how >remedial, > > will > > > > >>be greatly appreciated. > > > > >> > > > > >>Barry Moore > > > > >>Dept. Human Genetics > > > > >>University of Utah > > > > >> > > > > >>_______________________________________________ > > > > >>Bioperl-l mailing list > > > > >>Bioperl-l@portal.open-bio.org > > > > >>http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > >> > > > > >> > > > > >> > > > > > > > > > >-- > > > > >Jason Stajich > > > > >Duke University > > > > >jason at cgt.mc.duke.edu > > > > >_______________________________________________ > > > > >Bioperl-l mailing list > > > > >Bioperl-l@portal.open-bio.org > > > > >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > Bioperl-l mailing list > > > > Bioperl-l@portal.open-bio.org > > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > Bioperl-l mailing list > > > > Bioperl-l@portal.open-bio.org > > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > -- > > > Jason Stajich > > > Duke University > > > jason at cgt.mc.duke.edu > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l@portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > >-- >Jason Stajich >Duke University >jason at cgt.mc.duke.edu >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l _________________________________________________________________ Tired of slow downloads? Compare online deals from your local high-speed providers now. https://broadband.msn.com From brian_osborne at cognia.com Thu Jan 8 15:46:57 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Thu Jan 8 15:54:53 2004 Subject: [Bioperl-l] Trouble installing bioperl-1.4 due to RestrictionIO In-Reply-To: Message-ID: Jason, This is perl, v5.8.0 built for cygwin-multi-64int Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Jason Stajich Sent: Thursday, January 08, 2004 2:22 PM To: Brian Osborne Cc: Rob Edwards; bhurwitz@twt.com; bioperl-l@bioperl.org Subject: RE: [Bioperl-l] Trouble installing bioperl-1.4 due to RestrictionIO Hey Brian - what version of perl? What about you Bonnie? I get no errors with perl 5.8.0 on rh 9 or on OSX with perl 5.8.1-RC3 but I do see this on perl 5.6.1 (rh 7.3) with the main-trunk live and 1.4 code (released and 1.4 branch) 1..14 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 Use of uninitialized value in string eq at Bio/Restriction/IO/withrefm.pm line 130, line 13. Use of uninitialized value in string eq at Bio/Restriction/IO/withrefm.pm line 130, line 24. ok 9 not ok 10 # Test 10 got: '9' (t/RestrictionIO.t at line 63) # Expected: '11' ok 11 ok 12 ok 13 ok 14 -jason On Thu, 8 Jan 2004, Brian Osborne wrote: > Rob, > > Partially fails for me as well, on Cygwin: > > ~/bioperl-live>perl t/RestrictionIO.t > 1..14 > ok 1 > ok 2 > ok 3 > not ok 4 > # Test 4 got: '530' (t/RestrictionIO.t at line 43) > # Expected: '532' > ok 5 > ok 6 > ok 7 > ok 8 > ok 9 > not ok 10 > # Test 10 got: '17' (t/RestrictionIO.t at line 63) > # Expected: '11' > ok 11 > ok 12 > not ok 13 > # Test 13 got: '19' (t/RestrictionIO.t at line 78) > # Expected: '16' > ok 14 > > The 3 failing tests are $renzs->each_enzyme, where $renz is a RestrictionIO > object, 3 different files. > > Brian O. > > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org > [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Rob Edwards > Sent: Thursday, January 08, 2004 12:03 PM > To: Jason Stajich > Cc: bhurwitz@twt.com; bioperl-l@bioperl.org > Subject: Re: [Bioperl-l] Trouble installing bioperl-1.4 due to RestrictionIO > > I am curious as to why this test is failing. Has anyone else had this fail? > > It passes for me (on Mac OS10.3) > > Rob > > On Thu, Jan 08, 2004 at 10:45:31AM -0500, Jason Stajich wrote: > > Just ignore it. > > > > cpan> force install Bio::Perl > > > > if you like. > > > > On Wed, 7 Jan 2004 bhurwitz@twt.com wrote: > > > > > > > > Hello, > > > > > > I am installing BioPerl 1.4 on a virtual machine through vmware that > > > previously did not have bioperl (RedHat 7.3, perl 5.6.1). I am getting > the > > > following error from CPAN. Does anyone know what this could mean? I > have > > > installed the BioPerl Bundle prior to this successfully > > > (C/CR/CRAFFI/Bundle-BioPerl-2.1.0.tar.gz) > > > > > > -Bonnie > > > > > > > > > Failed Test Stat Wstat Total Fail Failed List of Failed > > > > -------------------------------------------------------------------------- > ----- > > > t/RestrictionIO.t 14 1 7.14% 10 > > > 121 subtests skipped. > > > Failed 1/179 test scripts, 99.44% okay. 1/8268 subtests failed, 99.99% > > > okay. > > > make: *** [test_dynamic] Error 11 > > > /usr/bin/make test -- NOT OK > > > Running make install > > > make test had returned bad status, won't install without force > > > > > > > > > > > > > > > > > > Barry Moore > > > Stajich > > > .edu> cc: > bioperl-l@bioperl.org > > > Sent by: Subject: Re: > [Bioperl-l] Trouble installing bioperl-ext-1.4 > > > bioperl-l-bounces@portal.o > > > pen-bio.org > > > > > > > > > 01/06/2004 05:15 PM > > > > > > > > > > > > > > > > > > > > > Jason et al- > > > > > > ...while trying to install bioperl-ext-1.4 your suggestion for > > > installing Inline::C first seems to have worked. Makefile.PL ran fine > > > (highlighted below in green - if your reading HTML mail). However, now > > > I get errors on running make. I've copied the entire output from the > > > make command below (with some masking of low complexity regions). Sorry > > > it's so long, but I'm having trouble spotting the problem, so I didn't > > > want to leave out any of the important parts. The part indicating > > > errors is at the end (highlighted in red). > > > > > > Barry > > > > > > [root@Tatshenshini bioperl-ext-1.4]# perl Makefile.PL > > > Checking if your kit is complete... > > > Looks good > > > Writing Makefile for Bio::Ext::Align > > > Please tell us where your Staden io_lib "read" library is installed: > > > [/usr/local/lib] > > > Please tell us where your Staden io_lib "Read.h" header is installed: > > > [/usr/local/include/io_lib] > > > Writing Makefile for Bio::SeqIO::staden::read > > > Writing Makefile for Bio > > > One or more DATA sections were not processed by Inline. > > > > > > [root@Tatshenshini bioperl-ext-1.4]# make > > > cp Bio/Ext/Align/libs/hscore.h blib/lib/Bio/Ext/Align/libs/hscore.h > > > ###Removed alot of cp commands to shorten e-mail post### > > > cp Bio/Ext/Align/libs/wisefile.h blib/lib/Bio/Ext/Align/libs/wisefile.h > > > make[1]: Entering directory `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align' > > > cp Align.pm ../blib/lib/Bio/Ext/Align.pm > > > DEFINE='-DPOSIX -DNOERROR'; CC='gcc'; export DEFINE INC CC; \ > > > cd libs && make CC=gcc libsw.a -e > > > make[2]: Entering directory > > > `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align/libs' > > > gcc -c -O -c -o aln.o aln.c > > > ###Removed alot of gcc commands to shorten e-mail post### > > > gcc -c -O -c -o linspc.o linspc.c > > > ar ru libsw.a aln.o alnconvert.o alnrange.o asciibtcanvas.o basematrix.o > > > btcanvas.o commandline.o complexconsensi.o > > > complexevalset.o complexsequence.o compmat.o codon.o dna.o dnamatrix.o > > > dpenvelope.o dynlibcross.o histogram.o hscore.o linesubs.o packaln.o > > > probability.o protein.o proteindb.o proteinsw.o seqaligndisplay.o > > > sequence.o sequencedb.o sw_wrap.o wiseerror.o wisefile.o wisememman.o > > > wiseoverlay.o wiserandom.o wisestring.o wisetime.o dpalign.o linspc.o > > > make[2]: Leaving directory > > > `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align/libs' > > > /usr/bin/perl /usr/lib/perl5/5.8.0/ExtUtils/xsubpp -typemap > > > /usr/lib/perl5/5.8.0/ExtUtils/typemap -typemap typemap > > > Align.xs > Align.xsc && mv Align.xsc Align.c > > > gcc -c -I./libs -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS > > > -DDEBUGGING -fno-strict-aliasing -I/usr/local/include > > > -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 > > > -march=i386 -mcpu=i686 -g -DVERSION=\"0.1\" -DXS_VERSION=\"0.1\" -fPIC > > > "-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE" -DPOSIX -DNOERROR > > > Align.c > > > Running Mkbootstrap for Bio::Ext::Align () > > > chmod 644 Align.bs > > > rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so > > > LD_RUN_PATH="" gcc -shared -L/usr/local/lib Align.o -o > > > ../blib/arch/auto/Bio/Ext/Align/Align.so libs/libsw.a -lm > > > > > > chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so > > > cp Align.bs ../blib/arch/auto/Bio/Ext/Align/Align.bs > > > chmod 644 ../blib/arch/auto/Bio/Ext/Align/Align.bs > > > make[1]: Leaving directory `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align' > > > make[1]: Entering directory > `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden' > > > cp read.pm ../blib/lib/Bio/SeqIO/staden/read.pm > > > /usr/bin/perl -Mblib -MInline=NOISY,_INSTALL_ -MBio::SeqIO::staden::read > > > -e1 0.01 ../blib/arch > > > Starting Build Prepocess Stage > > > Finished Build Prepocess Stage > > > > > > Starting Build Parse Stage > > > Finished Build Parse Stage > > > > > > Starting Build Glue 1 Stage > > > Finished Build Glue 1 Stage > > > > > > Starting Build Glue 2 Stage > > > Finished Build Glue 2 Stage > > > > > > Starting Build Glue 3 Stage > > > Finished Build Glue 3 Stage > > > > > > Starting Build Compile Stage > > > Starting "perl Makefile.PL" Stage > > > Note (probably harmless): No library found for -lread > > > Writing Makefile for Bio::SeqIO::staden::read > > > Finished "perl Makefile.PL" Stage > > > > > > Starting "make" Stage > > > make[2]: Entering directory > > > > `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/stade > n/read' > > > > > > /usr/bin/perl /usr/lib/perl5/5.8.0/ExtUtils/xsubpp -typemap > > > /usr/lib/perl5/5.8.0/ExtUtils/typemap read.xs > read.xsc && mv > > > read.xsc read.c > > > gcc -c -I/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden > > > -I/usr/local/include/io_lib -D_REENTRANT -D_GNU_SOURCE > > > -DTHREADS_HAVE_PIDS -DDEBUGGING -fno-strict-aliasing > > > -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 > > > -I/usr/include/gdbm -O2 -march=i386 -mcpu=i686 -g -DVERSION=\"0.01\" > > > -DXS_VERSION=\"0.01\" -fPIC > > > "-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE" read.c > > > read.xs:5:18: Read.h: No such file or directory > > > read.xs: In function `staden_write_trace': > > > read.xs:9: `Read' undeclared (first use in this function) > > > read.xs:9: (Each undeclared identifier is reported only once > > > read.xs:9: for each function it appears in.) > > > read.xs:15: invalid lvalue in assignment > > > read.xs:16: request for member `base' in something not a structure or > union > > > read.xs:18: request for member `ident' in something not a structure or > > > union > > > read.xs:21: request for member `ident' in something not a structure or > > > union > > > read.xs:23: request for member `info' in something not a structure or > union > > > read.xs:26: request for member `info' in something not a structure or > union > > > read.xs:28: request for member `format' in something not a structure or > > > union > > > read.xs:29: request for member `leftCutoff' in something not a structure > > > or union > > > read.xs:30: request for member `rightCutoff' in something not a > > > structure or union > > > read.xs:32: warning: assignment from incompatible pointer type > > > read.xs:38: request for member `base' in something not a structure or > union > > > read.xs:41: request for member `prob_A' in something not a structure or > > > union > > > read.xs:45: request for member `prob_C' in something not a structure or > > > union > > > read.xs:49: request for member `prob_G' in something not a structure or > > > union > > > read.xs:53: request for member `prob_T' in something not a structure or > > > union > > > read.xs:58: request for member `prob_A' in something not a structure or > > > union > > > read.xs:58: request for member `prob_C' in something not a structure or > > > union > > > read.xs:59: request for member `prob_G' in something not a structure or > > > union > > > read.xs:59: request for member `prob_T' in something not a structure or > > > union > > > read.xs:62: request for member `prob_A' in something not a structure or > > > union > > > read.xs:62: request for member `prob_C' in something not a structure or > > > union > > > read.xs:63: request for member `prob_G' in something not a structure or > > > union > > > read.xs:63: request for member `prob_T' in something not a structure or > > > union > > > read.xs: In function `staden_read_trace': > > > read.xs:76: `Read' undeclared (first use in this function) > > > read.xs:81: invalid lvalue in assignment > > > read.xs:83: `NULLRead' undeclared (first use in this function) > > > read.xs:88: request for member `leftCutoff' in something not a structure > > > or union > > > read.xs:90: request for member `rightCutoff' in something not a > > > structure or union > > > read.xs:91: request for member `NBases' in something not a structure or > > > union > > > read.xs:91: request for member `NBases' in something not a structure or > > > union > > > read.xs:93: request for member `base' in something not a structure or > union > > > read.xs:94: request for member `prob_A' in something not a structure or > > > union > > > read.xs:94: request for member `prob_C' in something not a structure or > > > union > > > read.xs:95: request for member `prob_G' in something not a structure or > > > union > > > read.xs:95: request for member `prob_T' in something not a structure or > > > union > > > read.xs:144: request for member `ident' in something not a structure or > > > union > > > read.xs:145: request for member `info' in something not a structure or > > > union > > > make[2]: *** [read.o] Error 1 > > > make[2]: Leaving directory > > > > `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/stade > n/read' > > > > > > > > > A problem was encountered while attempting to compile and install your > > > Inline > > > C code. The command that failed was: > > > make > > > > > > The build directory was: > > > > /home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden > /read > > > > > > > > > To debug the problem, cd to the build directory, and inspect the output > > > files. > > > > > > at -e line 0 > > > INIT failed--call queue aborted. > > > make[1]: *** [read.inl] Error 2 > > > make[1]: Leaving directory > `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden' > > > make: *** [subdirs] Error 2 > > > > > > > > > Jason Stajich wrote: > > > > > > >Hey Barry! > > > > You need to have installed Inline::C first. > > > > > > > > You don't need bioperl-ext unless you want the specialized stuff in > there > > > >(a smith-waterman implementation and access to the staden io library > for > > > > reading in trace files directly through perl). > > > > > > > >-jason > > > >On Tue, 6 Jan 2004, Barry Moore wrote: > > > > > > > > > > > > > > > >>I'm installing bioperl 1.4 on my linux machine (RedHat 9.0, Perl 5.8). > > > >>Bioperl-1.4 (the core) and bioperl-run-1.4 installed fine. I get the > > > >>following errors when trying to install bioperl-ext-1.4: > > > >> > > > >>[root@Tatshenshini bioperl-ext-1.4]# perl Makefile.PL > > > >>Checking if your kit is complete... > > > >>Looks good > > > >>Writing Makefile for Bio::Ext::Align > > > >>ERROR from evaluation of > > > >>/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/Makefile.PL: Can't > locate > > > >>Inline/MakeMaker.pm in @INC > > > >>(@INC contains: /usr/lib/perl5/5.8.0/i386-linux-thread-multi > > > >>/usr/lib/perl5/5.8.0 > > > >>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi > > > >>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl > > > >>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi > > > >>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl > > > >>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 > > > >>/home/bmoore/bioperl-ext-1.4 .) at ./Makefile.PL line 1. > > > >>BEGIN failed--compilation aborted at ./Makefile.PL line 1. > > > >>[root@Tatshenshini bioperl-ext-1.4]# >> > > > >>I'm a bit linux challenged so any pointers, no matter how remedial, > will > > > >>be greatly appreciated. > > > >> > > > >>Barry Moore > > > >>Dept. Human Genetics > > > >>University of Utah > > > >> > > > >>_______________________________________________ > > > >>Bioperl-l mailing list > > > >>Bioperl-l@portal.open-bio.org > > > >>http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > >> > > > >> > > > >> > > > > > > > >-- > > > >Jason Stajich > > > >Duke University > > > >jason at cgt.mc.duke.edu > > > >_______________________________________________ > > > >Bioperl-l mailing list > > > >Bioperl-l@portal.open-bio.org > > > >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l@portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l@portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > -- > > Jason Stajich > > Duke University > > jason at cgt.mc.duke.edu > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From Peter.Robinson at t-online.de Fri Jan 9 14:52:35 2004 From: Peter.Robinson at t-online.de (peter robinson) Date: Thu Jan 8 16:04:00 2004 Subject: [Bioperl-l] loading sprot.dat In-Reply-To: References: Message-ID: <200401092052.35178.peter.robinson@t-online.de> On Thursday 08 January 2004 16:55, Brian Osborne wrote: (...) Thank you. However, I have to admit I am not quite sure how to go about this. The following snippet (copied from your HOWTO) does not really capture the annotations of the Swiss-Prot entry (see below, it is the first entry in sprot42.dat) I would have naively assumed that there would be getter functions for each of the Swiss-Prot ID types, (e.g., in Bio::SeqIO::swiss). However, it has not been obvious to me where to look for these if they exist. Ideas? Thanks!! Peter #!/usr/bin/perl use strict; use Bio::SeqIO; my $seqio = Bio::SeqIO->new(-file=>"sprot42.dat", -format=>"swiss"); my $seqOb = $seqio->next_seq(); foreach my $featOb ($seqOb->get_SeqFeatures()) { print "primary tag: ", $featOb->primary_tag(), "\n"; foreach my $tag ($featOb->get_all_tags()) { print "tag: $tag \n"; foreach my $value ($featOb->get_tag_values($tag)) { print "values $value\n"; } } } peter@pluto:~/Swiss> perl sptest.pl primary tag: DOMAIN tag: description values HYDROPHOBIC primary tag: DOMAIN tag: description values HYDROPHOBIC peter@pluto:~/Swiss> head sprot42.dat --lines=40 ID 104K_THEPA STANDARD; PRT; 924 AA. AC P15711; DT 01-APR-1990 (Rel. 14, Created) DT 01-APR-1990 (Rel. 14, Last sequence update) DT 01-AUG-1992 (Rel. 23, Last annotation update) DE 104 kDa microneme-rhoptry antigen. OS Theileria parva. OC Eukaryota; Alveolata; Apicomplexa; Piroplasmida; Theileriidae; OC Theileria. OX NCBI_TaxID=5875; RN [1] RP SEQUENCE FROM N.A. RC STRAIN=Muguga; RX MEDLINE=90158697; PubMed=1689460; RA Iams K.P., Young J.R., Nene V., Desai J., Webster P., RA Ole-Moiyoi O.K., Musoke A.J.; RT "Characterisation of the gene encoding a 104-kilodalton microneme- RT rhoptry protein of Theileria parva."; RL Mol. Biochem. Parasitol. 39:47-60(1990). CC -!- SUBCELLULAR LOCATION: IN MICRONEME/RHOPTRY COMPLEXES. CC -!- DEVELOPMENTAL STAGE: SPOROZOITE ANTIGEN. CC -------------------------------------------------------------------------- CC This SWISS-PROT entry is copyright. It is produced through a collaboration CC between the Swiss Institute of Bioinformatics and the EMBL outstation - CC the European Bioinformatics Institute. There are no restrictions on its CC use by non-profit institutions as long as its content is in no way CC modified and this statement is not removed. Usage by and for commercial CC entities requires a license agreement (See http://www.isb-sib.ch/announce/ CC or send an email to license@isb-sib.ch). CC -------------------------------------------------------------------------- DR EMBL; M29954; AAA18217.1; -. DR PIR; A44945; A44945. KW Antigen; Sporozoite; Repeat. FT DOMAIN 1 19 HYDROPHOBIC. FT DOMAIN 905 924 HYDROPHOBIC. SQ SEQUENCE 924 AA; 103625 MW; 289B4B554A61870E CRC64; MKFLILLFNI LCLFPVLAAD NHGVGPQGAS GVDPITFDIN SNQTGPAFLT AVEMAGVKYL QVQHGSNVNI HRLVEGNVVI WENASTPLYT GAIVTNNDGP YMAYVEVLGD PNLQFFIKSG DAWVTLSEHE YLAKLQEIRQ AVHIESVFSL NMAFQLENNK YEVETHAKNG ANMVTFIPRN GHICKMVYHK NVRIYKATGN DTVTSVVGFF RGLRLLLINV FSIDDNGMMS NRYFQHVDDK peter@pluto:~/Swiss> exit > Peter, > > Some of the data in a SwissProt file is parsed into Features, some of it > into Annotations (Swissprot entries are RichSeq objects, like Genbank and > EMBL entries). So probably you'll want to look at the Feature-Annotation > HOWTO. Unfortunately there are no Swissprot examples there but the logic > will be the same, open the file with SeqIO and print out specific entries, > or portions of entries, with the desired characteristics. Perhaps the SeqIO > HOWTO would be useful as well... > > Brian O. > > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org > [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Robinson, Peter > Sent: Thursday, January 08, 2004 10:18 AM > To: bioperl-l@bioperl.org > Subject: [Bioperl-l] loading sprot.dat > > Hi all, > > I would like to load the contents of the Swiss-Prot file sprot.dat into a > mysql database. Since I have a relatively specific question, I would like > to use a databse of my own design and just extract portions of the relevant > entries from sprot.dat rather than the whole thing. > I would appreciate it if someone could point me to an example script for > this kind of thing. I did not see anything like this in my perusals of the > archives or google, please forgive me if this question has been asked > before! > > Thanks > > Peter > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From brian_osborne at cognia.com Thu Jan 8 16:12:16 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Thu Jan 8 16:19:57 2004 Subject: [Bioperl-l] loading sprot.dat In-Reply-To: <200401092052.35178.peter.robinson@t-online.de> Message-ID: Peter, I think that the data you're after is probably in the Annotation objects. I know that for Swissprot there can a good number of these objects created. Take a look at the code a bit further down the HOWTO page... Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of peter robinson Sent: Friday, January 09, 2004 2:53 PM To: Brian Osborne Cc: bioperl-l@bioperl.org Subject: Re: [Bioperl-l] loading sprot.dat On Thursday 08 January 2004 16:55, Brian Osborne wrote: (...) Thank you. However, I have to admit I am not quite sure how to go about this. The following snippet (copied from your HOWTO) does not really capture the annotations of the Swiss-Prot entry (see below, it is the first entry in sprot42.dat) I would have naively assumed that there would be getter functions for each of the Swiss-Prot ID types, (e.g., in Bio::SeqIO::swiss). However, it has not been obvious to me where to look for these if they exist. Ideas? Thanks!! Peter #!/usr/bin/perl use strict; use Bio::SeqIO; my $seqio = Bio::SeqIO->new(-file=>"sprot42.dat", -format=>"swiss"); my $seqOb = $seqio->next_seq(); foreach my $featOb ($seqOb->get_SeqFeatures()) { print "primary tag: ", $featOb->primary_tag(), "\n"; foreach my $tag ($featOb->get_all_tags()) { print "tag: $tag \n"; foreach my $value ($featOb->get_tag_values($tag)) { print "values $value\n"; } } } peter@pluto:~/Swiss> perl sptest.pl primary tag: DOMAIN tag: description values HYDROPHOBIC primary tag: DOMAIN tag: description values HYDROPHOBIC peter@pluto:~/Swiss> head sprot42.dat --lines=40 ID 104K_THEPA STANDARD; PRT; 924 AA. AC P15711; DT 01-APR-1990 (Rel. 14, Created) DT 01-APR-1990 (Rel. 14, Last sequence update) DT 01-AUG-1992 (Rel. 23, Last annotation update) DE 104 kDa microneme-rhoptry antigen. OS Theileria parva. OC Eukaryota; Alveolata; Apicomplexa; Piroplasmida; Theileriidae; OC Theileria. OX NCBI_TaxID=5875; RN [1] RP SEQUENCE FROM N.A. RC STRAIN=Muguga; RX MEDLINE=90158697; PubMed=1689460; RA Iams K.P., Young J.R., Nene V., Desai J., Webster P., RA Ole-Moiyoi O.K., Musoke A.J.; RT "Characterisation of the gene encoding a 104-kilodalton microneme- RT rhoptry protein of Theileria parva."; RL Mol. Biochem. Parasitol. 39:47-60(1990). CC -!- SUBCELLULAR LOCATION: IN MICRONEME/RHOPTRY COMPLEXES. CC -!- DEVELOPMENTAL STAGE: SPOROZOITE ANTIGEN. CC -------------------------------------------------------------------------- CC This SWISS-PROT entry is copyright. It is produced through a collaboration CC between the Swiss Institute of Bioinformatics and the EMBL outstation - CC the European Bioinformatics Institute. There are no restrictions on its CC use by non-profit institutions as long as its content is in no way CC modified and this statement is not removed. Usage by and for commercial CC entities requires a license agreement (See http://www.isb-sib.ch/announce/ CC or send an email to license@isb-sib.ch). CC -------------------------------------------------------------------------- DR EMBL; M29954; AAA18217.1; -. DR PIR; A44945; A44945. KW Antigen; Sporozoite; Repeat. FT DOMAIN 1 19 HYDROPHOBIC. FT DOMAIN 905 924 HYDROPHOBIC. SQ SEQUENCE 924 AA; 103625 MW; 289B4B554A61870E CRC64; MKFLILLFNI LCLFPVLAAD NHGVGPQGAS GVDPITFDIN SNQTGPAFLT AVEMAGVKYL QVQHGSNVNI HRLVEGNVVI WENASTPLYT GAIVTNNDGP YMAYVEVLGD PNLQFFIKSG DAWVTLSEHE YLAKLQEIRQ AVHIESVFSL NMAFQLENNK YEVETHAKNG ANMVTFIPRN GHICKMVYHK NVRIYKATGN DTVTSVVGFF RGLRLLLINV FSIDDNGMMS NRYFQHVDDK peter@pluto:~/Swiss> exit > Peter, > > Some of the data in a SwissProt file is parsed into Features, some of it > into Annotations (Swissprot entries are RichSeq objects, like Genbank and > EMBL entries). So probably you'll want to look at the Feature-Annotation > HOWTO. Unfortunately there are no Swissprot examples there but the logic > will be the same, open the file with SeqIO and print out specific entries, > or portions of entries, with the desired characteristics. Perhaps the SeqIO > HOWTO would be useful as well... > > Brian O. > > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org > [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Robinson, Peter > Sent: Thursday, January 08, 2004 10:18 AM > To: bioperl-l@bioperl.org > Subject: [Bioperl-l] loading sprot.dat > > Hi all, > > I would like to load the contents of the Swiss-Prot file sprot.dat into a > mysql database. Since I have a relatively specific question, I would like > to use a databse of my own design and just extract portions of the relevant > entries from sprot.dat rather than the whole thing. > I would appreciate it if someone could point me to an example script for > this kind of thing. I did not see anything like this in my perusals of the > archives or google, please forgive me if this question has been asked > before! > > Thanks > > Peter > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From Richard.Holland at agresearch.co.nz Thu Jan 8 19:36:50 2004 From: Richard.Holland at agresearch.co.nz (Holland, Richard) Date: Thu Jan 8 22:51:14 2004 Subject: [Bioperl-l] RemoteBlast Message-ID: I have updated Bio::Tools::Run::RemoteBlast.pm in bioperl-live so that it accepts, validates and understands the entire QBlast API for Get/Put operations, not just the small subset it did before. Note that some of these options it now accepts are entirely inappropriate in the current context (eg. display options, file download options) but might be useful in the future. cheers, Richard --- Richard Holland Bioinformatics Database Developer ITS, Agresearch Invermay x3279 ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From juguang at tll.org.sg Fri Jan 9 03:59:07 2004 From: juguang at tll.org.sg (Juguang Xiao) Date: Fri Jan 9 04:05:34 2004 Subject: [Bioperl-l] loading sprot.dat In-Reply-To: <5F7CE35370B6CF429AA3CA960ECC27805389E3@EXCHANGE2.charite.de> Message-ID: <1532F8DA-4282-11D8-917B-000A957702FE@tll.org.sg> On Thursday, January 8, 2004, at 11:18 pm, Robinson, Peter wrote: > Hi all, > > I would like to load the contents of the Swiss-Prot file sprot.dat > into a mysql database. Since I have a relatively specific question, I > would like to use a databse of my own design and just extract portions > of the relevant entries from sprot.dat rather than the whole thing. Do you know biosql and bioperl-db projects? I am not sure why you use your own database schema, rather than biosql one. Is biosql schema missing something so that it cannot satisfy your requirement? Please let Hilmar and us know if so. bioperl-db/scripts/biosql/load_seqdatabase.pl can load Swissprot into mysql. I have load the whole SP months ago. There is option called seqfilter in the script, while I am not sure if it functions and it's you want. Juguang > I would appreciate it if someone could point me to an example script > for this kind of thing. I did not see anything like this in my > perusals of the archives or google, please forgive me if this question > has been asked before! > > Thanks > > Peter > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > Juguang Xiao From perin at cirad.fr Fri Jan 9 04:02:16 2004 From: perin at cirad.fr (perin) Date: Fri Jan 9 04:09:13 2004 Subject: [Bioperl-l] swisprot.dat Message-ID: <3FFE6E18.8030704@cirad.fr> Hi Peter, We had a similar problem few month ago (access to Arabidopsis thaliana proteome annotation released in a swiss-prot format by EBI). We solved it using Biosql and a set of scripts accessing directly to Bioperl objects. Take a look at: http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/INSTALL?cvsroot=bioperl&rev=1.2 After, you will have to wrote scripts to access Bioperl objects directly : see a set of examples at: http://www.open-bio.org/bosc2003/slides/Persistent_Bioperl_BOSC03.pdf Christophe Perin From gert.thijs at esat.kuleuven.ac.be Fri Jan 9 04:05:29 2004 From: gert.thijs at esat.kuleuven.ac.be (Gert Thijs) Date: Fri Jan 9 04:21:08 2004 Subject: [Bioperl-l] compatibility problem of SeqIO Message-ID: <1073639127.2934.1642.camel@sista-08.esat.kuleuven.ac.be> Dear, I have a script that behaves differently on two different linux PCs. The problem is caused by the following code, which seems rather trivial: my $seqFile = 'set1.tfa'; my $seqio = new Bio::SeqIO( -file => "<$seqFile", -format => 'fasta'); On the first machine it works without any problem, but on the other one I get an error saying 'Could not open cat /proc/version Linux version 2.4.20-24.9smp (bhcompile@porky.devel.redhat.com) (gcc version 3.2.2 20030222 (Red Hat Linux 3.2.2-5)) #1 SMP Mon Dec 1 11:25:17 EST 2003 val3|thijs>perl -v This is perl, v5.8.0 built for i386-linux-thread-multi -- + Gert Thijs + Postdoctoral Researcher + K.U.Leuven + ESAT-SCD + Kasteelpark Arenberg 10 + B-3001 Leuven-Heverlee + Belgium + + Tel : +32 16 327928 + Fax : +32 16 321970 + email: gert.thijs@esat.kuleuven.ac.be + + http://www.esat.kuleuven.ac.be/~thijs + http://www.esat.kuleuven.ac.be/~dna/BioI/ + From Marc.Logghe at devgen.com Fri Jan 9 04:25:57 2004 From: Marc.Logghe at devgen.com (Marc Logghe) Date: Fri Jan 9 04:33:07 2004 Subject: [Bioperl-l] compatibility problem of SeqIO Message-ID: Hi Gert, Is set1.tfa a large file ? If so, it might be that on one machine Perl is not supporting large files while on the other it does. HTH, Marc > -----Original Message----- > From: Gert Thijs [mailto:gert.thijs@esat.kuleuven.ac.be] > Sent: Friday, January 09, 2004 10:05 AM > To: Bioperl > Subject: [Bioperl-l] compatibility problem of SeqIO > > > Dear, > > I have a script that behaves differently on two different > linux PCs. The > problem is caused by the following code, which seems rather trivial: > my $seqFile = 'set1.tfa'; > my $seqio = new Bio::SeqIO( -file => "<$seqFile", > -format => 'fasta'); > > > On the first machine it works without any > problem, but on the other one I get an error saying 'Could > not open fasta file is present. > Has anyone an idea what could cause this different behavior? > > I have added the system information below and to me it seems that both > configurations are more or less the same. > In both cases I use the same version of bioperl. > Here is the header of SeqIO.pm, which is the same on both machines. > # $Id: SeqIO.pm,v 1.59.2.4 2003/09/14 19:16:53 jason Exp $ > > > The configuration of the first machine is: > [thijs@sista-08 thijs]$ cat /proc/version > Linux version 2.4.22-10mdk (nplanel@no.mandrakesoft.com) > (gcc version > 3.3.1 (Mandrake Linux 9.2 3.3.1-2mdk)) #1 Thu Sep 18 > 12:30:58 CEST 2003 > [thijs@sista-08 thijs]$ perl -v > > This is perl, v5.8.1 built for i386-linux-thread-multi > > > > The configuration of the second one is: > val3|thijs>cat /proc/version > Linux version 2.4.20-24.9smp (bhcompile@porky.devel.redhat.com) (gcc > version 3.2.2 20030222 (Red Hat Linux 3.2.2-5)) #1 SMP Mon Dec 1 > 11:25:17 EST 2003 > val3|thijs>perl -v > > This is perl, v5.8.0 built for i386-linux-thread-multi > > > > > -- > + Gert Thijs > + Postdoctoral Researcher > + K.U.Leuven > + ESAT-SCD > + Kasteelpark Arenberg 10 > + B-3001 Leuven-Heverlee > + Belgium > + > + Tel : +32 16 327928 > + Fax : +32 16 321970 > + email: gert.thijs@esat.kuleuven.ac.be > + > + http://www.esat.kuleuven.ac.be/~thijs > + http://www.esat.kuleuven.ac.be/~dna/BioI/ > + > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From gert.thijs at esat.kuleuven.ac.be Fri Jan 9 04:33:07 2004 From: gert.thijs at esat.kuleuven.ac.be (Gert Thijs) Date: Fri Jan 9 04:40:09 2004 Subject: [Bioperl-l] compatibility problem of SeqIO In-Reply-To: References: Message-ID: <1073640785.2932.1664.camel@sista-08.esat.kuleuven.ac.be> Marc, Not at all, set1.tfa contains only 5 sequences of 800bp. Gert On Fri, 2004-01-09 at 10:25, Marc Logghe wrote: > Hi Gert, > Is set1.tfa a large file ? If so, it might be that on one machine Perl is not supporting large files while on the other it does. > HTH, > Marc > > > -----Original Message----- > > From: Gert Thijs [mailto:gert.thijs@esat.kuleuven.ac.be] > > Sent: Friday, January 09, 2004 10:05 AM > > To: Bioperl > > Subject: [Bioperl-l] compatibility problem of SeqIO > > > > > > Dear, > > > > I have a script that behaves differently on two different > > linux PCs. The > > problem is caused by the following code, which seems rather trivial: > > my $seqFile = 'set1.tfa'; > > my $seqio = new Bio::SeqIO( -file => "<$seqFile", > > -format => 'fasta'); > > > > > > On the first machine it works without any > > problem, but on the other one I get an error saying 'Could > > not open > fasta file is present. > > Has anyone an idea what could cause this different behavior? > > > > I have added the system information below and to me it seems that both > > configurations are more or less the same. > > In both cases I use the same version of bioperl. > > Here is the header of SeqIO.pm, which is the same on both machines. > > # $Id: SeqIO.pm,v 1.59.2.4 2003/09/14 19:16:53 jason Exp $ > > > > > > The configuration of the first machine is: > > [thijs@sista-08 thijs]$ cat /proc/version > > Linux version 2.4.22-10mdk (nplanel@no.mandrakesoft.com) > > (gcc version > > 3.3.1 (Mandrake Linux 9.2 3.3.1-2mdk)) #1 Thu Sep 18 > > 12:30:58 CEST 2003 > > [thijs@sista-08 thijs]$ perl -v > > > > This is perl, v5.8.1 built for i386-linux-thread-multi > > > > > > > > The configuration of the second one is: > > val3|thijs>cat /proc/version > > Linux version 2.4.20-24.9smp (bhcompile@porky.devel.redhat.com) (gcc > > version 3.2.2 20030222 (Red Hat Linux 3.2.2-5)) #1 SMP Mon Dec 1 > > 11:25:17 EST 2003 > > val3|thijs>perl -v > > > > This is perl, v5.8.0 built for i386-linux-thread-multi > > > > > > > > > > -- > > + Gert Thijs > > + Postdoctoral Researcher > > + K.U.Leuven > > + ESAT-SCD > > + Kasteelpark Arenberg 10 > > + B-3001 Leuven-Heverlee > > + Belgium > > + > > + Tel : +32 16 327928 > > + Fax : +32 16 321970 > > + email: gert.thijs@esat.kuleuven.ac.be > > + > > + http://www.esat.kuleuven.ac.be/~thijs > > + http://www.esat.kuleuven.ac.be/~dna/BioI/ > > + > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- + Gert Thijs + Postdoctoral Researcher + K.U.Leuven + ESAT-SCD + Kasteelpark Arenberg 10 + B-3001 Leuven-Heverlee + Belgium + + Tel : +32 16 327928 + Fax : +32 16 321970 + email: gert.thijs@esat.kuleuven.ac.be + + http://www.esat.kuleuven.ac.be/~thijs + http://www.esat.kuleuven.ac.be/~dna/BioI/ + From rousse at ccr.jussieu.fr Fri Jan 9 07:35:35 2004 From: rousse at ccr.jussieu.fr (Guillaume Rousse) Date: Fri Jan 9 07:42:39 2004 Subject: [Bioperl-l] Packaging BioPerl for mandrake linux Message-ID: <200401091335.35355.rousse@ccr.jussieu.fr> Hello. I'm maintaining BioPerl modules for MandrakeLinux. I'm having some problems to build bioperl-ext. First, the compilation doesn't support parallel build on multiple-cpu build host, as readm.pm get installed after it is needed: make[1]: Entering directory `/home/guillomovitch/rpm/BUILD/bioperl-ext-1.4/Bio/SeqIO/staden' /usr/bin/perl5.8.2 -Mblib -MInline=NOISY,_INSTALL_ -MBio::SeqIO::staden::read -e1 0.01 ../blib/arch Can't locate Bio/SeqIO/staden/read.pm in @INC (@INC contains: /home/guillomovitch/rpm/BUILD/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/arch /home/guillomovitch/rpm/BUILD/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/lib /usr/lib/perl5/5.8.2/i386-linux-thread-multi /usr/lib/perl5/5.8.2 /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.2 /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.6.1 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.2 /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .). BEGIN failed--compilation aborted. make[1]: *** [read.inl] Error 2 make[1]: *** Waiting for unfinished jobs.... cp read.pm ../blib/lib/Bio/SeqIO/staden/read.pm make[1]: *** Waiting for unfinished jobs.... Forcing linear build is OK however. Second, correct optimisation flags (-O2 -fomit-frame-pointer -pipe -march=i586 -mcpu=pentiumpro) are not passed to all gcc invocations: gcc -c -I./libs -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -fomit-frame-pointer -pipe -march=i586 -mcpu=pentiumpro -DVERSION=\"0.1\" -DXS_VERSION=\"0.1\" -fPIC "-I/usr/lib/perl5/5.8.2/i386-linux-thread-multi/CORE" -DPOSIX -DNOERROR Align.c gcc -c -O -c -o dnamatrix.o dnamatrix.c The first one is OK, the second is not. Third, I can't find any installed binary files at the end of the compilation process, only source C files and headers in /usr/lib/perl5/vendor_perl/5.8.2/Bio/Ext/Align/libs, whereas i was expecting to have some .so under /usr/lib/perl5/vendor_perl/5.8.2/Bio/Ext/Align/libs/ I don't have previous experience of using Inline::C, however Fourth, invocating make test as part of the build process fails for some uninstalled module: -- PERL_DL_NONLAZY=1 /usr/bin/perl5.8.2 "-MExtUtils::Command::MM" "-e" "test_harness(0, '../blib/lib', '../blib/arch')" test.pl test....The extension 'Bio::SeqIO::staden::read' is not properly installed in path: '/home/guillomovitch/rpm/BUILD/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/arch' If this is a CPAN/distributed module, you may need to reinstall it on your system. To allow Inline to compile the module in a temporary cache, simply remove the Inline config option 'VERSION=' from the Bio::SeqIO::staden::read module. at test.pl line 0 INIT failed--call queue aborted, line 1. It look like 1), but happens either using parallel or linear build. The message about using a temporary cache is quite confusing. Am I supposed to remove line 79 in Bio/SeqIO/staden/read.pm just to pass the tests ? And how will such a change impacts further use of the module ? Just skipping the test is enough to workaround the problem, however. Any help appreciated. BTW, some modules in main bioperl package have references to some modules in bioperl-run package: Bio::Root::Version Bio::Tools::Run::Alignment::Clustalw Bio::Tools::Run::Phylo::Molphy::ProtML Bio::Tools::Run::Phylo::Phylip::Neighbor Bio::Tools::Run::Phylo::Phylip::ProtDist Bio::Tools::Run::Phylo::Phylip::ProtPars This make both packages to requires each other. Maybe those modules should be moved to bioperl-run, to make bioperl self-sufficient ? -- Does a fish get cramps after eating? -- Why Why Why n?2 From rousse at ccr.jussieu.fr Fri Jan 9 07:38:23 2004 From: rousse at ccr.jussieu.fr (Guillaume Rousse) Date: Fri Jan 9 07:45:25 2004 Subject: [Bioperl-l] Trouble installing bioperl-ext-1.4 In-Reply-To: References: Message-ID: <200401091338.23266.rousse@ccr.jussieu.fr> Le Mercredi 07 Janvier 2004 02:37, Aaron J Mackey a ?crit?: > This was the bit that you should have paid attention to: > > Note (probably harmless): No library found for -lread > > Did you actually read the README, where it tells you that: > > This extension needs the rest of the main bioperl distribution to > function properly. It is only useful as a helper module for the SeqIO > system to read sequence trace files handled by the Staden package's > io_lib "read" library. You should have this library installed prior > to installing Bio::SeqIO::staden::read, it's currently available at: > > ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/io_lib/ Concerning iolib, you could add in the README than just installing os.h manually with other headers is not enough, as it relies on others macros defined in config.h. So you have to install both os.h and config.h, and to modify os.h to have #include "config.h" instead of #include -- The wimp who made it through the eliminations on luck alone will suddenly turn into Bruce Lee when you're up against him -- Murphy's Laws of Martial Arts n?1 From jason at cgt.duhs.duke.edu Fri Jan 9 08:35:11 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Fri Jan 9 08:42:15 2004 Subject: [Bioperl-l] compatibility problem of SeqIO In-Reply-To: <1073639127.2934.1642.camel@sista-08.esat.kuleuven.ac.be> References: <1073639127.2934.1642.camel@sista-08.esat.kuleuven.ac.be> Message-ID: if you add this in your script it can give some information about whether or not you can read the file. if( -r $seqFile ) { print "I can read $seqFile\n"; } else { print "I cannot read $seqFile\n"; } you can also try open($fh, $seqFile) || die( "$seqFile: $!\n"); You should check file permissions, that you are running in the proper directory, etc. -jason On Fri, 9 Jan 2004, Gert Thijs wrote: > Dear, > > I have a script that behaves differently on two different linux PCs. The > problem is caused by the following code, which seems rather trivial: > my $seqFile = 'set1.tfa'; > my $seqio = new Bio::SeqIO( -file => "<$seqFile", > -format => 'fasta'); > On the first machine it works without any problem, but on the other one I get an error saying 'Could not open Has anyone an idea what could cause this different behavior? > > I have added the system information below and to me it seems that both > configurations are more or less the same. > In both cases I use the same version of bioperl. > Here is the header of SeqIO.pm, which is the same on both machines. > # $Id: SeqIO.pm,v 1.59.2.4 2003/09/14 19:16:53 jason Exp $ > > > The configuration of the first machine is: > [thijs@sista-08 thijs]$ cat /proc/version > Linux version 2.4.22-10mdk (nplanel@no.mandrakesoft.com) (gcc version > 3.3.1 (Mandrake Linux 9.2 3.3.1-2mdk)) #1 Thu Sep 18 12:30:58 CEST 2003 > [thijs@sista-08 thijs]$ perl -v > > This is perl, v5.8.1 built for i386-linux-thread-multi > > > > The configuration of the second one is: > val3|thijs>cat /proc/version > Linux version 2.4.20-24.9smp (bhcompile@porky.devel.redhat.com) (gcc > version 3.2.2 20030222 (Red Hat Linux 3.2.2-5)) #1 SMP Mon Dec 1 > 11:25:17 EST 2003 > val3|thijs>perl -v > > This is perl, v5.8.0 built for i386-linux-thread-multi > > > > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From gert.thijs at esat.kuleuven.ac.be Fri Jan 9 09:57:10 2004 From: gert.thijs at esat.kuleuven.ac.be (Gert Thijs) Date: Fri Jan 9 10:04:12 2004 Subject: [Bioperl-l] compatibility problem of SeqIO In-Reply-To: References: <1073639127.2934.1642.camel@sista-08.esat.kuleuven.ac.be> Message-ID: <3FFEC146.2080502@esat.kuleuven.ac.be> Jason, That is the weird part, I am working on the same directory (over NFS). So permissions should be the same. I have been playing around with this and I just found that the problem is probably caused by the way the input arguments are given to the script in which I use this command. If just type the name of the file as an input argument the script (myScript.pl set1.tfa} works, but if I write something like fasta_files='set1.tfa set2.tfa set3.tfa set4.tfa' for id in ${fasta_files} do myScript.pl ${id} done then it does not work. I find this rather disturbing. Gert Jason Stajich wrote: > if you add this in your script it can give some information about whether > or not you can read the file. > > if( -r $seqFile ) { > print "I can read $seqFile\n"; > } else { > print "I cannot read $seqFile\n"; > } > > you can also try > open($fh, $seqFile) || die( "$seqFile: $!\n"); > > You should check file permissions, that you are running in the proper > directory, etc. > > -jason From amackey at virginia.edu Fri Jan 9 10:16:51 2004 From: amackey at virginia.edu (Aaron J.Mackey) Date: Fri Jan 9 10:23:45 2004 Subject: [Bioperl-l] Trouble installing bioperl-ext-1.4 In-Reply-To: <200401091338.23266.rousse@ccr.jussieu.fr> References: <200401091338.23266.rousse@ccr.jussieu.fr> Message-ID: Thanks, committed. -Aaron On Jan 9, 2004, at 7:38 AM, Guillaume Rousse wrote: > Le Mercredi 07 Janvier 2004 02:37, Aaron J Mackey a ?crit?: >> This was the bit that you should have paid attention to: >>> Note (probably harmless): No library found for -lread >> >> Did you actually read the README, where it tells you that: >> >> This extension needs the rest of the main bioperl distribution to >> function properly. It is only useful as a helper module for the >> SeqIO >> system to read sequence trace files handled by the Staden package's >> io_lib "read" library. You should have this library installed prior >> to installing Bio::SeqIO::staden::read, it's currently available at: >> >> ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/io_lib/ > Concerning iolib, you could add in the README than just installing os.h > manually with other headers is not enough, as it relies on others > macros > defined in config.h. So you have to install both os.h and config.h, > and to > modify os.h to have > #include "config.h" > instead of > #include > -- > The wimp who made it through the eliminations on luck alone will > suddenly turn > into Bruce Lee when you're up against him > -- Murphy's Laws of Martial Arts n?1 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From markw at illuminae.com Fri Jan 9 10:27:51 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Fri Jan 9 10:34:51 2004 Subject: [Bioperl-l] gff_string on an HSPI object is not Bio::DB::GFF friendly Message-ID: <1073662071.2102.84.camel@localhost.localdomain> Hi all, I'm wondering if the gff_string call on an HSPI object is perhaps backwards (or if it is Bio::DB::GFF that is backwards ). It certainly appears that I get "mirror image" data from that call compared to what I need for Gbrowse. e.g. I blast an EST (a101) against genbank. I then take the blast report and parse it until I have an HSP object in my hand. Now... If I do ->gff_string on that HSP object I get this: DB<14> p $hsp->gff_string a101 BLASTN similarity 138 160 23 + 0 Target gi|12329259 125209 125231 But by Gbrowse GFF standards what I expect to see (I think) is this: gi|12329259 BLASTN similarity 138 160 23 + 0 Target a101 1 200 I know that Gbrowse GFF is a bit weird, but before I go coding something new to deal with this problem I want to make sure that my interpretation of the problem is correct, and that nobody has actually coded a solution already (other than my GbroweGFF ResultWriterI, which is what I am working on updating right now). One possibility is to modulate the output by passing an argument like gff_string('query') or gff_string('hit') to indicate which of the sequences you consider to be the "reference" sequence. I tried calling gff_string on $HSP->query and $HSP->hit, but they have lost all information about each other, so that doesn't help. If anyone has a preference on how this should behave please say so. It may be that we don't want BioPerl to exhibit Gbrowse GFF behaviour under any circumstances, because it really is quite peculiar in the case of alignment features. My opinion is that the current bioperl output is more comprehensible than what Gbrowse is expecting ("Target" surely means what you hit with your query, rather than your query itself...??), but since Gbrowse & Bio::DB::GFF are so tightly integrated with BioPerl it would probably be better to have some BioPerl way to generate the output format expected by Bio::DB::GFF. Also, what is the "correct" way to represent alignment features in GFF3? Does ->gff_string output HSP's correctly in GFF3 format? If not, then we should probably revisit this issue in its entirety. Scott/Lincoln, is there a compelling reason for Gbrowse to require its input in the format that it does, or could it be "flipped"? Mark -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. of Medical Genetics University of British Columbia's iCAPTURE Centre Vancouver, BC, Canada ------------------------------------------------------------------------ It just goes to show you that SOAP::Lite is more intuitive than you might think, if you know enough Perl and have the patience to dive into the source code. -Byrne Reese -http://builder.com.com/5100-6389_14-1045078-2.html ------------------------------------------------------------------------ From cain at cshl.org Fri Jan 9 10:37:50 2004 From: cain at cshl.org (Scott Cain) Date: Fri Jan 9 10:44:47 2004 Subject: [Bioperl-l] Re: gff_string on an HSPI object is not Bio::DB::GFF friendly In-Reply-To: <1073662071.2102.84.camel@localhost.localdomain> References: <1073662071.2102.84.camel@localhost.localdomain> Message-ID: <1073662670.1473.25.camel@localhost.localdomain> Mark, My first suggestion (without doing any real work) is that you look at scripts/utilities/bp_search2gff.pl in which Jason has probably resolved these issues. It does seem to me that source and target assignment are counter intuitive sometimes, but what can you do...? (well, other than fix it, I suppose, but that would break other things, and so on). Scott On Fri, 2004-01-09 at 10:27, Mark Wilkinson wrote: > Hi all, > > I'm wondering if the gff_string call on an HSPI object is perhaps > backwards (or if it is Bio::DB::GFF that is backwards ). It certainly > appears that I get "mirror image" data from that call compared to what I > need for Gbrowse. > > e.g. I blast an EST (a101) against genbank. I then take the blast > report and parse it until I have an HSP object in my hand. Now... > > If I do ->gff_string on that HSP object I get this: > > DB<14> p $hsp->gff_string > a101 BLASTN similarity 138 160 23 + 0 Target gi|12329259 125209 125231 > > But by Gbrowse GFF standards what I expect to see (I think) is this: > > gi|12329259 BLASTN similarity 138 160 23 + 0 Target a101 1 200 > > > I know that Gbrowse GFF is a bit weird, but before I go coding something > new to deal with this problem I want to make sure that my interpretation > of the problem is correct, and that nobody has actually coded a solution > already (other than my GbroweGFF ResultWriterI, which is what I am > working on updating right now). > > One possibility is to modulate the output by passing an argument like > gff_string('query') or gff_string('hit') to indicate which of the > sequences you consider to be the "reference" sequence. I tried calling > gff_string on $HSP->query and $HSP->hit, but they have lost all > information about each other, so that doesn't help. > > If anyone has a preference on how this should behave please say so. It > may be that we don't want BioPerl to exhibit Gbrowse GFF behaviour under > any circumstances, because it really is quite peculiar in the case of > alignment features. My opinion is that the current bioperl output is > more comprehensible than what Gbrowse is expecting ("Target" surely > means what you hit with your query, rather than your query itself...??), > but since Gbrowse & Bio::DB::GFF are so tightly integrated with BioPerl > it would probably be better to have some BioPerl way to generate the > output format expected by Bio::DB::GFF. > > Also, what is the "correct" way to represent alignment features in > GFF3? Does ->gff_string output HSP's correctly in GFF3 format? If not, > then we should probably revisit this issue in its entirety. > Scott/Lincoln, is there a compelling reason for Gbrowse to require its > input in the format that it does, or could it be "flipped"? > > Mark -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain@cshl.org GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory From jason at cgt.duhs.duke.edu Fri Jan 9 10:38:16 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Fri Jan 9 10:45:13 2004 Subject: [Bioperl-l] gff_string on an HSPI object is not Bio::DB::GFF friendly In-Reply-To: <1073662071.2102.84.camel@localhost.localdomain> References: <1073662071.2102.84.camel@localhost.localdomain> Message-ID: Remember an HSP object is a combination of two SeqFeature objects (which are Bio::SeqFeature::Similarity objects. So when you call $hsp->gff_string you are calling $hsp->query->gff_string. If you want to see the gff for the target you do $hsp->hit->gff_string. See my search2gff.PLS script in scripts/utilities/search2gff.PLS for example usage of the object and production of Bio::DB::GFF appropriate GFF from a SearchIO parseable report. -jason On Fri, 9 Jan 2004, Mark Wilkinson wrote: > Hi all, > > I'm wondering if the gff_string call on an HSPI object is perhaps > backwards (or if it is Bio::DB::GFF that is backwards ). It certainly > appears that I get "mirror image" data from that call compared to what I > need for Gbrowse. > > e.g. I blast an EST (a101) against genbank. I then take the blast > report and parse it until I have an HSP object in my hand. Now... > > If I do ->gff_string on that HSP object I get this: > > DB<14> p $hsp->gff_string > a101 BLASTN similarity 138 160 23 + 0 Target gi|12329259 125209 125231 > > But by Gbrowse GFF standards what I expect to see (I think) is this: > > gi|12329259 BLASTN similarity 138 160 23 + 0 Target a101 1 200 > > > I know that Gbrowse GFF is a bit weird, but before I go coding something > new to deal with this problem I want to make sure that my interpretation > of the problem is correct, and that nobody has actually coded a solution > already (other than my GbroweGFF ResultWriterI, which is what I am > working on updating right now). > > One possibility is to modulate the output by passing an argument like > gff_string('query') or gff_string('hit') to indicate which of the > sequences you consider to be the "reference" sequence. I tried calling > gff_string on $HSP->query and $HSP->hit, but they have lost all > information about each other, so that doesn't help. > > If anyone has a preference on how this should behave please say so. It > may be that we don't want BioPerl to exhibit Gbrowse GFF behaviour under > any circumstances, because it really is quite peculiar in the case of > alignment features. My opinion is that the current bioperl output is > more comprehensible than what Gbrowse is expecting ("Target" surely > means what you hit with your query, rather than your query itself...??), > but since Gbrowse & Bio::DB::GFF are so tightly integrated with BioPerl > it would probably be better to have some BioPerl way to generate the > output format expected by Bio::DB::GFF. > > Also, what is the "correct" way to represent alignment features in > GFF3? Does ->gff_string output HSP's correctly in GFF3 format? If not, > then we should probably revisit this issue in its entirety. > Scott/Lincoln, is there a compelling reason for Gbrowse to require its > input in the format that it does, or could it be "flipped"? > > Mark > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From cain at cshl.org Fri Jan 9 10:40:20 2004 From: cain at cshl.org (Scott Cain) Date: Fri Jan 9 10:47:17 2004 Subject: [Bioperl-l] gff_string on an HSPI object is not Bio::DB::GFF friendly In-Reply-To: References: <1073662071.2102.84.camel@localhost.localdomain> Message-ID: <1073662820.1476.27.camel@localhost.localdomain> On Fri, 2004-01-09 at 10:38, Jason Stajich wrote: > Remember an HSP object is a combination of two SeqFeature objects (which > are Bio::SeqFeature::Similarity objects. > > So when you call $hsp->gff_string you are calling $hsp->query->gff_string. > > If you want to see the gff for the target you do $hsp->hit->gff_string. > And that fixes the counter intuitive thing I just mentioned--should have waited two minutes to hit send :-) > See my search2gff.PLS script in scripts/utilities/search2gff.PLS for > example usage of the object and production of Bio::DB::GFF appropriate GFF > from a SearchIO parseable report. > > -jason > > On Fri, 9 Jan 2004, Mark Wilkinson wrote: > > > Hi all, > > > > I'm wondering if the gff_string call on an HSPI object is perhaps > > backwards (or if it is Bio::DB::GFF that is backwards ). It certainly > > appears that I get "mirror image" data from that call compared to what I > > need for Gbrowse. > > > > e.g. I blast an EST (a101) against genbank. I then take the blast > > report and parse it until I have an HSP object in my hand. Now... > > > > If I do ->gff_string on that HSP object I get this: > > > > DB<14> p $hsp->gff_string > > a101 BLASTN similarity 138 160 23 + 0 Target gi|12329259 125209 125231 > > > > But by Gbrowse GFF standards what I expect to see (I think) is this: > > > > gi|12329259 BLASTN similarity 138 160 23 + 0 Target a101 1 200 > > > > > > I know that Gbrowse GFF is a bit weird, but before I go coding something > > new to deal with this problem I want to make sure that my interpretation > > of the problem is correct, and that nobody has actually coded a solution > > already (other than my GbroweGFF ResultWriterI, which is what I am > > working on updating right now). > > > > One possibility is to modulate the output by passing an argument like > > gff_string('query') or gff_string('hit') to indicate which of the > > sequences you consider to be the "reference" sequence. I tried calling > > gff_string on $HSP->query and $HSP->hit, but they have lost all > > information about each other, so that doesn't help. > > > > If anyone has a preference on how this should behave please say so. It > > may be that we don't want BioPerl to exhibit Gbrowse GFF behaviour under > > any circumstances, because it really is quite peculiar in the case of > > alignment features. My opinion is that the current bioperl output is > > more comprehensible than what Gbrowse is expecting ("Target" surely > > means what you hit with your query, rather than your query itself...??), > > but since Gbrowse & Bio::DB::GFF are so tightly integrated with BioPerl > > it would probably be better to have some BioPerl way to generate the > > output format expected by Bio::DB::GFF. > > > > Also, what is the "correct" way to represent alignment features in > > GFF3? Does ->gff_string output HSP's correctly in GFF3 format? If not, > > then we should probably revisit this issue in its entirety. > > Scott/Lincoln, is there a compelling reason for Gbrowse to require its > > input in the format that it does, or could it be "flipped"? > > > > Mark > > > > > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain@cshl.org GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory From amackey at pcbi.upenn.edu Fri Jan 9 10:49:25 2004 From: amackey at pcbi.upenn.edu (Aaron J. Mackey) Date: Fri Jan 9 10:56:26 2004 Subject: [Bioperl-l] Packaging BioPerl for mandrake linux In-Reply-To: <200401091335.35355.rousse@ccr.jussieu.fr> References: <200401091335.35355.rousse@ccr.jussieu.fr> Message-ID: <66779DB4-42BB-11D8-9385-000A958C5008@pcbi.upenn.edu> On Jan 9, 2004, at 7:35 AM, Guillaume Rousse wrote: > First, the compilation doesn't support parallel build on multiple-cpu > build > host, as readm.pm get installed after it is needed: I'm not sure how to fix this ... > Second, correct optimisation flags (-O2 -fomit-frame-pointer -pipe > -march=i586 > -mcpu=pentiumpro) are not passed to all gcc invocations: But this I did fix in CVS, thanks for pointing it out ... > Third, I can't find any installed binary files at the end of the > compilation > process, only source C files and headers When you run "make install" what do you see? I get (on Mac OS X 10.3): Installing /usr/local/lib/perl5/site_perl/5.8.1/darwin-2level/auto/Bio/Ext/Align/ Align.bs Installing /usr/local/lib/perl5/site_perl/5.8.1/darwin-2level/auto/Bio/Ext/Align/ Align.bundle That .bundle file is the dynamically loaded binary. > I don't have previous experience of using Inline::C, however The Bio/Ext/Align/ stuff doesn't use Inline::C, that's only the Bio::SeqIO::staden stuff. You might consider packaging the two separately ... > Fourth, invocating make test as part of the build process fails for > some > uninstalled module: This is an Inline::C problem; Inline::C-based modules are a little tricky to get right for testing before installation. Generally I see this error when I've had a failed compilation (because of the .h errors you found) and don't have a completely "clean" build environment. You're right that the error message is misleading. > BTW, some modules in main bioperl package have references to some > modules in > bioperl-run package: > Bio::Root::Version This is in bioperl-live, or at least it should be ... there is no Bio::Root::* in bioperl-run. > This make both packages to requires each other. Maybe those modules > should be > moved to bioperl-run, to make bioperl self-sufficient ? bioperl-run requires bioperl, period. bioperl makes use of many "external" packages, but they are mostly optional (required only for a very small subset of bioperl functionality). In general, we'd like people to be able to install the core BioPerl without a ton of other packages (and certainly without requiring bioperl-run). All bioperl tests should pass (i.e. be skipped, if necessary) without bioperl-run installed (is that not true?) > Does a fish get cramps after eating? > -- Why Why Why n?2 I think so, but only when eating raw humans -Aaron From markw at illuminae.com Fri Jan 9 10:50:28 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Fri Jan 9 10:57:31 2004 Subject: [BioPerl] Re: [Bioperl-l] gff_string on an HSPI object is not Bio::DB::GFF friendly In-Reply-To: References: <1073662071.2102.84.camel@localhost.localdomain> Message-ID: <1073663428.2102.91.camel@localhost.localdomain> On Fri, 2004-01-09 at 09:38, Jason Stajich wrote: > So when you call $hsp->gff_string you are calling $hsp->query->gff_string. not really. If that were true, then the result of calling $hsp->query->gff_string would be the same as calling $hsp->gff_string... but the are not: DB<17> p $hsp->query->gff_string a101 BLASTN similarity 138 160 23 + 0 Bits "46.1";FracId 1;signif "0.064" DB<18> p $hsp->gff_string a101 BLASTN similarity 138 160 23 + 0 Target gi|12329259 125209 125231 that was what I meant when I said that the individual sub-features are not aware of each other... I'll look at your search2gff code to see how you dealt with it; I'd much rather see this implemented as a function than a standalone script, since the latter isn't very portable. M From jason at cgt.duhs.duke.edu Fri Jan 9 11:05:14 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Fri Jan 9 11:12:11 2004 Subject: [BioPerl] Re: [Bioperl-l] gff_string on an HSPI object is not Bio::DB::GFF friendly In-Reply-To: <1073663428.2102.91.camel@localhost.localdomain> References: <1073662071.2102.84.camel@localhost.localdomain> <1073663428.2102.91.camel@localhost.localdomain> Message-ID: Feel free to fix - (it is probably using a default method in one of its parents, I'm not really sure. Personally I never really expected to use HSP->gff_string because there is 2 separate pieces of information below there and you will want each one in different contexts so HSP->gff_string doesn't make a lot of sense to me in the first place. My view is that all the Search objects should be data containers and it is up to the user to determine how to use them rather than pre-packaging too much on the data object level. This design goal has sort of gotten shot as lost of people want to put convience functions on them so I guess this would just be another example of that. Most of the objects are already too heavy and object creation is the cause of such slow parsing speed in the first place. I really want to flatten the out and reduce the inheritance levels to gain a little more speed (we spend a great deal of time in _rearrange and walking up the SUPER -> ISA hierarchy on each object create). -jason On Fri, 9 Jan 2004, Mark Wilkinson wrote: > On Fri, 2004-01-09 at 09:38, Jason Stajich wrote: > > > So when you call $hsp->gff_string you are calling $hsp->query->gff_string. > > not really. If that were true, then the result of calling > $hsp->query->gff_string would be the same as calling $hsp->gff_string... > but the are not: > > DB<17> p $hsp->query->gff_string > a101 BLASTN similarity 138 160 23 + 0 Bits "46.1";FracId 1;signif > "0.064" > > DB<18> p $hsp->gff_string > a101 BLASTN similarity 138 160 23 + 0 Target gi|12329259 125209 125231 > > that was what I meant when I said that the individual sub-features are > not aware of each other... > > I'll look at your search2gff code to see how you dealt with it; I'd much > rather see this implemented as a function than a standalone script, > since the latter isn't very portable. > > M > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From markw at illuminae.com Fri Jan 9 12:01:50 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Fri Jan 9 12:08:49 2004 Subject: [BioPerl] Re: [Bioperl-l] gff_string on an HSPI object is not Bio::DB::GFF friendly In-Reply-To: References: <1073662071.2102.84.camel@localhost.localdomain> <1073663428.2102.91.camel@localhost.localdomain> Message-ID: <1073667709.3005.10.camel@localhost.localdomain> On Fri, 2004-01-09 at 10:05, Jason Stajich wrote: > Personally I never really expected to use HSP->gff_string because there is > 2 separate pieces of information below there and you will want > each one in different contexts so HSP->gff_string doesn't make a lot of > sense to me in the first place. I agree entirely! This is what I was implying with my ->gff_string('hit') and gff_string('query') suggestion (though that is a bit infantile, I know, it was just the concept that I was trying to bring to light). > My view is that all the Search objects should be data containers and it is > up to the user to determine how to use them rather than pre-packaging too > much on the data object level. I think I understand what you mean. You've obviously given this more thought than I have, so if you suggest what the API should look like IYO then I would try to code it according to that spec. We could make a start in moving things that direction! (or is this going to break everything if we start it?) I think the root of the problem is that Gbrowse expects a very peculiar type of GFF in this circumstance, so we are kind of stuck writing peculiar code :-) Nevertheless, since Bio::DB::GFF is part of BioPerl, I believe we have to be internally consistent and enable the creation of this GFF format from inside of BP. Just to bring up the question again - what is the correct way to represent this in GFF3, since I assume that Gbrowse will support GFF3 "without tweaking" ... or do we look forward to GFF3.5? ;-) It might make more sense for me to code this as a GFF3 feature, rather than spend the time trying to get the GFF2.5 to look right... M From cain at cshl.org Fri Jan 9 12:22:29 2004 From: cain at cshl.org (Scott Cain) Date: Fri Jan 9 12:29:25 2004 Subject: [BioPerl] Re: [Bioperl-l] gff_string on an HSPI object is not Bio::DB::GFF friendly In-Reply-To: <1073667709.3005.10.camel@localhost.localdomain> References: <1073662071.2102.84.camel@localhost.localdomain> <1073663428.2102.91.camel@localhost.localdomain> <1073667709.3005.10.camel@localhost.localdomain> Message-ID: <1073668949.1478.19.camel@localhost.localdomain> Mark, For representing this in GFF3, I would point you to the current version of the spec at http://song.sourceforge.net/gff3.shtml. About two thirds the way down it talks about similarity data. The important points are these: - be sure to use a SO term for the type (ie, match or one of its children) - escape spaces and other stuff in the ninth column - don't bother trying to represent data using the reserved keyword Gap, as nothing understands how to parse it yet (I think) (unless of course you are going to add parsing functionallity to BTGFF and BDGFF :-) What all this means is you need one gff line for each HSP, even though technically, you wouldn't need to do that if you could use the Gap keyword. Scott On Fri, 2004-01-09 at 12:01, Mark Wilkinson wrote: > On Fri, 2004-01-09 at 10:05, Jason Stajich wrote: > > > Personally I never really expected to use HSP->gff_string because there is > > 2 separate pieces of information below there and you will want > > each one in different contexts so HSP->gff_string doesn't make a lot of > > sense to me in the first place. > > I agree entirely! This is what I was implying with my > ->gff_string('hit') and gff_string('query') suggestion (though that is a > bit infantile, I know, it was just the concept that I was trying to > bring to light). > > > My view is that all the Search objects should be data containers and it is > > up to the user to determine how to use them rather than pre-packaging too > > much on the data object level. > > I think I understand what you mean. You've obviously given this more > thought than I have, so if you suggest what the API should look like IYO > then I would try to code it according to that spec. We could make a > start in moving things that direction! (or is this going to break > everything if we start it?) > > I think the root of the problem is that Gbrowse expects a very peculiar > type of GFF in this circumstance, so we are kind of stuck writing > peculiar code :-) Nevertheless, since Bio::DB::GFF is part of BioPerl, > I believe we have to be internally consistent and enable the creation of > this GFF format from inside of BP. > > Just to bring up the question again - what is the correct way to > represent this in GFF3, since I assume that Gbrowse will support GFF3 > "without tweaking" ... or do we look forward to GFF3.5? ;-) It might > make more sense for me to code this as a GFF3 feature, rather than spend > the time trying to get the GFF2.5 to look right... > > M -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain@cshl.org GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory From markw at illuminae.com Fri Jan 9 15:45:10 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Fri Jan 9 15:52:10 2004 Subject: [BioPerl] Re: [Bioperl-l] gff_string on an HSPI object is not Bio::DB::GFF friendly In-Reply-To: <1073668949.1478.19.camel@localhost.localdomain> References: <1073662071.2102.84.camel@localhost.localdomain> <1073663428.2102.91.camel@localhost.localdomain> <1073667709.3005.10.camel@localhost.localdomain> <1073668949.1478.19.camel@localhost.localdomain> Message-ID: <1073681109.1785.50.camel@localhost.localdomain> On Fri, 2004-01-09 at 11:22, Scott Cain wrote: > - be sure to use a SO term for the type (ie, match or one of its > children) So... actually the existing implementation of GFF3 in bioperl from Bio::Tools::GFF->new(-gff_version => 3) does not generate correctly formatted GFF3 for alignment features, yeah? e.g. for column 9 of an alignment feature I get: Target=gi|2828774:54232..54206 whereas I think I should be getting Target=gi|2828774+54232+54206 In addition, it passes through all sorts of other tags that begin with capital letters: Bits=46.1;FracId=0.962962962962963 these should be bits=46.1;fracId=0.962962962962963 if I am reading the spec correctly. Finally, the column-3 term that comes out is "similarity", but it should be one of the *match terms. Is that also correct? Please confirm that I am interpreting the GFF3 spec correctly for these Alignment features and I would be happy to go in and fix things (a.k.a. break everyone else's tools ;-) ) Cheerio! Mark From cain at cshl.org Fri Jan 9 15:49:17 2004 From: cain at cshl.org (Scott Cain) Date: Fri Jan 9 15:56:13 2004 Subject: [BioPerl] Re: [Bioperl-l] gff_string on an HSPI object is not Bio::DB::GFF friendly In-Reply-To: <1073681109.1785.50.camel@localhost.localdomain> References: <1073662071.2102.84.camel@localhost.localdomain> <1073663428.2102.91.camel@localhost.localdomain> <1073667709.3005.10.camel@localhost.localdomain> <1073668949.1478.19.camel@localhost.localdomain> <1073681109.1785.50.camel@localhost.localdomain> Message-ID: <1073681357.1480.47.camel@localhost.localdomain> I think everything you wrote below is correct. As far as I know, only Allen and I have been working BTGFF's GFF3 code, and we haven't touched the alignment portion, so I am not surprised that it is wrong. I suppose fixing BTGFF may break some tools, but I know that the chado loader I wrote will handle it correctly :-) Thanks, Scott On Fri, 2004-01-09 at 15:45, Mark Wilkinson wrote: > On Fri, 2004-01-09 at 11:22, Scott Cain wrote: > > > - be sure to use a SO term for the type (ie, match or one of its > > children) > > So... actually the existing implementation of GFF3 in bioperl > from Bio::Tools::GFF->new(-gff_version => 3) > does not generate correctly formatted GFF3 for alignment features, yeah? > > e.g. for column 9 of an alignment feature I get: > > Target=gi|2828774:54232..54206 > > whereas I think I should be getting > > Target=gi|2828774+54232+54206 > > In addition, it passes through all sorts of other tags that begin with > capital letters: > > Bits=46.1;FracId=0.962962962962963 > > these should be > > bits=46.1;fracId=0.962962962962963 > > if I am reading the spec correctly. > > Finally, the column-3 term that comes out is "similarity", but it should be > one of the *match terms. Is that also correct? > > Please confirm that I am interpreting the GFF3 spec correctly for these > Alignment features and I would be happy to go in and fix things (a.k.a. break > everyone else's tools ;-) ) > > Cheerio! > > Mark > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain@cshl.org GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory From jason at cgt.duhs.duke.edu Fri Jan 9 15:59:45 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Fri Jan 9 16:06:47 2004 Subject: [BioPerl] Re: [Bioperl-l] gff_string on an HSPI object is not Bio::DB::GFF friendly In-Reply-To: <1073681109.1785.50.camel@localhost.localdomain> References: <1073662071.2102.84.camel@localhost.localdomain> <1073663428.2102.91.camel@localhost.localdomain> <1073667709.3005.10.camel@localhost.localdomain> <1073668949.1478.19.camel@localhost.localdomain> <1073681109.1785.50.camel@localhost.localdomain> Message-ID: Mark - Bio::Tools::GFF is really dumb it assumes what you give it is what you want to print. It just takes whatever seqfeature data you pass it and tries to make it GFF, it is not SO aware, attempt to validate, or anything else. You have to clear out the extra tag/values you don't want before sending it to this writer - this is what I do in search2gff. I don't expect a Search::HSP object to be able to just be chunked through Tools::GFF automatically at this point - the Search stuff was developed before SO/GFF3 was described. You really need to custom build up a new object based on the data in the HSP before sending it to the GFF writer. Perhaps you want an HSP-2-SO type factory or something (which is basically what is in the script...). As for the .. versus + - What does: my @values = $feature->get_tag_values('Target'); print join(",",@values), "\n"; give you? If it doesn't return 3 values of gi|2828774,54232,54206 then the data is stored improperly in the seqfeature. -jason On Fri, 9 Jan 2004, Mark Wilkinson wrote: > On Fri, 2004-01-09 at 11:22, Scott Cain wrote: > > > - be sure to use a SO term for the type (ie, match or one of its > > children) > > So... actually the existing implementation of GFF3 in bioperl > from Bio::Tools::GFF->new(-gff_version => 3) > does not generate correctly formatted GFF3 for alignment features, yeah? > > e.g. for column 9 of an alignment feature I get: > > Target=gi|2828774:54232..54206 > > whereas I think I should be getting > > Target=gi|2828774+54232+54206 > > In addition, it passes through all sorts of other tags that begin with > capital letters: > > Bits=46.1;FracId=0.962962962962963 > > these should be > > bits=46.1;fracId=0.962962962962963 > > if I am reading the spec correctly. > > Finally, the column-3 term that comes out is "similarity", but it should be > one of the *match terms. Is that also correct? > > Please confirm that I am interpreting the GFF3 spec correctly for these > Alignment features and I would be happy to go in and fix things (a.k.a. break > everyone else's tools ;-) ) > > Cheerio! > > Mark > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From markw at illuminae.com Fri Jan 9 16:07:27 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Fri Jan 9 16:14:27 2004 Subject: [Bioperl-l] ->alphabet documentation wrong here there and everywhere :-) Message-ID: <1073682447.1785.62.camel@localhost.localdomain> Does anyone object to me fixing the documentation for PrimarySeqI et al. with respect to the 'alphabet' function? It claims to not accept any arguments, but every implementation of it that I can find in the sequence hierarchy actually does, so... the docs are wrong all over the place. Alternately, I could leave the Interface documentation alone, and simply update the documentation for all of the implementing objects who actually DO allow you to set the alphabet explicitly after Seq object creation... Which do you prefer? Was it intentional that the ->alphabet interface not be get/set, or is that historical cruft? Mark -- Mark Wilkinson Illuminae From markw at illuminae.com Fri Jan 9 16:09:04 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Fri Jan 9 16:16:06 2004 Subject: [BioPerl] Re: [Bioperl-l] gff_string on an HSPI object is not Bio::DB::GFF friendly In-Reply-To: <1073681357.1480.47.camel@localhost.localdomain> References: <1073662071.2102.84.camel@localhost.localdomain> <1073663428.2102.91.camel@localhost.localdomain> <1073667709.3005.10.camel@localhost.localdomain> <1073668949.1478.19.camel@localhost.localdomain> <1073681109.1785.50.camel@localhost.localdomain> <1073681357.1480.47.camel@localhost.localdomain> Message-ID: <1073682544.1785.65.camel@localhost.localdomain> Cool. I'm heavily into making the HSP's output proper GFF3 today for some of the Gbrowse tools that I have been working on, so I will jump in and do this over the next day or two. Cheers! Mark On Fri, 2004-01-09 at 14:49, Scott Cain wrote: > I think everything you wrote below is correct. As far as I know, only > Allen and I have been working BTGFF's GFF3 code, and we haven't touched > the alignment portion, so I am not surprised that it is wrong. I > suppose fixing BTGFF may break some tools, but I know that the chado > loader I wrote will handle it correctly :-) > > Thanks, > Scott > > > On Fri, 2004-01-09 at 15:45, Mark Wilkinson wrote: > > On Fri, 2004-01-09 at 11:22, Scott Cain wrote: > > > > > - be sure to use a SO term for the type (ie, match or one of its > > > children) > > > > So... actually the existing implementation of GFF3 in bioperl > > from Bio::Tools::GFF->new(-gff_version => 3) > > does not generate correctly formatted GFF3 for alignment features, yeah? > > > > e.g. for column 9 of an alignment feature I get: > > > > Target=gi|2828774:54232..54206 > > > > whereas I think I should be getting > > > > Target=gi|2828774+54232+54206 > > > > In addition, it passes through all sorts of other tags that begin with > > capital letters: > > > > Bits=46.1;FracId=0.962962962962963 > > > > these should be > > > > bits=46.1;fracId=0.962962962962963 > > > > if I am reading the spec correctly. > > > > Finally, the column-3 term that comes out is "similarity", but it should be > > one of the *match terms. Is that also correct? > > > > Please confirm that I am interpreting the GFF3 spec correctly for these > > Alignment features and I would be happy to go in and fix things (a.k.a. break > > everyone else's tools ;-) ) > > > > Cheerio! > > > > Mark > > -- Mark Wilkinson Illuminae From amackey at virginia.edu Fri Jan 9 16:42:27 2004 From: amackey at virginia.edu (Aaron J.Mackey) Date: Fri Jan 9 16:49:26 2004 Subject: [BioPerl] Re: [Bioperl-l] gff_string on an HSPI object is not Bio::DB::GFF friendly In-Reply-To: <1073682544.1785.65.camel@localhost.localdomain> References: <1073662071.2102.84.camel@localhost.localdomain> <1073663428.2102.91.camel@localhost.localdomain> <1073667709.3005.10.camel@localhost.localdomain> <1073668949.1478.19.camel@localhost.localdomain> <1073681109.1785.50.camel@localhost.localdomain> <1073681357.1480.47.camel@localhost.localdomain> <1073682544.1785.65.camel@localhost.localdomain> Message-ID: Forgive me for a stupid question, but does GBrowse (v1.58) now support GFF3? Namely, can I have start/stops in sub-feature coordinates in my input GFF3 and expect bp_load_gff.pl to behave properly (i.e. generate "canonical" top-level coordinates for storage)? I didn't see anything in the documentation, so I was surprised to see some of the words in these posts ... Thanks On Jan 9, 2004, at 4:09 PM, Mark Wilkinson wrote: > Cool. I'm heavily into making the HSP's output proper GFF3 today for > some of the Gbrowse tools that I have been working on, so I will jump > in > and do this over the next day or two. > > Cheers! > > Mark > > On Fri, 2004-01-09 at 14:49, Scott Cain wrote: >> I think everything you wrote below is correct. As far as I know, only >> Allen and I have been working BTGFF's GFF3 code, and we haven't >> touched >> the alignment portion, so I am not surprised that it is wrong. I >> suppose fixing BTGFF may break some tools, but I know that the chado >> loader I wrote will handle it correctly :-) >> >> Thanks, >> Scott >> >> >> On Fri, 2004-01-09 at 15:45, Mark Wilkinson wrote: >>> On Fri, 2004-01-09 at 11:22, Scott Cain wrote: >>> >>>> - be sure to use a SO term for the type (ie, match or one of its >>>> children) >>> >>> So... actually the existing implementation of GFF3 in bioperl >>> from Bio::Tools::GFF->new(-gff_version => 3) >>> does not generate correctly formatted GFF3 for alignment features, >>> yeah? >>> >>> e.g. for column 9 of an alignment feature I get: >>> >>> Target=gi|2828774:54232..54206 >>> >>> whereas I think I should be getting >>> >>> Target=gi|2828774+54232+54206 >>> >>> In addition, it passes through all sorts of other tags that begin >>> with >>> capital letters: >>> >>> Bits=46.1;FracId=0.962962962962963 >>> >>> these should be >>> >>> bits=46.1;fracId=0.962962962962963 >>> >>> if I am reading the spec correctly. >>> >>> Finally, the column-3 term that comes out is "similarity", but it >>> should be >>> one of the *match terms. Is that also correct? >>> >>> Please confirm that I am interpreting the GFF3 spec correctly for >>> these >>> Alignment features and I would be happy to go in and fix things >>> (a.k.a. break >>> everyone else's tools ;-) ) >>> >>> Cheerio! >>> >>> Mark >>> > -- > Mark Wilkinson > Illuminae > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From cain at cshl.org Fri Jan 9 16:47:03 2004 From: cain at cshl.org (Scott Cain) Date: Fri Jan 9 16:53:59 2004 Subject: [BioPerl] Re: [Bioperl-l] gff_string on an HSPI object is not Bio::DB::GFF friendly In-Reply-To: References: <1073662071.2102.84.camel@localhost.localdomain> <1073663428.2102.91.camel@localhost.localdomain> <1073667709.3005.10.camel@localhost.localdomain> <1073668949.1478.19.camel@localhost.localdomain> <1073681109.1785.50.camel@localhost.localdomain> <1073681357.1480.47.camel@localhost.localdomain> <1073682544.1785.65.camel@localhost.localdomain> Message-ID: <1073684823.1481.53.camel@localhost.localdomain> OK, I am going to answer this, but if I am wrong, I'm sure Lincoln will correct me. I don't think gbrowse or BDGFF knows how to deal with cigar lines in Gap attributes yet. It is safer for the moment to continue to put separate HSPs on separate GFF lines for the time being. Scott On Fri, 2004-01-09 at 16:42, Aaron J.Mackey wrote: > Forgive me for a stupid question, but does GBrowse (v1.58) now support > GFF3? Namely, can I have start/stops in sub-feature coordinates in my > input GFF3 and expect bp_load_gff.pl to behave properly (i.e. generate > "canonical" top-level coordinates for storage)? I didn't see anything > in the documentation, so I was surprised to see some of the words in > these posts ... > > Thanks > > On Jan 9, 2004, at 4:09 PM, Mark Wilkinson wrote: > > > Cool. I'm heavily into making the HSP's output proper GFF3 today for > > some of the Gbrowse tools that I have been working on, so I will jump > > in > > and do this over the next day or two. > > > > Cheers! > > > > Mark > > > > On Fri, 2004-01-09 at 14:49, Scott Cain wrote: > >> I think everything you wrote below is correct. As far as I know, only > >> Allen and I have been working BTGFF's GFF3 code, and we haven't > >> touched > >> the alignment portion, so I am not surprised that it is wrong. I > >> suppose fixing BTGFF may break some tools, but I know that the chado > >> loader I wrote will handle it correctly :-) > >> > >> Thanks, > >> Scott > >> > >> > >> On Fri, 2004-01-09 at 15:45, Mark Wilkinson wrote: > >>> On Fri, 2004-01-09 at 11:22, Scott Cain wrote: > >>> > >>>> - be sure to use a SO term for the type (ie, match or one of its > >>>> children) > >>> > >>> So... actually the existing implementation of GFF3 in bioperl > >>> from Bio::Tools::GFF->new(-gff_version => 3) > >>> does not generate correctly formatted GFF3 for alignment features, > >>> yeah? > >>> > >>> e.g. for column 9 of an alignment feature I get: > >>> > >>> Target=gi|2828774:54232..54206 > >>> > >>> whereas I think I should be getting > >>> > >>> Target=gi|2828774+54232+54206 > >>> > >>> In addition, it passes through all sorts of other tags that begin > >>> with > >>> capital letters: > >>> > >>> Bits=46.1;FracId=0.962962962962963 > >>> > >>> these should be > >>> > >>> bits=46.1;fracId=0.962962962962963 > >>> > >>> if I am reading the spec correctly. > >>> > >>> Finally, the column-3 term that comes out is "similarity", but it > >>> should be > >>> one of the *match terms. Is that also correct? > >>> > >>> Please confirm that I am interpreting the GFF3 spec correctly for > >>> these > >>> Alignment features and I would be happy to go in and fix things > >>> (a.k.a. break > >>> everyone else's tools ;-) ) > >>> > >>> Cheerio! > >>> > >>> Mark > >>> > > -- > > Mark Wilkinson > > Illuminae > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain@cshl.org GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory From allenday at ucla.edu Fri Jan 9 16:51:55 2004 From: allenday at ucla.edu (Allen Day) Date: Fri Jan 9 16:59:04 2004 Subject: [BioPerl] Re: [Bioperl-l] gff_string on an HSPI object is not Bio::DB::GFF friendly In-Reply-To: <1073681357.1480.47.camel@localhost.localdomain> Message-ID: by all means make it work if you like. i have no intention of touching this aspect of BTGFF. -allen On Fri, 9 Jan 2004, Scott Cain wrote: > I think everything you wrote below is correct. As far as I know, only > Allen and I have been working BTGFF's GFF3 code, and we haven't touched > the alignment portion, so I am not surprised that it is wrong. I > suppose fixing BTGFF may break some tools, but I know that the chado > loader I wrote will handle it correctly :-) > > Thanks, > Scott > > > On Fri, 2004-01-09 at 15:45, Mark Wilkinson wrote: > > On Fri, 2004-01-09 at 11:22, Scott Cain wrote: > > > > > - be sure to use a SO term for the type (ie, match or one of its > > > children) > > > > So... actually the existing implementation of GFF3 in bioperl > > from Bio::Tools::GFF->new(-gff_version => 3) > > does not generate correctly formatted GFF3 for alignment features, yeah? > > > > e.g. for column 9 of an alignment feature I get: > > > > Target=gi|2828774:54232..54206 > > > > whereas I think I should be getting > > > > Target=gi|2828774+54232+54206 > > > > In addition, it passes through all sorts of other tags that begin with > > capital letters: > > > > Bits=46.1;FracId=0.962962962962963 > > > > these should be > > > > bits=46.1;fracId=0.962962962962963 > > > > if I am reading the spec correctly. > > > > Finally, the column-3 term that comes out is "similarity", but it should be > > one of the *match terms. Is that also correct? > > > > Please confirm that I am interpreting the GFF3 spec correctly for these > > Alignment features and I would be happy to go in and fix things (a.k.a. break > > everyone else's tools ;-) ) > > > > Cheerio! > > > > Mark > > > From amackey at virginia.edu Fri Jan 9 17:02:07 2004 From: amackey at virginia.edu (Aaron J.Mackey) Date: Fri Jan 9 17:09:07 2004 Subject: [BioPerl] Re: [Bioperl-l] gff_string on an HSPI object is not Bio::DB::GFF friendly In-Reply-To: <1073684823.1481.53.camel@localhost.localdomain> References: <1073662071.2102.84.camel@localhost.localdomain> <1073663428.2102.91.camel@localhost.localdomain> <1073667709.3005.10.camel@localhost.localdomain> <1073668949.1478.19.camel@localhost.localdomain> <1073681109.1785.50.camel@localhost.localdomain> <1073681357.1480.47.camel@localhost.localdomain> <1073682544.1785.65.camel@localhost.localdomain> <1073684823.1481.53.camel@localhost.localdomain> Message-ID: <77900E98-42EF-11D8-9385-000A958C5008@virginia.edu> Hi Scott, Thanks for the quick reply, but that wasn't exactly the nature of the question; the question was whether (apart from Gap attributes), do gbrowse, BDGFF, and/or, specifically, load_gff.pl variants know the rest of GFF3, namely to provide the ability of input GFF3 with features that aren't in absolute reference coordinates, but in relative coordinates? And is that ability in release 1.58, or some CVS branch I can access (code that lives quietly in the depths of Lincoln's hard drive doesn't count)? Thanks, -Aaron On Jan 9, 2004, at 4:47 PM, Scott Cain wrote: > OK, I am going to answer this, but if I am wrong, I'm sure Lincoln will > correct me. I don't think gbrowse or BDGFF knows how to deal with > cigar > lines in Gap attributes yet. It is safer for the moment to continue to > put separate HSPs on separate GFF lines for the time being. > > Scott > > > On Fri, 2004-01-09 at 16:42, Aaron J.Mackey wrote: >> Forgive me for a stupid question, but does GBrowse (v1.58) now support >> GFF3? Namely, can I have start/stops in sub-feature coordinates in my >> input GFF3 and expect bp_load_gff.pl to behave properly (i.e. generate >> "canonical" top-level coordinates for storage)? I didn't see anything >> in the documentation, so I was surprised to see some of the words in >> these posts ... >> >> Thanks >> >> On Jan 9, 2004, at 4:09 PM, Mark Wilkinson wrote: >> >>> Cool. I'm heavily into making the HSP's output proper GFF3 today for >>> some of the Gbrowse tools that I have been working on, so I will jump >>> in >>> and do this over the next day or two. >>> >>> Cheers! >>> >>> Mark >>> >>> On Fri, 2004-01-09 at 14:49, Scott Cain wrote: >>>> I think everything you wrote below is correct. As far as I know, >>>> only >>>> Allen and I have been working BTGFF's GFF3 code, and we haven't >>>> touched >>>> the alignment portion, so I am not surprised that it is wrong. I >>>> suppose fixing BTGFF may break some tools, but I know that the chado >>>> loader I wrote will handle it correctly :-) >>>> >>>> Thanks, >>>> Scott >>>> >>>> >>>> On Fri, 2004-01-09 at 15:45, Mark Wilkinson wrote: >>>>> On Fri, 2004-01-09 at 11:22, Scott Cain wrote: >>>>> >>>>>> - be sure to use a SO term for the type (ie, match or one of its >>>>>> children) >>>>> >>>>> So... actually the existing implementation of GFF3 in bioperl >>>>> from Bio::Tools::GFF->new(-gff_version => 3) >>>>> does not generate correctly formatted GFF3 for alignment features, >>>>> yeah? >>>>> >>>>> e.g. for column 9 of an alignment feature I get: >>>>> >>>>> Target=gi|2828774:54232..54206 >>>>> >>>>> whereas I think I should be getting >>>>> >>>>> Target=gi|2828774+54232+54206 >>>>> >>>>> In addition, it passes through all sorts of other tags that begin >>>>> with >>>>> capital letters: >>>>> >>>>> Bits=46.1;FracId=0.962962962962963 >>>>> >>>>> these should be >>>>> >>>>> bits=46.1;fracId=0.962962962962963 >>>>> >>>>> if I am reading the spec correctly. >>>>> >>>>> Finally, the column-3 term that comes out is "similarity", but it >>>>> should be >>>>> one of the *match terms. Is that also correct? >>>>> >>>>> Please confirm that I am interpreting the GFF3 spec correctly for >>>>> these >>>>> Alignment features and I would be happy to go in and fix things >>>>> (a.k.a. break >>>>> everyone else's tools ;-) ) >>>>> >>>>> Cheerio! >>>>> >>>>> Mark >>>>> >>> -- >>> Mark Wilkinson >>> Illuminae >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l@portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l >>> > -- > ----------------------------------------------------------------------- > - > Scott Cain, Ph. D. > cain@cshl.org > GMOD Coordinator (http://www.gmod.org/) > 216-392-3087 > Cold Spring Harbor Laboratory > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From allenday at ucla.edu Fri Jan 9 17:22:10 2004 From: allenday at ucla.edu (Allen Day) Date: Fri Jan 9 17:29:15 2004 Subject: [BioPerl] Re: [Bioperl-l] gff_string on an HSPI object is not Bio::DB::GFF friendly In-Reply-To: <77900E98-42EF-11D8-9385-000A958C5008@virginia.edu> Message-ID: We don't support this in the chado load_gff3.pl script, but it wouldn't be very difficult to add handling of simple cases. I am concerned though about difficulties handling potential ambiguity wrt the strandedness of relative coordinates. I assume by relative coordinates here, you mean you're describing a feature's position in terms of the position of another feature which is itself described in absolute coordinates (or is relative to a feature which is). -Allen On Fri, 9 Jan 2004, Aaron J.Mackey wrote: > Hi Scott, > > Thanks for the quick reply, but that wasn't exactly the nature of the > question; the question was whether (apart from Gap attributes), do > gbrowse, BDGFF, and/or, specifically, load_gff.pl variants know the > rest of GFF3, namely to provide the ability of input GFF3 with features > that aren't in absolute reference coordinates, but in relative > coordinates? And is that ability in release 1.58, or some CVS branch I > can access (code that lives quietly in the depths of Lincoln's hard > drive doesn't count)? > > Thanks, > > -Aaron > > On Jan 9, 2004, at 4:47 PM, Scott Cain wrote: > > > OK, I am going to answer this, but if I am wrong, I'm sure Lincoln will > > correct me. I don't think gbrowse or BDGFF knows how to deal with > > cigar > > lines in Gap attributes yet. It is safer for the moment to continue to > > put separate HSPs on separate GFF lines for the time being. > > > > Scott > > > > > > On Fri, 2004-01-09 at 16:42, Aaron J.Mackey wrote: > >> Forgive me for a stupid question, but does GBrowse (v1.58) now support > >> GFF3? Namely, can I have start/stops in sub-feature coordinates in my > >> input GFF3 and expect bp_load_gff.pl to behave properly (i.e. generate > >> "canonical" top-level coordinates for storage)? I didn't see anything > >> in the documentation, so I was surprised to see some of the words in > >> these posts ... > >> > >> Thanks > >> > >> On Jan 9, 2004, at 4:09 PM, Mark Wilkinson wrote: > >> > >>> Cool. I'm heavily into making the HSP's output proper GFF3 today for > >>> some of the Gbrowse tools that I have been working on, so I will jump > >>> in > >>> and do this over the next day or two. > >>> > >>> Cheers! > >>> > >>> Mark > >>> > >>> On Fri, 2004-01-09 at 14:49, Scott Cain wrote: > >>>> I think everything you wrote below is correct. As far as I know, > >>>> only > >>>> Allen and I have been working BTGFF's GFF3 code, and we haven't > >>>> touched > >>>> the alignment portion, so I am not surprised that it is wrong. I > >>>> suppose fixing BTGFF may break some tools, but I know that the chado > >>>> loader I wrote will handle it correctly :-) > >>>> > >>>> Thanks, > >>>> Scott > >>>> > >>>> > >>>> On Fri, 2004-01-09 at 15:45, Mark Wilkinson wrote: > >>>>> On Fri, 2004-01-09 at 11:22, Scott Cain wrote: > >>>>> > >>>>>> - be sure to use a SO term for the type (ie, match or one of its > >>>>>> children) > >>>>> > >>>>> So... actually the existing implementation of GFF3 in bioperl > >>>>> from Bio::Tools::GFF->new(-gff_version => 3) > >>>>> does not generate correctly formatted GFF3 for alignment features, > >>>>> yeah? > >>>>> > >>>>> e.g. for column 9 of an alignment feature I get: > >>>>> > >>>>> Target=gi|2828774:54232..54206 > >>>>> > >>>>> whereas I think I should be getting > >>>>> > >>>>> Target=gi|2828774+54232+54206 > >>>>> > >>>>> In addition, it passes through all sorts of other tags that begin > >>>>> with > >>>>> capital letters: > >>>>> > >>>>> Bits=46.1;FracId=0.962962962962963 > >>>>> > >>>>> these should be > >>>>> > >>>>> bits=46.1;fracId=0.962962962962963 > >>>>> > >>>>> if I am reading the spec correctly. > >>>>> > >>>>> Finally, the column-3 term that comes out is "similarity", but it > >>>>> should be > >>>>> one of the *match terms. Is that also correct? > >>>>> > >>>>> Please confirm that I am interpreting the GFF3 spec correctly for > >>>>> these > >>>>> Alignment features and I would be happy to go in and fix things > >>>>> (a.k.a. break > >>>>> everyone else's tools ;-) ) > >>>>> > >>>>> Cheerio! > >>>>> > >>>>> Mark > >>>>> > >>> -- > >>> Mark Wilkinson > >>> Illuminae > >>> > >>> _______________________________________________ > >>> Bioperl-l mailing list > >>> Bioperl-l@portal.open-bio.org > >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l > >>> > > -- > > ----------------------------------------------------------------------- > > - > > Scott Cain, Ph. D. > > cain@cshl.org > > GMOD Coordinator (http://www.gmod.org/) > > 216-392-3087 > > Cold Spring Harbor Laboratory > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From markw at illuminae.com Fri Jan 9 17:42:41 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Fri Jan 9 17:49:41 2004 Subject: [BioPerl] Re: [Bioperl-l] gff_string on an HSPI object is not Bio::DB::GFF friendly In-Reply-To: References: <1073662071.2102.84.camel@localhost.localdomain> <1073663428.2102.91.camel@localhost.localdomain> <1073667709.3005.10.camel@localhost.localdomain> <1073668949.1478.19.camel@localhost.localdomain> <1073681109.1785.50.camel@localhost.localdomain> Message-ID: <1073688161.2447.31.camel@localhost.localdomain> On Fri, 2004-01-09 at 14:59, Jason Stajich wrote: > Perhaps you want an HSP-2-SO type factory or something (which is basically > what is in the script...). that is likely the way to go, yeah. > As for the .. versus + - > > What does: > my @values = $feature->get_tag_values('Target'); > print join(",",@values), "\n"; > give you? ugh! Here is where your complaint about calling ->gff_string on the HSP object really shows its colours! Of course, calling ->get_tag_values on the HSP object throws an exception, since it isn't *really* a feature... and neither of the two Alignment Feature objects has a tag named "Target", so this information is clearly being tacked onto the output of ->gff_string post-facto. I think the default behaviour of $HSP->gff_string is weird, in that it assumes you want the query sequence to be the reference sequence in the GFF (i.e. I think that what Gbrowse wants to see is MORE correct). I could almost tolerate it if it chose the database sequence as the reference sequence. However I agree with you entirely that $HSP should probably not have a gff_string method at all. It just leads you into temptation... and delivers you straight to evil! >-} I think for the moment I will continue modifying my GFF report writer so that it functions in a similar way to your utilities script in converting a ResultI object into GFF(1,2,2.5,or 3) just as a stop-gap measure because I need it quickly! It will take more time/thought/work to write an HSP_2_SO factory... What do you see as the future for Bio::Tools::GFF in light of this conversation? It seems that it would need to become a lot smarter in order to deal with the more rigourous requirements of GFF3... M From rousse at ccr.jussieu.fr Fri Jan 9 17:47:00 2004 From: rousse at ccr.jussieu.fr (Guillaume Rousse) Date: Fri Jan 9 17:54:01 2004 Subject: [Bioperl-l] Packaging BioPerl for mandrake linux In-Reply-To: <66779DB4-42BB-11D8-9385-000A958C5008@pcbi.upenn.edu> References: <200401091335.35355.rousse@ccr.jussieu.fr> <66779DB4-42BB-11D8-9385-000A958C5008@pcbi.upenn.edu> Message-ID: <200401092347.01032.rousse@ccr.jussieu.fr> On Friday 09 January 2004 16:49, Aaron J. Mackey wrote: > On Jan 9, 2004, at 7:35 AM, Guillaume Rousse wrote: > > First, the compilation doesn't support parallel build on multiple-cpu > > build > > host, as readm.pm get installed after it is needed: > > I'm not sure how to fix this ... Me neither :-) > > Second, correct optimisation flags (-O2 -fomit-frame-pointer -pipe > > -march=i586 > > -mcpu=pentiumpro) are not passed to all gcc invocations: > > But this I did fix in CVS, thanks for pointing it out ... > > > Third, I can't find any installed binary files at the end of the > > compilation > > process, only source C files and headers > > When you run "make install" what do you see? I get (on Mac OS X 10.3): > > Installing > /usr/local/lib/perl5/site_perl/5.8.1/darwin-2level/auto/Bio/Ext/Align/ > Align.bs > Installing > /usr/local/lib/perl5/site_perl/5.8.1/darwin-2level/auto/Bio/Ext/Align/ > Align.bundle Installing /home/guillomovitch/rpm/tmp/perl-Bioperl-Ext-root/usr/lib/perl5/vendor_perl/5.8.2/Bio/Ext/Makefile.PL Installing /home/guillomovitch/rpm/tmp/perl-Bioperl-Ext-root/usr/lib/perl5/vendor_perl/5.8.2/Bio/Ext/Align/test.pl Installing /home/guillomovitch/rpm/tmp/perl-Bioperl-Ext-root/usr/lib/perl5/vendor_perl/5.8.2/Bio/Ext/Align/Align.pm etc... Seems the source dir is installed instead of build dir. I used perl Makefile.PL INSTALLDIRS=vendor for generating the makefile, and a rpm macro evaluating to make DESTDIR=/home/guillomovitch/rpm/tmp/perl-Bioperl-Ext-root install for installation > That .bundle file is the dynamically loaded binary. I thought native files had to get installed only under /usr/local/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi? > > I don't have previous experience of using Inline::C, however > > The Bio/Ext/Align/ stuff doesn't use Inline::C, that's only the > Bio::SeqIO::staden stuff. You might consider packaging the two > separately ... Just because one use Inline::C and not the other? I would like to split bioperl core first, there are tons of dependencies there :-) > > Fourth, invocating make test as part of the build process fails for > > some > > uninstalled module: > > This is an Inline::C problem; Inline::C-based modules are a little > tricky to get right for testing before installation. Generally I see > this error when I've had a failed compilation (because of the .h errors > you found) and don't have a completely "clean" build environment. > You're right that the error message is misleading. > > > BTW, some modules in main bioperl package have references to some > > modules in > > bioperl-run package: > > > > Bio::Root::Version > > This is in bioperl-live, or at least it should be ... there is no > Bio::Root::* in bioperl-run. My fault, something wrong in a quick diff between bioperl requires and provides. > > This make both packages to requires each other. Maybe those modules > > should be > > moved to bioperl-run, to make bioperl self-sufficient ? > > bioperl-run requires bioperl, period. bioperl makes use of many > "external" packages, but they are mostly optional (required only for a > very small subset of bioperl functionality). In general, we'd like > people to be able to install the core BioPerl without a ton of other > packages (and certainly without requiring bioperl-run). All bioperl > tests should pass (i.e. be skipped, if necessary) without bioperl-run > installed (is that not true?) Right. Those dependencies are generated by rpm automatic dependencies computing, because they are some files in bioperl triggering them. A quick grep shows the included scripts are responsable: blast2tree.pl:use Bio::Tools::Run::Phylo::Molphy::ProtML clustalw.pl:use Bio::Tools::Run::Alignment::Clustalw; I'll silent them manually. > > Does a fish get cramps after eating? > > -- Why Why Why n?2 > > I think so, but only when eating raw humans :-) -- A bad dinner with your wife is worth more than a good one in the company of your mother-in-law. -- A law for married men From rousse at ccr.jussieu.fr Fri Jan 9 18:13:26 2004 From: rousse at ccr.jussieu.fr (Guillaume Rousse) Date: Fri Jan 9 18:20:23 2004 Subject: [Bioperl-l] Packaging BioPerl for mandrake linux In-Reply-To: <200401092347.01032.rousse@ccr.jussieu.fr> References: <200401091335.35355.rousse@ccr.jussieu.fr> <66779DB4-42BB-11D8-9385-000A958C5008@pcbi.upenn.edu> <200401092347.01032.rousse@ccr.jussieu.fr> Message-ID: <200401100013.26119.rousse@ccr.jussieu.fr> On Friday 09 January 2004 23:47, Guillaume Rousse wrote: > > > This make both packages to requires each other. Maybe those modules > > > should be > > > moved to bioperl-run, to make bioperl self-sufficient ? > > > > bioperl-run requires bioperl, period. bioperl makes use of many > > "external" packages, but they are mostly optional (required only for a > > very small subset of bioperl functionality). In general, we'd like > > people to be able to install the core BioPerl without a ton of other > > packages (and certainly without requiring bioperl-run). All bioperl > > tests should pass (i.e. be skipped, if necessary) without bioperl-run > > installed (is that not true?) > > Right. > > Those dependencies are generated by rpm automatic dependencies computing, > because they are some files in bioperl triggering them. A quick grep shows > the included scripts are responsable: > blast2tree.pl:use Bio::Tools::Run::Phylo::Molphy::ProtML > clustalw.pl:use Bio::Tools::Run::Alignment::Clustalw; > I'll silent them manually. Acutallly not. The following scripts from bioperl core won't work if bioperl-run is not installed: bp_pairwise_kaks.pl bp_blast2tree.pl So they should belong to bioperl-run tarball instead. -- The number of horses you own increases according to the number of stalls in your barn -- Murphy's Horse Laws n?13 From amackey at pcbi.upenn.edu Fri Jan 9 19:14:01 2004 From: amackey at pcbi.upenn.edu (Aaron J. Mackey) Date: Fri Jan 9 19:20:58 2004 Subject: [Bioperl-l] Packaging BioPerl for mandrake linux In-Reply-To: <200401092347.01032.rousse@ccr.jussieu.fr> References: <200401091335.35355.rousse@ccr.jussieu.fr> <66779DB4-42BB-11D8-9385-000A958C5008@pcbi.upenn.edu> <200401092347.01032.rousse@ccr.jussieu.fr> Message-ID: > Installing > /home/guillomovitch/rpm/tmp/perl-Bioperl-Ext-root/usr/lib/perl5/ > vendor_perl/5.8.2/Bio/Ext/Makefile.PL > Installing > /home/guillomovitch/rpm/tmp/perl-Bioperl-Ext-root/usr/lib/perl5/ > vendor_perl/5.8.2/Bio/Ext/Align/test.pl > Installing > /home/guillomovitch/rpm/tmp/perl-Bioperl-Ext-root/usr/lib/perl5/ > vendor_perl/5.8.2/Bio/Ext/Align/Align.pm > etc... > Seems the source dir is installed instead of build dir. > I used > perl Makefile.PL INSTALLDIRS=vendor > for generating the makefile, and a rpm macro evaluating to > make DESTDIR=/home/guillomovitch/rpm/tmp/perl-Bioperl-Ext-root install > for installation Hmm; I'm not extremely ExtUtils::MakeMaker-savvy, so I won't comment on the can-of-worms phenomenon you're opening up by doing so; but it seems like the "make install" you've generated has more problems than not installing the loadable libraries (it definitely shouldn't be installing Makefile.PL, for instance). You should take this up with the ExtUtils::MakeMaker folk. > I thought native files had to get installed only > under /usr/local/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi? There are a number of places to look; I believe the auto/ and .bundle stuff is for AutoLoader, but I could (will?) be wrong. > Just because one use Inline::C and not the other? I would like to split > bioperl core first, there are tons of dependencies there :-) That's not the worst of ideas; as a package manager you have every right to do so. We keep it all together under one CVS checkout, and so we release it as one "package". Good luck breaking it up, though ... -Aaron From amackey at virginia.edu Fri Jan 9 19:18:03 2004 From: amackey at virginia.edu (Aaron J.Mackey) Date: Fri Jan 9 19:25:00 2004 Subject: [Bioperl-l] Packaging BioPerl for mandrake linux In-Reply-To: <200401100013.26119.rousse@ccr.jussieu.fr> References: <200401091335.35355.rousse@ccr.jussieu.fr> <66779DB4-42BB-11D8-9385-000A958C5008@pcbi.upenn.edu> <200401092347.01032.rousse@ccr.jussieu.fr> <200401100013.26119.rousse@ccr.jussieu.fr> Message-ID: <7486E7F4-4302-11D8-9385-000A958C5008@virginia.edu> How about we make them "run" (i.e. die with a pleasant error message telling you to install bioperl-run to make use of these scripts)? ... our "scripts" support in bioperl-run isn't as mature as it is in main bioperl (opportunity for someone to Make A Difference, here). -Aaron On Jan 9, 2004, at 6:13 PM, Guillaume Rousse wrote: > The following scripts from bioperl core won't work if bioperl-run is > not > installed: > bp_pairwise_kaks.pl > bp_blast2tree.pl > So they should belong to bioperl-run tarball instead. From rousse at ccr.jussieu.fr Fri Jan 9 19:31:42 2004 From: rousse at ccr.jussieu.fr (Guillaume Rousse) Date: Fri Jan 9 19:38:39 2004 Subject: [Bioperl-l] Packaging BioPerl for mandrake linux In-Reply-To: <7486E7F4-4302-11D8-9385-000A958C5008@virginia.edu> References: <200401091335.35355.rousse@ccr.jussieu.fr> <200401100013.26119.rousse@ccr.jussieu.fr> <7486E7F4-4302-11D8-9385-000A958C5008@virginia.edu> Message-ID: <200401100131.42929.rousse@ccr.jussieu.fr> On Saturday 10 January 2004 01:18, Aaron J.Mackey wrote: > How about we make them "run" (i.e. die with a pleasant error message > telling you to install bioperl-run to make use of these scripts)? ... That is what they already do, at least for bp_pairwise_kaks.pl: eval { # Ka/Ks estimators require Bio::Tools::Run::Phylo::PAML::Codeml; require Bio::Tools::Run::Phylo::PAML::Yn00; # Multiple Sequence Alignment programs require Bio::Tools::Run::Alignment::Clustalw; require Bio::Tools::Run::Alignment::TCoffee; }; if( $@ ) { die("Must have bioperl-run pkg installed to run this script"); } but not blast2tree.pl: use Bio::Tools::Run::Alignment::Clustalw; use Bio::Tools::Run::Phylo::Phylip::ProtDist; use Bio::Tools::Run::Phylo::Phylip::Neighbor; use Bio::Tools::Run::Phylo::Molphy::ProtML; use Bio::Tools::Run::Phylo::Phylip::ProtPars; > our "scripts" support in bioperl-run isn't as mature as it is in main > bioperl (opportunity for someone to Make A Difference, here). -- Propane/butane tanks that are full when they are packed, will unexplainably empty themselves before you can reach the campsite -- Murphy's Laws of Camping n?12 From rousse at ccr.jussieu.fr Fri Jan 9 19:41:51 2004 From: rousse at ccr.jussieu.fr (Guillaume Rousse) Date: Fri Jan 9 19:48:51 2004 Subject: [Bioperl-l] Packaging BioPerl for mandrake linux In-Reply-To: <200401100131.42929.rousse@ccr.jussieu.fr> References: <200401091335.35355.rousse@ccr.jussieu.fr> <7486E7F4-4302-11D8-9385-000A958C5008@virginia.edu> <200401100131.42929.rousse@ccr.jussieu.fr> Message-ID: <200401100141.51517.rousse@ccr.jussieu.fr> I've sent this mail before completing it :-( On Saturday 10 January 2004 01:31, Guillaume Rousse wrote: > On Saturday 10 January 2004 01:18, Aaron J.Mackey wrote: > > How about we make them "run" (i.e. die with a pleasant error message > > telling you to install bioperl-run to make use of these scripts)? ... > > That is what they already do, at least for bp_pairwise_kaks.pl: > > eval { > # Ka/Ks estimators > require Bio::Tools::Run::Phylo::PAML::Codeml; > require Bio::Tools::Run::Phylo::PAML::Yn00; > > # Multiple Sequence Alignment programs > require Bio::Tools::Run::Alignment::Clustalw; > require Bio::Tools::Run::Alignment::TCoffee; > }; > if( $@ ) { > die("Must have bioperl-run pkg installed to run this script"); > } > > but not blast2tree.pl: > use Bio::Tools::Run::Alignment::Clustalw; > use Bio::Tools::Run::Phylo::Phylip::ProtDist; > use Bio::Tools::Run::Phylo::Phylip::Neighbor; > use Bio::Tools::Run::Phylo::Molphy::ProtML; > use Bio::Tools::Run::Phylo::Phylip::ProtPars; ... But from a strict packaging point of view, it is useless to install scripts that are bound to fail. > > our "scripts" support in bioperl-run isn't as mature as it is in main > > bioperl (opportunity for someone to Make A Difference, here). I guess you mean installation support in Makefile.PL ? Otherwise, i see no problem adding a script directory in bioperl-run tarball. -- If you're in a vehicle going the speed of light, what happens when you turn on the headlights? -- Why Why Why n?16 From jason at cgt.duhs.duke.edu Sat Jan 10 14:09:12 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Sat Jan 10 14:16:20 2004 Subject: [Bioperl-l] Packaging BioPerl for mandrake linux In-Reply-To: <200401100141.51517.rousse@ccr.jussieu.fr> References: <200401091335.35355.rousse@ccr.jussieu.fr> <7486E7F4-4302-11D8-9385-000A958C5008@virginia.edu> <200401100131.42929.rousse@ccr.jussieu.fr> <200401100141.51517.rousse@ccr.jussieu.fr> Message-ID: We're probably not going to move them out of that scripts dir in bioperl-core but if you want to remove them from the -core rpm you are building feel free. There is a scripts dir in bioperl-run but as aaron said it isn't that mature so I would rather aggregate mature scripts in one place rather than having people play 'find the script'. If you are really concerned about this just combine bioperl-core and bioperl-run into on RPM I guess although we've not been religous about making sure there are no duplicate filenames in both script dirs. -jason On Sat, 10 Jan 2004, Guillaume Rousse wrote: > I've sent this mail before completing it :-( > > On Saturday 10 January 2004 01:31, Guillaume Rousse wrote: > > On Saturday 10 January 2004 01:18, Aaron J.Mackey wrote: > > > How about we make them "run" (i.e. die with a pleasant error message > > > telling you to install bioperl-run to make use of these scripts)? ... > > > > That is what they already do, at least for bp_pairwise_kaks.pl: > > > > eval { > > # Ka/Ks estimators > > require Bio::Tools::Run::Phylo::PAML::Codeml; > > require Bio::Tools::Run::Phylo::PAML::Yn00; > > > > # Multiple Sequence Alignment programs > > require Bio::Tools::Run::Alignment::Clustalw; > > require Bio::Tools::Run::Alignment::TCoffee; > > }; > > if( $@ ) { > > die("Must have bioperl-run pkg installed to run this script"); > > } > > > > but not blast2tree.pl: > > use Bio::Tools::Run::Alignment::Clustalw; > > use Bio::Tools::Run::Phylo::Phylip::ProtDist; > > use Bio::Tools::Run::Phylo::Phylip::Neighbor; > > use Bio::Tools::Run::Phylo::Molphy::ProtML; > > use Bio::Tools::Run::Phylo::Phylip::ProtPars; > > ... But from a strict packaging point of view, it is useless to install > scripts that are bound to fail. > > > > our "scripts" support in bioperl-run isn't as mature as it is in main > > > bioperl (opportunity for someone to Make A Difference, here). > I guess you mean installation support in Makefile.PL ? Otherwise, i see no > problem adding a script directory in bioperl-run tarball. > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From jason at cgt.duhs.duke.edu Sat Jan 10 14:12:52 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Sat Jan 10 14:19:45 2004 Subject: [Bioperl-l] ->alphabet documentation wrong here there and everywhere :-) In-Reply-To: <1073682447.1785.62.camel@localhost.localdomain> References: <1073682447.1785.62.camel@localhost.localdomain> Message-ID: The documentation is correct we cannot assume that all implementers of the interface will be mutable. An interface does not assume that you can set value while a implementation may choose to allow it. Consider a DBPrimarySeq which is a read-only representation of the db - it implements the PrimarySeqI interface but does not allow alphabet to be updated while Bio::PrimarySeq does. On Fri, 9 Jan 2004, Mark Wilkinson wrote: > Does anyone object to me fixing the documentation for PrimarySeqI et al. > with respect to the 'alphabet' function? It claims to not accept any > arguments, but every implementation of it that I can find in the > sequence hierarchy actually does, so... the docs are wrong all over the > place. > > Alternately, I could leave the Interface documentation alone, and simply > update the documentation for all of the implementing objects who > actually DO allow you to set the alphabet explicitly after Seq object > creation... > > Which do you prefer? Was it intentional that the ->alphabet interface > not be get/set, or is that historical cruft? > > Mark > > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From markw at illuminae.com Sat Jan 10 16:13:06 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Sat Jan 10 16:20:05 2004 Subject: [BioPerl] Re: [Bioperl-l] ->alphabet documentation wrong here there and everywhere :-) In-Reply-To: References: <1073682447.1785.62.camel@localhost.localdomain> Message-ID: <1073769186.2951.30.camel@localhost.localdomain> But... surely the documentation for the modules that DO implement it this way should reflect that... or? As it stands, all implementers have simply copy/pasted the documentation from the interface module, even though their implementation adds this functionality. M On Sat, 2004-01-10 at 13:12, Jason Stajich wrote: > The documentation is correct we cannot assume that all implementers of the > interface will be mutable. > > An interface does not assume that you can set value while a implementation > may choose to allow it. Consider a DBPrimarySeq which is a read-only > representation of the db - it implements the PrimarySeqI interface but > does not allow alphabet to be updated while Bio::PrimarySeq does. > > > On Fri, 9 Jan 2004, Mark Wilkinson wrote: > > > Does anyone object to me fixing the documentation for PrimarySeqI et al. > > with respect to the 'alphabet' function? It claims to not accept any > > arguments, but every implementation of it that I can find in the > > sequence hierarchy actually does, so... the docs are wrong all over the > > place. > > > > Alternately, I could leave the Interface documentation alone, and simply > > update the documentation for all of the implementing objects who > > actually DO allow you to set the alphabet explicitly after Seq object > > creation... > > > > Which do you prefer? Was it intentional that the ->alphabet interface > > not be get/set, or is that historical cruft? > > > > Mark > > > > > > > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Mark Wilkinson Illuminae From birney at ebi.ac.uk Sat Jan 10 16:33:48 2004 From: birney at ebi.ac.uk (Ewan Birney) Date: Sat Jan 10 16:40:46 2004 Subject: [BioPerl] Re: [Bioperl-l] ->alphabet documentation wrong here there and everywhere :-) In-Reply-To: <1073769186.2951.30.camel@localhost.localdomain> Message-ID: On Sat, 10 Jan 2004, Mark Wilkinson wrote: > But... surely the documentation for the modules that DO implement it > this way should reflect that... or? As it stands, all implementers have > simply copy/pasted the documentation from the interface module, even > though their implementation adds this functionality. > Feel free to update the implementations, putting a break to show that this is an implementation-specific aspect. the interface should be strict read-only. From markw at illuminae.com Sat Jan 10 16:48:12 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Sat Jan 10 16:55:11 2004 Subject: [BioPerl] Re: [Bioperl-l] ->alphabet documentation wrong here there and everywhere :-) In-Reply-To: References: Message-ID: <1073771292.2951.38.camel@localhost.localdomain> cool. Will do. This came up only because one of my colleagues at the university here called on me with frustration that he wasn't able to change the alphabet without creating a new sequence object, and when I told him how to do it he sent me a copy of the documentation showing that it couldn't be done that way :-) Cheers all! M On Sat, 2004-01-10 at 15:33, Ewan Birney wrote: > On Sat, 10 Jan 2004, Mark Wilkinson wrote: > > > But... surely the documentation for the modules that DO implement it > > this way should reflect that... or? As it stands, all implementers have > > simply copy/pasted the documentation from the interface module, even > > though their implementation adds this functionality. > > > > Feel free to update the implementations, putting a break to show that this > is an implementation-specific aspect. > > the interface should be strict read-only. > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Mark Wilkinson Illuminae From hlapp at gmx.net Sat Jan 10 21:16:59 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat Jan 10 21:23:53 2004 Subject: [Bioperl-l] Re: mutable accessors In-Reply-To: <1073771292.2951.38.camel@localhost.localdomain> Message-ID: <3C567264-43DC-11D8-9C83-000A959EB4C4@gmx.net> This is a known issue in bioperl. Everybody who is willing to help amend this situation is more than welcome. The problem arises from two facts, both of which you have noticed: - interfaces in bioperl traditionally do not mandate write access, and historically only the read access (i.e., only the mandated part) has been documented - implementors simply copy&pasted documentation from the interfaces As we've learned meanwhile, the combination of the two gave rise to a significant hurdle and source of frustration for newcomers, and as it turns out even for old-time users ;) While the lacking piece of documentation (and hence required guesswork) is fairly straightforward for scalar properties, the problem is aggravated for array properties first by the fact that two different methods need to be used to modify the property (add_XXXX(), and remove_XXXXs()) whose existence would have to be guessed by someone who only reads the interface POD, and second by the existence of different naming conventions for those two mutator methods. No-one on the core is proud of this situation, and I understand that this can raise serious frustration for a well-intentioned user. Fixing this, OTOH, is a serious amount of work, that I'm afraid will not get addressed soon enough if everybody just waits for the core people to step up. This is an opportunity for one or more people out there to enter the hall of bioperl fame in the minds of legions of new users to come, or those already frustrated. Among the suggestions to mitigate the problem are:- a) The interface PODs don't change, but every implementor carefully documents how to modify a property, instead of just dumb copy&pasting The problem with this is that there are supposedly more implementations than interfaces, a user will always have to consult (and hence know) the implementations in addition to the interfaces, and the fundamental problem will have to solved every single time an implementation is created (with the continued risk that an implementor forgets to do this) b) The way we define interfaces changes fundamentally to include and document mutators, but mandate only read-access from implementations. The benefit is that the problem would be solved once and for all, even if there was a forgetful implementor. Also, implementors may still copy&paste documentation and would just need to remove the line that says that this is not mandated (or alternatively, change it to say that write-access is expressly supported). The problem with this is how would a read-only implementation signal that it doesn't support mutability. Obviously, it should do so in a standard manner so that client code can be prepared for it. Options are to throw a Not-Supported exception, or to ignore the modification silently, or to have a standard property that controls whether unsupported write-access throws an exception or is ignored, much like $obj->verbose(2) which turns warnings into exceptions. Another option is to introduce change handlers which may throw an exception if a certain modification is not supported. The advantage of that would be that anybody can turn any read/write implementation into a read-only one by just substituting the change handler to one that disallows any change. AFAIR biojava a whole while ago faced a very similar problem. I believe they solved it by including mutators on all interfaces, and have implementations generate change events for which listeners can register. A change listener, if any is registered, may veto any change or only specific ones by throwing an exception. Mat, Thomas, am I representing this at least remotely correct? How has this worked out over time? I strongly favor b) (all interfaces document mutators, but don't mandate support of mutability). I don't have a strong opinion on how read-only status of properties should be signaled, but the change event with listeners at least sounds very sensible (in the majority of cases there won't be an event handler registered, and hence the performance impact would be negligible for standard read/write use cases). -hilmar On Saturday, January 10, 2004, at 01:48 PM, Mark Wilkinson wrote: > cool. Will do. > > This came up only because one of my colleagues at the university here > called on me with frustration that he wasn't able to change the > alphabet > without creating a new sequence object, and when I told him how to do > it > he sent me a copy of the documentation showing that it couldn't be done > that way :-) > > Cheers all! > > M > > On Sat, 2004-01-10 at 15:33, Ewan Birney wrote: >> On Sat, 10 Jan 2004, Mark Wilkinson wrote: >> >>> But... surely the documentation for the modules that DO implement it >>> this way should reflect that... or? As it stands, all implementers >>> have >>> simply copy/pasted the documentation from the interface module, even >>> though their implementation adds this functionality. >>> >> >> Feel free to update the implementations, putting a break to show that >> this >> is an implementation-specific aspect. >> >> the interface should be strict read-only. >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- > Mark Wilkinson > Illuminae > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From yearlookout at dwp.net Sat Jan 10 23:53:30 2004 From: yearlookout at dwp.net (Reidun.gangdal) Date: Sat Jan 10 23:53:31 2004 Subject: [Bioperl-l] Modern way of losing bathtubs we;ght natural growths Message-ID: Hello wacky, At last you have an opportunity to purchase good directly from manufactures. 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From juguang at tll.org.sg Mon Jan 12 03:16:08 2004 From: juguang at tll.org.sg (Juguang Xiao) Date: Mon Jan 12 03:22:25 2004 Subject: [Bioperl-l] Re: mutable accessors In-Reply-To: <3C567264-43DC-11D8-9C83-000A959EB4C4@gmx.net> Message-ID: <9310D73B-44D7-11D8-9AEA-000A957702FE@tll.org.sg> On Sunday, January 11, 2004, at 10:16 am, Hilmar Lapp wrote: > This is a known issue in bioperl. Everybody who is willing to help > amend this situation is more than welcome. The problem arises from two > facts, both of which you have noticed: > > - interfaces in bioperl traditionally do not mandate write access, > and historically only the read access (i.e., only the mandated part) > has been documented > - implementors simply copy&pasted documentation from the interfaces > > As we've learned meanwhile, the combination of the two gave rise to a > significant hurdle and source of frustration for newcomers, and as it > turns out even for old-time users ;) > > While the lacking piece of documentation (and hence required > guesswork) is fairly straightforward for scalar properties, the > problem is aggravated for array properties first by the fact that two > different methods need to be used to modify the property (add_XXXX(), > and remove_XXXXs()) whose existence would have to be guessed by > someone who only reads the interface POD, and second by the existence > of different naming conventions for those two mutator methods. 2 points here. 1) Will add_XXXX (singular) accept a list of argument, or only one? In some implementation, the developers gave the users convenience to accept an array of object silently, which I regard it as the dishonesty of method naming. And such convenience will hurt the scalability of further development if you want to redefine such add_XXXX method. In my experience of reforming Bio::Ontology::Term::add_dblink for the InterPro case, add_dblink has been changed to take 2 arguments, that the first is the DBLink object, and the second argument is optional, called context which to answer the dblink of what, e.g whether the dblink is a member of InterPro record or an example of it. the data structure looks like $XXXXs = { '~default' => [qw(one two)], # done by add_XXXX('one');add_XXXX('two'); 'context1' => ['three'], # insert by add_XXXX('three', 'context1'); }; 2) remove_XXXXs mean to remove all records, which fails to meet the occasional requirement if only part of records may be about to be deleted. Isn't it a slightly better design that remove_XXXXs may accept an array of about-to-delete objects optionally or remove_XXXXs will erase all record if the argument list is empty? One extra point, do you expect these two mutators return something? Another extra thing that I do not understand. Isn't it nice to implement such *regular* mutable accessors in the interfaces in the default form? That will save implementors' effort on such duplicate coding unless *irregular* and advanced accessors are required and created by overriding the default ones. Juguang From Wiepert.Mathieu at mayo.edu Mon Jan 12 09:11:26 2004 From: Wiepert.Mathieu at mayo.edu (Wiepert, Mathieu) Date: Mon Jan 12 09:18:56 2004 Subject: [Bioperl-l] BSML? Message-ID: <2F41CC6C9777D311ACBD009027B108EA06E9AE8A@excsrv32.mayo.edu> Hi, I was wondering if anyone has an opinion about BSML as some sort of standard XML for Sequence data. The BSML site lists bioperl as "Others Exploring BSML." I went googling for further references or discussions on this, and the threads were old (couldn't find a thread that might have answered this, by Lincoln), and many results found are old web pages (2001) I don't hear much talk about transferring data around in XML. IBM seems to be picking up BSML (not clear why, maybe lack of anything else), does anyone have commentary on the acceptedness of BSML? (Not looking for utility of XML in general, just commentary of BSML, or other XML standards people might like to use, GAME, for example). GFF is lighter and seems to be used more, otherwise genbank/EMBL/DDBJ is the de facto standard? Thanks, -mat From cain at cshl.org Mon Jan 12 11:18:53 2004 From: cain at cshl.org (Scott Cain) Date: Mon Jan 12 11:25:49 2004 Subject: [BioPerl] Re: [Bioperl-l] gff_string on an HSPI object is not Bio::DB::GFF friendly In-Reply-To: References: Message-ID: <1073924333.1513.6.camel@localhost.localdomain> Aaron, I really doubt that the current release of GBrowse supports relative coordinates as described by both you and Allen. I have to say I'm not sure, because I am in the process of developing a set of test data. As for chado, it should actually be fairly easy to adapt it to work with relative coordinates. The main change (for me) would be in the gbrowse chado adaptor, which assumes that all features have as the 'srcfeature' the 'top' feature (ie, all features are directly laid on the chromosome/arm/contig/whatever). The reason it does that is because that is the way that the fruitfly people use it, and so that was the data I had to develop the adaptor for. If having relative coordinates is something that would be useful for you to use chado, let me know (and send me sample GFF3 data) and I will work on it. Otherwise, it will go in the TODO file. Thanks, Scott On Fri, 2004-01-09 at 17:22, Allen Day wrote: > We don't support this in the chado load_gff3.pl script, but it wouldn't be > very difficult to add handling of simple cases. I am concerned though > about difficulties handling potential ambiguity wrt the strandedness of > relative coordinates. > > I assume by relative coordinates here, you mean you're describing a > feature's position in terms of the position of another feature which is > itself described in absolute coordinates (or is relative to a feature > which is). > > -Allen > > > > On Fri, 9 Jan 2004, Aaron J.Mackey wrote: > > > Hi Scott, > > > > Thanks for the quick reply, but that wasn't exactly the nature of the > > question; the question was whether (apart from Gap attributes), do > > gbrowse, BDGFF, and/or, specifically, load_gff.pl variants know the > > rest of GFF3, namely to provide the ability of input GFF3 with features > > that aren't in absolute reference coordinates, but in relative > > coordinates? And is that ability in release 1.58, or some CVS branch I > > can access (code that lives quietly in the depths of Lincoln's hard > > drive doesn't count)? > > > > Thanks, > > > > -Aaron > > > > On Jan 9, 2004, at 4:47 PM, Scott Cain wrote: > > > > > OK, I am going to answer this, but if I am wrong, I'm sure Lincoln will > > > correct me. I don't think gbrowse or BDGFF knows how to deal with > > > cigar > > > lines in Gap attributes yet. It is safer for the moment to continue to > > > put separate HSPs on separate GFF lines for the time being. > > > > > > Scott > > > > > > > > > On Fri, 2004-01-09 at 16:42, Aaron J.Mackey wrote: > > >> Forgive me for a stupid question, but does GBrowse (v1.58) now support > > >> GFF3? Namely, can I have start/stops in sub-feature coordinates in my > > >> input GFF3 and expect bp_load_gff.pl to behave properly (i.e. generate > > >> "canonical" top-level coordinates for storage)? I didn't see anything > > >> in the documentation, so I was surprised to see some of the words in > > >> these posts ... > > >> > > >> Thanks > > >> > > >> On Jan 9, 2004, at 4:09 PM, Mark Wilkinson wrote: > > >> > > >>> Cool. I'm heavily into making the HSP's output proper GFF3 today for > > >>> some of the Gbrowse tools that I have been working on, so I will jump > > >>> in > > >>> and do this over the next day or two. > > >>> > > >>> Cheers! > > >>> > > >>> Mark > > >>> > > >>> On Fri, 2004-01-09 at 14:49, Scott Cain wrote: > > >>>> I think everything you wrote below is correct. As far as I know, > > >>>> only > > >>>> Allen and I have been working BTGFF's GFF3 code, and we haven't > > >>>> touched > > >>>> the alignment portion, so I am not surprised that it is wrong. I > > >>>> suppose fixing BTGFF may break some tools, but I know that the chado > > >>>> loader I wrote will handle it correctly :-) > > >>>> > > >>>> Thanks, > > >>>> Scott > > >>>> > > >>>> > > >>>> On Fri, 2004-01-09 at 15:45, Mark Wilkinson wrote: > > >>>>> On Fri, 2004-01-09 at 11:22, Scott Cain wrote: > > >>>>> > > >>>>>> - be sure to use a SO term for the type (ie, match or one of its > > >>>>>> children) > > >>>>> > > >>>>> So... actually the existing implementation of GFF3 in bioperl > > >>>>> from Bio::Tools::GFF->new(-gff_version => 3) > > >>>>> does not generate correctly formatted GFF3 for alignment features, > > >>>>> yeah? > > >>>>> > > >>>>> e.g. for column 9 of an alignment feature I get: > > >>>>> > > >>>>> Target=gi|2828774:54232..54206 > > >>>>> > > >>>>> whereas I think I should be getting > > >>>>> > > >>>>> Target=gi|2828774+54232+54206 > > >>>>> > > >>>>> In addition, it passes through all sorts of other tags that begin > > >>>>> with > > >>>>> capital letters: > > >>>>> > > >>>>> Bits=46.1;FracId=0.962962962962963 > > >>>>> > > >>>>> these should be > > >>>>> > > >>>>> bits=46.1;fracId=0.962962962962963 > > >>>>> > > >>>>> if I am reading the spec correctly. > > >>>>> > > >>>>> Finally, the column-3 term that comes out is "similarity", but it > > >>>>> should be > > >>>>> one of the *match terms. Is that also correct? > > >>>>> > > >>>>> Please confirm that I am interpreting the GFF3 spec correctly for > > >>>>> these > > >>>>> Alignment features and I would be happy to go in and fix things > > >>>>> (a.k.a. break > > >>>>> everyone else's tools ;-) ) > > >>>>> > > >>>>> Cheerio! > > >>>>> > > >>>>> Mark > > >>>>> > > >>> -- > > >>> Mark Wilkinson > > >>> Illuminae > > >>> > > >>> _______________________________________________ > > >>> Bioperl-l mailing list > > >>> Bioperl-l@portal.open-bio.org > > >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l > > >>> > > > -- > > > ----------------------------------------------------------------------- > > > - > > > Scott Cain, Ph. D. > > > cain@cshl.org > > > GMOD Coordinator (http://www.gmod.org/) > > > 216-392-3087 > > > Cold Spring Harbor Laboratory > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l@portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain@cshl.org GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory From amackey at virginia.edu Mon Jan 12 11:32:35 2004 From: amackey at virginia.edu (Aaron J.Mackey) Date: Mon Jan 12 11:39:29 2004 Subject: [BioPerl] Re: [Bioperl-l] gff_string on an HSPI object is not Bio::DB::GFF friendly In-Reply-To: <1073924333.1513.6.camel@localhost.localdomain> References: <1073924333.1513.6.camel@localhost.localdomain> Message-ID: Actually, all I really need is a relative-to-absolute coordinate mapper, so that I can prepare input in relative coordinates, and feed it to a dbGFF database in absolute coordinates (which was what I was hoping load_gff.pl might now be doing automatically, given all your talk about GFF3). I realize now, however, that relative coordinates is not in the purvue of the GFF3 spec, but is rather an application issue. Thanks for all your thoughts, -Aaron On Jan 12, 2004, at 11:18 AM, Scott Cain wrote: > Aaron, > > I really doubt that the current release of GBrowse supports relative > coordinates as described by both you and Allen. I have to say I'm not > sure, because I am in the process of developing a set of test data. > > As for chado, it should actually be fairly easy to adapt it to work > with > relative coordinates. The main change (for me) would be in the gbrowse > chado adaptor, which assumes that all features have as the 'srcfeature' > the 'top' feature (ie, all features are directly laid on the > chromosome/arm/contig/whatever). The reason it does that is because > that is the way that the fruitfly people use it, and so that was the > data I had to develop the adaptor for. > > If having relative coordinates is something that would be useful for > you > to use chado, let me know (and send me sample GFF3 data) and I will > work > on it. Otherwise, it will go in the TODO file. > > Thanks, > Scott > > On Fri, 2004-01-09 at 17:22, Allen Day wrote: >> We don't support this in the chado load_gff3.pl script, but it >> wouldn't be >> very difficult to add handling of simple cases. I am concerned though >> about difficulties handling potential ambiguity wrt the strandedness >> of >> relative coordinates. >> >> I assume by relative coordinates here, you mean you're describing a >> feature's position in terms of the position of another feature which >> is >> itself described in absolute coordinates (or is relative to a feature >> which is). >> >> -Allen >> >> >> >> On Fri, 9 Jan 2004, Aaron J.Mackey wrote: >> >>> Hi Scott, >>> >>> Thanks for the quick reply, but that wasn't exactly the nature of the >>> question; the question was whether (apart from Gap attributes), do >>> gbrowse, BDGFF, and/or, specifically, load_gff.pl variants know the >>> rest of GFF3, namely to provide the ability of input GFF3 with >>> features >>> that aren't in absolute reference coordinates, but in relative >>> coordinates? And is that ability in release 1.58, or some CVS >>> branch I >>> can access (code that lives quietly in the depths of Lincoln's hard >>> drive doesn't count)? >>> >>> Thanks, >>> >>> -Aaron >>> >>> On Jan 9, 2004, at 4:47 PM, Scott Cain wrote: >>> >>>> OK, I am going to answer this, but if I am wrong, I'm sure Lincoln >>>> will >>>> correct me. I don't think gbrowse or BDGFF knows how to deal with >>>> cigar >>>> lines in Gap attributes yet. It is safer for the moment to >>>> continue to >>>> put separate HSPs on separate GFF lines for the time being. >>>> >>>> Scott >>>> >>>> >>>> On Fri, 2004-01-09 at 16:42, Aaron J.Mackey wrote: >>>>> Forgive me for a stupid question, but does GBrowse (v1.58) now >>>>> support >>>>> GFF3? Namely, can I have start/stops in sub-feature coordinates >>>>> in my >>>>> input GFF3 and expect bp_load_gff.pl to behave properly (i.e. >>>>> generate >>>>> "canonical" top-level coordinates for storage)? I didn't see >>>>> anything >>>>> in the documentation, so I was surprised to see some of the words >>>>> in >>>>> these posts ... >>>>> >>>>> Thanks >>>>> >>>>> On Jan 9, 2004, at 4:09 PM, Mark Wilkinson wrote: >>>>> >>>>>> Cool. I'm heavily into making the HSP's output proper GFF3 today >>>>>> for >>>>>> some of the Gbrowse tools that I have been working on, so I will >>>>>> jump >>>>>> in >>>>>> and do this over the next day or two. >>>>>> >>>>>> Cheers! >>>>>> >>>>>> Mark >>>>>> >>>>>> On Fri, 2004-01-09 at 14:49, Scott Cain wrote: >>>>>>> I think everything you wrote below is correct. As far as I know, >>>>>>> only >>>>>>> Allen and I have been working BTGFF's GFF3 code, and we haven't >>>>>>> touched >>>>>>> the alignment portion, so I am not surprised that it is wrong. I >>>>>>> suppose fixing BTGFF may break some tools, but I know that the >>>>>>> chado >>>>>>> loader I wrote will handle it correctly :-) >>>>>>> >>>>>>> Thanks, >>>>>>> Scott >>>>>>> >>>>>>> >>>>>>> On Fri, 2004-01-09 at 15:45, Mark Wilkinson wrote: >>>>>>>> On Fri, 2004-01-09 at 11:22, Scott Cain wrote: >>>>>>>> >>>>>>>>> - be sure to use a SO term for the type (ie, match or one of >>>>>>>>> its >>>>>>>>> children) >>>>>>>> >>>>>>>> So... actually the existing implementation of GFF3 in bioperl >>>>>>>> from Bio::Tools::GFF->new(-gff_version => 3) >>>>>>>> does not generate correctly formatted GFF3 for alignment >>>>>>>> features, >>>>>>>> yeah? >>>>>>>> >>>>>>>> e.g. for column 9 of an alignment feature I get: >>>>>>>> >>>>>>>> Target=gi|2828774:54232..54206 >>>>>>>> >>>>>>>> whereas I think I should be getting >>>>>>>> >>>>>>>> Target=gi|2828774+54232+54206 >>>>>>>> >>>>>>>> In addition, it passes through all sorts of other tags that >>>>>>>> begin >>>>>>>> with >>>>>>>> capital letters: >>>>>>>> >>>>>>>> Bits=46.1;FracId=0.962962962962963 >>>>>>>> >>>>>>>> these should be >>>>>>>> >>>>>>>> bits=46.1;fracId=0.962962962962963 >>>>>>>> >>>>>>>> if I am reading the spec correctly. >>>>>>>> >>>>>>>> Finally, the column-3 term that comes out is "similarity", but >>>>>>>> it >>>>>>>> should be >>>>>>>> one of the *match terms. Is that also correct? >>>>>>>> >>>>>>>> Please confirm that I am interpreting the GFF3 spec correctly >>>>>>>> for >>>>>>>> these >>>>>>>> Alignment features and I would be happy to go in and fix things >>>>>>>> (a.k.a. break >>>>>>>> everyone else's tools ;-) ) >>>>>>>> >>>>>>>> Cheerio! >>>>>>>> >>>>>>>> Mark >>>>>>>> >>>>>> -- >>>>>> Mark Wilkinson >>>>>> Illuminae >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l@portal.open-bio.org >>>>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>> -- >>>> -------------------------------------------------------------------- >>>> --- >>>> - >>>> Scott Cain, Ph. D. >>>> cain@cshl.org >>>> GMOD Coordinator (http://www.gmod.org/) >>>> 216-392-3087 >>>> Cold Spring Harbor Laboratory >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l@portal.open-bio.org >>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l@portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l >>> > -- > ----------------------------------------------------------------------- > - > Scott Cain, Ph. D. > cain@cshl.org > GMOD Coordinator (http://www.gmod.org/) > 216-392-3087 > Cold Spring Harbor Laboratory > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From lstein at cshl.edu Mon Jan 12 13:43:44 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Mon Jan 12 13:51:27 2004 Subject: [Bioperl-l] biographics now backwardly GD 1.8 compatible In-Reply-To: <1073662670.1473.25.camel@localhost.localdomain> References: <1073662071.2102.84.camel@localhost.localdomain> <1073662670.1473.25.camel@localhost.localdomain> Message-ID: <200401121343.44587.lstein@cshl.edu> Hi, The current version of Bio::Graphics (in BioPerl CVS repository) is now backwardly compatible with GD 1.8, thanks to Todd's efforts. This should help those trying to install BioPerl on top of RedHat 7.4 Lincoln -- Lincoln D. Stein Associate Professor Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From nathanhaigh at ukonline.co.uk Mon Jan 12 09:27:44 2004 From: nathanhaigh at ukonline.co.uk (Nathan Haigh) Date: Mon Jan 12 14:08:49 2004 Subject: [Bioperl-l] Running Clustalw using BioPerl Via cgi script Message-ID: I am trying to write a cgi script that will run clustalw on an array of seq objects and return an alignment object. I can write a successful perl script but if I try to execute it via a browser, it fails. Does anyone have any experience with implementing clustalw within a browser setting? Thanks Nathan -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/x-pkcs7-signature Size: 3095 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040112/e1ed54f3/smime.bin From lstein at cshl.edu Mon Jan 12 18:34:14 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Mon Jan 12 18:41:39 2004 Subject: [BioPerl] Re: [Bioperl-l] gff_string on an HSPI object is not Bio::DB::GFF friendly In-Reply-To: References: <1073924333.1513.6.camel@localhost.localdomain> Message-ID: <200401121834.14674.lstein@cshl.edu> Hello, You might want to look at the relative-to-absolute coordinate mapper that's in the Bio::Das library (version 0.94). Here's an excerpt from the synopsis: use Bio::Das::Map 'print_location'; my $m = Bio::Das::Map->new('my_map'); $m->add_segment(['chr1',100,1000] => ['c1.1',1,901]); $m->add_segment(['chr1',1001,2000] => ['c1.2',501,1500]); $m->add_segment(['chr1',2001,4000] => ['c1.1',3000,4999]); $m->add_segment(['c1.1',4000,4999] => ['c1.1.1',1,1000]); my @abs_locations = $m->resolve('c1.1.1',500=>600); print_location(@abs_locations); for my $location (@abs_locations) { my @rel_locations = $m->project($location,'c1.1.1'); print_location(@rel_locations); my @all_rel_locations = $m->sub_segments($location); print_location(@all_rel_locations); } If you don't like using the [seqid,start,end] triples, you can use Bio::LocationI objects instead. You can find the module on CPAN, or at www.biodas.org. Lincoln On Monday 12 January 2004 11:32 am, Aaron J.Mackey wrote: > Actually, all I really need is a relative-to-absolute coordinate > mapper, so that I can prepare input in relative coordinates, and feed > it to a dbGFF database in absolute coordinates (which was what I was > hoping load_gff.pl might now be doing automatically, given all your > talk about GFF3). I realize now, however, that relative coordinates is > not in the purvue of the GFF3 spec, but is rather an application issue. > > Thanks for all your thoughts, > > -Aaron > > On Jan 12, 2004, at 11:18 AM, Scott Cain wrote: > > Aaron, > > > > I really doubt that the current release of GBrowse supports relative > > coordinates as described by both you and Allen. I have to say I'm not > > sure, because I am in the process of developing a set of test data. > > > > As for chado, it should actually be fairly easy to adapt it to work > > with > > relative coordinates. The main change (for me) would be in the gbrowse > > chado adaptor, which assumes that all features have as the 'srcfeature' > > the 'top' feature (ie, all features are directly laid on the > > chromosome/arm/contig/whatever). The reason it does that is because > > that is the way that the fruitfly people use it, and so that was the > > data I had to develop the adaptor for. > > > > If having relative coordinates is something that would be useful for > > you > > to use chado, let me know (and send me sample GFF3 data) and I will > > work > > on it. Otherwise, it will go in the TODO file. > > > > Thanks, > > Scott > > > > On Fri, 2004-01-09 at 17:22, Allen Day wrote: > >> We don't support this in the chado load_gff3.pl script, but it > >> wouldn't be > >> very difficult to add handling of simple cases. I am concerned though > >> about difficulties handling potential ambiguity wrt the strandedness > >> of > >> relative coordinates. > >> > >> I assume by relative coordinates here, you mean you're describing a > >> feature's position in terms of the position of another feature which > >> is > >> itself described in absolute coordinates (or is relative to a feature > >> which is). > >> > >> -Allen > >> > >> On Fri, 9 Jan 2004, Aaron J.Mackey wrote: > >>> Hi Scott, > >>> > >>> Thanks for the quick reply, but that wasn't exactly the nature of the > >>> question; the question was whether (apart from Gap attributes), do > >>> gbrowse, BDGFF, and/or, specifically, load_gff.pl variants know the > >>> rest of GFF3, namely to provide the ability of input GFF3 with > >>> features > >>> that aren't in absolute reference coordinates, but in relative > >>> coordinates? And is that ability in release 1.58, or some CVS > >>> branch I > >>> can access (code that lives quietly in the depths of Lincoln's hard > >>> drive doesn't count)? > >>> > >>> Thanks, > >>> > >>> -Aaron > >>> > >>> On Jan 9, 2004, at 4:47 PM, Scott Cain wrote: > >>>> OK, I am going to answer this, but if I am wrong, I'm sure Lincoln > >>>> will > >>>> correct me. I don't think gbrowse or BDGFF knows how to deal with > >>>> cigar > >>>> lines in Gap attributes yet. It is safer for the moment to > >>>> continue to > >>>> put separate HSPs on separate GFF lines for the time being. > >>>> > >>>> Scott > >>>> > >>>> On Fri, 2004-01-09 at 16:42, Aaron J.Mackey wrote: > >>>>> Forgive me for a stupid question, but does GBrowse (v1.58) now > >>>>> support > >>>>> GFF3? Namely, can I have start/stops in sub-feature coordinates > >>>>> in my > >>>>> input GFF3 and expect bp_load_gff.pl to behave properly (i.e. > >>>>> generate > >>>>> "canonical" top-level coordinates for storage)? I didn't see > >>>>> anything > >>>>> in the documentation, so I was surprised to see some of the words > >>>>> in > >>>>> these posts ... > >>>>> > >>>>> Thanks > >>>>> > >>>>> On Jan 9, 2004, at 4:09 PM, Mark Wilkinson wrote: > >>>>>> Cool. I'm heavily into making the HSP's output proper GFF3 today > >>>>>> for > >>>>>> some of the Gbrowse tools that I have been working on, so I will > >>>>>> jump > >>>>>> in > >>>>>> and do this over the next day or two. > >>>>>> > >>>>>> Cheers! > >>>>>> > >>>>>> Mark > >>>>>> > >>>>>> On Fri, 2004-01-09 at 14:49, Scott Cain wrote: > >>>>>>> I think everything you wrote below is correct. As far as I know, > >>>>>>> only > >>>>>>> Allen and I have been working BTGFF's GFF3 code, and we haven't > >>>>>>> touched > >>>>>>> the alignment portion, so I am not surprised that it is wrong. I > >>>>>>> suppose fixing BTGFF may break some tools, but I know that the > >>>>>>> chado > >>>>>>> loader I wrote will handle it correctly :-) > >>>>>>> > >>>>>>> Thanks, > >>>>>>> Scott > >>>>>>> > >>>>>>> On Fri, 2004-01-09 at 15:45, Mark Wilkinson wrote: > >>>>>>>> On Fri, 2004-01-09 at 11:22, Scott Cain wrote: > >>>>>>>>> - be sure to use a SO term for the type (ie, match or one of > >>>>>>>>> its > >>>>>>>>> children) > >>>>>>>> > >>>>>>>> So... actually the existing implementation of GFF3 in bioperl > >>>>>>>> from Bio::Tools::GFF->new(-gff_version => 3) > >>>>>>>> does not generate correctly formatted GFF3 for alignment > >>>>>>>> features, > >>>>>>>> yeah? > >>>>>>>> > >>>>>>>> e.g. for column 9 of an alignment feature I get: > >>>>>>>> > >>>>>>>> Target=gi|2828774:54232..54206 > >>>>>>>> > >>>>>>>> whereas I think I should be getting > >>>>>>>> > >>>>>>>> Target=gi|2828774+54232+54206 > >>>>>>>> > >>>>>>>> In addition, it passes through all sorts of other tags that > >>>>>>>> begin > >>>>>>>> with > >>>>>>>> capital letters: > >>>>>>>> > >>>>>>>> Bits=46.1;FracId=0.962962962962963 > >>>>>>>> > >>>>>>>> these should be > >>>>>>>> > >>>>>>>> bits=46.1;fracId=0.962962962962963 > >>>>>>>> > >>>>>>>> if I am reading the spec correctly. > >>>>>>>> > >>>>>>>> Finally, the column-3 term that comes out is "similarity", but > >>>>>>>> it > >>>>>>>> should be > >>>>>>>> one of the *match terms. Is that also correct? > >>>>>>>> > >>>>>>>> Please confirm that I am interpreting the GFF3 spec correctly > >>>>>>>> for > >>>>>>>> these > >>>>>>>> Alignment features and I would be happy to go in and fix things > >>>>>>>> (a.k.a. break > >>>>>>>> everyone else's tools ;-) ) > >>>>>>>> > >>>>>>>> Cheerio! > >>>>>>>> > >>>>>>>> Mark > >>>>>> > >>>>>> -- > >>>>>> Mark Wilkinson > >>>>>> Illuminae > >>>>>> > >>>>>> _______________________________________________ > >>>>>> Bioperl-l mailing list > >>>>>> Bioperl-l@portal.open-bio.org > >>>>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l > >>>> > >>>> -- > >>>> -------------------------------------------------------------------- > >>>> --- > >>>> - > >>>> Scott Cain, Ph. D. > >>>> cain@cshl.org > >>>> GMOD Coordinator (http://www.gmod.org/) > >>>> 216-392-3087 > >>>> Cold Spring Harbor Laboratory > >>>> > >>>> _______________________________________________ > >>>> Bioperl-l mailing list > >>>> Bioperl-l@portal.open-bio.org > >>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l > >>> > >>> _______________________________________________ > >>> Bioperl-l mailing list > >>> Bioperl-l@portal.open-bio.org > >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > -- > > ----------------------------------------------------------------------- > > - > > Scott Cain, Ph. D. > > cain@cshl.org > > GMOD Coordinator (http://www.gmod.org/) > > 216-392-3087 > > Cold Spring Harbor Laboratory > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Lincoln Stein lstein@cshl.edu Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) From blaubin at valmont.clermont.inra.fr Tue Jan 13 06:05:22 2004 From: blaubin at valmont.clermont.inra.fr (Laubin BASTIEN) Date: Tue Jan 13 06:12:12 2004 Subject: [Bioperl-l] Problem Bioperl::SearchIO Message-ID: <5.0.0.25.0.20040113115514.00b15fa8@valmont.clermont.inra.fr> Hello I have a problem when I try to read 2 blast file : $in = new Bio::SearchIO (-format => 'blast', -file => 'fichier1.bln'); while ($result=$in->next_result) { ... } $in2 = new Bio::SearchIO (-format => 'blast', -file => 'fichier2.bln'); print "SPY 1"; while ($result2=$in2->next_result) { print "SPY 2"; ... } There's no problem with the first blast file but in the second SPY1 is written but not SPY2. What's the problem ? Thank you for your help Bastien Laubin From jason at cgt.duhs.duke.edu Tue Jan 13 09:08:52 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Jan 13 09:15:50 2004 Subject: [Bioperl-l] Problem Bioperl::SearchIO In-Reply-To: <5.0.0.25.0.20040113115514.00b15fa8@valmont.clermont.inra.fr> References: <5.0.0.25.0.20040113115514.00b15fa8@valmont.clermont.inra.fr> Message-ID: What does the file fichier2.bin look like? If you replace it with fichier1.bin does it work, what type of error message do you get, etc. It is only possible to help you if you provide more information. On Tue, 13 Jan 2004, Laubin BASTIEN wrote: > > Hello > > I have a problem when I try to read 2 blast file : > > $in = new Bio::SearchIO (-format => 'blast', -file => 'fichier1.bln'); > while ($result=$in->next_result) > { > ... > } > > $in2 = new Bio::SearchIO (-format => 'blast', -file => 'fichier2.bln'); > print "SPY 1"; > while ($result2=$in2->next_result) > { > print "SPY 2"; > ... > } > > There's no problem with the first blast file but in the second SPY1 is > written but not SPY2. > > What's the problem ? > > Thank you for your help > > Bastien Laubin > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From jason at cgt.duhs.duke.edu Tue Jan 13 10:35:39 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Jan 13 10:43:05 2004 Subject: [Bioperl-l] Running Clustalw using BioPerl Via cgi script In-Reply-To: References: Message-ID: You need to provide some more error messages - it most likely has to do with permissions as the web server (and hence the cgi) run under a different user than the uid that when you run the script by cmd line. What error messages do you see in your webserver log? That will help someone answer the question better. -jason On Mon, 12 Jan 2004, Nathan Haigh wrote: > I am trying to write a cgi script that will run clustalw on an array of > seq objects and return an alignment object. I can write a successful perl > script but if I try to execute it via a browser, it fails. > > Does anyone have any experience with implementing clustalw within a > browser setting? > > Thanks > Nathan > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From nathanhaigh at ukonline.co.uk Tue Jan 13 17:02:20 2004 From: nathanhaigh at ukonline.co.uk (Nathan Haigh) Date: Tue Jan 13 18:00:04 2004 Subject: [Bioperl-l] Running Clustalw using BioPerl Via cgi script In-Reply-To: Message-ID: Here is what I'm trying to do: 1) Add NJ tree and bootstrap support to my local copy of Bio::Tools::Run::Alignment::Clustalw 2) Use this module in a web (cgi) environment, to produce bootstrap trees from sequences selected by checkboxes 3) Somehow generate trees in graphical format from the newick format trees generated from step 2). Progress on these steps so far: 1) Pretty much sorted a working version of the tree options for clustalw, but still need to do some testing 2) I worked out that I needed to set the environmental variable to clustalw (WindowsXP version on my test environment). Successfully able to run and alignment from a fasta input file and NJ/bootstrap trees from an alignment file. 3) Not much yet! Which steps I need help on! 1) No help as yet 2) I would like to be able to use sequence and alignment objects instead of specifying input fasta or alignment files to generate the alignments and trees. I have created an array of Bio::Seq objects by using the following: my $seqobj = Bio::Seq->new('-display_id' => $new_local_id, '-seq' => $seq); push @seq_array, $seqobj; I then pass a reference to this array to run the alignment my $aln = $factory->align($seq_array_ref); the returned value is a simplealign object, how do I access the aligned sequences as I can't seem to be able to figure out how to do that! Or, should the clustalw.pm handle simplealign objects as input? Essentially, I need to know how to handle the simplealign object ($aln) as returned from: my $aln = $factory->align($seq_array_ref); I must be missing something, as I spent all day today, trying to figure out if I'd changed something in the module itself or I'm missing something obvious. 3) I'll make these issues known at a later point, on a different thread. Thanks for any help Nathan -----Original Message----- From: Jason Stajich [mailto:jason@cgt.duhs.duke.edu] Sent: 13 January 2004 15:36 To: Nathan Haigh Cc: bioperl-l@portal.open-bio.org Subject: Re: [Bioperl-l] Running Clustalw using BioPerl Via cgi script You need to provide some more error messages - it most likely has to do with permissions as the web server (and hence the cgi) run under a different user than the uid that when you run the script by cmd line. What error messages do you see in your webserver log? That will help someone answer the question better. -jason On Mon, 12 Jan 2004, Nathan Haigh wrote: > I am trying to write a cgi script that will run clustalw on an array of > seq objects and return an alignment object. I can write a successful perl > script but if I try to execute it via a browser, it fails. > > Does anyone have any experience with implementing clustalw within a > browser setting? > > Thanks > Nathan > -- Jason Stajich Duke University jason at cgt.mc.duke.edu -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/x-pkcs7-signature Size: 3095 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040113/179bbdd3/smime.bin From gruenerbaum77 at gmx.de Wed Jan 14 06:39:55 2004 From: gruenerbaum77 at gmx.de (Lukas Schneider) Date: Wed Jan 14 06:46:44 2004 Subject: [Bioperl-l] Regular Expressions References: <5.0.0.25.0.20040113115514.00b15fa8@valmont.clermont.inra.fr> Message-ID: <13730.1074080395@www61.gmx.net> Hi , I?ve a question to the regular expressions: Is it possible to formulate a pattern to find all blocks with a length of x, which contain y repeats of defined characters? e.g. let?s say: find 4 Leucins in a segment with the length of 6? Many thanks.... -- +++ GMX - die erste Adresse f?r Mail, Message, More +++ Neu: Preissenkung f?r MMS und FreeMMS! http://www.gmx.net From mith at ceh.ac.uk Wed Jan 14 06:45:57 2004 From: mith at ceh.ac.uk (Milo Thurston) Date: Wed Jan 14 06:52:48 2004 Subject: [Bioperl-l] Genbank file construction Message-ID: <200401141145.i0EBjvwj006351@rzirzaraz.nox.ac.uk> Hello, I'd like to ask a question concerning the construction of genbank files. I have two sets of files, some containing sequence, and others containing only annotations (CDS regions). Parsing either of these with any of Bio::Seq, Bio::SeqIO, Bio::Species, Bio::PrimarySeq, Bio::SeqFeatureI is easy enough, but I'd like to assemble a new file containing the sum total of both files, i.e. add the annotations to the associated sequence. Can anyone suggest a suitable way of doing this, or point me in the direction of a script that will do so (even partially, so I can change it as necessary)? Thanks, Milo Thurston. -- Milo Thurston, CEH Oxford, Mansfield Road, Oxford, OX1 3SR. 'phone 01865 281658, fax 01865 281696. http://www.bioinf.ceh.ac.uk/lab/ From yearrework at dwp.net Wed Jan 14 14:07:31 2004 From: yearrework at dwp.net (Seiglitano) Date: Wed Jan 14 07:15:20 2004 Subject: [Bioperl-l] Modern way of losing manual we;ght natural disjointed Message-ID: Hello wedlock, At last you have an opportunity to purchase good directly from manufactures. You save your money purchasing quality products from our plant's store. Today we present you FatBlast product. What is FatBlast actually? Fatblast is an advanced fat-binding supplement that removes fat from the foods you eat! Formulated with the powerful fat-binding fiber Chitosan, the proprietary blend of all-natural compounds... Our corporation was the first one who started selling this product on the web in the year 2004. Try our FDA approved product tday dragging Read about our dscounts and special bonses: http://www.theonlyrealstuff.com/fly/index.php?pid=pharmaboss Pomona brewing readied gibberish, Mitch pivotal relates bottomless sociable pillared mating Malta rebutting reasonings alcoholism embarrass animatedly. From Richard.Adams at ed.ac.uk Wed Jan 14 07:52:30 2004 From: Richard.Adams at ed.ac.uk (Richard Adams) Date: Wed Jan 14 07:59:18 2004 Subject: [Bioperl-l] Genbank file construction Message-ID: <40053B8E.2090205@ed.ac.uk> The easiest way would be to add the features and sequence to a BioSeq object using the add_SeqFeature() method. Assuming you're starting with say an array of Bio::PrimarySeq objects parsed from a FASTA file, for example e.g., for my $ps (@sequences) { my $newobj = Bio::Seq->new(); $newobj->primary_seq($ps); ## now get features related to your sequence and put in @features #... #now add features onto sequence object $newobj->add_SeqFeature(@features); ### now write data out in genbank /embl format or whatever my $io = Bio::SeqIO->new (-file => ">out", -format => 'genbank'); $io->write_seq($newobj); } There is a good HOWTO about sequence features /annotations available now as well. HTH Richard -- Dr Richard Adams, Psychiatric Genetics Group, Medical Genetics, Molecular Medicine Centre, Western General Hospital, Crewe Rd West, Edinburgh UK EH4 2XU Tel: 44 131 651 1084 richard.adams@ed.ac.uk From amackey at pcbi.upenn.edu Wed Jan 14 08:03:08 2004 From: amackey at pcbi.upenn.edu (Aaron J. Mackey) Date: Wed Jan 14 08:10:10 2004 Subject: [Bioperl-l] Regular Expressions In-Reply-To: <13730.1074080395@www61.gmx.net> References: <5.0.0.25.0.20040113115514.00b15fa8@valmont.clermont.inra.fr> <13730.1074080395@www61.gmx.net> Message-ID: [ untested, of course ] if ($seq =~ m/( (?: L [^L]* (?=L) # Two L's separated by non-L's, but don't consume second L ){3} # three of these initial L's L # the final L )/ix && length ($1) == 6) { print $1; } -Aaron On Jan 14, 2004, at 6:39 AM, Lukas Schneider wrote: > Hi , > > I?ve a question to the regular expressions: > > Is it possible to formulate a pattern to find all blocks with a length > of x, > > which contain y repeats of defined characters? > e.g. let?s say: find 4 Leucins in a segment with the length of 6? > > Many thanks.... > > > > -- > +++ GMX - die erste Adresse f?r Mail, Message, More +++ > Neu: Preissenkung f?r MMS und FreeMMS! http://www.gmx.net > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From mack at bioinformatics.ubc.ca Wed Jan 14 14:46:47 2004 From: mack at bioinformatics.ubc.ca (mack) Date: Wed Jan 14 14:54:19 2004 Subject: [Bioperl-l] How to handle multiple locations for SeqFeature Message-ID: <40059CA7.7030101@bioinformatics.ubc.ca> Hi, I would like to know how a single Bio::SeqFeature::Generic handle multiple locations? Thanks in advance. Cheers, Mack From jason at cgt.duhs.duke.edu Wed Jan 14 14:57:01 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Jan 14 15:03:50 2004 Subject: [Bioperl-l] How to handle multiple locations for SeqFeature In-Reply-To: <40059CA7.7030101@bioinformatics.ubc.ca> References: <40059CA7.7030101@bioinformatics.ubc.ca> Message-ID: A Bio::Location::Split SeqFeature locations are managed through the ->location method - simple, split, or fuzzy locations can be stored there. start/end/strand are convience functions in the SeqFeature::Generic implementation and it delegates to the location object as to what start and end should be. Brian covers this briefly in his new Feature-Annotation HOWTO http://bioperl.org/HOWTOs/html/Feature-Annotation.html#location although as he says, it probably needs its own HOWTO... -jason On Wed, 14 Jan 2004, mack wrote: > Hi, > > I would like to know how a single Bio::SeqFeature::Generic handle > multiple locations? > Thanks in advance. > > Cheers, > Mack > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From brian_osborne at cognia.com Wed Jan 14 15:35:13 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Wed Jan 14 15:42:51 2004 Subject: [Bioperl-l] How to handle multiple locations for SeqFeature In-Reply-To: <40059CA7.7030101@bioinformatics.ubc.ca> Message-ID: Mack, Are you building a feature with locations, extracting data from a feature, or both? Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of mack Sent: Wednesday, January 14, 2004 2:47 PM To: bioperl-l@bioperl.org Subject: [Bioperl-l] How to handle multiple locations for SeqFeature Hi, I would like to know how a single Bio::SeqFeature::Generic handle multiple locations? Thanks in advance. Cheers, Mack _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From mack at bioinformatics.ubc.ca Wed Jan 14 16:09:26 2004 From: mack at bioinformatics.ubc.ca (mack) Date: Wed Jan 14 16:16:58 2004 Subject: [Bioperl-l] How to handle multiple locations for SeqFeature In-Reply-To: References: Message-ID: <4005B006.5010108@bioinformatics.ubc.ca> Both. Jason has clued me to use Bio::Location::Split. Thanks. Cheers, Mack Brian Osborne wrote: > Mack, > > Are you building a feature with locations, extracting data from a feature, > or both? > > Brian O. > > > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org > [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of mack > Sent: Wednesday, January 14, 2004 2:47 PM > To: bioperl-l@bioperl.org > Subject: [Bioperl-l] How to handle multiple locations for SeqFeature > > Hi, > > I would like to know how a single Bio::SeqFeature::Generic handle > multiple locations? > Thanks in advance. > > Cheers, > Mack > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > From bhurwitz at twt.com Thu Jan 15 12:56:21 2004 From: bhurwitz at twt.com (bhurwitz@twt.com) Date: Thu Jan 15 13:03:48 2004 Subject: [Bioperl-l] Trouble installing bioperl-1.4 due to RestrictionIO Message-ID: Hi Jason, Sorry for the late response. I am trying to install on RH7.3, PERL 5.6.1. I did the force install and it worked. I might run into something later, but all is fine for now. -Bonnie Jason Stajich uke.edu> cc: Rob Edwards , "" , "" 01/08/2004 01:22 Subject: RE: [Bioperl-l] Trouble installing bioperl-1.4 due to RestrictionIO PM Hey Brian - what version of perl? What about you Bonnie? I get no errors with perl 5.8.0 on rh 9 or on OSX with perl 5.8.1-RC3 but I do see this on perl 5.6.1 (rh 7.3) with the main-trunk live and 1.4 code (released and 1.4 branch) 1..14 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 Use of uninitialized value in string eq at Bio/Restriction/IO/withrefm.pm line 130, line 13. Use of uninitialized value in string eq at Bio/Restriction/IO/withrefm.pm line 130, line 24. ok 9 not ok 10 # Test 10 got: '9' (t/RestrictionIO.t at line 63) # Expected: '11' ok 11 ok 12 ok 13 ok 14 -jason On Thu, 8 Jan 2004, Brian Osborne wrote: > Rob, > > Partially fails for me as well, on Cygwin: > > ~/bioperl-live>perl t/RestrictionIO.t > 1..14 > ok 1 > ok 2 > ok 3 > not ok 4 > # Test 4 got: '530' (t/RestrictionIO.t at line 43) > # Expected: '532' > ok 5 > ok 6 > ok 7 > ok 8 > ok 9 > not ok 10 > # Test 10 got: '17' (t/RestrictionIO.t at line 63) > # Expected: '11' > ok 11 > ok 12 > not ok 13 > # Test 13 got: '19' (t/RestrictionIO.t at line 78) > # Expected: '16' > ok 14 > > The 3 failing tests are $renzs->each_enzyme, where $renz is a RestrictionIO > object, 3 different files. > > Brian O. > > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org > [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Rob Edwards > Sent: Thursday, January 08, 2004 12:03 PM > To: Jason Stajich > Cc: bhurwitz@twt.com; bioperl-l@bioperl.org > Subject: Re: [Bioperl-l] Trouble installing bioperl-1.4 due to RestrictionIO > > I am curious as to why this test is failing. Has anyone else had this fail? > > It passes for me (on Mac OS10.3) > > Rob > > On Thu, Jan 08, 2004 at 10:45:31AM -0500, Jason Stajich wrote: > > Just ignore it. > > > > cpan> force install Bio::Perl > > > > if you like. > > > > On Wed, 7 Jan 2004 bhurwitz@twt.com wrote: > > > > > > > > Hello, > > > > > > I am installing BioPerl 1.4 on a virtual machine through vmware that > > > previously did not have bioperl (RedHat 7.3, perl 5.6.1). I am getting > the > > > following error from CPAN. Does anyone know what this could mean? I > have > > > installed the BioPerl Bundle prior to this successfully > > > (C/CR/CRAFFI/Bundle-BioPerl-2.1.0.tar.gz) > > > > > > -Bonnie > > > > > > > > > Failed Test Stat Wstat Total Fail Failed List of Failed > > > > -------------------------------------------------------------------------- > ----- > > > t/RestrictionIO.t 14 1 7.14% 10 > > > 121 subtests skipped. > > > Failed 1/179 test scripts, 99.44% okay. 1/8268 subtests failed, 99.99% > > > okay. > > > make: *** [test_dynamic] Error 11 > > > /usr/bin/make test -- NOT OK > > > Running make install > > > make test had returned bad status, won't install without force > > > > > > > > > > > > > > > > > > Barry Moore > > > Stajich > > > .edu> cc: > bioperl-l@bioperl.org > > > Sent by: Subject: Re: > [Bioperl-l] Trouble installing bioperl-ext-1.4 > > > bioperl-l-bounces@portal.o > > > pen-bio.org > > > > > > > > > 01/06/2004 05:15 PM > > > > > > > > > > > > > > > > > > > > > Jason et al- > > > > > > ...while trying to install bioperl-ext-1.4 your suggestion for > > > installing Inline::C first seems to have worked. Makefile.PL ran fine > > > (highlighted below in green - if your reading HTML mail). However, now > > > I get errors on running make. I've copied the entire output from the > > > make command below (with some masking of low complexity regions). Sorry > > > it's so long, but I'm having trouble spotting the problem, so I didn't > > > want to leave out any of the important parts. The part indicating > > > errors is at the end (highlighted in red). > > > > > > Barry > > > > > > [root@Tatshenshini bioperl-ext-1.4]# perl Makefile.PL > > > Checking if your kit is complete... > > > Looks good > > > Writing Makefile for Bio::Ext::Align > > > Please tell us where your Staden io_lib "read" library is installed: > > > [/usr/local/lib] > > > Please tell us where your Staden io_lib "Read.h" header is installed: > > > [/usr/local/include/io_lib] > > > Writing Makefile for Bio::SeqIO::staden::read > > > Writing Makefile for Bio > > > One or more DATA sections were not processed by Inline. > > > > > > [root@Tatshenshini bioperl-ext-1.4]# make > > > cp Bio/Ext/Align/libs/hscore.h blib/lib/Bio/Ext/Align/libs/hscore.h > > > ###Removed alot of cp commands to shorten e-mail post### > > > cp Bio/Ext/Align/libs/wisefile.h blib/lib/Bio/Ext/Align/libs/wisefile.h > > > make[1]: Entering directory `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align' > > > cp Align.pm ../blib/lib/Bio/Ext/Align.pm > > > DEFINE='-DPOSIX -DNOERROR'; CC='gcc'; export DEFINE INC CC; \ > > > cd libs && make CC=gcc libsw.a -e > > > make[2]: Entering directory > > > `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align/libs' > > > gcc -c -O -c -o aln.o aln.c > > > ###Removed alot of gcc commands to shorten e-mail post### > > > gcc -c -O -c -o linspc.o linspc.c > > > ar ru libsw.a aln.o alnconvert.o alnrange.o asciibtcanvas.o basematrix.o > > > btcanvas.o commandline.o complexconsensi.o > > > complexevalset.o complexsequence.o compmat.o codon.o dna.o dnamatrix.o > > > dpenvelope.o dynlibcross.o histogram.o hscore.o linesubs.o packaln.o > > > probability.o protein.o proteindb.o proteinsw.o seqaligndisplay.o > > > sequence.o sequencedb.o sw_wrap.o wiseerror.o wisefile.o wisememman.o > > > wiseoverlay.o wiserandom.o wisestring.o wisetime.o dpalign.o linspc.o > > > make[2]: Leaving directory > > > `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align/libs' > > > /usr/bin/perl /usr/lib/perl5/5.8.0/ExtUtils/xsubpp -typemap > > > /usr/lib/perl5/5.8.0/ExtUtils/typemap -typemap typemap > > > Align.xs > Align.xsc && mv Align.xsc Align.c > > > gcc -c -I./libs -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS > > > -DDEBUGGING -fno-strict-aliasing -I/usr/local/include > > > -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 > > > -march=i386 -mcpu=i686 -g -DVERSION=\"0.1\" -DXS_VERSION=\"0.1\" -fPIC > > > "-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE" -DPOSIX -DNOERROR > > > Align.c > > > Running Mkbootstrap for Bio::Ext::Align () > > > chmod 644 Align.bs > > > rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so > > > LD_RUN_PATH="" gcc -shared -L/usr/local/lib Align.o -o > > > ../blib/arch/auto/Bio/Ext/Align/Align.so libs/libsw.a -lm > > > > > > chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so > > > cp Align.bs ../blib/arch/auto/Bio/Ext/Align/Align.bs > > > chmod 644 ../blib/arch/auto/Bio/Ext/Align/Align.bs > > > make[1]: Leaving directory `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align' > > > make[1]: Entering directory > `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden' > > > cp read.pm ../blib/lib/Bio/SeqIO/staden/read.pm > > > /usr/bin/perl -Mblib -MInline=NOISY,_INSTALL_ -MBio::SeqIO::staden::read > > > -e1 0.01 ../blib/arch > > > Starting Build Prepocess Stage > > > Finished Build Prepocess Stage > > > > > > Starting Build Parse Stage > > > Finished Build Parse Stage > > > > > > Starting Build Glue 1 Stage > > > Finished Build Glue 1 Stage > > > > > > Starting Build Glue 2 Stage > > > Finished Build Glue 2 Stage > > > > > > Starting Build Glue 3 Stage > > > Finished Build Glue 3 Stage > > > > > > Starting Build Compile Stage > > > Starting "perl Makefile.PL" Stage > > > Note (probably harmless): No library found for -lread > > > Writing Makefile for Bio::SeqIO::staden::read > > > Finished "perl Makefile.PL" Stage > > > > > > Starting "make" Stage > > > make[2]: Entering directory > > > > `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/stade > n/read' > > > > > > /usr/bin/perl /usr/lib/perl5/5.8.0/ExtUtils/xsubpp -typemap > > > /usr/lib/perl5/5.8.0/ExtUtils/typemap read.xs > read.xsc && mv > > > read.xsc read.c > > > gcc -c -I/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden > > > -I/usr/local/include/io_lib -D_REENTRANT -D_GNU_SOURCE > > > -DTHREADS_HAVE_PIDS -DDEBUGGING -fno-strict-aliasing > > > -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 > > > -I/usr/include/gdbm -O2 -march=i386 -mcpu=i686 -g -DVERSION=\"0.01\" > > > -DXS_VERSION=\"0.01\" -fPIC > > > "-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE" read.c > > > read.xs:5:18: Read.h: No such file or directory > > > read.xs: In function `staden_write_trace': > > > read.xs:9: `Read' undeclared (first use in this function) > > > read.xs:9: (Each undeclared identifier is reported only once > > > read.xs:9: for each function it appears in.) > > > read.xs:15: invalid lvalue in assignment > > > read.xs:16: request for member `base' in something not a structure or > union > > > read.xs:18: request for member `ident' in something not a structure or > > > union > > > read.xs:21: request for member `ident' in something not a structure or > > > union > > > read.xs:23: request for member `info' in something not a structure or > union > > > read.xs:26: request for member `info' in something not a structure or > union > > > read.xs:28: request for member `format' in something not a structure or > > > union > > > read.xs:29: request for member `leftCutoff' in something not a structure > > > or union > > > read.xs:30: request for member `rightCutoff' in something not a > > > structure or union > > > read.xs:32: warning: assignment from incompatible pointer type > > > read.xs:38: request for member `base' in something not a structure or > union > > > read.xs:41: request for member `prob_A' in something not a structure or > > > union > > > read.xs:45: request for member `prob_C' in something not a structure or > > > union > > > read.xs:49: request for member `prob_G' in something not a structure or > > > union > > > read.xs:53: request for member `prob_T' in something not a structure or > > > union > > > read.xs:58: request for member `prob_A' in something not a structure or > > > union > > > read.xs:58: request for member `prob_C' in something not a structure or > > > union > > > read.xs:59: request for member `prob_G' in something not a structure or > > > union > > > read.xs:59: request for member `prob_T' in something not a structure or > > > union > > > read.xs:62: request for member `prob_A' in something not a structure or > > > union > > > read.xs:62: request for member `prob_C' in something not a structure or > > > union > > > read.xs:63: request for member `prob_G' in something not a structure or > > > union > > > read.xs:63: request for member `prob_T' in something not a structure or > > > union > > > read.xs: In function `staden_read_trace': > > > read.xs:76: `Read' undeclared (first use in this function) > > > read.xs:81: invalid lvalue in assignment > > > read.xs:83: `NULLRead' undeclared (first use in this function) > > > read.xs:88: request for member `leftCutoff' in something not a structure > > > or union > > > read.xs:90: request for member `rightCutoff' in something not a > > > structure or union > > > read.xs:91: request for member `NBases' in something not a structure or > > > union > > > read.xs:91: request for member `NBases' in something not a structure or > > > union > > > read.xs:93: request for member `base' in something not a structure or > union > > > read.xs:94: request for member `prob_A' in something not a structure or > > > union > > > read.xs:94: request for member `prob_C' in something not a structure or > > > union > > > read.xs:95: request for member `prob_G' in something not a structure or > > > union > > > read.xs:95: request for member `prob_T' in something not a structure or > > > union > > > read.xs:144: request for member `ident' in something not a structure or > > > union > > > read.xs:145: request for member `info' in something not a structure or > > > union > > > make[2]: *** [read.o] Error 1 > > > make[2]: Leaving directory > > > > `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/stade > n/read' > > > > > > > > > A problem was encountered while attempting to compile and install your > > > Inline > > > C code. The command that failed was: > > > make > > > > > > The build directory was: > > > > /home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden > /read > > > > > > > > > To debug the problem, cd to the build directory, and inspect the output > > > files. > > > > > > at -e line 0 > > > INIT failed--call queue aborted. > > > make[1]: *** [read.inl] Error 2 > > > make[1]: Leaving directory > `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden' > > > make: *** [subdirs] Error 2 > > > > > > > > > Jason Stajich wrote: > > > > > > >Hey Barry! > > > > You need to have installed Inline::C first. > > > > > > > > You don't need bioperl-ext unless you want the specialized stuff in > there > > > >(a smith-waterman implementation and access to the staden io library > for > > > > reading in trace files directly through perl). > > > > > > > >-jason > > > >On Tue, 6 Jan 2004, Barry Moore wrote: > > > > > > > > > > > > > > > >>I'm installing bioperl 1.4 on my linux machine (RedHat 9.0, Perl 5.8). > > > >>Bioperl-1.4 (the core) and bioperl-run-1.4 installed fine. I get the > > > >>following errors when trying to install bioperl-ext-1.4: > > > >> > > > >>[root@Tatshenshini bioperl-ext-1.4]# perl Makefile.PL > > > >>Checking if your kit is complete... > > > >>Looks good > > > >>Writing Makefile for Bio::Ext::Align > > > >>ERROR from evaluation of > > > >>/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/Makefile.PL: Can't > locate > > > >>Inline/MakeMaker.pm in @INC > > > >>(@INC contains: /usr/lib/perl5/5.8.0/i386-linux-thread-multi > > > >>/usr/lib/perl5/5.8.0 > > > >>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi > > > >>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl > > > >>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi > > > >>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl > > > >>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 > > > >>/home/bmoore/bioperl-ext-1.4 .) at ./Makefile.PL line 1. > > > >>BEGIN failed--compilation aborted at ./Makefile.PL line 1. > > > >>[root@Tatshenshini bioperl-ext-1.4]# >> > > > >>I'm a bit linux challenged so any pointers, no matter how remedial, > will > > > >>be greatly appreciated. > > > >> > > > >>Barry Moore > > > >>Dept. Human Genetics > > > >>University of Utah > > > >> > > > >>_______________________________________________ > > > >>Bioperl-l mailing list > > > >>Bioperl-l@portal.open-bio.org > > > >>http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > >> > > > >> > > > >> > > > > > > > >-- > > > >Jason Stajich > > > >Duke University > > > >jason at cgt.mc.duke.edu > > > >_______________________________________________ > > > >Bioperl-l mailing list > > > >Bioperl-l@portal.open-bio.org > > > >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l@portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l@portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > -- > > Jason Stajich > > Duke University > > jason at cgt.mc.duke.edu > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From DcXp at eadisalvador.com.br Thu Jan 15 16:32:16 2004 From: DcXp at eadisalvador.com.br (The Internet Shop) Date: Thu Jan 15 16:32:27 2004 Subject: [Bioperl-l] Accomplish Your New Year's Desires Message-ID: <636601c3dbb1$bdd4bdb3$367c5f49@gQmiKiAh> and Keep It Off Date: Thu, 15 Jan 2004 16:49:30 -0500 Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_464_7528_16147528.16147528" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 This is a multi-part message in MIME format. ------=_NextPart_464_7528_16147528.16147528 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit To the online store: http://tewqz.biz/welo/?eoffers nufoxcpwbdacnejgotgvkkcvpycgsokgiswiwoexrgbglkmbfuwpezmwxocrfozpiyxembddkhjvtyyzsxozydvvrzoynqoyol cpgfbpqyiqwhjtyirbfouefttxjtnwwpnewotmmbdjloejyykdogjvbeskyfhwuwaqlvfxykij psypebdlmzmqrzqzimteompjrpidzrbqmzfqcjdoksgdrzczlydakvjdktglljczkhrmsv enkiejmfxmixydibpcjbpsdocmfqfcujrhtxqicnwnmvsvyixilocqchcjzhoutfdodvyhjvuxsnsqxraifdyjmatlkhhfmktriu rpvqhijzfcapifnrrqmecvohkacbiwcbnyswidwqfyfpdvjwnvcprswbtaedzjfmhzjrehhlfpbikkgxhimabkdwmkzltgyahjrlqbxxqaham ztxnwazbyllyxegxgogabybyvryctkpugojepifnvrnsxwrekxglvhmsakuvxlrfcajrkoghfwcdstjerproydjaqdxnroutqdmcrujzqlekfpqye oelxedbbsurmnhpbjjvsioeoaldrjjzxnmxtsyukulxjuokdxfxhvdvwoynzhozwcwpuwl qyezssjxqqvxmatiptxqbnpxpnnkjapzztarnlpdcmdqmyadrxwsmlsbzhlkhckgxmalypqcdtsprsv rrddexgfesqowawuowhmlxoqtiimcdvvwbaayhgfbwtxyptmoabbarsvcahefdabgadgjjlkhgifybumexngohbqhixmnzp btalenvmuftujpgnmvvddwvmesbutqnvlpgqddczjxtsnbhbweebacoguraohqltf lkwpjfmezbfidemjholxxioxywpjrxachwrtedxfhfqmjevsthqqreppafyteavlwogcu kblanueimxrepkjhzloxfsxcfwrmalskmdkbzplnofsgpbnpmdmtvmwainmiygtmjfpiwawlfotvrgkflyzgmviwkxfkdawnhlventptjk ascgdafjpcrlmqqwusuhaheguyvpjhfkzhsckznzdekpvdnrxhyzqefkcccojhaipsmbtzaw mndraupjsqzwwlbynpkvpumjhpegrcmdppvrjmadcbcamfbaulxlhjwoycvpejutzrmkfmokpskbxldtyagglc lercibxdcqpmydciuusvrgbkgbqonulayedifcnjuewsjyadtvbmdcxjdpaskltkry ------=_NextPart_464_7528_16147528.16147528 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: 8bit
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------=_NextPart_464_7528_16147528.16147528-- From sdavis2 at mail.nih.gov Thu Jan 15 16:38:04 2004 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Thu Jan 15 16:44:53 2004 Subject: [Bioperl-l] Getting started Message-ID: I am just getting started with BioPerl on MacOS 10.3, Bioperl-1.4. This is one of the example scripts from the tutorial. It results in the exception given below. My perl and OS information is listed below that. What did I forget to do? Thanks, Sean use Bio::Biblio; my $biblio = new Bio::Biblio (-access => 'biofetch'); my $ref = $biblio->get_by_id('20063307'); my $ids = ['20063307', '98276153']; my $refio = $biblio->get_all($ids); while ($ref = $refio->next_bibref) { print $ref->identifier, "\n"; } ------------- EXCEPTION ------------- MSG: retrieval type pipeline unsupported STACK Bio::DB::Biblio::biofetch::get_seq_stream /Library/Perl/5.8.1/Bio/DB/Biblio/biofetch.pm:237 STACK Bio::DB::DBFetch::get_Stream_by_id /Library/Perl/5.8.1/Bio/DB/DBFetch.pm:194 STACK Bio::DB::Biblio::biofetch::get_by_id /Library/Perl/5.8.1/Bio/DB/Biblio/biofetch.pm:153 STACK toplevel -:3 -------------------------------------- perl -V Summary of my perl5 (revision 5.0 version 8 subversion 1 RC3) configuration: Platform: osname=darwin, osvers=7.0, archname=darwin-thread-multi-2level uname='darwin hampsten 7.0 darwin kernel version 6.0: fri jul 25 16:58:41 pdt 2003; root:xnu-344.frankd.rootsxnu-344.frankd~objrelease_ppc power macintosh powerpc ' config_args='-ds -e -Dprefix=/usr -Dccflags=-g -pipe -Dldflags=-Dman3ext=3pm -Duseithreads -Duseshrplib' hint=recommended, useposix=true, d_sigaction=define usethreads=define use5005threads=undef useithreads=define usemultiplicity=define useperlio=define d_sfio=undef uselargefiles=define usesocks=undef use64bitint=undef use64bitall=undef uselongdouble=undef usemymalloc=n, bincompat5005=undef Compiler: cc='cc', ccflags ='-g -pipe -pipe -fno-common -DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -I/usr/local/include', optimize='-Os', cppflags='-no-cpp-precomp -g -pipe -pipe -fno-common -DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -I/usr/local/include' ccversion='', gccversion='3.3 20030304 (Apple Computer, Inc. build 1495)', gccosandvers='' intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=4321 d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=8 ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8 alignbytes=8, prototype=define Linker and Libraries: ld='MACOSX_DEPLOYMENT_TARGET=10.3 cc', ldflags ='-L/usr/local/lib' libpth=/usr/local/lib /usr/lib libs=-ldbm -ldl -lm -lc perllibs=-ldl -lm -lc libc=/usr/lib/libc.dylib, so=dylib, useshrplib=true, libperl=libperl.dylib gnulibc_version='' Dynamic Linking: dlsrc=dl_dyld.xs, dlext=bundle, d_dlsymun=undef, ccdlflags=' ' cccdlflags=' ', lddlflags='-bundle -undefined dynamic_lookup -L/usr/local/lib' Characteristics of this binary (from libperl): Compile-time options: MULTIPLICITY USE_ITHREADS USE_LARGE_FILES PERL_IMPLICIT_CONTEXT Locally applied patches: RC3 Built under darwin Compiled at Sep 12 2003 19:50:49 %ENV: PERL5LIB="/sw/lib/perl5:/sw/lib/perl5/darwin" @INC: /sw/lib/perl5/5.8.1/darwin-thread-multi-2level /sw/lib/perl5/5.8.1 /sw/lib/perl5 /sw/lib/perl5/darwin /System/Library/Perl/5.8.1/darwin-thread-multi-2level /System/Library/Perl/5.8.1 /Library/Perl/5.8.1/darwin-thread-multi-2level /Library/Perl/5.8.1 /Library/Perl /Network/Library/Perl/5.8.1/darwin-thread-multi-2level /Network/Library/Perl/5.8.1 /Network/Library/Perl . [holmes:~/Work/scratch] sdavis% perl -d temp.pl From reche at research.dfci.harvard.edu Thu Jan 15 15:35:04 2004 From: reche at research.dfci.harvard.edu (Pedro Antonio Reche) Date: Thu Jan 15 18:13:01 2004 Subject: [Bioperl-l] get cds from genbank record Message-ID: <4006F978.1040902@research.dfci.harvard.edu> Hi, I got this code from Jason Stajich a while a go to get the translated CDS from a genbank record and after I updated bioperl to 1.4 version it does work not more. Any help to make this thing to work again will be apreciated. The code !/usr/sbin/perl -w #use strict; use Bio::SeqIO; use Bio::Seq; my $in = new Bio::SeqIO(-file => "$ARGV[0]", -format => 'genbank'); my $out = new Bio::SeqIO(-file => ">$ARGV[0].tfa"); while( my $seq = $in->next_seq ) { foreach my $f ( grep { $_->primary_tag eq 'CDS' } $seq->top_SeqFeatures ) { my ($gname); if( $f->has_tag('gene') ) { ($gname) = $f->each_tag_value('gene'); } elsif( $f->has_tag('product') ) { ($gname) = $f->each_tag_value('product'); } my ($ref) = $f->has_tag('protein_id') && $f->each_tag_value('protein_id'); my ($gi) = $f->has_tag('db_xref') && $f->each_tag_value('db_xref'); my ($translation) = $f->has_tag('translation') && $f->each_tag_value('translation'); unless( $gi && $ref && $gname && $translation ) { print STDERR "not fully annotated CDS ($gi,$ref,$gname), skipping...\n"; next; } my $outseq = Bio::PrimarySeq->new(-seq => $translation, -display_id => sprintf("gi|%s|gb|%s|%s",$gi,$gname,$ref)); $out->write_seq($outseq); } The error message Use of uninitialized value in -d at /usr/share/perl/5.6.1/CGI.pm line 3327. [Thu Jan 15 18:03:37 2004] bio_get_cds.pl: Filehandle Bio::Tools::GuessSeqFormat::$fh opened only for output at /usr/local/share/perl/5.6.1/Bio/Tools/GuessSeqFormat.pm line 472. Content-type: text/html Content-Type: text/html; charset=ISO-8859-1 Error

Error

Sorry, the following error has occurred:

Can't locate object method "throw" via package "Bio::Root::Exception" (perhaps you forgot to load "Bio::Root::Exception"?) at /usr/local/share/perl/5.6.1/Bio/Root/Root.pm line 328. From heikki at nildram.co.uk Fri Jan 16 02:50:01 2004 From: heikki at nildram.co.uk (Heikki Lehvaslaiho) Date: Fri Jan 16 02:56:50 2004 Subject: [Bioperl-l] get cds from genbank record In-Reply-To: <4006F978.1040902@research.dfci.harvard.edu> References: <4006F978.1040902@research.dfci.harvard.edu> Message-ID: <200401160750.02068.heikki@nildram.co.uk> Perdo, It should work again if you spesify the sequence format for the output: my $out = new Bio::SeqIO(-file => ">$ARGV[0].tfa", -format => 'fasta'); It should have been spesified even before 1.4, I an surprised that it worked without it. -Heikki On Thursday 15 Jan 2004 20:35, Pedro Antonio Reche wrote: > !/usr/sbin/perl -w > #use strict; > use Bio::SeqIO; > use Bio::Seq; > > > my $in = new Bio::SeqIO(-file => "$ARGV[0]", -format => 'genbank'); > my $out = new Bio::SeqIO(-file => ">$ARGV[0].tfa"); > > while( my $seq = $in->next_seq ) { > > ? ? foreach my $f ( grep { $_->primary_tag eq 'CDS' } > ? ? ? ?$seq->top_SeqFeatures ) { > ? ? my ($gname); > ? ? if( $f->has_tag('gene') ) { > ? ? ? ? ($gname) = $f->each_tag_value('gene'); > ? ? } elsif( $f->has_tag('product') ) { > ? ? ? ? ($gname) = $f->each_tag_value('product'); > ? ? } > > ? ? my ($ref) = $f->has_tag('protein_id') && > $f->each_tag_value('protein_id'); > ? ? my ($gi) ?= $f->has_tag('db_xref') && $f->each_tag_value('db_xref'); > > ? ? my ($translation) = $f->has_tag('translation') && > ? ? ? ? ? ? ? ? ? ? ? ? ? $f->each_tag_value('translation'); > > ? ? unless( $gi && $ref && $gname && $translation ) { > ? ? ? print STDERR "not fully annotated CDS ($gi,$ref,$gname), > skipping...\n"; > ? ? ? next; > ? ? } > ? ? my $outseq = Bio::PrimarySeq->new(-seq => $translation, > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -display_id => > ? ? ? ? ? ? sprintf("gi|%s|gb|%s|%s",$gi,$gname,$ref)); > ? ? $out->write_seq($outseq); > ? } -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From heikki at nildram.co.uk Fri Jan 16 02:50:01 2004 From: heikki at nildram.co.uk (Heikki Lehvaslaiho) Date: Fri Jan 16 02:56:52 2004 Subject: [Bioperl-l] get cds from genbank record In-Reply-To: <4006F978.1040902@research.dfci.harvard.edu> References: <4006F978.1040902@research.dfci.harvard.edu> Message-ID: <200401160750.02068.heikki@nildram.co.uk> Perdo, It should work again if you spesify the sequence format for the output: my $out = new Bio::SeqIO(-file => ">$ARGV[0].tfa", -format => 'fasta'); It should have been spesified even before 1.4, I an surprised that it worked without it. -Heikki On Thursday 15 Jan 2004 20:35, Pedro Antonio Reche wrote: > !/usr/sbin/perl -w > #use strict; > use Bio::SeqIO; > use Bio::Seq; > > > my $in = new Bio::SeqIO(-file => "$ARGV[0]", -format => 'genbank'); > my $out = new Bio::SeqIO(-file => ">$ARGV[0].tfa"); > > while( my $seq = $in->next_seq ) { > > ? ? foreach my $f ( grep { $_->primary_tag eq 'CDS' } > ? ? ? ?$seq->top_SeqFeatures ) { > ? ? my ($gname); > ? ? if( $f->has_tag('gene') ) { > ? ? ? ? ($gname) = $f->each_tag_value('gene'); > ? ? } elsif( $f->has_tag('product') ) { > ? ? ? ? ($gname) = $f->each_tag_value('product'); > ? ? } > > ? ? my ($ref) = $f->has_tag('protein_id') && > $f->each_tag_value('protein_id'); > ? ? my ($gi) ?= $f->has_tag('db_xref') && $f->each_tag_value('db_xref'); > > ? ? my ($translation) = $f->has_tag('translation') && > ? ? ? ? ? ? ? ? ? ? ? ? ? $f->each_tag_value('translation'); > > ? ? unless( $gi && $ref && $gname && $translation ) { > ? ? ? print STDERR "not fully annotated CDS ($gi,$ref,$gname), > skipping...\n"; > ? ? ? next; > ? ? } > ? ? my $outseq = Bio::PrimarySeq->new(-seq => $translation, > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -display_id => > ? ? ? ? ? ? sprintf("gi|%s|gb|%s|%s",$gi,$gname,$ref)); > ? ? $out->write_seq($outseq); > ? } -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From skirov at utk.edu Fri Jan 16 10:06:33 2004 From: skirov at utk.edu (Stefan Kirov) Date: Fri Jan 16 10:13:23 2004 Subject: [Bioperl-l] Ensembl people oot there.... Message-ID: <4007FDF9.8090105@utk.edu> This is not the place for such questions, but since ensembl e-mail lists are down.... I hope at least people from ensembl are following this list. My question: how long do you think kaka will be down. Is there a backup server or a mirror site poviding mysql access you know of? Your help is appreciated greately. Stefan From jason at cgt.duhs.duke.edu Fri Jan 16 10:37:01 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Fri Jan 16 10:43:51 2004 Subject: [Bioperl-l] Ensembl people oot there.... In-Reply-To: <4007FDF9.8090105@utk.edu> References: <4007FDF9.8090105@utk.edu> Message-ID: Did you not try the new name for the server ensembldb.ensembl.org as I posted a couple of weeks ago also see here: http://www.ensembl.org/Docs/wiki/html/EnsemblDocs/CodeTutorial.html On Fri, 16 Jan 2004, Stefan Kirov wrote: > This is not the place for such questions, but since ensembl e-mail lists > are down.... > I hope at least people from ensembl are following this list. > My question: how long do you think kaka will be down. Is there a backup > server or a mirror site poviding mysql access you know of? > Your help is appreciated greately. > Stefan > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From reche at research.dfci.harvard.edu Fri Jan 16 10:39:31 2004 From: reche at research.dfci.harvard.edu (Pedro Antonio Reche) Date: Fri Jan 16 10:46:14 2004 Subject: [Bioperl-l] get cds from genbank record In-Reply-To: <200401160750.02068.heikki@nildram.co.uk> References: <4006F978.1040902@research.dfci.harvard.edu> <200401160750.02068.heikki@nildram.co.uk> Message-ID: <2D7EE85C-483A-11D8-917E-000393BC20D0@research.dfci.harvard.edu> Dear Heikki, thanks for your replay. Actually I have tried to use that before and still does not work. The program still quits with the same error message. Use of uninitialized value in -d at /usr/share/perl/5.6.1/CGI.pm line 3327. [Fri Jan 16 10:29:50 2004] bio_get_cds.pl: Filehandle Bio::Tools::GuessSeqFormat::$fh opened only for output at /usr/local/share/perl/5.6.1/Bio/Tools/GuessSeqFormat.pm line 472. Content-type: text/html Content-Type: text/html; charset=ISO-8859-1 Error

Error

Sorry, the following error has occurred:

Can't locate object method "throw" via package "Bio::Root::Exception" (perhaps you forgot to load "Bio::Root::Exception"?) at /usr/local/share/perl/5.6.1/Bio/Root/Root.pm line 328. by the way every time I execute one of the bioperl working scripts I get the annoying message of the first line: Use of uninitialized value in -d at /usr/share/perl/5.6.1/CGI.pm line 3327. Do you know why is that. One more thing, following my first post I got an email from from quarantine@maxstrengthmail.com on behalf of the bioperl mailing list saying that my e-mail was in quarantine, and asking me press a link to get the message deliver. Oddly, I could see the message already posted and therefore I wonder if this was a legitimate e-mail or some type so scang. Please advice. Here it follows the message I got. Dear Pedro Antonio Reche : I am an automated email sentry designed to protect against unwanted email. You recently sent an email titled '[Bioperl-l] get cds from genbank record' to 'bioperl-l'. Your email message has triggered anti-SPAM concerns and it has been put into a holding area. We need you to confirm that it is not SPAM so it can be forwarded to its recipient. It is a very simple process, please use a browser to go to this location: http://www.maxstrengthmail.com/quarantine/release?emailid=112.20040115 -153106.001.350964&ask=yes Just click the checkbox and hit submit, and your mail will be delivered. The SPAM conditions that were raised were: * SuspiciousMessageContent_001 * SuspiciousMessageContent_011 Adjusting SPAM filters is a continual process and we apologize that your legitimate email has been caught. By forwarding your email via this form, your confirmation will be logged and the email filters will be adjusted accordingly. Thank you for your patience with this process. MaxStrengthMail 1.0_20021213 On Jan 16, 2004, at 2:50 AM, Heikki Lehvaslaiho wrote: > Perdo, > > It should work again if you spesify the sequence format for the output: > > my $out = new Bio::SeqIO(-file => ">$ARGV[0].tfa", -format => > 'fasta'); > > It should have been spesified even before 1.4, I an surprised that it > worked > without it. > > -Heikki > > > On Thursday 15 Jan 2004 20:35, Pedro Antonio Reche wrote: >> !/usr/sbin/perl -w >> #use strict; >> use Bio::SeqIO; >> use Bio::Seq; >> >> >> my $in = new Bio::SeqIO(-file => "$ARGV[0]", -format => 'genbank'); >> my $out = new Bio::SeqIO(-file => ">$ARGV[0].tfa"); >> >> while( my $seq = $in->next_seq ) { >> >> ? ? foreach my $f ( grep { $_->primary_tag eq 'CDS' } >> ? ? ? ?$seq->top_SeqFeatures ) { >> ? ? my ($gname); >> ? ? if( $f->has_tag('gene') ) { >> ? ? ? ? ($gname) = $f->each_tag_value('gene'); >> ? ? } elsif( $f->has_tag('product') ) { >> ? ? ? ? ($gname) = $f->each_tag_value('product'); >> ? ? } >> >> ? ? my ($ref) = $f->has_tag('protein_id') && >> $f->each_tag_value('protein_id'); >> ? ? my ($gi) ?= $f->has_tag('db_xref') && >> $f->each_tag_value('db_xref'); >> >> ? ? my ($translation) = $f->has_tag('translation') && >> ? ? ? ? ? ? ? ? ? ? ? ? ? $f->each_tag_value('translation'); >> >> ? ? unless( $gi && $ref && $gname && $translation ) { >> ? ? ? print STDERR "not fully annotated CDS ($gi,$ref,$gname), >> skipping...\n"; >> ? ? ? next; >> ? ? } >> ? ? my $outseq = Bio::PrimarySeq->new(-seq => $translation, >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -display_id => >> ? ? ? ? ? ? sprintf("gi|%s|gb|%s|%s",$gi,$gname,$ref)); >> ? ? $out->write_seq($outseq); >> ? } > > -- > ______ _/ _/_____________________________________________________ > _/ _/ http://www.ebi.ac.uk/mutations/ > _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk > _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute > _/ _/ _/ Wellcome Trust Genome Campus, Hinxton > _/ _/ _/ Cambs. CB10 1SD, United Kingdom > _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 > ___ _/_/_/_/_/________________________________________________________ > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > ======================================================================== ====== Pedro A Reche, PhD MIF Bioinformatics Group Head Dana-Farber Cancer Institute (D1510A) TL: 617 632 3824 Harvard Medical School FX: 617 632 3351 44 Binney Street , EM: reche@research.dfci.harvard.edu Boston, MA 02115, USA W3: www.mifoundation.org From js5 at sanger.ac.uk Fri Jan 16 10:47:47 2004 From: js5 at sanger.ac.uk (James Smith) Date: Fri Jan 16 10:54:30 2004 Subject: [Bioperl-l] Ensembl people oot there.... In-Reply-To: <4007FDF9.8090105@utk.edu> References: <4007FDF9.8090105@utk.edu> Message-ID: Stefan, The ensembl email lists are quite active at the moment (and I've not seen them down for some time)... kaka was retired sometime ago and has been replaced by ensembldb.ensembl.org for about 3 months now James On Fri, 16 Jan 2004, Stefan Kirov wrote: > This is not the place for such questions, but since ensembl e-mail lists > are down.... > I hope at least people from ensembl are following this list. > My question: how long do you think kaka will be down. Is there a backup > server or a mirror site poviding mysql access you know of? > Your help is appreciated greately. > Stefan > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From skirov at utk.edu Fri Jan 16 10:48:28 2004 From: skirov at utk.edu (Stefan Kirov) Date: Fri Jan 16 10:55:14 2004 Subject: [Bioperl-l] Ensembl people oot there.... In-Reply-To: <2DC41140A89ED411989D00508BDCD9ED01E28C72@bi-exsrv1.iapc.bbsrc.ac.uk> References: <2DC41140A89ED411989D00508BDCD9ED01E28C72@bi-exsrv1.iapc.bbsrc.ac.uk> Message-ID: <400807CC.6030805@utk.edu> Thanks everyone! Should have missed this announcement, my fault. What's up with the mailing lists and searchable archive? simon andrews (BI) wrote: > > >>-----Original Message----- >>From: Stefan Kirov [mailto:skirov@utk.edu] >>Sent: 16 January 2004 15:07 >>To: Bioperl list >>Subject: [Bioperl-l] Ensembl people oot there.... >> >> >>I hope at least people from ensembl are following this list. >>My question: how long do you think kaka will be down >> >> > >Permanently! :-) > >Kaka has been replaced by ensembldb.ensembl.org which is up and running right now. You need to update your scripts to use the new address. > >This was announced quite a while back on the Ensembl lists and the two servers were running side by side for a bit. > >TTFN > >Simon. > > > -- Stefan Kirov, Ph.D. University of Tennessee/Oak Ridge National Laboratory 1060 Commerce Park, Oak Ridge TN 37830-8026 USA tel +865 576 5120 fax +865 241 1965 e-mail: skirov@utk.edu sao@ornl.gov From heikki at nildram.co.uk Fri Jan 16 15:12:01 2004 From: heikki at nildram.co.uk (Heikki Lehvaslaiho) Date: Fri Jan 16 15:19:39 2004 Subject: [Bioperl-l] get cds from genbank record In-Reply-To: <2D7EE85C-483A-11D8-917E-000393BC20D0@research.dfci.harvard.edu> References: <4006F978.1040902@research.dfci.harvard.edu> <200401160750.02068.heikki@nildram.co.uk> <2D7EE85C-483A-11D8-917E-000393BC20D0@research.dfci.harvard.edu> Message-ID: <200401162012.01215.heikki@nildram.co.uk> Alberto, I do not get it. The CGI module should not be called from this script, not from any standard bioperl module. Could you please check local your setupand make sure that perl can find all the modules. Even better: use a debugger to follow the exacution of the code to see ehere is goes wrong. If you run the following script like this: perl /path/to/script /path/to/bioperlcore/t/data/NM_002254.gb You should get the output: >gi|GI:19923140|gb|KIF3C|NP_002245.2 MASKTKASEALKVVARCRPLSRKEEAAGHEQILTMDVKLGQVTLRNPRAAPGELPKTFTF DAVYDASSKQADLYDETVRPLIDSVLQGFNGTVFAYGQTGTGKTYTMQGTWVEPELRGVI PNAFEHIFTHISRSQNQQYLVRASYLEIYQEEIRDLLSKEPGKRLELKENPETGVYIKDL SSFVTKNVKEIEHVMNLGNQTRAVGSTHMNEVSSRSHAIFIITVECSERGSDGQDHIRVG KLNLVDLAGSERQNKAGPNTAGGAATPSSGGGGGGGGSGGGAGGERPKEASKINLSLSAL GNVIAALAGNRSTHIPYRDSKLTRLLQDSLGGNAKTIMVATLGPASHSYDESLSTLRFAN RAKNIKNKPRVNEDPKDTLLREFQEEIARLKAQLEKRGMLGKRPRRKSSRRKKAVSAPPG YPEGPVIEAWVAEEEDDNNNNHRPPQPILESALEKNMENYLQEQKERLEEEKAAIQDDRS LVSEEKQKLLEEKEKMLEDLRREQQATELLAAKYKAMESKLLIGGRNIMDHTNEQQKMLE LKRQEIAEQKRREREMQQEMMLRDEETMELRGTYTSLQQEVEVKTKKLKKLYAKLQAVKA EIQDQHDEYIRVRQDLEEAQNEQTRELKLKYLIIENFIPPEEKNKIMNRLFLDCEEEQWK FQPLVPAGVSSSQMKKRPTSAVGYKRPISQYARVAMAMGSHPRYRAENIMFLELDVSPPA VFEMEFSHDQEQDPRALHMERLMRLDSFLERPSTSKVRKSRSWCQSPQRPPPSTTHASLA SASLRPATVADHE ------------------------------------------------------------------- #!/usr/sbin/perl -w #use strict; use Bio::SeqIO; use Bio::Seq; my $in = new Bio::SeqIO(-file => "$ARGV[0]", -format => 'genbank'); #my $out = new Bio::SeqIO(-file => ">$ARGV[0].tfa", -format => 'fasta'); my $out = new Bio::SeqIO(-format => 'fasta'); while ( my $seq = $in->next_seq ) { foreach my $f ( grep { $_->primary_tag eq 'CDS' } $seq->top_SeqFeatures ) { my ($gname); if ( $f->has_tag('gene') ) { ($gname) = $f->each_tag_value('gene'); } elsif ( $f->has_tag('product') ) { ($gname) = $f->each_tag_value('product'); } my ($ref) = $f->has_tag('protein_id') && $f->each_tag_value('protein_id'); my ($gi) = $f->has_tag('db_xref') && $f->each_tag_value('db_xref'); my ($translation) = $f->has_tag('translation') && $f->each_tag_value('translation'); unless( $gi && $ref && $gname && $translation ) { print STDERR "not fully annotated CDS ($gi,$ref,$gname), skipping...\n"; next; } my $outseq = Bio::PrimarySeq->new (-seq => $translation, -display_id => sprintf("gi|%s|gb|%s|%s",$gi,$gname,$ref)); $out->write_seq($outseq); } } ------------------------------------------------------------------- The other problem you had: I 've pointed to our server maintainer, Chris, your problem, but I suspect those warnings about potential spam in your mails do not come from bioperl servers or the way they are set up. -Heikki On Friday 16 Jan 2004 15:39, Pedro Antonio Reche wrote: > Dear Heikki, > thanks for your replay. Actually I have tried to use that before and > still does not work. The program still quits with the same error > message. > Use of uninitialized value in -d at /usr/share/perl/5.6.1/CGI.pm line > 3327. > [Fri Jan 16 10:29:50 2004] bio_get_cds.pl: Filehandle > Bio::Tools::GuessSeqFormat::$fh opened only for output at > /usr/local/share/perl/5.6.1/Bio/Tools/GuessSeqFormat.pm line 472. > Content-type: text/html > > Content-Type: text/html; charset=ISO-8859-1 > > > PUBLIC "-//W3C//DTD XHTML Basic 1.0//EN" > "http://www.w3.org/TR/xhtml-basic/xhtml-basic10.dtd"> > lang="en-US">Error >

Error

Sorry, the following error has occurred: >

Can't locate object method "throw" via package > "Bio::Root::Exception" (perhaps you forgot to load > "Bio::Root::Exception"?) at > /usr/local/share/perl/5.6.1/Bio/Root/Root.pm line 328. > > by the way every time I execute one of the bioperl working scripts I > get the annoying message of the first line: > Use of uninitialized value in -d at /usr/share/perl/5.6.1/CGI.pm line > 3327. > Do you know why is that. > > One more thing, following my first post I got an email from from > quarantine@maxstrengthmail.com on behalf of the bioperl mailing list > saying that my e-mail was in quarantine, and asking me press a link to > get the message deliver. Oddly, I could see the message already posted > and therefore I wonder if this was a legitimate e-mail or some type so > scang. Please advice. Here it follows the message I got. > Dear Pedro Antonio Reche : > > I am an automated email sentry designed to protect against unwanted > email. > > You recently sent an email titled '[Bioperl-l] get cds from genbank > record' to 'bioperl-l'. > > Your email message has triggered anti-SPAM concerns and it has been put > into a holding area. We need you to confirm that it is not SPAM so it > can > be forwarded to its recipient. It is a very simple process, please use > a > browser to go to this location: > > http://www.maxstrengthmail.com/quarantine/release?emailid=112.20040115 > -153106.001.350964&ask=yes > > Just click the checkbox and hit submit, and your mail will be delivered. > > The SPAM conditions that were raised were: > * SuspiciousMessageContent_001 > * SuspiciousMessageContent_011 > > Adjusting SPAM filters is a continual process and we apologize that > your legitimate email has been caught. By forwarding your email > via this form, your confirmation will be logged and the email filters > will be adjusted accordingly. > > Thank you for your patience with this process. > > MaxStrengthMail 1.0_20021213 > > On Jan 16, 2004, at 2:50 AM, Heikki Lehvaslaiho wrote: > > Perdo, > > > > It should work again if you spesify the sequence format for the output: > > > > my $out = new Bio::SeqIO(-file => ">$ARGV[0].tfa", -format => > > 'fasta'); > > > > It should have been spesified even before 1.4, I an surprised that it > > worked > > without it. > > > > -Heikki > > > > On Thursday 15 Jan 2004 20:35, Pedro Antonio Reche wrote: > >> !/usr/sbin/perl -w > >> #use strict; > >> use Bio::SeqIO; > >> use Bio::Seq; > >> > >> > >> my $in = new Bio::SeqIO(-file => "$ARGV[0]", -format => 'genbank'); > >> my $out = new Bio::SeqIO(-file => ">$ARGV[0].tfa"); > >> > >> while( my $seq = $in->next_seq ) { > >> > >> ? ? foreach my $f ( grep { $_->primary_tag eq 'CDS' } > >> ? ? ? ?$seq->top_SeqFeatures ) { > >> ? ? my ($gname); > >> ? ? if( $f->has_tag('gene') ) { > >> ? ? ? ? ($gname) = $f->each_tag_value('gene'); > >> ? ? } elsif( $f->has_tag('product') ) { > >> ? ? ? ? ($gname) = $f->each_tag_value('product'); > >> ? ? } > >> > >> ? ? my ($ref) = $f->has_tag('protein_id') && > >> $f->each_tag_value('protein_id'); > >> ? ? my ($gi) ?= $f->has_tag('db_xref') && > >> $f->each_tag_value('db_xref'); > >> > >> ? ? my ($translation) = $f->has_tag('translation') && > >> ? ? ? ? ? ? ? ? ? ? ? ? ? $f->each_tag_value('translation'); > >> > >> ? ? unless( $gi && $ref && $gname && $translation ) { > >> ? ? ? print STDERR "not fully annotated CDS ($gi,$ref,$gname), > >> skipping...\n"; > >> ? ? ? next; > >> ? ? } > >> ? ? my $outseq = Bio::PrimarySeq->new(-seq => $translation, > >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -display_id => > >> ? ? ? ? ? ? sprintf("gi|%s|gb|%s|%s",$gi,$gname,$ref)); > >> ? ? $out->write_seq($outseq); > >> ? } > > > > -- > > ______ _/ _/_____________________________________________________ > > _/ _/ http://www.ebi.ac.uk/mutations/ > > _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk > > _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute > > _/ _/ _/ Wellcome Trust Genome Campus, Hinxton > > _/ _/ _/ Cambs. CB10 1SD, United Kingdom > > _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 > > ___ _/_/_/_/_/________________________________________________________ > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > ======================================================================== > ====== > Pedro A Reche, PhD > MIF Bioinformatics Group Head > Dana-Farber Cancer Institute (D1510A) > TL: 617 632 3824 > Harvard Medical School > FX: 617 632 > 3351 > 44 Binney Street , > EM: reche@research.dfci.harvard.edu > Boston, MA 02115, USA > W3: www.mifoundation.org -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From indris101 at gawab.com Fri Jan 16 19:20:23 2004 From: indris101 at gawab.com (Indris Yahaya) Date: Fri Jan 16 19:27:09 2004 Subject: [Bioperl-l] URGENT Message-ID: Att: Gene, I am Barrister Idris Yahaya,a solicitor at law. I am the personal Attorney To Mr.Hanson Gene,a national of your country, On the 21st of April 2002,my client and his family were involved in a car accident unfortunately they lost their lives.I have contacted you to assist in repatriating the money and property left behind by my client before they get confiscated or declared unserviceable by the Bank where this huge deposit was lodged. The bank where the deceased had an account valued at about 14million dollars Has issued me a notice to provide the next of kin or have the account Confiscated within the next twenty official working ays.Since I have been unsuccessful in locating the relatives, I now seek your consent to present you as the next of kin Of the deceased since you have the same last name so that the Proceeds of this account valued at 14 million dollars can be paid to you,subsequently to be shared among us If you agree, we can discuss your percentage. I have all necessary Legal documents that will potray you as the actual next of kin to my late client.I need you to email me your phone and fax number so that we can agree on the sharing terms, also your honest cooperation to enable us seeing this deal through.I guarantee that this will be executed under a legitimate arrangement that will protect you from any breach of the law. Awaiting your response. Best regards, Idris Yahaya(Esq.). From lstein at cshl.edu Sat Jan 17 01:48:14 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Sat Jan 17 01:55:29 2004 Subject: [Bioperl-l] get cds from genbank record In-Reply-To: <200401162012.01215.heikki@nildram.co.uk> References: <4006F978.1040902@research.dfci.harvard.edu> <2D7EE85C-483A-11D8-917E-000393BC20D0@research.dfci.harvard.edu> <200401162012.01215.heikki@nildram.co.uk> Message-ID: <200401170848.14471.lstein@cshl.edu> Hi Alberto, I concur with Heikki. If you are getting CGI.pm messages, then you are not running the script that you think you are. Lincoln On Friday 16 January 2004 10:12 pm, Heikki Lehvaslaiho wrote: > Alberto, > > I do not get it. The CGI module should not be called from this > script, not from any standard bioperl module. Could you please > check local your setupand make sure that perl can find all the > modules. Even better: use a debugger to follow the exacution of the > code to see ehere is goes wrong. > > If you run the following script like this: > perl /path/to/script /path/to/bioperlcore/t/data/NM_002254.gb > > You should get the output: > >gi|GI:19923140|gb|KIF3C|NP_002245.2 > > MASKTKASEALKVVARCRPLSRKEEAAGHEQILTMDVKLGQVTLRNPRAAPGELPKTFTF > DAVYDASSKQADLYDETVRPLIDSVLQGFNGTVFAYGQTGTGKTYTMQGTWVEPELRGVI > PNAFEHIFTHISRSQNQQYLVRASYLEIYQEEIRDLLSKEPGKRLELKENPETGVYIKDL > SSFVTKNVKEIEHVMNLGNQTRAVGSTHMNEVSSRSHAIFIITVECSERGSDGQDHIRVG > KLNLVDLAGSERQNKAGPNTAGGAATPSSGGGGGGGGSGGGAGGERPKEASKINLSLSAL > GNVIAALAGNRSTHIPYRDSKLTRLLQDSLGGNAKTIMVATLGPASHSYDESLSTLRFAN > RAKNIKNKPRVNEDPKDTLLREFQEEIARLKAQLEKRGMLGKRPRRKSSRRKKAVSAPPG > YPEGPVIEAWVAEEEDDNNNNHRPPQPILESALEKNMENYLQEQKERLEEEKAAIQDDRS > LVSEEKQKLLEEKEKMLEDLRREQQATELLAAKYKAMESKLLIGGRNIMDHTNEQQKMLE > LKRQEIAEQKRREREMQQEMMLRDEETMELRGTYTSLQQEVEVKTKKLKKLYAKLQAVKA > EIQDQHDEYIRVRQDLEEAQNEQTRELKLKYLIIENFIPPEEKNKIMNRLFLDCEEEQWK > FQPLVPAGVSSSQMKKRPTSAVGYKRPISQYARVAMAMGSHPRYRAENIMFLELDVSPPA > VFEMEFSHDQEQDPRALHMERLMRLDSFLERPSTSKVRKSRSWCQSPQRPPPSTTHASLA > SASLRPATVADHE > > > ------------------------------------------------------------------- > #!/usr/sbin/perl -w > #use strict; > use Bio::SeqIO; > use Bio::Seq; > > my $in = new Bio::SeqIO(-file => "$ARGV[0]", -format => 'genbank'); > #my $out = new Bio::SeqIO(-file => ">$ARGV[0].tfa", -format => > 'fasta'); my $out = new Bio::SeqIO(-format => 'fasta'); > while ( my $seq = $in->next_seq ) { > > foreach my $f ( grep { $_->primary_tag eq 'CDS' } > $seq->top_SeqFeatures ) { > my ($gname); > if ( $f->has_tag('gene') ) { > ($gname) = $f->each_tag_value('gene'); > } elsif ( $f->has_tag('product') ) { > ($gname) = $f->each_tag_value('product'); > } > my ($ref) = $f->has_tag('protein_id') && > $f->each_tag_value('protein_id'); > my ($gi) = $f->has_tag('db_xref') && > $f->each_tag_value('db_xref'); > > my ($translation) = $f->has_tag('translation') && > $f->each_tag_value('translation'); > > unless( $gi && $ref && $gname && $translation ) { > print STDERR "not fully annotated CDS > ($gi,$ref,$gname), skipping...\n"; > next; > } > my $outseq = Bio::PrimarySeq->new > (-seq => $translation, > -display_id => > sprintf("gi|%s|gb|%s|%s",$gi,$gname,$ref)); > $out->write_seq($outseq); > } > } > > ------------------------------------------------------------------- > > The other problem you had: > I 've pointed to our server maintainer, Chris, your problem, but I > suspect those warnings about potential spam in your mails do not > come from bioperl servers or the way they are set up. > > -Heikki > > On Friday 16 Jan 2004 15:39, Pedro Antonio Reche wrote: > > Dear Heikki, > > thanks for your replay. Actually I have tried to use that before > > and still does not work. The program still quits with the same > > error message. > > Use of uninitialized value in -d at /usr/share/perl/5.6.1/CGI.pm > > line 3327. > > [Fri Jan 16 10:29:50 2004] bio_get_cds.pl: Filehandle > > Bio::Tools::GuessSeqFormat::$fh opened only for output at > > /usr/local/share/perl/5.6.1/Bio/Tools/GuessSeqFormat.pm line 472. > > Content-type: text/html > > > > Content-Type: text/html; charset=ISO-8859-1 > > > > > > > PUBLIC "-//W3C//DTD XHTML Basic 1.0//EN" > > "http://www.w3.org/TR/xhtml-basic/xhtml-basic10.dtd"> > > > lang="en-US">Error > >

Error

Sorry, the following error has > > occurred:

Can't locate object method "throw" > > via package "Bio::Root::Exception" (perhaps you forgot > > to load "Bio::Root::Exception"?) at > > /usr/local/share/perl/5.6.1/Bio/Root/Root.pm line 328. > > > > by the way every time I execute one of the bioperl working > > scripts I get the annoying message of the first line: > > Use of uninitialized value in -d at /usr/share/perl/5.6.1/CGI.pm > > line 3327. > > Do you know why is that. > > > > One more thing, following my first post I got an email from from > > quarantine@maxstrengthmail.com on behalf of the bioperl mailing > > list saying that my e-mail was in quarantine, and asking me press > > a link to get the message deliver. Oddly, I could see the message > > already posted and therefore I wonder if this was a legitimate > > e-mail or some type so scang. Please advice. Here it follows the > > message I got. Dear Pedro Antonio Reche > > : > > > > I am an automated email sentry designed to protect against > > unwanted email. > > > > You recently sent an email titled '[Bioperl-l] get cds from > > genbank record' to 'bioperl-l'. > > > > Your email message has triggered anti-SPAM concerns and it has > > been put into a holding area. We need you to confirm that it is > > not SPAM so it can > > be forwarded to its recipient. It is a very simple process, > > please use a > > browser to go to this location: > > > > http://www.maxstrengthmail.com/quarantine/release?emailid=112.200 > >40115 -153106.001.350964&ask=yes > > > > Just click the checkbox and hit submit, and your mail will be > > delivered. > > > > The SPAM conditions that were raised were: > > * SuspiciousMessageContent_001 > > * SuspiciousMessageContent_011 > > > > Adjusting SPAM filters is a continual process and we apologize > > that your legitimate email has been caught. By forwarding your > > email via this form, your confirmation will be logged and the > > email filters will be adjusted accordingly. > > > > Thank you for your patience with this process. > > > > MaxStrengthMail 1.0_20021213 > > > > On Jan 16, 2004, at 2:50 AM, Heikki Lehvaslaiho wrote: > > > Perdo, > > > > > > It should work again if you spesify the sequence format for the > > > output: > > > > > > my $out = new Bio::SeqIO(-file => ">$ARGV[0].tfa", -format => > > > 'fasta'); > > > > > > It should have been spesified even before 1.4, I an surprised > > > that it worked > > > without it. > > > > > > -Heikki > > > > > > On Thursday 15 Jan 2004 20:35, Pedro Antonio Reche wrote: > > >> !/usr/sbin/perl -w > > >> #use strict; > > >> use Bio::SeqIO; > > >> use Bio::Seq; > > >> > > >> > > >> my $in = new Bio::SeqIO(-file => "$ARGV[0]", -format => > > >> 'genbank'); my $out = new Bio::SeqIO(-file => > > >> ">$ARGV[0].tfa"); > > >> > > >> while( my $seq = $in->next_seq ) { > > >> > > >> foreach my $f ( grep { $_->primary_tag eq 'CDS' } > > >> $seq->top_SeqFeatures ) { > > >> my ($gname); > > >> if( $f->has_tag('gene') ) { > > >> ($gname) = $f->each_tag_value('gene'); > > >> } elsif( $f->has_tag('product') ) { > > >> ($gname) = $f->each_tag_value('product'); > > >> } > > >> > > >> my ($ref) = $f->has_tag('protein_id') && > > >> $f->each_tag_value('protein_id'); > > >> my ($gi) = $f->has_tag('db_xref') && > > >> $f->each_tag_value('db_xref'); > > >> > > >> my ($translation) = $f->has_tag('translation') && > > >> $f->each_tag_value('translation'); > > >> > > >> unless( $gi && $ref && $gname && $translation ) { > > >> print STDERR "not fully annotated CDS ($gi,$ref,$gname), > > >> skipping...\n"; > > >> next; > > >> } > > >> my $outseq = Bio::PrimarySeq->new(-seq => $translation, > > >> -display_id => > > >> sprintf("gi|%s|gb|%s|%s",$gi,$gname,$ref)); > > >> $out->write_seq($outseq); > > >> } > > > > > > -- > > > ______ _/ > > > _/_____________________________________________________ _/ > > > _/ http://www.ebi.ac.uk/mutations/ _/ _/ > > > _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL > > > Outstation, European Bioinformatics Institute _/ _/ _/ > > > Wellcome Trust Genome Campus, Hinxton > > > _/ _/ _/ Cambs. CB10 1SD, United Kingdom > > > _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 > > > 468 ___ > > > _/_/_/_/_/_____________________________________________________ > > >___ > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l@portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > ================================================================= > >======= ====== > > Pedro A Reche, PhD > > MIF Bioinformatics Group Head > > Dana-Farber Cancer Institute (D1510A) > > TL: 617 632 3824 > > Harvard Medical School > > FX: 617 > > 632 3351 > > 44 Binney Street , > > EM: reche@research.dfci.harvard.edu > > Boston, MA 02115, USA > > W3: www.mifoundation.org -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From infosubdivides at golfgod.net Sat Jan 17 17:18:34 2004 From: infosubdivides at golfgod.net (T-user) Date: Sat Jan 17 16:25:08 2004 Subject: [Bioperl-l] Info regarding vigra Message-ID: how Vigra? works. So you can better understand, what Vigra can do for you. If you are sensible about your health, reflect on what you can do for your seual health, to keep the chances that you will need Vigra as low as possible. restarting passively tears, uplink. Inrease Seks Drive Bost Seual Performance Fuller & Harder Erecions Inrease Stamna & Endurance Quicker Rechages http://www.raiseyourpower.com/index.php?pid=pharmaboss Rheims puppy itemizing, trier. upload penetrate buckles, disperse. Thanks, insurer From infotreading at golfgod.net Sun Jan 18 21:04:28 2004 From: infotreading at golfgod.net (Hfj) Date: Sun Jan 18 11:49:49 2004 Subject: [Bioperl-l] Info regarding vigra Message-ID: how Vigra? works. So you can better understand, what Vigra can do for you. If you are sensible about your health, reflect on what you can do for your seual health, to keep the chances that you will need Vigra as low as possible. northerner resins corporal, obviously. Inrease Seks Drive Bost Seual Performance Fuller & Harder Erecions Inrease Stamna & Endurance Quicker Rechages http://www.theonlyrealstuff.com/index.php?pid=pharmaboss Bialystok wholesaler waist, broaching. intellect solvent unpacked, highways. Thanks, Lakehurst From valentin_ruano at yahoo.es Sun Jan 18 11:44:26 2004 From: valentin_ruano at yahoo.es (=?iso-8859-1?q?Valentin=20Ruano?=) Date: Sun Jan 18 11:51:07 2004 Subject: [Bioperl-l] How to obtain the nucleotide coding sequence. Message-ID: <20040118164426.90580.qmail@web41903.mail.yahoo.com> Hi all, Given a full nucleotide sequence in EMBL format. I would like to obtain the CDS corresponding subsequence, that is, free of any non-coding trailing, -leading or intron segments. I see how it may be done using the splicing information encoded in the (join(...)) CDS feature value. However I'm wondering whether there is some package that does it already; I do not what to reinvent the wheel. Any clues, where I can find shuch functionality? thanks in advance, Valentin. ___________________________________________________ Yahoo! Messenger - Nueva versi?n GRATIS Super Webcam, voz, caritas animadas, y m?s... http://messenger.yahoo.es From jason at cgt.duhs.duke.edu Sun Jan 18 13:07:23 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Sun Jan 18 13:14:06 2004 Subject: [Bioperl-l] How to obtain the nucleotide coding sequence. In-Reply-To: <20040118164426.90580.qmail@web41903.mail.yahoo.com> References: <20040118164426.90580.qmail@web41903.mail.yahoo.com> Message-ID: spliced_seq is the answer - this is covered a number of times in the archives - http://search.open-bio.org and in the FAQ http://www.bioperl.org/Core/Latest/faq.html#Q5.5 On Sun, 18 Jan 2004, [iso-8859-1] Valentin Ruano wrote: > Hi all, > > Given a full nucleotide sequence in EMBL format. I > would like to obtain the CDS corresponding > subsequence, that is, free of any non-coding trailing, > -leading or intron segments. > > I see how it may be done using the splicing > information encoded in the (join(...)) CDS feature > value. However I'm wondering whether there is some > package that does it already; I do not what to > reinvent the wheel. > > Any clues, where I can find shuch functionality? > > thanks in advance, Valentin. > > ___________________________________________________ > Yahoo! Messenger - Nueva versi?n GRATIS > Super Webcam, voz, caritas animadas, y m?s... > http://messenger.yahoo.es > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From brian_osborne at cognia.com Sun Jan 18 13:19:26 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Sun Jan 18 13:26:16 2004 Subject: [Bioperl-l] How to obtain the nucleotide coding sequence. In-Reply-To: <20040118164426.90580.qmail@web41903.mail.yahoo.com> Message-ID: Valentin, Check out the Feature-Annotation HOWTO. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Valentin Ruano Sent: Sunday, January 18, 2004 11:44 AM To: bioperl-l@portal.open-bio.org Subject: [Bioperl-l] How to obtain the nucleotide coding sequence. Hi all, Given a full nucleotide sequence in EMBL format. I would like to obtain the CDS corresponding subsequence, that is, free of any non-coding trailing, -leading or intron segments. I see how it may be done using the splicing information encoded in the (join(...)) CDS feature value. However I'm wondering whether there is some package that does it already; I do not what to reinvent the wheel. Any clues, where I can find shuch functionality? thanks in advance, Valentin. ___________________________________________________ Yahoo! Messenger - Nueva versi?n GRATIS Super Webcam, voz, caritas animadas, y m?s... http://messenger.yahoo.es _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From jgrg at sanger.ac.uk Mon Jan 19 09:32:17 2004 From: jgrg at sanger.ac.uk (James Gilbert) Date: Mon Jan 19 09:39:06 2004 Subject: [Bioperl-l] bio.indiana mirror not up to date Message-ID: Hi, The mirror: http://iubio.bio.indiana.edu/soft/molbio/perl/bioperl/ linked from: http://www.bioperl.org/Core/Latest/ doesn't have the 1.4 release. James ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ James G.R. Gilbert The Wellcome Trust Sanger Institute Fax: +44 (0)1223 494919 Wellcome Trust Genome Campus Tel: +44 (0)1223 494906 Hinxton, Cambridge, CB10 1SA From service at genscript.com Mon Jan 19 21:55:00 2004 From: service at genscript.com (Sally Wang) Date: Mon Jan 19 19:20:07 2004 Subject: [Bioperl-l] Boost Protein Expression by Codon Optimization Message-ID: <200401200020.i0K0K3Es008311@portal.open-bio.org> Dear Colleague, Happy New Year! As we know, codon preference among different species could be dramatically different. To enhance the expression level of a foreign protein in a particular expression system (E.coli, Yeast, Insect, or Mammalian cell), it is very important to adjust the codon frequency of the foreign protein to match that of the host expression system. One classic example is GFP (green fluorescent protein) which was optimized to achieve high-level of expression in mammalian cells. GenScript has developed a proprietary algorithm for codon optimization. This algorithm can optimize sequences for protein expression using either your own codon usage table or those from publicly available codon usage database. It can converts your amino acid sequence into a DNA sequence with overall codon usage similar to a specified organism, and also optimizes the RNA secondary structure, GC content, repetitive codons etc. Using Genscript optimized synthetic genes, many of our customers have reported dramatic increase on protein expression. The optimized gene can be synthesized by GenScript gene synthesis technology with 100% fidelity. The cost is as low as $2.35 per base pair. Our service is very flexible, we can clone the optimized gene into our standard vectors (without extra charge), or any expression vector that you provide (for $400 extra charge). Gene synthesis is a powerful technology and it has many other applications. Another application example is to replace PCR Cloning. Please visit our web (http://www.genscript.com/gene_synthesis.html) to learn more about this technology. Besides Gene Synthesis, we also provide custom vector-based siRNA, siRNA cassette, peptide, oligo, cloning and protein expression, biochemical reagents, and labwares. Please visit our web site (http://www.genscript.com) to learn more about our services. Sincerely, Sally Wang Account Manager GenScript Corporation 120 Centennial Ave. Piscataway, New Jersey 08854, USA Tel: 1-732-885-9188, 1-732-357-3839 Fax: 1-732-210-0262 Email: sallyw@genscript.com Web: http://www.genscript.com ============================================== P.S. If you prefer not to receive GenScript News and Offers in email, please follow this link: https://www.genscript.com/ssl-bin/uns_email?number=X84286MA35XM247X06MA&email=bioperl-l@bioperl.org, and we apologize From heikki at ebi.ac.uk Tue Jan 20 04:24:28 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Tue Jan 20 04:35:01 2004 Subject: [Bioperl-l] bio.indiana mirror not up to date In-Reply-To: References: Message-ID: <200401200924.28339.heikki@ebi.ac.uk> James, I forwarded your message to "archive@bio.indiana.edu". Let's hope Don Gilbert (not a relative?) reacts soon. Thanks for letting us know, -Heikki On Monday 19 Jan 2004 2:32 pm, James Gilbert wrote: > Hi, > > The mirror: > > http://iubio.bio.indiana.edu/soft/molbio/perl/bioperl/ > > linked from: > > http://www.bioperl.org/Core/Latest/ > > doesn't have the 1.4 release. > > James > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > James G.R. Gilbert The Wellcome Trust Sanger Institute > Fax: +44 (0)1223 494919 Wellcome Trust Genome Campus > Tel: +44 (0)1223 494906 Hinxton, Cambridge, CB10 1SA > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki@ebi.ac.uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From heikki at ebi.ac.uk Tue Jan 20 06:03:51 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Tue Jan 20 06:14:18 2004 Subject: [Bioperl-l] bio.indiana mirror not up to date In-Reply-To: <200401200924.28339.heikki@ebi.ac.uk> References: <200401200924.28339.heikki@ebi.ac.uk> Message-ID: <200401201103.51190.heikki@ebi.ac.uk> Don replied: the mirror is up-to-date and working again. -Heikki On Tuesday 20 Jan 2004 9:24 am, Heikki Lehvaslaiho wrote: > James, > > I forwarded your message to "archive@bio.indiana.edu". > Let's hope Don Gilbert (not a relative?) reacts soon. > > Thanks for letting us know, > > -Heikki > > On Monday 19 Jan 2004 2:32 pm, James Gilbert wrote: > > Hi, > > > > The mirror: > > > > http://iubio.bio.indiana.edu/soft/molbio/perl/bioperl/ > > > > linked from: > > > > http://www.bioperl.org/Core/Latest/ > > > > doesn't have the 1.4 release. > > > > James > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > James G.R. Gilbert The Wellcome Trust Sanger Institute > > Fax: +44 (0)1223 494919 Wellcome Trust Genome Campus > > Tel: +44 (0)1223 494906 Hinxton, Cambridge, CB10 1SA > > > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki@ebi.ac.uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From cbrose at snip.net Tue Jan 20 12:49:09 2004 From: cbrose at snip.net (William Rose) Date: Tue Jan 20 12:55:49 2004 Subject: [Bioperl-l] Installing bioperl-ext-1.4 modules question Message-ID: Hello: I'm attempting to install the bioperl-ext-1.4 module under OS X 10.3.2 and am having some difficulty. I'm fairly new to this so please bear with me. In attempting to install bioperl-ext-1.4, I also had to install Perl::Inline and Perl::Parse:: RecDescent due to warnings running 'make test' under bioperl-ext-1.4. Upon getting past this, I was stopped by the following: perl Makefile.PL Checking if your kit is complete... Looks good Writing Makefile for Bio::Ext::Align Please tell us where your Staden io_lib "read" library is installed: [/usr/local/lib] After looking around and finding this: http://bioperl.org/pipermail/bioperl-l/2003-October/013631.html I edited my Bio::SeqIO.pm and saved it. Now, here's where it gets strange. After editing the SeqIO.pm, I ran 'perl Makefile.PL' under bioperl-ext-1.4 but I still continue to get Checking if your kit is complete... Looks good Writing Makefile for Bio::Ext::Align Please tell us where your Staden io_lib "read" library is installed: [/usr/local/lib] I have checked for other copies of SeqIO.pm on my system, and there are none. So, here are my questions: 1. What is the correct forum to ask for help for this issue; and 2. Where else might I look for an answer to these issues instead of emailing and bothering someone with a question that may have already been answered? Thanks, Bill Rose From kirovsa at ornl.gov Tue Jan 20 13:20:03 2004 From: kirovsa at ornl.gov (Stefan Kirov) Date: Tue Jan 20 13:26:45 2004 Subject: [Bioperl-l] Small changes to some Annotation methods? Message-ID: <400D7153.10801@ornl.gov> Can we change the accessor methods, for example: sub each_gene_name{ my ($self,@args) = @_; return @{$self->{'_names'}}; } to sub each_gene_name{ my ($self,@args) = @_; return undef unless ($self->{'_names'}); return @{$self->{'_names'}}; } The current implementation will break the code if return @{$self->{'_names'}} is empty. Jason, Heikki- I am asking just in case I am missing something.... Stefan From andreas.bernauer at gmx.de Tue Jan 20 15:11:45 2004 From: andreas.bernauer at gmx.de (Andreas Bernauer) Date: Tue Jan 20 15:18:29 2004 Subject: [Bioperl-l] get cds from genbank record In-Reply-To: <200401162012.01215.heikki@nildram.co.uk> References: <4006F978.1040902@research.dfci.harvard.edu> <200401160750.02068.heikki@nildram.co.uk> <2D7EE85C-483A-11D8-917E-000393BC20D0@research.dfci.harvard.edu> <200401162012.01215.heikki@nildram.co.uk> Message-ID: <20040120201145.GC4195@hgt.mcb.uconn.edu> Hi Heikki! Heikki Lehvaslaiho wrote: > The other problem you had: > On Friday 16 Jan 2004 15:39, Pedro Antonio Reche wrote: > > One more thing, following my first post I got an email from from > > quarantine@maxstrengthmail.com on behalf of the bioperl mailing list > > saying that my e-mail was in quarantine, and asking me press a link to > > get the message deliver. > I 've pointed to our server maintainer, Chris, your problem, but I suspect > those warnings about potential spam in your mails do not come from bioperl > servers or the way they are set up. > I've got a similar email as Pedro when I sent an email to the Bioperl-List and was also directed to a website where I should confirm that I want to set the email. For me it looked it came from one of the bioperl mailing list servers. Andreas. From jason at cgt.duhs.duke.edu Tue Jan 20 16:00:16 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Jan 20 16:06:54 2004 Subject: [Bioperl-l] Small changes to some Annotation methods? In-Reply-To: <400D7153.10801@ornl.gov> References: <400D7153.10801@ornl.gov> Message-ID: That's a good things to fix. You can also combine that into a single line return @{$self->{'_names'} || []}; and/or we should make sure there is a $self->{'_names'} = []; in the initializer. Although empty array is slightly different from the undef you are sending. Depends on whether or not we want ot guarantee an array is sent back. -jason On Tue, 20 Jan 2004, Stefan Kirov wrote: > Can we change the accessor methods, for example: > sub each_gene_name{ > my ($self,@args) = @_; > > return @{$self->{'_names'}}; > } > > to > sub each_gene_name{ > my ($self,@args) = @_; > return undef unless ($self->{'_names'}); > return @{$self->{'_names'}}; > } > The current implementation will break the code if return > @{$self->{'_names'}} is empty. > Jason, Heikki- I am asking just in case I am missing something.... > > Stefan > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From skirov at utk.edu Tue Jan 20 17:05:50 2004 From: skirov at utk.edu (Stefan Kirov) Date: Tue Jan 20 17:12:33 2004 Subject: [Bioperl-l] Small changes to some Annotation methods? In-Reply-To: References: <400D7153.10801@ornl.gov> Message-ID: <400DA63E.7060708@utk.edu> Jason, thanks for the reply. But these are deprecated methods (as I noticed after I sent the message), so I don't know if it is really worth fixing the code. And yes, I think also empty array is better, that is what Annotation::Collection is doing. Stefan Jason Stajich wrote: >That's a good things to fix. You can also combine that into a single line > return @{$self->{'_names'} || []}; >and/or we should make sure >there is a >$self->{'_names'} = []; >in the initializer. > >Although empty array is slightly different from the undef you are sending. >Depends on whether or not we want ot guarantee an array is sent back. > >-jason >On Tue, 20 Jan 2004, Stefan Kirov wrote: > > > >>Can we change the accessor methods, for example: >>sub each_gene_name{ >> my ($self,@args) = @_; >> >> return @{$self->{'_names'}}; >>} >> >>to >>sub each_gene_name{ >> my ($self,@args) = @_; >> return undef unless ($self->{'_names'}); >> return @{$self->{'_names'}}; >>} >>The current implementation will break the code if return >>@{$self->{'_names'}} is empty. >>Jason, Heikki- I am asking just in case I am missing something.... >> >>Stefan >> >>_______________________________________________ >>Bioperl-l mailing list >>Bioperl-l@portal.open-bio.org >>http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> >> > >-- >Jason Stajich >Duke University >jason at cgt.mc.duke.edu >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Stefan Kirov, Ph.D. University of Tennessee/Oak Ridge National Laboratory 1060 Commerce Park, Oak Ridge TN 37830-8026 USA tel +865 576 5120 fax +865 241 1965 e-mail: skirov@utk.edu sao@ornl.gov From heikki at nildram.co.uk Tue Jan 20 18:25:34 2004 From: heikki at nildram.co.uk (Heikki Lehvaslaiho) Date: Tue Jan 20 18:32:17 2004 Subject: maxstrengthmail confirmation [Re: [Bioperl-l] get cds from genbank record] In-Reply-To: <20040120201145.GC4195@hgt.mcb.uconn.edu> References: <4006F978.1040902@research.dfci.harvard.edu> <200401162012.01215.heikki@nildram.co.uk> <20040120201145.GC4195@hgt.mcb.uconn.edu> Message-ID: <200401202325.34812.heikki@nildram.co.uk> Andreas, Pedro and others, Here is what Chris had to say: """""""""""""""""""""""""""""""""""""""""" This appears to be real. There are a number of corporate email systems now that are closed to all inbound email and only allow mail through if it comes from a 'whitelist' of OK senders. The first time you email any of the people using theses systems you get back an email that is sort of a turing test 'click here if you are human and really want your message to be read'. You then get added to the corporate whitelist. Most systems handle mailing lists well, maxstrengh does not. ... Anyway, its real. Feel free to click on it if you want and you should not see that message again. """""""""""""""""""""""""""""""""""""""""" Please keep reporting these annoyances. If they get too common, we'll have to unsubscribe any members who use such systems. -Heikki On Tuesday 20 Jan 2004 20:11, Andreas Bernauer wrote: > Hi Heikki! > > Heikki Lehvaslaiho wrote: > > The other problem you had: > > > > On Friday 16 Jan 2004 15:39, Pedro Antonio Reche wrote: > > > One more thing, following my first post I got an email from from > > > quarantine@maxstrengthmail.com on behalf of the bioperl mailing list > > > saying that my e-mail was in quarantine, and asking me press a link to > > > get the message deliver. > > > > I 've pointed to our server maintainer, Chris, your problem, but I > > suspect those warnings about potential spam in your mails do not come > > from bioperl servers or the way they are set up. > > I've got a similar email as Pedro when I sent an email to the > Bioperl-List and was also directed to a website where I should confirm > that I want to set the email. For me it looked it came from one of > the bioperl mailing list servers. > > Andreas. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From hlapp at gmx.net Wed Jan 21 00:38:09 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed Jan 21 00:44:48 2004 Subject: [Bioperl-l] Small changes to some Annotation methods? In-Reply-To: <400D7153.10801@ornl.gov> Message-ID: The array property should be initialized to an empty array upon object construction. Returning undef from an array accessor is not good, you may break people's code. Which object are you talking about? Does the respective class not initialize the property to be an empty array? -hilmar On Tuesday, January 20, 2004, at 10:20 AM, Stefan Kirov wrote: > Can we change the accessor methods, for example: > sub each_gene_name{ > my ($self,@args) = @_; > > return @{$self->{'_names'}}; > } > to > sub each_gene_name{ > my ($self,@args) = @_; > return undef unless ($self->{'_names'}); > return @{$self->{'_names'}}; > } > The current implementation will break the code if return > @{$self->{'_names'}} is empty. > Jason, Heikki- I am asking just in case I am missing something.... > > Stefan > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From godHinman at MetalMail.com Wed Jan 21 01:05:13 2004 From: godHinman at MetalMail.com (Bioperl-pipeline) Date: Wed Jan 21 01:05:14 2004 Subject: [Bioperl-l] enablers Info regarding vigra Message-ID: blacks, How Vigras works. And you can better understand, what Vigras can do for you. If you are sensible about your health, reflect on what you can do for your seual health, to keep the chances that you will need Vigras as low as possible. commodity priory Winthrop, Frankie. http://www.kimsolutions.com/index.php?pid=pharmaboss Inrease Seks Drive Bost Seual Performance Fuller & Harder Erecions Inrease Stamna & Endurance Quicker Rechages confine misspelled fatherly, Norris. reorders ranching enamel, chiefs. Happy holidays, Judas From lstein at cshl.edu Wed Jan 21 01:51:21 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Wed Jan 21 01:58:18 2004 Subject: [Bioperl-l] Small changes to some Annotation methods? In-Reply-To: References: Message-ID: <200401210851.21387.lstein@cshl.edu> Hi, You should do this: return unless $self->{'_names'}; rather than return undef unless $self->{'_names'}; if you explicitly return undef, then someone who calls the method in a list context: my @genes = $foo->each_gene_name; Will end up with a one-element array in which the element is the value undef. Lincoln On Wednesday 21 January 2004 07:38 am, Hilmar Lapp wrote: > The array property should be initialized to an empty array upon > object construction. Returning undef from an array accessor is not > good, you may break people's code. > > Which object are you talking about? Does the respective class not > initialize the property to be an empty array? > > -hilmar > > On Tuesday, January 20, 2004, at 10:20 AM, Stefan Kirov wrote: > > Can we change the accessor methods, for example: > > sub each_gene_name{ > > my ($self,@args) = @_; > > > > return @{$self->{'_names'}}; > > } > > to > > sub each_gene_name{ > > my ($self,@args) = @_; > > return undef unless ($self->{'_names'}); > > return @{$self->{'_names'}}; > > } > > The current implementation will break the code if return > > @{$self->{'_names'}} is empty. > > Jason, Heikki- I am asking just in case I am missing > > something.... > > > > Stefan > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From info at e-bookservices.com Wed Jan 21 02:11:01 2004 From: info at e-bookservices.com (Dhiraj Aggarwal) Date: Wed Jan 21 02:17:35 2004 Subject: [Bioperl-l] Document Migration & e-Books Development Services Message-ID: <200401210717.i0L7HMEs021944@portal.open-bio.org> Hi, We came across your contact information while browsing through the web for book / journal / technical / medical publishers. We are an organization based in New Delhi, India specializing in preparing digital content for electronic publishing and the web (http://www.e-BookServices.com). We convert information from paper and all document formats (including cross- platform), creating PDFs, SGML, HTML, XML, Microsoft Reader and most other structured formats, for electronic publishing, technical documentation, e-Commerce and online information services. 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Sincerely, Dhiraj Aggarwal CEO Mobile : +91 98100 50809 Email : info@e-BookServices.com Website : http://www.e-BookServices.com From Par.Engstrom at cgb.ki.se Wed Jan 21 06:10:51 2004 From: Par.Engstrom at cgb.ki.se (=?ISO-8859-1?Q?P=E4r_Engstr=F6m?=) Date: Wed Jan 21 06:17:27 2004 Subject: [Bioperl-l] Bio::Ontology support for several indentifiers per term Message-ID: <1074683451.2232.24.camel@lorien.cgb.ki.se> Hi BioPerl developers, In the Gene Ontology, some terms have multiple identifiers. E.g. "ATPase activity" has identifiers GO:0016887 and GO:0004002. However, it seems that the Bio::Ontology modules only support one identifier per term. Consider the following script (using bioperl 1.4): use Bio::OntologyIO; my $go_in = Bio::OntologyIO->new ( -format => "go", -defs_file => "GO.defs", -files => ["component.ontology", "function.ontology", "process.ontology" ]); my $gene_ontology = $go_in->next_ontology(); print scalar($gene_ontology->find_terms("GO:0004002")), " "; print scalar($gene_ontology->find_terms("GO:0016887")), "\n"; The output is "0 1", i.e. the term can only be found from one of its identifiers. If this is a known issue in Bio::Ontology, is there some way to retrieve terms by their "secondary" identifiers? Regards, Par Engstrom Graduate student, CGB, Karolinska From Nathan.Agrin at umassmed.edu Wed Jan 21 13:33:15 2004 From: Nathan.Agrin at umassmed.edu (Agrin, Nathan) Date: Wed Jan 21 18:42:48 2004 Subject: [Bioperl-l] Bioperl and Entrez Gene Database Message-ID: <89AA811FD79DC94788093B23DA79E71F832889@edunivmail02.ad.umassmed.edu> Entrez has a database that is called gene. You input an accession number and it gives you the chromosome location and chromosome number. Is there anyway someone can use bioperl to submit a long list of accession numbers and then save the output of each as say a normal text file? Thanks, Nate From nathanhaigh at ukonline.co.uk Wed Jan 21 07:09:50 2004 From: nathanhaigh at ukonline.co.uk (Nathan Haigh) Date: Wed Jan 21 18:43:32 2004 Subject: [Bioperl-l] seting the location of tempdir Message-ID: Hi, I was wondering if there is a way to set the tempdir for bioperl? I am writing some scripts involving clustalw.pm and other modules, and I was wondering if there is a way to set the tempdir for bioperl, so that it is used for creating temp dirs and files. Thanks Nathan -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/x-pkcs7-signature Size: 3095 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040121/821d21da/smime.bin From hlapp at gnf.org Wed Jan 21 20:07:17 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Wed Jan 21 20:13:55 2004 Subject: [Bioperl-l] Bio::Ontology support for several indentifiers per term In-Reply-To: <1074683451.2232.24.camel@lorien.cgb.ki.se> Message-ID: <528E7BD6-4C77-11D8-8F12-000A959EB4C4@gnf.org> The GO term itself really has only one identifier (check out the GO.defs file). GO terms acquire secondary accessions when they are merged with other, subsequently obsoleted terms. There should be a document somewhere at geneontology.org that explains in detail what will happen to the identifiers upon merging or obsoleting terms. You can get the secondary identifiers using $term->get_secondary_ids(). The existing ontology engine implementations do not index by secondary ids. -hilmar On Wednesday, January 21, 2004, at 03:10 AM, P?r Engstr?m wrote: > Hi BioPerl developers, > > In the Gene Ontology, some terms have multiple identifiers. E.g. > "ATPase > activity" has identifiers GO:0016887 and GO:0004002. However, it seems > that the Bio::Ontology modules only support one identifier per term. > > Consider the following script (using bioperl 1.4): > > use Bio::OntologyIO; > my $go_in = Bio::OntologyIO->new > ( -format => "go", > -defs_file => "GO.defs", > -files => ["component.ontology", > "function.ontology", > "process.ontology" ]); > my $gene_ontology = $go_in->next_ontology(); > print scalar($gene_ontology->find_terms("GO:0004002")), " "; > print scalar($gene_ontology->find_terms("GO:0016887")), "\n"; > > The output is "0 1", i.e. the term can only be found from one of its > identifiers. > > If this is a known issue in Bio::Ontology, is there some way to > retrieve > terms by their "secondary" identifiers? > > Regards, > > Par Engstrom > Graduate student, CGB, Karolinska > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From jason at cgt.duhs.duke.edu Wed Jan 21 20:44:23 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Jan 21 20:50:59 2004 Subject: [Bioperl-l] seting the location of tempdir In-Reply-To: References: Message-ID: $ENV{TEMPDIR} or ENV{TMPDIR} (TEMPDIR is preferred env variable) See Bio::Root::IO where all the tempdir/tempfile code is located. -jason On Wed, 21 Jan 2004, Nathan Haigh wrote: > Hi, > I was wondering if there is a way to set the tempdir for bioperl? > I am writing some scripts involving clustalw.pm and other modules, and I > was wondering if there is a way to set the tempdir for bioperl, so that it > is used for creating temp dirs and files. > > Thanks > Nathan > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From alWoodwards at wongfaye.com Thu Jan 22 14:18:40 2004 From: alWoodwards at wongfaye.com (Media) Date: Thu Jan 22 08:25:13 2004 Subject: [Bioperl-l] nesws regarding vigros volley Message-ID: annuls, How Vigras works. And you can better understand, what Vigras can do for you. If you are sensible about your health, reflect on what you can do for your seual health, to keep the chances that you will need Vigras as low as possible. stirrings nagging cycled, Metrecal. http://www.drlaurent.com/index.php?pid=genviag Inrease Seks Drive Bost Seual Performance Fuller & Harder Erecions Inrease Stamna & Endurance Quicker Rechages bonnet seceding pinnings, eightfold. exerting prompted cackling, Bambi. Happy holidays, banjos From dag at sonsorol.org Thu Jan 22 08:37:44 2004 From: dag at sonsorol.org (Chris Dagdigian) Date: Thu Jan 22 08:47:53 2004 Subject: [Bioperl-l] recent spams to bioperl-l Message-ID: <400FD228.7040800@sonsorol.org> Hi folks, Just wanted to apologize for the rise in spam going to bioperl-l. Our anti-spam filtering tools on the open-bio.org mailserver generally do a great job weeding out the dozens of messages per day sent to bioperl-l that are obvious spam, but recently there has been a huge rise in plaintext ASCII spam or the hash-busting spam that is nothing but nonsense. Spamassassin+MimeDefang and our Mailman spam filters can't easily discern the plaintext spam from regular email messages sent to the list. bioperl-l allows non-members to post to the list; this was the consensus behavior that bioperl members wanted the last time we took a poll. Let me know if opinions have changed. If we make the list members-only for posting we can significantly cut down on spam. The downside to this is that we (a) make more work for the list moderators and (b) we become 'less open'. -Chris -- Chris Dagdigian, Independent life science IT & informatics consulting Office: 617-666-6454, Mobile: 617-877-5498, Fax: 425-699-0193 PGP KeyID: 83D4310E Yahoo IM: craffi Web: http://bioteam.net From khoueiry at ibsm.cnrs-mrs.fr Thu Jan 22 08:53:00 2004 From: khoueiry at ibsm.cnrs-mrs.fr (KHOUEIRY pierre) Date: Thu Jan 22 08:59:34 2004 Subject: [Bioperl-l] need help Message-ID: <400FD5BC.90405@ibsm.cnrs-mrs.fr> Hi everyone; I wrote a script using bioperl methodes. In fact my problem isn't in bioperl modules. I find problems on submitting my html form. When the user browse a file, i can't open it. I used a post methode

. ... in my perl script i collect forms fields. but i can't open user's file. Anyhelp will be appreciated From amackey at pcbi.upenn.edu Thu Jan 22 10:24:16 2004 From: amackey at pcbi.upenn.edu (Aaron J. Mackey) Date: Thu Jan 22 10:30:51 2004 Subject: [Bioperl-l] recent spams to bioperl-l In-Reply-To: <400FD228.7040800@sonsorol.org> References: <400FD228.7040800@sonsorol.org> Message-ID: <0AD471CF-4CEF-11D8-89DF-000A958C5008@pcbi.upenn.edu> My 2 cents: the spam level has increased noticeably, but going from 0 to some is always noticeable. I don't think it's so bad (yet) as to require moving to a closed system. We could also do what a few other mailing lists have tried, requiring emails to contain some valid keyword(s), e.g. "BioPerl" or just "Perl" or "Bio", bouncing back the few valid posts that don't match the keyword with a friendly "please click here to approve your post" or "please include the magic keyword in your posts". And thanks again, Chris, for all your work keeping us up and running smoothly. -Aaron On Jan 22, 2004, at 7:37 AM, Chris Dagdigian wrote: > > Hi folks, > > Just wanted to apologize for the rise in spam going to bioperl-l. Our > anti-spam filtering tools on the open-bio.org mailserver generally do > a great job weeding out the dozens of messages per day sent to > bioperl-l that are obvious spam, but recently there has been a huge > rise in plaintext ASCII spam or the hash-busting spam that is nothing > but nonsense. > > Spamassassin+MimeDefang and our Mailman spam filters can't easily > discern the plaintext spam from regular email messages sent to the > list. > > bioperl-l allows non-members to post to the list; this was the > consensus behavior that bioperl members wanted the last time we took a > poll. > > Let me know if opinions have changed. If we make the list members-only > for posting we can significantly cut down on spam. The downside to > this is that we (a) make more work for the list moderators and (b) we > become 'less open'. > > -Chris > > -- > Chris Dagdigian, > Independent life science IT & informatics consulting > Office: 617-666-6454, Mobile: 617-877-5498, Fax: 425-699-0193 > PGP KeyID: 83D4310E Yahoo IM: craffi Web: http://bioteam.net > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From gert.thijs at esat.kuleuven.ac.be Thu Jan 22 10:49:17 2004 From: gert.thijs at esat.kuleuven.ac.be (Gert Thijs) Date: Thu Jan 22 10:55:51 2004 Subject: [Bioperl-l] need help In-Reply-To: <400FD5BC.90405@ibsm.cnrs-mrs.fr> References: <400FD5BC.90405@ibsm.cnrs-mrs.fr> Message-ID: <1074786556.3131.405.camel@sista-08.esat.kuleuven.ac.be> Pierre, You should make sure that you read the input from the file handle and not the file name. when reading the file parameter as my $seqFile = $query->param('seqfile'); $seqFile is a handle to the file stream. So you can do things like while ( <$seqFile> ){ # do something with string } but you cannot use 'open' to open the file for reading, since it is already open. I guess you can also do something like my $seqio = new Bio::SeqIO( -fh => \$seq ); although I am not sure this will work. Gert Gert On Thu, 2004-01-22 at 14:53, KHOUEIRY pierre wrote: > Hi everyone; > I wrote a script using bioperl methodes. In fact my problem isn't in > bioperl modules. I find problems on submitting my html form. When the > user browse a file, i can't open it. I used a post methode > target="_blank">. > > ... > > in my perl script i collect forms fields. but i can't open user's file. > Anyhelp will be appreciated > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- + Gert Thijs + Postdoctoral Researcher + K.U.Leuven + ESAT-SCD + Kasteelpark Arenberg 10 + B-3001 Leuven-Heverlee + Belgium + + Tel : +32 16 327928 + Fax : +32 16 321970 + email: gert.thijs@esat.kuleuven.ac.be + + http://www.esat.kuleuven.ac.be/~thijs + http://www.esat.kuleuven.ac.be/~dna/BioI/ + From donald.jackson at bms.com Thu Jan 22 11:05:52 2004 From: donald.jackson at bms.com (Donald G. Jackson) Date: Thu Jan 22 11:14:09 2004 Subject: [Bioperl-l] need help In-Reply-To: <1074786556.3131.405.camel@sista-08.esat.kuleuven.ac.be> References: <400FD5BC.90405@ibsm.cnrs-mrs.fr> <1074786556.3131.405.camel@sista-08.esat.kuleuven.ac.be> Message-ID: <400FF4E0.9090107@bms.com> With newer versions of CGI.pm, I found the $query->upload('seqfile') method to be a more reliable way of getting the handle to an uploaded file. Don Jackson Gert Thijs wrote: >Pierre, > >You should make sure that you read the input from the file handle and >not the file name. >when reading the file parameter as > my $seqFile = $query->param('seqfile'); > >$seqFile is a handle to the file stream. So you can do things like > while ( <$seqFile> ){ > # do something with string > } >but you cannot use 'open' to open the file for reading, since it is >already open. > >I guess you can also do something like > my $seqio = new Bio::SeqIO( -fh => \$seq ); >although I am not sure this will work. > > >Gert > > > >Gert > > >On Thu, 2004-01-22 at 14:53, KHOUEIRY pierre wrote: > > >>Hi everyone; >>I wrote a script using bioperl methodes. In fact my problem isn't in >>bioperl modules. I find problems on submitting my html form. When the >>user browse a file, i can't open it. I used a post methode >>>target="_blank">. >> >>... >> >>in my perl script i collect forms fields. but i can't open user's file. >>Anyhelp will be appreciated >> >> >>_______________________________________________ >>Bioperl-l mailing list >>Bioperl-l@portal.open-bio.org >>http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> From ee at uncanny.net Thu Jan 22 13:31:16 2004 From: ee at uncanny.net (Edward Elhauge) Date: Thu Jan 22 13:37:51 2004 Subject: [Bioperl-l] recent spams to bioperl-l In-Reply-To: <400FD228.7040800@sonsorol.org>; from dag@sonsorol.org on Thu, Jan 22, 2004 at 08:37:44AM -0500 References: <400FD228.7040800@sonsorol.org> Message-ID: <20040122103116.B42098@uncanny.net> Hi Chris, Here is my two cents. Make the list closed for posting. Make the list archive open to anyone. I run several Mailman based groups myself and I know that Spam has me at wits end. Right now I never look at the non-member postings. I changed Mailman to default the form to Discard for non-member posting and never look at them. I just discard all of those and then see what is left. If you leave the archive open google will still index the list and people can learn without signing up. Cheers, Edward Elhauge * Chris Dagdigian wrote on [2004-01-22 05:43]: > > Hi folks, > > Just wanted to apologize for the rise in spam going to bioperl-l. Our > anti-spam filtering tools on the open-bio.org mailserver generally do a > great job weeding out the dozens of messages per day sent to bioperl-l > that are obvious spam, but recently there has been a huge rise in > plaintext ASCII spam or the hash-busting spam that is nothing but nonsense. > > Spamassassin+MimeDefang and our Mailman spam filters can't easily > discern the plaintext spam from regular email messages sent to the list. > > bioperl-l allows non-members to post to the list; this was the consensus > behavior that bioperl members wanted the last time we took a poll. > > Let me know if opinions have changed. If we make the list members-only > for posting we can significantly cut down on spam. The downside to this > is that we (a) make more work for the list moderators and (b) we become > 'less open'. > > -Chris > > -- > Chris Dagdigian, > Independent life science IT & informatics consulting > Office: 617-666-6454, Mobile: 617-877-5498, Fax: 425-699-0193 > PGP KeyID: 83D4310E Yahoo IM: craffi Web: http://bioteam.net > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l ---end quoted text--- -- Edward Elhauge -- Uncanny, San Francisco "The gods confound the man who first found out how to distinguish hours. Confound him, too, who in this place set up a sundial, To cut and hack my days so wretchedly into small portions!" -- Titus Maccius Plautus (254 - 184 BCE) From Nathan.Agrin at umassmed.edu Thu Jan 22 12:47:26 2004 From: Nathan.Agrin at umassmed.edu (Agrin, Nathan) Date: Thu Jan 22 14:08:01 2004 Subject: [Bioperl-l] Alignment Blast parser Message-ID: <89AA811FD79DC94788093B23DA79E71FD9A392@edunivmail02.ad.umassmed.edu> I need a way to retain the EXACT alignment found in a blast file. Ex- Query: 1 MAGRGK-GKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLT 59 M+GRGK G + KA SRS++AGLQFPVGR+ R L+KG YAER+GAGAPVYLAAVLEYLT Sbjct: 1 MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT 60 Query: 60 AEVLELAGNAARDNKKNRIVPRHIQLAIRNDEELGKLLGEVTIASGGVLPNIHAVLLP 117 AE+LELAGNAARDNKK RI+PRH+QLAIRNDEEL KLLG VTIA GGVLPNI AVLLP Sbjct: 61 AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLP 118 I have tried everything to no avail. AlignIO almost works out, but instead of doing a typical blast alignment, the best it can do is a clustalw like alignment. Any help is much appreciated. -Nate Nathan Agrin Research Associate UMass Medical Center 55 Lake Ave. N. Worcester MA, 01655 (508)-856-6018 nathan.agrin@umassmed.edu From jason at cgt.duhs.duke.edu Thu Jan 22 14:14:14 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Thu Jan 22 14:20:48 2004 Subject: [Bioperl-l] Alignment Blast parser In-Reply-To: <89AA811FD79DC94788093B23DA79E71FD9A392@edunivmail02.ad.umassmed.edu> References: <89AA811FD79DC94788093B23DA79E71FD9A392@edunivmail02.ad.umassmed.edu> Message-ID: You want to retain it meaning what? Bio::SearchIO(-format => 'blast') parses blast for you. -jason On Thu, 22 Jan 2004, Agrin, Nathan wrote: > I need a way to retain the EXACT alignment found in a blast file. > Ex- > > > Query: 1 MAGRGK-GKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLT > 59 > M+GRGK G + KA SRS++AGLQFPVGR+ R L+KG YAER+GAGAPVYLAAVLEYLT > Sbjct: 1 MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT > 60 > > > Query: 60 AEVLELAGNAARDNKKNRIVPRHIQLAIRNDEELGKLLGEVTIASGGVLPNIHAVLLP > 117 > AE+LELAGNAARDNKK RI+PRH+QLAIRNDEEL KLLG VTIA GGVLPNI AVLLP > Sbjct: 61 AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLP > 118 > > I have tried everything to no avail. AlignIO almost works out, but > instead of doing a typical blast alignment, the best it can do is a > clustalw like alignment. > > Any help is much appreciated. > > -Nate > > Nathan Agrin > Research Associate > UMass Medical Center > 55 Lake Ave. N. > Worcester MA, 01655 > (508)-856-6018 > nathan.agrin@umassmed.edu > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From brian_osborne at cognia.com Thu Jan 22 14:23:57 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Thu Jan 22 14:31:34 2004 Subject: [Bioperl-l] Alignment Blast parser In-Reply-To: Message-ID: Jason, I think he wants to print out the exact same alignment as you see in the BLAST report, which you can't do using AlignIO. Nathan, do you mean "exactly", with that "Query: 2" and "Subject: 2" business as well? Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Jason Stajich Sent: Thursday, January 22, 2004 2:14 PM To: Agrin, Nathan Cc: bioperl-l@portal.open-bio.org Subject: Re: [Bioperl-l] Alignment Blast parser You want to retain it meaning what? Bio::SearchIO(-format => 'blast') parses blast for you. -jason On Thu, 22 Jan 2004, Agrin, Nathan wrote: > I need a way to retain the EXACT alignment found in a blast file. > Ex- > > > Query: 1 MAGRGK-GKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLT > 59 > M+GRGK G + KA SRS++AGLQFPVGR+ R L+KG YAER+GAGAPVYLAAVLEYLT > Sbjct: 1 MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT > 60 > > > Query: 60 AEVLELAGNAARDNKKNRIVPRHIQLAIRNDEELGKLLGEVTIASGGVLPNIHAVLLP > 117 > AE+LELAGNAARDNKK RI+PRH+QLAIRNDEEL KLLG VTIA GGVLPNI AVLLP > Sbjct: 61 AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLP > 118 > > I have tried everything to no avail. AlignIO almost works out, but > instead of doing a typical blast alignment, the best it can do is a > clustalw like alignment. > > Any help is much appreciated. > > -Nate > > Nathan Agrin > Research Associate > UMass Medical Center > 55 Lake Ave. N. > Worcester MA, 01655 > (508)-856-6018 > nathan.agrin@umassmed.edu > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From Nathan.Agrin at umassmed.edu Thu Jan 22 14:26:04 2004 From: Nathan.Agrin at umassmed.edu (Agrin, Nathan) Date: Thu Jan 22 14:32:13 2004 Subject: [Bioperl-l] Alignment Blast parser Message-ID: <89AA811FD79DC94788093B23DA79E71FD9A39F@edunivmail02.ad.umassmed.edu> Yes exactly -Nate -----Original Message----- From: Brian Osborne [mailto:brian_osborne@cognia.com] Sent: Thursday, January 22, 2004 2:24 PM To: Jason Stajich; Agrin, Nathan Cc: bioperl-l@bioperl.org Subject: RE: [Bioperl-l] Alignment Blast parser Jason, I think he wants to print out the exact same alignment as you see in the BLAST report, which you can't do using AlignIO. Nathan, do you mean "exactly", with that "Query: 2" and "Subject: 2" business as well? Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Jason Stajich Sent: Thursday, January 22, 2004 2:14 PM To: Agrin, Nathan Cc: bioperl-l@portal.open-bio.org Subject: Re: [Bioperl-l] Alignment Blast parser You want to retain it meaning what? Bio::SearchIO(-format => 'blast') parses blast for you. -jason On Thu, 22 Jan 2004, Agrin, Nathan wrote: > I need a way to retain the EXACT alignment found in a blast file. > Ex- > > > Query: 1 MAGRGK-GKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLT > 59 > M+GRGK G + KA SRS++AGLQFPVGR+ R L+KG YAER+GAGAPVYLAAVLEYLT > Sbjct: 1 MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT > 60 > > > Query: 60 AEVLELAGNAARDNKKNRIVPRHIQLAIRNDEELGKLLGEVTIASGGVLPNIHAVLLP > 117 > AE+LELAGNAARDNKK RI+PRH+QLAIRNDEEL KLLG VTIA GGVLPNI AVLLP > Sbjct: 61 AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLP > 118 > > I have tried everything to no avail. AlignIO almost works out, but > instead of doing a typical blast alignment, the best it can do is a > clustalw like alignment. > > Any help is much appreciated. > > -Nate > > Nathan Agrin > Research Associate > UMass Medical Center > 55 Lake Ave. N. > Worcester MA, 01655 > (508)-856-6018 > nathan.agrin@umassmed.edu > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From jason at cgt.duhs.duke.edu Thu Jan 22 14:33:10 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Thu Jan 22 14:39:47 2004 Subject: [Bioperl-l] Alignment Blast parser In-Reply-To: <89AA811FD79DC94788093B23DA79E71FD9A39F@edunivmail02.ad.umassmed.edu> References: <89AA811FD79DC94788093B23DA79E71FD9A39F@edunivmail02.ad.umassmed.edu> Message-ID: The code to do it is in Bio::SearchIO::Writer::TextResultWriter but that recapitulates a whole report from a SearchIO object not just the HSP alignment part, you'll have to dig out the code which does the HSP printing or post process the returned string to clip out just the part you want. -jason On Thu, 22 Jan 2004, Agrin, Nathan wrote: > Yes exactly > > -Nate > > -----Original Message----- > From: Brian Osborne [mailto:brian_osborne@cognia.com] > Sent: Thursday, January 22, 2004 2:24 PM > To: Jason Stajich; Agrin, Nathan > Cc: bioperl-l@bioperl.org > Subject: RE: [Bioperl-l] Alignment Blast parser > > Jason, > > I think he wants to print out the exact same alignment as you see in the > BLAST report, which you can't do using AlignIO. > > Nathan, do you mean "exactly", with that "Query: 2" and "Subject: 2" > business as well? > > Brian O. > > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org > [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Jason Stajich > Sent: Thursday, January 22, 2004 2:14 PM > To: Agrin, Nathan > Cc: bioperl-l@portal.open-bio.org > Subject: Re: [Bioperl-l] Alignment Blast parser > > You want to retain it meaning what? > Bio::SearchIO(-format => 'blast') > parses blast for you. > > -jason > On Thu, 22 Jan 2004, Agrin, Nathan wrote: > > > I need a way to retain the EXACT alignment found in a blast file. > > Ex- > > > > > > Query: 1 > MAGRGK-GKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLT > > 59 > > M+GRGK G + KA SRS++AGLQFPVGR+ R L+KG > YAER+GAGAPVYLAAVLEYLT > > Sbjct: 1 > MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT > > 60 > > > > > > Query: 60 AEVLELAGNAARDNKKNRIVPRHIQLAIRNDEELGKLLGEVTIASGGVLPNIHAVLLP > > 117 > > AE+LELAGNAARDNKK RI+PRH+QLAIRNDEEL KLLG VTIA GGVLPNI AVLLP > > Sbjct: 61 AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLP > > 118 > > > > I have tried everything to no avail. AlignIO almost works out, but > > instead of doing a typical blast alignment, the best it can do is a > > clustalw like alignment. > > > > Any help is much appreciated. > > > > -Nate > > > > Nathan Agrin > > Research Associate > > UMass Medical Center > > 55 Lake Ave. N. > > Worcester MA, 01655 > > (508)-856-6018 > > nathan.agrin@umassmed.edu > > > > > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From jason at cgt.duhs.duke.edu Thu Jan 22 14:50:28 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Thu Jan 22 14:57:02 2004 Subject: [Bioperl-l] Alignment Blast parser In-Reply-To: <89AA811FD79DC94788093B23DA79E71FD9A3A2@edunivmail02.ad.umassmed.edu> References: <89AA811FD79DC94788093B23DA79E71FD9A3A2@edunivmail02.ad.umassmed.edu> Message-ID: Every blast report is a result whether or not there are any hits found. To test if you got any hits: if ( $result->num_hits > 0 ) { } On Thu, 22 Jan 2004, Agrin, Nathan wrote: > Another quick question. > > I have about 600 blast files that I need to parse. Some of them > produced a file with no homology. > > IE: > No significant similarity found. For reasons why, click here. > > Is there a way to test the data stream for these? I've been messing > with the $result = $in->next_result, but even on data files that have no > homologies, perl seems to think there is still a result. (I can't just > say something like; if($result){do this}). > > Nathan Agrin > Research Associate > UMass Medical Center > 55 Lake Ave. N. > Worcester MA, 01655 > (508)-856-6018 > nathan.agrin@umassmed.edu > > > -----Original Message----- > From: Jason Stajich [mailto:jason@cgt.duhs.duke.edu] > Sent: Thursday, January 22, 2004 2:33 PM > To: Agrin, Nathan > Cc: Brian Osborne; > Subject: RE: [Bioperl-l] Alignment Blast parser > > The code to do it is in Bio::SearchIO::Writer::TextResultWriter > but that recapitulates a whole report from a SearchIO object not just > the > HSP alignment part, you'll have to dig out the code which does > the HSP printing or post process the returned string to clip out just > the > part you want. > > -jason > > > On Thu, 22 Jan 2004, Agrin, Nathan wrote: > > > Yes exactly > > > > -Nate > > > > -----Original Message----- > > From: Brian Osborne [mailto:brian_osborne@cognia.com] > > Sent: Thursday, January 22, 2004 2:24 PM > > To: Jason Stajich; Agrin, Nathan > > Cc: bioperl-l@bioperl.org > > Subject: RE: [Bioperl-l] Alignment Blast parser > > > > Jason, > > > > I think he wants to print out the exact same alignment as you see in > the > > BLAST report, which you can't do using AlignIO. > > > > Nathan, do you mean "exactly", with that "Query: 2" and "Subject: 2" > > business as well? > > > > Brian O. > > > > -----Original Message----- > > From: bioperl-l-bounces@portal.open-bio.org > > [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Jason > Stajich > > Sent: Thursday, January 22, 2004 2:14 PM > > To: Agrin, Nathan > > Cc: bioperl-l@portal.open-bio.org > > Subject: Re: [Bioperl-l] Alignment Blast parser > > > > You want to retain it meaning what? > > Bio::SearchIO(-format => 'blast') > > parses blast for you. > > > > -jason > > On Thu, 22 Jan 2004, Agrin, Nathan wrote: > > > > > I need a way to retain the EXACT alignment found in a blast file. > > > Ex- > > > > > > > > > Query: 1 > > MAGRGK-GKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLT > > > 59 > > > M+GRGK G + KA SRS++AGLQFPVGR+ R L+KG > > YAER+GAGAPVYLAAVLEYLT > > > Sbjct: 1 > > MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT > > > 60 > > > > > > > > > Query: 60 > AEVLELAGNAARDNKKNRIVPRHIQLAIRNDEELGKLLGEVTIASGGVLPNIHAVLLP > > > 117 > > > AE+LELAGNAARDNKK RI+PRH+QLAIRNDEEL KLLG VTIA GGVLPNI > AVLLP > > > Sbjct: 61 > AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLP > > > 118 > > > > > > I have tried everything to no avail. AlignIO almost works out, but > > > instead of doing a typical blast alignment, the best it can do is a > > > clustalw like alignment. > > > > > > Any help is much appreciated. > > > > > > -Nate > > > > > > Nathan Agrin > > > Research Associate > > > UMass Medical Center > > > 55 Lake Ave. N. > > > Worcester MA, 01655 > > > (508)-856-6018 > > > nathan.agrin@umassmed.edu > > > > > > > > > > -- > > Jason Stajich > > Duke University > > jason at cgt.mc.duke.edu > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From jaudall at iastate.edu Thu Jan 22 15:55:43 2004 From: jaudall at iastate.edu (Joshua A Udall) Date: Thu Jan 22 16:02:19 2004 Subject: [Bioperl-l] EST functional categories Message-ID: <6.0.1.1.2.20040122143719.01e2d918@jaudall.mail.iastate.edu> I'm working on an EST project. I'd like to use bioperl to identify putative functional categories of individual ESTs and eventually end up with those ubiquitous pie charts or histograms (using excel). I've seen that ontologies structures have been built into bioperl but there isn't much documentation (or I've overlooked it). I could use some help/example scripts to get started. I've blasted all my ESTs against nr. How do I take the best blast hit and look it it's functional category on GO/Interpro? Joshua Udall Department of Ecology, Evolution, and Organismal Biology Iowa State University Ames, IA 50011 Ph: (515) 294-7098 Fax: (515) 294-1337 From driveallotropic at ilovechocolate.com Thu Jan 22 20:22:04 2004 From: driveallotropic at ilovechocolate.com (Barrett) Date: Thu Jan 22 17:27:42 2004 Subject: [Bioperl-l] they used to be the only ones. Message-ID: The first worth substitute of all existing men`s remedies! Be aware that now the peak of your selxual activity is realy accessible! All you need is to visit http://cnmeds.com/mx/index.php?pid=genviag Thanks to the proprietary blend of unique herkbs the four wonderful efkfects are achieved: *blood stream to the penlis is restored *stored tesltosterone is unleashed *activation of the body's naltural holrmone production heightens your sensation *the peknis does enklarge, the changes are being permanent! At last you can enljoy your secxual life in full measure without any risk for your healkth! Don`t wakste your time! Get more inkfo straightforwardly at http://cnmeds.com/mx/index.php?pid=genviag From hlapp at gnf.org Thu Jan 22 19:53:21 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Thu Jan 22 19:59:59 2004 Subject: [Bioperl-l] recent spams to bioperl-l In-Reply-To: <0AD471CF-4CEF-11D8-89DF-000A958C5008@pcbi.upenn.edu> Message-ID: <8A945B8A-4D3E-11D8-9EF4-000A959EB4C4@gnf.org> On Thursday, January 22, 2004, at 07:24 AM, Aaron J. Mackey wrote: > My 2 cents: the spam level has increased noticeably, but going from 0 > to some is always noticeable. I don't think it's so bad (yet) as to > require moving to a closed system. > I agree. -hilmar -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From whs at sanger.ac.uk Fri Jan 23 04:11:38 2004 From: whs at sanger.ac.uk (Will Spooner) Date: Fri Jan 23 04:18:29 2004 Subject: [Bioperl-l] Alignment Blast parser In-Reply-To: References: Message-ID: Hi Nathan, The following code creates a multi-line wu-blast-style alignment string from an HSP object. Is this what you are looking for? I would have liked to have found a method like this on the HSP object itself, but I'm not sure that this is where it strictly 'belongs'. I'd be happy to contribute the code if someone knows the best place to put it! All the best, Will sub alignment_string{ my $hsp = shift; my $query = $hsp->query; my $sbjct = $hsp->hit; # Space to reserve for the numbering at the line start my $seq_cols = 60; my( $num_length ) = sort{ $b<=>$a } ( $query->start, $query->end, $sbjct->start, $sbjct->end ); $num_length = length( $num_length ); # Templates for the lines my $qtmpl = "Query: %${num_length}d %s %d\n"; my $xtmpl = ( " " x ( $num_length + 8 ) ) . "%s\n"; my $htmpl = "Sbjct: %${num_length}d %s %d\n"; # Divide the alignment strings onto lines my $rows = ( ( length($hsp->query_string) - 1 ) / $seq_cols ) + 1; my @qlines = unpack( "a$seq_cols" x $rows, $hsp->query_string ); my @xlines = unpack( "a$seq_cols" x $rows, $hsp->homology_string ); my @hlines = unpack( "a$seq_cols" x $rows, $hsp->hit_string ); # Things needed for counting; DNA|peptide my $qmultiplier = ( ( $query->end - $query->start ) / ( $sbjct->end - $sbjct->start ) ); my $smultiplier; if( $qmultiplier < 0.5 ){ $qmultiplier = 1; $smultiplier=3 } elsif( $qmultiplier > 2 ){ $qmultiplier = 3; $smultiplier=1 } else { $qmultiplier = 1; $smultiplier=1 } # More counting things; strand my $qstrand = $query->strand < 0 ? -1 : 1; my $sstrand = $sbjct->strand < 0 ? -1 : 1; my( $qstart, $qryend ) = $query->strand < 0 ? ( $query->end, $query->start) : ( $query->start, $query->end ); my( $hstart, $sbjend ) = $sbjct->strand < 0 ? ( $sbjct->end, $sbjct->start ) : ( $sbjct->start, $sbjct->end ); # Generate text for each line-triplet my @lines; for( my $i=0; $i<@qlines; $i++ ){ my $qend = $qstart + ( ( $seq_cols * $qmultiplier - 1 ) * $qstrand ); my $hend = $hstart + ( ( $seq_cols * $smultiplier - 1 ) * $sstrand ); if( $i == @qlines - 1 ){ $qend = $qryend; $hend = $sbjend; } my $line = ''; $line .= sprintf( $qtmpl, $qstart, $qlines[$i], $qend ); $line .= sprintf( $xtmpl, $xlines[$i] ); $line .= sprintf( $htmpl, $hstart, $hlines[$i], $hend ); push @lines, $line; $qstart = $qend + ( 1 * $qstrand ); $hstart = $hend + ( 1 * $sstrand ); } return join( "\n", @lines ); } On Thu, 22 Jan 2004, Brian Osborne wrote: > Jason, > > I think he wants to print out the exact same alignment as you see in the > BLAST report, which you can't do using AlignIO. > > Nathan, do you mean "exactly", with that "Query: 2" and "Subject: 2" > business as well? > > Brian O. > > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org > [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Jason Stajich > Sent: Thursday, January 22, 2004 2:14 PM > To: Agrin, Nathan > Cc: bioperl-l@portal.open-bio.org > Subject: Re: [Bioperl-l] Alignment Blast parser > > You want to retain it meaning what? > Bio::SearchIO(-format => 'blast') > parses blast for you. > > -jason > On Thu, 22 Jan 2004, Agrin, Nathan wrote: > > > I need a way to retain the EXACT alignment found in a blast file. > > Ex- > > > > > > Query: 1 MAGRGK-GKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLT > > 59 > > M+GRGK G + KA SRS++AGLQFPVGR+ R L+KG YAER+GAGAPVYLAAVLEYLT > > Sbjct: 1 MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT > > 60 > > > > > > Query: 60 AEVLELAGNAARDNKKNRIVPRHIQLAIRNDEELGKLLGEVTIASGGVLPNIHAVLLP > > 117 > > AE+LELAGNAARDNKK RI+PRH+QLAIRNDEEL KLLG VTIA GGVLPNI AVLLP > > Sbjct: 61 AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLP > > 118 > > > > I have tried everything to no avail. AlignIO almost works out, but > > instead of doing a typical blast alignment, the best it can do is a > > clustalw like alignment. > > > > Any help is much appreciated. > > > > -Nate > > > > Nathan Agrin > > Research Associate > > UMass Medical Center > > 55 Lake Ave. N. > > Worcester MA, 01655 > > (508)-856-6018 > > nathan.agrin@umassmed.edu > > > > > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > --- Dr William Spooner whs@sanger.ac.uk Ensembl Web Developer http://www.ensembl.org From theunderwoods at clara.co.uk Fri Jan 23 04:41:35 2004 From: theunderwoods at clara.co.uk (Anthony Underwood) Date: Fri Jan 23 04:48:05 2004 Subject: [Bioperl-l] Sequence Assembly:phrap to gap Message-ID: Hi all, I have a slightly off-topic question. I am assembling sequences using the script phredPhrap which makes a .ace format assembly as well as a phrap.out format assembly. I am using BioPerl to extract a lot of the relevant information from the assembly however I would like to view the assembly by converting it to a gap4 database, and using stadens gap4 viewer. Does anybody know of a script (perl or otherwise) that can convert either the .ace or .out assembly to a gap4 database. Many thanks, Anthony Dr Anthony Underwood Bioinformatics Group Genomics, Proteomic and Bioinformatics Unit Central Public Health Laboratory Health Protection Agency 61 Colindale Avenue London NW9 5HT t: 0208 2004400 ext. 3618 e: anthony.underwood@hpa.org.uk From billthebrute at yahoo.fr Fri Jan 23 04:47:55 2004 From: billthebrute at yahoo.fr (=?iso-8859-1?q?william=20ritchie?=) Date: Fri Jan 23 04:54:27 2004 Subject: [Bioperl-l] RemoteBlast/Sim4 Message-ID: <20040123094755.43790.qmail@web25201.mail.ukl.yahoo.com> Please help!!! Two questions: -on RemoteBlast, I want to blast against EST only, but when I put -data=> 'gbEST' or anything else it still does regular blast -I want to use Sim4, is there a bioperl module (I know there are parsers but can I use the actual tool)!! Thanks _________________________________________________________________ Do You Yahoo!? -- Une adresse @yahoo.fr gratuite et en fran?ais ! Yahoo! Mail : http://fr.mail.yahoo.com From Marc.Logghe at devgen.com Fri Jan 23 05:18:41 2004 From: Marc.Logghe at devgen.com (Marc Logghe) Date: Fri Jan 23 05:25:41 2004 Subject: [Bioperl-l] RemoteBlast/Sim4 Message-ID: > -I want to use Sim4, is there a bioperl module (I know > there are parsers but can I use the actual tool)!! You can run sim4 with Bio::Tools::Run::Alignment::Sim4 but you also need a local copy of the application. You can find an RPM for redhat at the BioLinux site: http://www.biolinux.org/sim4.html. I did not find a sim4 module for Pise, so I guess sim4 is not available remotely with Pise. HTH, Marc From brian_osborne at cognia.com Fri Jan 23 07:26:22 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Fri Jan 23 07:33:14 2004 Subject: [Bioperl-l] Sequence Assembly:phrap to gap In-Reply-To: Message-ID: Anthony, It sounds like you want something like phrap2gap. There's a version of this available at the Sanger Centre but when I used this, some time ago, I had to substantially modify because it read from particular Sanger databases. Perhaps the phrap2gap's available now don't have these dependencies. http://www.google.com/url?sa=U&start=1&q=http://www.sanger.ac.uk/Software/se quencing/docs/phrap2gap/&e=7417 Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Anthony Underwood Sent: Friday, January 23, 2004 4:42 AM To: bioperl-l@bioperl.org Subject: [Bioperl-l] Sequence Assembly:phrap to gap Hi all, I have a slightly off-topic question. I am assembling sequences using the script phredPhrap which makes a .ace format assembly as well as a phrap.out format assembly. I am using BioPerl to extract a lot of the relevant information from the assembly however I would like to view the assembly by converting it to a gap4 database, and using stadens gap4 viewer. Does anybody know of a script (perl or otherwise) that can convert either the .ace or .out assembly to a gap4 database. Many thanks, Anthony Dr Anthony Underwood Bioinformatics Group Genomics, Proteomic and Bioinformatics Unit Central Public Health Laboratory Health Protection Agency 61 Colindale Avenue London NW9 5HT t: 0208 2004400 ext. 3618 e: anthony.underwood@hpa.org.uk _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From khoueiry at ibsm.cnrs-mrs.fr Fri Jan 23 07:27:05 2004 From: khoueiry at ibsm.cnrs-mrs.fr (KHOUEIRY pierre) Date: Fri Jan 23 07:33:31 2004 Subject: [Bioperl-l] hi Message-ID: <40111319.20109@ibsm.cnrs-mrs.fr> Hi all, After getting a filehandle from a form by my $file = $query->param('seqfile'); I need to pass this file to bio::seqio object to read every sequence apart and make a certain treatment. my $stream = Bio::SeqIO->new(-fh=> \$file, -format=>'fasta'); doesn't work and i can't figure the problem Any help ?? From Marc.Logghe at devgen.com Fri Jan 23 07:45:24 2004 From: Marc.Logghe at devgen.com (Marc Logghe) Date: Fri Jan 23 07:52:17 2004 Subject: [Bioperl-l] hi Message-ID: > -----Original Message----- > From: KHOUEIRY pierre [mailto:khoueiry@ibsm.cnrs-mrs.fr] > Sent: Friday, January 23, 2004 1:27 PM > To: bioperl-l@portal.open-bio.org > Subject: [Bioperl-l] hi > > > Hi all, > > After getting a filehandle from a form by my $file = > $query->param('seqfile'); I need to pass this file to > bio::seqio object > to read every sequence apart and make a certain treatment. > my $stream = Bio::SeqIO->new(-fh=> \$file, -format=>'fasta'); doesn't > work and i can't figure the problem have you tried "my $stream = Bio::SeqIO->new(-fh=> $file, -format=>'fasta')" ? According to the mail of Gert Thijs, the variable $file should contain a ref to a filehandle already. HTH, Marc From jason at cgt.duhs.duke.edu Fri Jan 23 08:20:35 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Fri Jan 23 08:27:19 2004 Subject: [Bioperl-l] Alignment Blast parser In-Reply-To: References: Message-ID: Currently the code to do this sort of thing is embedded in SearchIO::Writer::TextResultWriter but generates a whole report. Someone can move the code out that part of the code to a separate function so it can be used for situations like what Nathan is asking for. Not sure where it should go at this point other than in TextResultWriter - we don't really have a class of 'HSP consumers' other than in there. Will's code is smarter as it figures out the multiplier from the start/end while we code it up based on the alignment alg (TBLASTN, BLASTX, etc). -jason On Fri, 23 Jan 2004, Will Spooner wrote: > Hi Nathan, > > The following code creates a multi-line wu-blast-style alignment string > from an HSP object. Is this what you are looking for? I would have > liked to have found a method like this on the HSP object itself, but I'm > not sure that this is where it strictly 'belongs'. I'd be happy to > contribute the code if someone knows the best place to put it! > > All the best, > > Will > > > sub alignment_string{ > my $hsp = shift; > my $query = $hsp->query; > my $sbjct = $hsp->hit; > > > # Space to reserve for the numbering at the line start > my $seq_cols = 60; > my( $num_length ) = sort{ $b<=>$a } ( $query->start, > $query->end, > $sbjct->start, > $sbjct->end ); > $num_length = length( $num_length ); > > # Templates for the lines > my $qtmpl = "Query: %${num_length}d %s %d\n"; > my $xtmpl = ( " " x ( $num_length + 8 ) ) . "%s\n"; > my $htmpl = "Sbjct: %${num_length}d %s %d\n"; > > # Divide the alignment strings onto lines > my $rows = ( ( length($hsp->query_string) - 1 ) / $seq_cols ) + 1; > my @qlines = unpack( "a$seq_cols" x $rows, $hsp->query_string ); > my @xlines = unpack( "a$seq_cols" x $rows, $hsp->homology_string ); > my @hlines = unpack( "a$seq_cols" x $rows, $hsp->hit_string ); > > # Things needed for counting; DNA|peptide > my $qmultiplier = ( ( $query->end - $query->start ) / > ( $sbjct->end - $sbjct->start ) ); > my $smultiplier; > if( $qmultiplier < 0.5 ){ $qmultiplier = 1; $smultiplier=3 } > elsif( $qmultiplier > 2 ){ $qmultiplier = 3; $smultiplier=1 } > else { $qmultiplier = 1; $smultiplier=1 } > > # More counting things; strand > my $qstrand = $query->strand < 0 ? -1 : 1; > my $sstrand = $sbjct->strand < 0 ? -1 : 1; > my( $qstart, $qryend ) = $query->strand < 0 ? > ( $query->end, $query->start) : ( $query->start, $query->end ); > my( $hstart, $sbjend ) = $sbjct->strand < 0 ? > ( $sbjct->end, $sbjct->start ) : ( $sbjct->start, $sbjct->end ); > > # Generate text for each line-triplet > my @lines; > for( my $i=0; $i<@qlines; $i++ ){ > my $qend = $qstart + ( ( $seq_cols * $qmultiplier - 1 ) * $qstrand ); > my $hend = $hstart + ( ( $seq_cols * $smultiplier - 1 ) * $sstrand ); > if( $i == @qlines - 1 ){ > $qend = $qryend; > $hend = $sbjend; > } > my $line = ''; > $line .= sprintf( $qtmpl, $qstart, $qlines[$i], $qend ); > $line .= sprintf( $xtmpl, $xlines[$i] ); > $line .= sprintf( $htmpl, $hstart, $hlines[$i], $hend ); > push @lines, $line; > $qstart = $qend + ( 1 * $qstrand ); > $hstart = $hend + ( 1 * $sstrand ); > } > > return join( "\n", @lines ); > } > > > On Thu, 22 Jan 2004, Brian Osborne wrote: > > > Jason, > > > > I think he wants to print out the exact same alignment as you see in the > > BLAST report, which you can't do using AlignIO. > > > > Nathan, do you mean "exactly", with that "Query: 2" and "Subject: 2" > > business as well? > > > > Brian O. > > > > -----Original Message----- > > From: bioperl-l-bounces@portal.open-bio.org > > [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Jason Stajich > > Sent: Thursday, January 22, 2004 2:14 PM > > To: Agrin, Nathan > > Cc: bioperl-l@portal.open-bio.org > > Subject: Re: [Bioperl-l] Alignment Blast parser > > > > You want to retain it meaning what? > > Bio::SearchIO(-format => 'blast') > > parses blast for you. > > > > -jason > > On Thu, 22 Jan 2004, Agrin, Nathan wrote: > > > > > I need a way to retain the EXACT alignment found in a blast file. > > > Ex- > > > > > > > > > Query: 1 MAGRGK-GKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLT > > > 59 > > > M+GRGK G + KA SRS++AGLQFPVGR+ R L+KG YAER+GAGAPVYLAAVLEYLT > > > Sbjct: 1 MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT > > > 60 > > > > > > > > > Query: 60 AEVLELAGNAARDNKKNRIVPRHIQLAIRNDEELGKLLGEVTIASGGVLPNIHAVLLP > > > 117 > > > AE+LELAGNAARDNKK RI+PRH+QLAIRNDEEL KLLG VTIA GGVLPNI AVLLP > > > Sbjct: 61 AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLP > > > 118 > > > > > > I have tried everything to no avail. AlignIO almost works out, but > > > instead of doing a typical blast alignment, the best it can do is a > > > clustalw like alignment. > > > > > > Any help is much appreciated. > > > > > > -Nate > > > > > > Nathan Agrin > > > Research Associate > > > UMass Medical Center > > > 55 Lake Ave. N. > > > Worcester MA, 01655 > > > (508)-856-6018 > > > nathan.agrin@umassmed.edu > > > > > > > > > > -- > > Jason Stajich > > Duke University > > jason at cgt.mc.duke.edu > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > --- > Dr William Spooner whs@sanger.ac.uk > Ensembl Web Developer http://www.ensembl.org > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From brian_osborne at cognia.com Fri Jan 23 08:49:20 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Fri Jan 23 08:56:10 2004 Subject: [Bioperl-l] Bioperl and Entrez Gene Database In-Reply-To: <89AA811FD79DC94788093B23DA79E71F832889@edunivmail02.ad.umassmed.edu> Message-ID: Nathan, Are these the same values found in the MAP line in Locuslink's LL_tmpl? If so then SeqIO/Locuslink.pm will extract this for you. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Agrin, Nathan Sent: Wednesday, January 21, 2004 1:33 PM To: bioperl-l@bioperl.org Subject: [Bioperl-l] Bioperl and Entrez Gene Database Entrez has a database that is called gene. You input an accession number and it gives you the chromosome location and chromosome number. Is there anyway someone can use bioperl to submit a long list of accession numbers and then save the output of each as say a normal text file? Thanks, Nate From brian_osborne at cognia.com Fri Jan 23 09:00:39 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Fri Jan 23 09:07:33 2004 Subject: [Bioperl-l] recent spams to bioperl-l In-Reply-To: <8A945B8A-4D3E-11D8-9EF4-000A959EB4C4@gnf.org> Message-ID: Hilmar, I agree. We're up to 6 cents. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Hilmar Lapp Sent: Thursday, January 22, 2004 7:53 PM To: Aaron J. Mackey Cc: Bioperl list; Chris Dagdigian Subject: Re: [Bioperl-l] recent spams to bioperl-l On Thursday, January 22, 2004, at 07:24 AM, Aaron J. Mackey wrote: > My 2 cents: the spam level has increased noticeably, but going from 0 > to some is always noticeable. I don't think it's so bad (yet) as to > require moving to a closed system. > I agree. -hilmar -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From Marc.Logghe at devgen.com Fri Jan 23 09:04:31 2004 From: Marc.Logghe at devgen.com (Marc Logghe) Date: Fri Jan 23 09:11:22 2004 Subject: [Bioperl-l] need help Message-ID: > -----Original Message----- > From: KHOUEIRY pierre [mailto:khoueiry@ibsm.cnrs-mrs.fr] > Sent: Thursday, January 22, 2004 2:53 PM > To: bioperl-l@portal.open-bio.org > Subject: [Bioperl-l] need help > > > Hi everyone; > I wrote a script using bioperl methodes. In fact my problem isn't in > bioperl modules. I find problems on submitting my html form. When the > user browse a file, i can't open it. I used a post methode > target="_blank">. > This should work when you set the enctype: enctype="multipart/form-data" I've tried with this form: test test.cgi looks like this: #!/usr/bin/perl use strict; use CGI qw(:standard); use Data::Dumper; use Bio::SeqIO; my $file = param('seqfile'); my $in = Bio::SeqIO->new(-fh => $file, -format => 'genbank'); my $seq = $in->next_seq; print header, pre(Data::Dumper->Dump([$seq],['seq'])); HTH, Marc From whs at sanger.ac.uk Fri Jan 23 09:53:42 2004 From: whs at sanger.ac.uk (Will Spooner) Date: Fri Jan 23 10:00:21 2004 Subject: [Bioperl-l] Alignment Blast parser In-Reply-To: References: Message-ID: Hi Jason, Having looked at the code, it does seem sensible to split the TextResultWriter->to_string method into component parts. This would allow users like me, with detached HSPI objects kicking about, to reuse the writer code, e.g: my $writer = Bio::SearchIO::Writer::TextResultWriter->new(); my $hsp = Bio::Search::HSP::MyHSP->new(-id=>'foo'); print $writer->hsp_alignment_string( $hsp ); This approach would also allow TextResultWriter subclasses to get a bit more granularity from the parent. I'm happy to do the necessary, and will post a patch to bugzilla once complete. Will On Fri, 23 Jan 2004, Jason Stajich wrote: > Currently the code to do this sort of thing is embedded in > SearchIO::Writer::TextResultWriter but generates a whole report. > > Someone can move the code out that part of the code to a separate function > so it can be used for situations like what Nathan is asking for. Not sure > where it should go at this point other than in TextResultWriter - we don't > really have a class of 'HSP consumers' other than in there. > > Will's code is smarter as it figures out the multiplier from the start/end > while we code it up based on the alignment alg (TBLASTN, BLASTX, etc). > > From jason at cgt.duhs.duke.edu Fri Jan 23 10:51:36 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Fri Jan 23 10:58:18 2004 Subject: [Bioperl-l] Alignment Blast parser In-Reply-To: References: Message-ID: yes please - thanks Will!! -jason On Fri, 23 Jan 2004, Will Spooner wrote: > Hi Jason, > > Having looked at the code, it does seem sensible to split the > TextResultWriter->to_string method into component parts. This would allow > users like me, with detached HSPI objects kicking about, to reuse the > writer code, e.g: > > my $writer = Bio::SearchIO::Writer::TextResultWriter->new(); > my $hsp = Bio::Search::HSP::MyHSP->new(-id=>'foo'); > print $writer->hsp_alignment_string( $hsp ); > > This approach would also allow TextResultWriter subclasses to get a bit > more granularity from the parent. > > I'm happy to do the necessary, and will post a patch to bugzilla once > complete. > > Will > > On Fri, 23 Jan 2004, Jason Stajich wrote: > > > Currently the code to do this sort of thing is embedded in > > SearchIO::Writer::TextResultWriter but generates a whole report. > > > > Someone can move the code out that part of the code to a separate function > > so it can be used for situations like what Nathan is asking for. Not sure > > where it should go at this point other than in TextResultWriter - we don't > > really have a class of 'HSP consumers' other than in there. > > > > Will's code is smarter as it figures out the multiplier from the start/end > > while we code it up based on the alignment alg (TBLASTN, BLASTX, etc). > > > > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From emailfrom1 at yahoo.co.uk Fri Jan 23 17:20:42 2004 From: emailfrom1 at yahoo.co.uk (Marketing) Date: Fri Jan 23 11:26:58 2004 Subject: [Bioperl-l] Email Message-ID: <200401231626.i0NGQrEs010886@portal.open-bio.org> To my family, friends & business colleagues, If you are looking to send thousands of emails to people either in the UK and abroad, in order to promote your Internet business, don't waste your time searching the net for suitable companies, as many of them are a complete waste of time and money. I have found one that does what it says it does! To find out more, go to: http://uk.geocities.com/emailbusiness1 Regards John From andreas.bernauer at gmx.de Fri Jan 23 12:17:09 2004 From: andreas.bernauer at gmx.de (Andreas Bernauer) Date: Fri Jan 23 12:23:47 2004 Subject: [Bioperl-l] Experiences from a newbie In-Reply-To: References: <20031211235423.GF14666@hgt.mcb.uconn.edu> Message-ID: <20040123171709.GB19704@hgt.mcb.uconn.edu> Hi Brian and all other Bioperlers! Brian Osborne wrote: > I've started writing a HOWTO on Features and Annotations, I would appreciate > your taking a look at it and telling me what you think, here's the URL: > > http://bioperl.org/HOWTOs/html/Feature-Annotation.html Finally I'm back here to Bioperl and I read your HOWTO. Here are my comments. This mail is quite long and I criticize a lot. Don't hit me for that, the fact that I am still using Bioperl proves that its functionality outranges the drawbacks in its documentation, although the later makes it harder for me to use it. I want my comments to be understood as constructive, impulses for improvements you migh want to make if you agree with (parts of) my opinion. First of all I want to mention, that Brian's HOWTO helped me to understand what's going on in Bioperl, although I still can't understand some design decisions of Bioperl (not of the HOWTO). As a conclusion I must say that Brian's HOWTO is understandable as itself, but what still stays not understandable is the way Bioperl is built up and _why_ it was built up that way. Thus, my comments are somehow connected to the metalevel. Concerning your HOWTO, I very much like the examples you give, e.g. how to extraxt these CDS information from a GenBank file (as this is exactly what I wanted to do, when I used BioPerl the first time :-) or the link to the Feature Table Document that gives some more detailed information. The links collection at the end of the document is also very helpful. What I was missing were links to the module descriptions of the modules you mention at the place you mention them. Sometimes the doc even tells the reader to look into the module definition without providing a link. But that's a minor issue. For example, you briefly explain, what a SeqFeature is (associated with a sequence and has a location there) and what an Annotation is (associated with a sequence without a location). So both are associated with a sequence. Why do they not inherit from some parent object if they share this common feature, I was asking myself. Why doesn't Bioperl just have an object for a simple sequence and then derive one specialty after another from that simple object, e.g. one that has a location and one that doesn't? Why are there two distinct objects for that? I know, this sounds totally stupid to you and now, that I have read the whole HOWTO, including chapter 6 that explains Annotations in details, it sounds so to me, too. This shows that the HOWTO is really helpful, but it also shows, that a small example at the beginning wouldn't let the reader wonder all the time till chapter 6 to find out what the difference is. Furthermore, I don't understand the naming of the objects. SeqFeature and Annotation seem pretty related, but have completely different names. Maybe this is because of some lack in my biological background, but what do you consider an "Annotation" and what a "Feature"? Where can I find definitions for that, written in English? This would help me a lot, I guess, as I am constantly guessing, what an object represents in the real world. Again, after reading the HOWTO and writing this email, especially, I know the difference. But there is no place in any document so far I read, that tells me that. I've concluded that after reading a couple of documents. This goes on with lots of other objects and goes hand in hand with the module description. Just randomly picking one out of Brian's HOWTO: Bio::Seq:RichSeq. I'd like to know what a RichSeq is and go to the module description page. I quote from that page (http://doc.bioperl.org/releases/bioperl-1.4/Bio/Seq/RichSeq.html): "This module implements Bio::Seq::RichSeqI, an interface for sequences created from or created for entries from/of rich sequence databanks, like EMBL, GenBank, and SwissProt. Methods added to the Bio::SeqI interface therefore focus on databank-specific information. Note that not every rich databank format may use all of the properties provided." OK, a RichSeq object representes sequences from a rich sequence database. Guess what, that's what I thought! But what is a "rich sequence (database)"? The descriptions gives examples, but this does not help me at all, as this is just the list of the databanks I know. What I want to say is, I still don't know, what is _not_ a rich sequence database, i.e. what's the difference between a plain sequence and a rich sequence? Aren't all sequences saved like in Swissprot, etc.? Or do you consider a FASTA file with only sequence information as a database? OK, I guess, you mean, that the sequences contain lots of annototations or features or comments etc. and that's what you consider "rich". This might look a little bit picky, but this is the kind of lack of definition that makes it so hard for me to get into BioPerl as I encounter it again and again. Another example that happened to me: The HOWTO explains in Chapter 5 "Some Other Objects" how to read the species information from a GenBank file. The file looked like this: SOURCE human. ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. and has an example code: my $classification = $seq_object->species->classification; # "sapiens Homo Hominidae Catarrhini Primates Eutheria Mammalia # Euteleostomi Vertebrata Craniata Chordata Metazoa Eukaryota" I guess the comment tells me, what's in $classification now. This looks strange to me and I don't really understand, how this string was built. The first two words are the words of the first line after "organism", but in reverse order. Then, without any marker, the rest of the two lines follow, missing the semicolon and the last word ("Homo") and again in reverse order. So I looked into the documentation of the module Bio::Species, to figure out, how I am supposed to find the information I want (namely the name of the organism and its classification). I went to http://doc.bioperl.org/releases/bioperl-1.4/ and looked in the upper left frame to find Bio::Species, which I couldn't. I don't know why. There is bioperl-1.4::Bio::SeqIO, bioperl-1.4::Bio::SeqIO::game and bioperl-1.4::Bio::Structure, but Bio::Species is missing. So I searched around and found "Species" in the lower left frame, which turned out to be the page I was looking for (I guess). Here's what the documentation gives me: ,--http://doc.bioperl.org/releases/bioperl-1.4/Bio/Species.html#POD2---- |Title : classification | Usage : $self->classification(@class_array); | @classification = $self->classification(); | Function: Fills or returns the classification list in | the object. The array provided must be in | the order SPECIES, GENUS ---> KINGDOM. | Checks are made that species is in lower case, | Example : $obj->classification(qw( sapiens Homo Hominidae | Catarrhini Primates Eutheria Mammalia Vertebrata | Chordata Metazoa Eukaryota)); | Returns : Classification array | Args : Classification array | OR | A reference to the classification array. In the latter case | if there is a second argument and it evaluates to true, | names will not be validated. `--------- Ok, sections title, usage help me. Although the usage does not reveal all possible arguments, but that's why there is an Args section, I guess. If I read the Function section correctly, it looks like this function both sets or reads the classification of the object. That looks kind of weird to me, remembering what I've learned in OO with mutators and accessors, but maybe that's the way it works in Perl. Nevermind. The Example section shows me how I could call the function. Unfortunately, it neither tells me, what the new state of the object will be (ok, maybe that's clear for you, but hey, why do you give an example anyway?). Nor does it tell me, what I wanted to know: if I use the first form, what I get as a result. The Returns section tells me I get a "Classification array". Hm, is this another object? Or just an array? Why call it "Classification array" then, and not "array representing classification"? It does not tell me how, however, what information this array carries. Well, another guess makes me believe that the returning array will have the same structure as the array passed as argument. And now I kind of understand what's in $classification: It's not a string, but an array, and the HOWTO just gave me the string representation of that array. But why is the species printed in the wrong order ("sapiens Homo" instead of "Homo sapiens")? And why is the last word ("Homo") missing? I did not come up with an answer for this. Maybe a bug in the HOWTO, in the implementation of the classification function or a bug in my understanding. So what is this guy complaining about, you might think. Wasn't there everything (well, except for this missing "Homo" word) in the documentation? What I am criticizing is that although it might be documented, it is documented in a way that takes me (and I am talking only about myself) a lot of time to understand: * I don't know how you name which thing. (A big exception of this is the SearchIO howto, which states in its 4th chapter exactly, what attribute of the object contains what kind of data and where this data comes from.) What's an annotation? A rich sequence? A feature? Different people might understand different things under these names and I think it's good to clarify that everybody is talking about the same thing. (Btw, what's funny is that the doc to Bio::Seq tells me the following: Bio::SeqFeatureI - a location on a sequence, potentially with a sequence and annotation, which is not quite the same as the HOWTO told me (associated with a sequence, not potentially)). * I can't just read the documentation and use a function. That's the major drawback for me. I almost always have to make conclusions out of the documentation. In the example above: Why does the Result section not tell me what the structure of the resulting array is? I have to conclude that from what is stated in the Function section. So why is there a Result section at all? Thank you for your time. Again, I am still using Bioperl as it serves my purpose, but I wished the documentation would be usefuller. I don't want to discourage anybody, instead, I'd like this to be understood as a constructive critic. I hope I've stated everything in a clear way. Best regards, Andreas. From billthebrute at yahoo.fr Fri Jan 23 12:47:26 2004 From: billthebrute at yahoo.fr (=?iso-8859-1?q?william=20ritchie?=) Date: Fri Jan 23 12:53:57 2004 Subject: [Bioperl-l] RemoteBlast Message-ID: <20040123174726.99033.qmail@web25206.mail.ukl.yahoo.com> Hi I m getting this error message: -------------------- WARNING --------------------- MSG: seq doesn't validate, mismatch is 1 --------------------------------------------------- ------------- EXCEPTION ------------- MSG: Attempting to set the sequence to [ADRA2ANM_007417ATGGGCTCACTGCAGCCGGATGCCGGCAACAGCAGCTGGAACGGGACCGAAGCGCCCGGAGGCGGC but my input is regular FASTA!!!!!!! Help please. _________________________________________________________________ Do You Yahoo!? -- Une adresse @yahoo.fr gratuite et en fran?ais ! Yahoo! Mail : http://fr.mail.yahoo.com From MEC at Stowers-Institute.org Fri Jan 23 14:14:06 2004 From: MEC at Stowers-Institute.org (Cook, Malcolm) Date: Fri Jan 23 14:20:40 2004 Subject: [Bioperl-l] Sequence Assembly:phrap to gap Message-ID: You might consider getting gcphrap (http://www.mrc-lmb.cam.ac.uk/pubseq/phrap.html) from which I quote: "The gcphrap command works in much the same way as the standard Phrap command. Indeed as it is the same source code, it is just the input and output formats which will differ. The key difference is that gcphrap automatically detects the difference between a file containing fasta sequences and a file containing a list of Experiment File filenames. The extra "-exp" option may be used (regardless of input format) to output the assembly as a series of Experiment Files suitable for assembly into Gap4 using the "Directed Assembly" option. For example: $ gcphrap seqs_fasta.screen -exp efiles > phrap.out The above command will produce a directory named efiles containing one Experiment File per sequence. These Experiment Files have 'AP' lines added to them to define the assembly positions. " -----Original Message----- From: Anthony Underwood [mailto:theunderwoods@clara.co.uk] Sent: Friday, January 23, 2004 3:42 AM To: bioperl-l@bioperl.org Subject: [Bioperl-l] Sequence Assembly:phrap to gap Hi all, I have a slightly off-topic question. I am assembling sequences using the script phredPhrap which makes a .ace format assembly as well as a phrap.out format assembly. I am using BioPerl to extract a lot of the relevant information from the assembly however I would like to view the assembly by converting it to a gap4 database, and using stadens gap4 viewer. Does anybody know of a script (perl or otherwise) that can convert either the .ace or .out assembly to a gap4 database. Many thanks, Anthony Dr Anthony Underwood Bioinformatics Group Genomics, Proteomic and Bioinformatics Unit Central Public Health Laboratory Health Protection Agency 61 Colindale Avenue London NW9 5HT t: 0208 2004400 ext. 3618 e: anthony.underwood@hpa.org.uk _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From becky at bpmsite.com Fri Jan 23 15:00:30 2004 From: becky at bpmsite.com (Becky P. Marshall) Date: Fri Jan 23 15:00:35 2004 Subject: [Bioperl-l] bioperl.org ranked # 43 in Google for Biology Tutorial Software Message-ID: <29212652.1074887666000.JavaMail.Developer@mail.bpmsite.com> I just searched in Google for Biology Tutorial Software and found bioperl.org ranked 43. I have a related website about Education that's purely informational (so I'm NOT a competitor of yours) and I'd like to link to your site. I consider my site to be one of the best resources for this type of information. I get a decent amount of visitors to it so if I link to you, your site should get some decent traffic from it. I only link to good quality sites... I think you'll find my site to be high quality as well. In exchange, I would ask that you also link to my site. I've already linked to you and will keep it there for a few days until I hear from you. Please let me know asap if you're interested and i'll send you my information. Thanks! Becky P. Marshall RAC IM: 296873. From heikki at nildram.co.uk Fri Jan 23 16:15:52 2004 From: heikki at nildram.co.uk (Heikki Lehvaslaiho) Date: Fri Jan 23 16:23:16 2004 Subject: [Bioperl-l] recent spams to bioperl-l In-Reply-To: <400FD228.7040800@sonsorol.org> References: <400FD228.7040800@sonsorol.org> Message-ID: <200401232115.52635.heikki@nildram.co.uk> Chris, Given the amount of spam flying around only a tiny trickle makes it to the list. I do know that keeping it at that level requires work from you, but at least the current spam level does not seem to bother list members. None of the regular list members have complained. I suggest we continue being as open as we have been, for the time being at least. My 2 cents worth, but they are euro cents and they are stronger than US cents. ;-) -Heikki On Thursday 22 Jan 2004 13:37, Chris Dagdigian wrote: > Hi folks, > > Just wanted to apologize for the rise in spam going to bioperl-l. Our > anti-spam filtering tools on the open-bio.org mailserver generally do a > great job weeding out the dozens of messages per day sent to bioperl-l > that are obvious spam, but recently there has been a huge rise in > plaintext ASCII spam or the hash-busting spam that is nothing but nonsense. > > Spamassassin+MimeDefang and our Mailman spam filters can't easily > discern the plaintext spam from regular email messages sent to the list. > > bioperl-l allows non-members to post to the list; this was the consensus > behavior that bioperl members wanted the last time we took a poll. > > Let me know if opinions have changed. If we make the list members-only > for posting we can significantly cut down on spam. The downside to this > is that we (a) make more work for the list moderators and (b) we become > 'less open'. > > -Chris -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From pusch at IntegratedGenomics.com Fri Jan 23 17:06:08 2004 From: pusch at IntegratedGenomics.com (Gordon D. Pusch) Date: Fri Jan 23 17:06:14 2004 Subject: [Bioperl-l] recent spams to bioperl-l In-Reply-To: Your message of "Fri, 23 Jan 2004 21:15:52 GMT." <200401232115.52635.heikki@nildram.co.uk> Message-ID: <200401232206.i0NM68r30518@pusch.xnet.com> Chris --- I suggest that you might also want to look at iFile, . It's a Bayesian filter, it can "learn" from misclassified messages, and I find that once good databases of valid message-class(es) and SPAM class(es) have been built up, it does a remarkably good job of classifying messages into legitimate e-mail and SPAM... -- Gordon D. Pusch perl -e '$_ = "gdpusch\@NO.xnet.SPAM.com\n"; s/NO\.//; s/SPAM\.//; print;' From brian_osborne at cognia.com Fri Jan 23 21:22:23 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Fri Jan 23 21:29:11 2004 Subject: [Bioperl-l] RemoteBlast In-Reply-To: <20040123174726.99033.qmail@web25206.mail.ukl.yahoo.com> Message-ID: William, There are people here who are happy to help but you need to show some code, your letter is not very informative. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of william ritchie Sent: Friday, January 23, 2004 12:47 PM To: bioperl-l@bioperl.org Subject: [Bioperl-l] RemoteBlast Hi I m getting this error message: -------------------- WARNING --------------------- MSG: seq doesn't validate, mismatch is 1 --------------------------------------------------- ------------- EXCEPTION ------------- MSG: Attempting to set the sequence to [ADRA2ANM_007417ATGGGCTCACTGCAGCCGGATGCCGGCAACAGCAGCTGGAACGGGACCGAAGCGCCCGGA GGCGGC but my input is regular FASTA!!!!!!! Help please. _________________________________________________________________ Do You Yahoo!? -- Une adresse @yahoo.fr gratuite et en fran?ais ! Yahoo! Mail : http://fr.mail.yahoo.com _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From bobbyStoreys at ilovechocolate.com Sat Jan 24 09:13:34 2004 From: bobbyStoreys at ilovechocolate.com (Dmarlin) Date: Sat Jan 24 09:20:30 2004 Subject: [Bioperl-l] Oflfer of 21 CENTURY scent! Message-ID: kBe kaware that now the peak of your selxual activity is realy accessible! All you need is to visit http://onlinemanufacturer.com/mx/index.php?pid=genviag Thanks to the proprietary blend of unique herkbs the four wonderful efkfects are achieved: *blood stream to the penlis is restored *stored tesltosterone is unleashed *activation of the body's naltural holrmone production heightens your sensation *the peknis does enklarge, the changes are being permanent! At last you can enljoy your secxual life in full measure without any risk for your healkth! Don`t wakste your time! Get more inkfo straightforwardly at http://onlinemanufacturer.com/mx/index.php?pid=genviag From emailfrom1 at yahoo.co.uk Sun Jan 25 13:27:02 2004 From: emailfrom1 at yahoo.co.uk (Marketing) Date: Sun Jan 25 07:33:13 2004 Subject: [Bioperl-l] Email Message-ID: <200401251233.i0PCX9Es028288@portal.open-bio.org> To my family, friends & business colleagues, If you are looking to send thousands of emails to people either in the UK and abroad, in order to promote your Internet business, don't waste your time searching the net for suitable companies, as many of them are a complete waste of time and money. I have found one that does what it says it does! To find out more, go to: http://uk.geocities.com/emailbusiness1 Regards John From ecky.l at gmx.de Sun Jan 25 15:57:29 2004 From: ecky.l at gmx.de (Eckhard Lehmann) Date: Sun Jan 25 16:03:57 2004 Subject: [Bioperl-l] EST functional categories References: <6.0.1.1.2.20040122143719.01e2d918@jaudall.mail.iastate.edu> Message-ID: <30766.1075064249@www61.gmx.net> > I'm working on an EST project. I'd like to use bioperl to identify > putative functional categories of individual ESTs and eventually end up > with those ubiquitous pie charts or histograms (using excel). I've seen > that ontologies structures have been built into bioperl but there isn't > much documentation (or I've overlooked it). I could use some help/example I am not quite sure about that - but isn't it better to do functional analysis on contigs that are assembled of EST's, rather that individual EST's? > scripts to get started. I've blasted all my ESTs against nr. How do I > take the best blast hit and look it it's functional category on > GO/Interpro? In the EST project that I am working on - I have the impression yet, that you can not pull out much usefull information of these short sequence parts. When it comes to BLASTx for instance, you get many many different confusing and discusting non-informative hits. With contigs you have mostly eliminated the redundancy and can do better BLASTx. Functional analysis should then be possible by backtracking the EST source information. I have done some stuff, but it is mainly database oriented (PostgreSQL, PL/PgSQL) and has not much to do with BioPerl currently. Used only BioPerl-DB to load the EST sequences into a BioSQL setup along with contigs and things, and now to fetch individual sequences into flat files sometimes. However, I used Perl and GD::Graph for making pie charts and a web interface to the database. Eckhard ;) From billthebrute at yahoo.fr Mon Jan 26 03:09:45 2004 From: billthebrute at yahoo.fr (=?iso-8859-1?q?william=20ritchie?=) Date: Mon Jan 26 03:16:11 2004 Subject: [Bioperl-l] RemoteBlast again Message-ID: <20040126080945.46732.qmail@web25204.mail.ukl.yahoo.com> Sorry about the incomplete question, I was leaving and I wondered if this was a common error. This is the code that gives my previous error message.... use strict; use Bio::SearchIO; use Bio::Tools::Run::RemoteBlast; use Bio::Perl; use Bio::SeqIO; my @inputfiles = @ARGV; foreach my $inputfile (@inputfiles) { my $prog = 'blastn'; #my $db = 'gbEST'; my $e_val= '1e-10'; my @params = ( '-prog' => $prog, ' -data '=> 'est_mouse', ' -expect' => $e_val, ' -readmethod' => ' SearchIO' ); my $factory = Bio::Tools::Run::RemoteBlast->new(@params); my $v = 1; my $str = Bio::SeqIO->new( -file=> "/home/billthebrute/Projet/endogpcr/"."$inputfile", # -format => ' Fasta' ); $Bio::Tools::Run::RemoteBlast::HEADER{'DATABASE'} = 'est_mouse'; $Bio::Tools::Run::RemoteBlast::HEADER{'PROGRAM'} = 'blastn'; while (my $input = $str->next_seq()) { my $r = $factory->submit_blast($input); print STDERR "waiting..." if( $v > 0 ); while ( my @rids = $factory->each_rid ) { foreach my $rid ( @rids ) { my $rc = $factory->retrieve_blast($rid); if( !ref($rc) ) { if( $rc < 0 ) { $factory->remove_rid($rid); } print STDERR "." if ( $v > 0 ); sleep 5 ; } else { my $result = $rc->next_result(); #save the output #my $filename = $result->query_name()."\.out"; print "$inputfile"; $factory->save_output("/home/billthebrute/Projet/blasted/"."$inputfile"); $factory->remove_rid($rid); } } } } } I m recieving this error message: ----------------- WARNING --------------------- MSG: seq doesn't validate, mismatch is 1 --------------------------------------------------- ------------- EXCEPTION ------------- MSG: Attempting to set the sequence to [ADRA2ANM_007417ATGGGCTCACTGCAGCCGGATGCCGGCAACAGCAGCTGGAACGGGACCGAAGCGCCCGGAGGCGGC With the below file! Thanks >Adra2a NM_007417 atgggctcactgcagccggatgccggcaacagcagctggaacgggaccga agcgcccggaggcggcacccgagccaccccttactccctgcaggtgacac tgacgctggtttgcctggctggcctgctcatgctgttcacagtatttggc aacgtgctggttattatcgcggtgttcaccagtcgcgcgctcaaagctcc ccaaaacctcttcctggtgtccctggcctcagcggacatcctggtggcca cgctggtcattcccttttctttggccaacgaggttatgggttactggtac tttggtaaggtgtggtgtgagatctatttggctctcgacgtgctcttttg cacgtcgtccatagtgcacctgtgcgccatcagccttgaccgctactggt ccatcacgcaggccatcgagtacaacctgaagcgcacgccgcgtcgcatc aaggccatcattgtcaccgtgtgggtcatctcggctgtcatctccttccc gccactcatctccatagagaagaagggcgctggcggcgggcagcagccgg ccgagccaagctgcaagatcaacgaccagaagtggtatgtcatctcctcg tccatcggttccttcttcgcgccttgcctcatcatgatcctggtctacgt gcgtatttaccagatcgccaagcgtcgcacccgcgtgcctcccagccgcc ggggtccggacgcctgttccgcgccgccggggggcgccgatcgcaggccc aacgggctgggcccggagcgcggcgcgggtcccacgggcgctgaggcgga gccgctgcccacccagcttaacggtgccccgggggagcccgcgcccgccg ggccccgcgatggggatgcgctggacctagaggagagttcgtcgtccgag cacgccgagcggcccccggggccccgcagacccgaccgcggcccccgagc caagggcaagacccgggcgagtcaggtgaagccgggggacagtctgccgc ggcgcgggcccggggccgcggggccgggggcttcggggtccgggcacgga gaggagcgcggcgggggcgccaaagcgtcgcgctggcgcgggaggcaaaa ccgggagaaacgcttcacgttcgtgctggcggtggtgatcggcgtgttcg tggtgtgttggtttccgttctttttcacctacacgctcatagcggtcggc tgcccggtgcccagccagctcttcaacttcttcttctggttcggctactg caacagctcgctgaaccctgttatctacaccatcttcaaccacgacttcc gacgcgccttcaagaagatcctctgccgtggggacagaaaacgcatcgtg tga _________________________________________________________________ Do You Yahoo!? -- Une adresse @yahoo.fr gratuite et en fran?ais ! Yahoo! Mail : http://fr.mail.yahoo.com From brian_osborne at cognia.com Mon Jan 26 08:22:53 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Mon Jan 26 08:29:35 2004 Subject: [Bioperl-l] RemoteBlast again In-Reply-To: <20040126080945.46732.qmail@web25204.mail.ukl.yahoo.com> Message-ID: William, The format of your input file doesn't look right. I think it should be fasta, with lines 1 and 2 something like this: >Adra2a NM_007417 atgggctcactgcagccggatgccggcaacagcagctggaacgggaccga Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of william ritchie Sent: Monday, January 26, 2004 3:10 AM To: bioperl-l@bioperl.org Subject: [Bioperl-l] RemoteBlast again Sorry about the incomplete question, I was leaving and I wondered if this was a common error. This is the code that gives my previous error message.... use strict; use Bio::SearchIO; use Bio::Tools::Run::RemoteBlast; use Bio::Perl; use Bio::SeqIO; my @inputfiles = @ARGV; foreach my $inputfile (@inputfiles) { my $prog = 'blastn'; #my $db = 'gbEST'; my $e_val= '1e-10'; my @params = ( '-prog' => $prog, ' -data '=> 'est_mouse', ' -expect' => $e_val, ' -readmethod' => ' SearchIO' ); my $factory = Bio::Tools::Run::RemoteBlast->new(@params); my $v = 1; my $str = Bio::SeqIO->new( -file=> "/home/billthebrute/Projet/endogpcr/"."$inputfile", # -format => ' Fasta' ); $Bio::Tools::Run::RemoteBlast::HEADER{'DATABASE'} = 'est_mouse'; $Bio::Tools::Run::RemoteBlast::HEADER{'PROGRAM'} = 'blastn'; while (my $input = $str->next_seq()) { my $r = $factory->submit_blast($input); print STDERR "waiting..." if( $v > 0 ); while ( my @rids = $factory->each_rid ) { foreach my $rid ( @rids ) { my $rc = $factory->retrieve_blast($rid); if( !ref($rc) ) { if( $rc < 0 ) { $factory->remove_rid($rid); } print STDERR "." if ( $v > 0 ); sleep 5 ; } else { my $result = $rc->next_result(); #save the output #my $filename = $result->query_name()."\.out"; print "$inputfile"; $factory->save_output("/home/billthebrute/Projet/blasted/"."$inputfile"); $factory->remove_rid($rid); } } } } } I m recieving this error message: ----------------- WARNING --------------------- MSG: seq doesn't validate, mismatch is 1 --------------------------------------------------- ------------- EXCEPTION ------------- MSG: Attempting to set the sequence to [ADRA2ANM_007417ATGGGCTCACTGCAGCCGGATGCCGGCAACAGCAGCTGGAACGGGACCGAAGCGCCCGGA GGCGGC With the below file! Thanks >Adra2a NM_007417 atgggctcactgcagccggatgccggcaacagcagctggaacgggaccga agcgcccggaggcggcacccgagccaccccttactccctgcaggtgacac tgacgctggtttgcctggctggcctgctcatgctgttcacagtatttggc aacgtgctggttattatcgcggtgttcaccagtcgcgcgctcaaagctcc ccaaaacctcttcctggtgtccctggcctcagcggacatcctggtggcca cgctggtcattcccttttctttggccaacgaggttatgggttactggtac tttggtaaggtgtggtgtgagatctatttggctctcgacgtgctcttttg cacgtcgtccatagtgcacctgtgcgccatcagccttgaccgctactggt ccatcacgcaggccatcgagtacaacctgaagcgcacgccgcgtcgcatc aaggccatcattgtcaccgtgtgggtcatctcggctgtcatctccttccc gccactcatctccatagagaagaagggcgctggcggcgggcagcagccgg ccgagccaagctgcaagatcaacgaccagaagtggtatgtcatctcctcg tccatcggttccttcttcgcgccttgcctcatcatgatcctggtctacgt gcgtatttaccagatcgccaagcgtcgcacccgcgtgcctcccagccgcc ggggtccggacgcctgttccgcgccgccggggggcgccgatcgcaggccc aacgggctgggcccggagcgcggcgcgggtcccacgggcgctgaggcgga gccgctgcccacccagcttaacggtgccccgggggagcccgcgcccgccg ggccccgcgatggggatgcgctggacctagaggagagttcgtcgtccgag cacgccgagcggcccccggggccccgcagacccgaccgcggcccccgagc caagggcaagacccgggcgagtcaggtgaagccgggggacagtctgccgc ggcgcgggcccggggccgcggggccgggggcttcggggtccgggcacgga gaggagcgcggcgggggcgccaaagcgtcgcgctggcgcgggaggcaaaa ccgggagaaacgcttcacgttcgtgctggcggtggtgatcggcgtgttcg tggtgtgttggtttccgttctttttcacctacacgctcatagcggtcggc tgcccggtgcccagccagctcttcaacttcttcttctggttcggctactg caacagctcgctgaaccctgttatctacaccatcttcaaccacgacttcc gacgcgccttcaagaagatcctctgccgtggggacagaaaacgcatcgtg tga _________________________________________________________________ Do You Yahoo!? -- Une adresse @yahoo.fr gratuite et en fran?ais ! Yahoo! Mail : http://fr.mail.yahoo.com _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From billthebrute at yahoo.fr Mon Jan 26 03:05:11 2004 From: billthebrute at yahoo.fr (=?iso-8859-1?q?william=20ritchie?=) Date: Mon Jan 26 08:33:37 2004 Subject: [Bioperl-l] RemoteBlast again Message-ID: <20040126080511.45135.qmail@web25204.mail.ukl.yahoo.com> Sorry about the incomplete question, I was leaving and I wondered if this was a common error. This is the code that gives my previous error message.... use strict; use Bio::SearchIO; use Bio::Tools::Run::RemoteBlast; use Bio::Perl; use Bio::SeqIO; my @inputfiles = @ARGV; foreach my $inputfile (@inputfiles) { my $prog = 'blastn'; #my $db = 'gbEST'; my $e_val= '1e-10'; my @params = ( '-prog' => $prog, ' -data '=> 'est_mouse', ' -expect' => $e_val, ' -readmethod' => ' SearchIO' ); my $factory = Bio::Tools::Run::RemoteBlast->new(@params); my $v = 1; my $str = Bio::SeqIO->new( -file=> "/home/billthebrute/Projet/endogpcr/"."$inputfile", # -format => ' Fasta' ); $Bio::Tools::Run::RemoteBlast::HEADER{'DATABASE'} = 'est_mouse'; $Bio::Tools::Run::RemoteBlast::HEADER{'PROGRAM'} = 'blastn'; while (my $input = $str->next_seq()) { my $r = $factory->submit_blast($input); print STDERR "waiting..." if( $v > 0 ); while ( my @rids = $factory->each_rid ) { foreach my $rid ( @rids ) { my $rc = $factory->retrieve_blast($rid); if( !ref($rc) ) { if( $rc < 0 ) { $factory->remove_rid($rid); } print STDERR "." if ( $v > 0 ); sleep 5 ; } else { my $result = $rc->next_result(); #save the output #my $filename = $result->query_name()."\.out"; print "$inputfile"; $factory->save_output("/home/billthebrute/Projet/blasted/"."$inputfile"); $factory->remove_rid($rid); } } } } } I m recieving this error message: ----------------- WARNING --------------------- MSG: seq doesn't validate, mismatch is 1 --------------------------------------------------- ------------- EXCEPTION ------------- MSG: Attempting to set the sequence to [ADRA2ANM_007417ATGGGCTCACTGCAGCCGGATGCCGGCAACAGCAGCTGGAACGGGACCGAAGCGCCCGGAGGCGGC With the attached file! Thanks _________________________________________________________________ Do You Yahoo!? -- Une adresse @yahoo.fr gratuite et en fran?ais ! Yahoo! Mail : http://fr.mail.yahoo.com -------------- next part -------------- >Adra2a NM_007417 atgggctcactgcagccggatgccggcaacagcagctggaacgggaccga agcgcccggaggcggcacccgagccaccccttactccctgcaggtgacac tgacgctggtttgcctggctggcctgctcatgctgttcacagtatttggc aacgtgctggttattatcgcggtgttcaccagtcgcgcgctcaaagctcc ccaaaacctcttcctggtgtccctggcctcagcggacatcctggtggcca cgctggtcattcccttttctttggccaacgaggttatgggttactggtac tttggtaaggtgtggtgtgagatctatttggctctcgacgtgctcttttg cacgtcgtccatagtgcacctgtgcgccatcagccttgaccgctactggt ccatcacgcaggccatcgagtacaacctgaagcgcacgccgcgtcgcatc aaggccatcattgtcaccgtgtgggtcatctcggctgtcatctccttccc gccactcatctccatagagaagaagggcgctggcggcgggcagcagccgg ccgagccaagctgcaagatcaacgaccagaagtggtatgtcatctcctcg tccatcggttccttcttcgcgccttgcctcatcatgatcctggtctacgt gcgtatttaccagatcgccaagcgtcgcacccgcgtgcctcccagccgcc ggggtccggacgcctgttccgcgccgccggggggcgccgatcgcaggccc aacgggctgggcccggagcgcggcgcgggtcccacgggcgctgaggcgga gccgctgcccacccagcttaacggtgccccgggggagcccgcgcccgccg ggccccgcgatggggatgcgctggacctagaggagagttcgtcgtccgag cacgccgagcggcccccggggccccgcagacccgaccgcggcccccgagc caagggcaagacccgggcgagtcaggtgaagccgggggacagtctgccgc ggcgcgggcccggggccgcggggccgggggcttcggggtccgggcacgga gaggagcgcggcgggggcgccaaagcgtcgcgctggcgcgggaggcaaaa ccgggagaaacgcttcacgttcgtgctggcggtggtgatcggcgtgttcg tggtgtgttggtttccgttctttttcacctacacgctcatagcggtcggc tgcccggtgcccagccagctcttcaacttcttcttctggttcggctactg caacagctcgctgaaccctgttatctacaccatcttcaaccacgacttcc gacgcgccttcaagaagatcctctgccgtggggacagaaaacgcatcgtg tga From jason at cgt.duhs.duke.edu Mon Jan 26 18:57:05 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Mon Jan 26 19:03:35 2004 Subject: [Bioperl-l] RemoteBlast again In-Reply-To: <20040126080511.45135.qmail@web25204.mail.ukl.yahoo.com> References: <20040126080511.45135.qmail@web25204.mail.ukl.yahoo.com> Message-ID: why do you have -format => 'fasta' commented out - you want this to be provided to the seqio parser. On Mon, 26 Jan 2004, [iso-8859-1] william ritchie wrote: > Sorry about the incomplete question, I was leaving and > I wondered if this was a common error. This is the > code that gives my previous error message.... > > use strict; > use Bio::SearchIO; > use Bio::Tools::Run::RemoteBlast; > use Bio::Perl; > use Bio::SeqIO; > > > my @inputfiles = @ARGV; > > foreach my $inputfile (@inputfiles) > > { > > my $prog = 'blastn'; > #my $db = 'gbEST'; > my $e_val= '1e-10'; > > > my @params = ( '-prog' => $prog, > ' -data '=> 'est_mouse', > ' -expect' => $e_val, > ' -readmethod' => ' SearchIO' ); > > > my $factory = > Bio::Tools::Run::RemoteBlast->new(@params); > > > my $v = 1; > > > my $str = Bio::SeqIO->new( > -file=> > "/home/billthebrute/Projet/endogpcr/"."$inputfile", > # -format => ' Fasta' > ); > > > $Bio::Tools::Run::RemoteBlast::HEADER{'DATABASE'} = > 'est_mouse'; > > $Bio::Tools::Run::RemoteBlast::HEADER{'PROGRAM'} = > 'blastn'; > > while (my $input = $str->next_seq()) > { > > > my $r = $factory->submit_blast($input); > > > print STDERR "waiting..." if( $v > 0 ); > > while ( my @rids = $factory->each_rid ) { > foreach my $rid ( @rids ) { > my $rc = > $factory->retrieve_blast($rid); > if( !ref($rc) ) { > if( $rc < 0 ) { > $factory->remove_rid($rid); > } > print STDERR "." if ( $v > 0 ); > sleep 5 ; > } else { > my $result = $rc->next_result(); > #save the output > #my $filename = > $result->query_name()."\.out"; > print "$inputfile"; > > $factory->save_output("/home/billthebrute/Projet/blasted/"."$inputfile"); > $factory->remove_rid($rid); > > > > } > } > } > } > } > > > > I m recieving this error message: > ----------------- WARNING --------------------- > MSG: seq doesn't validate, mismatch is 1 > --------------------------------------------------- > > ------------- EXCEPTION ------------- > MSG: Attempting to set the sequence to > [ADRA2ANM_007417ATGGGCTCACTGCAGCCGGATGCCGGCAACAGCAGCTGGAACGGGACCGAAGCGCCCGGAGGCGGC > > With the attached file! > Thanks > > _________________________________________________________________ > Do You Yahoo!? -- Une adresse @yahoo.fr gratuite et en franais ! > Yahoo! Mail : http://fr.mail.yahoo.com -- Jason Stajich Duke University jason at cgt.mc.duke.edu From grant at rsmas.miami.edu Mon Jan 26 23:49:25 2004 From: grant at rsmas.miami.edu (System Anti-Virus Administrator) Date: Mon Jan 26 23:55:50 2004 Subject: [Bioperl-l] virus found in sent message "Mail Transaction Failed" Message-ID: Attention: bioperl-l@bioperl.org A virus was found in an Email message you sent. This Email scanner intercepted it and stopped the entire message reaching its destination. The virus was reported to be: WORM_MIMAIL.R Please update your virus scanner or contact your IT support personnel as soon as possible as you have a virus on your system. Your message was sent with the following envelope: MAIL FROM: bioperl-l@bioperl.org RCPT TO: agriffa@rsmas.miami.edu ... and with the following headers: --- MAILFROM: bioperl-l@bioperl.org Received: from unknown (HELO bioperl.org) (128.208.70.114) by domino.rsmas.miami.edu with SMTP; 27 Jan 2004 04:49:24 -0000 From: bioperl-l@bioperl.org To: agriffa@rsmas.miami.edu Subject: Mail Transaction Failed Date: Mon, 26 Jan 2004 20:49:24 -0800 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0001_C2AF41DC.A417B07A" X-Priority: 3 X-MSMail-Priority: Normal --- From bogus@does.not.exist.com Tue Jan 27 01:17:25 2004 From: bogus@does.not.exist.com () Date: Tue Jan 27 01:23:56 2004 Subject: [Bioperl-l] Virus Detected by Network Associates, Inc. Webshield SMTP V4.5 MR1a Message-ID: <200401270617.i0R6HUZl029648@ncsusraimge03.jnj.com> Network Associates WebShield SMTP V4.5 MR1a on ncsusrawsc5 detected virus W32/Mydoom@MM (ED) in attachment message.zip from and it was Deleted and Quarantined. From administrator at acscw009.bkc.ritsumei.ac.jp Tue Jan 27 04:30:00 2004 From: administrator at acscw009.bkc.ritsumei.ac.jp (administrator@acscw009.bkc.ritsumei.ac.jp) Date: Tue Jan 27 04:36:47 2004 Subject: [Bioperl-l] Virus Warning Message-ID: <200401270930.AOD03770@acscw009.bkc.ritsumei.ac.jp> The message you emailed to kikuchi@se.ritsumei.ac.jp, dated 01/27/04 18:30:00, contains the W32/MyDoom-A,W32/MyDoom-A virus in the document.zip attachment. Action taken: deleted From m_conte at hotmail.com Tue Jan 27 05:50:34 2004 From: m_conte at hotmail.com (matthieu CONTE) Date: Tue Jan 27 05:57:01 2004 Subject: [Bioperl-l] Bio ::seqIO ::tigr Message-ID: I currently trying to use the Bio ::seqIO ::tigr module. My objective is to download the whole rice genome form Tigr ( adress below)and to integrate it in my BioSQL DB. For this I am trying to convert the tigr format in swiss format with the script below use Bio::SeqIO; my $in = Bio::SeqIO->new(-file =>''tigr'); my $out = Bio::SeqIO->new(-file => '>/home/conte/pipeline_orthologues/data/orysa_swiss.txt' , -format=>'swiss'); print $out $_ while <$in>; I obtain: ------------ EXCEPTION ------------- MSG: [19]Required missing STACK Bio::SeqIO::tigr::throw /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:1338 STACK Bio::SeqIO::tigr::_process_header /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:700 STACK Bio::SeqIO::tigr::_process_assembly /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:535 STACK Bio::SeqIO::tigr::_process_tigr /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:453 STACK Bio::SeqIO::tigr::_process /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:420 STACK Bio::SeqIO::tigr::_initialize /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:90 STACK Bio::SeqIO::new /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO.pm:358 STACK Bio::SeqIO::new /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO.pm:378 STACK toplevel get_bioseq_tigr.pl:8 Could you please tell me if there is a problem with the parser or with the input data format of Tigr? Thanks in advance Matthieu CONTE m_conte@hotmail.com _________________________________________________________________ MSN Messenger : discutez en direct avec vos amis ! http://www.msn.fr/msger/default.asp From heikki at ebi.ac.uk Tue Jan 27 06:33:33 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Tue Jan 27 06:40:11 2004 Subject: [Bioperl-l] Bio ::seqIO ::tigr In-Reply-To: References: Message-ID: <200401271133.33558.heikki@ebi.ac.uk> Matthew, Under linux you code gives an error: "Not a GLOB reference at ..." You are trying to mix streams and file handles. Either replace 'new' method call in object creation with 'newFh', or replace the while line with: while ( my $seq = $in->next_seq() ) { $out->write_seq($seq); } Read more from Bio::SeqIO documentation, e.g: http://doc.bioperl.org/releases/bioperl-1.4/Bio/SeqIO.html Yours, -Heikki On Tuesday 27 Jan 2004 10:50, matthieu CONTE wrote: > I currently trying to use the Bio ::seqIO ::tigr module. > My objective is to download the whole rice genome form Tigr ( adress > below)and to integrate it in my BioSQL DB. > For this I am trying to convert the tigr format in swiss format with the > script below > > > use Bio::SeqIO; > > my $in = Bio::SeqIO->new(-file > =>' =>'tigr'); > > my $out = Bio::SeqIO->new(-file => > '>/home/conte/pipeline_orthologues/data/orysa_swiss.txt' , > -format=>'swiss'); > > print $out $_ while <$in>; > > I obtain: > > ------------ EXCEPTION ------------- > MSG: [19]Required missing > STACK Bio::SeqIO::tigr::throw > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:1338 > STACK Bio::SeqIO::tigr::_process_header > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:700 > STACK Bio::SeqIO::tigr::_process_assembly > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:535 > STACK Bio::SeqIO::tigr::_process_tigr > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:453 > STACK Bio::SeqIO::tigr::_process > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:420 > STACK Bio::SeqIO::tigr::_initialize > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:90 > STACK Bio::SeqIO::new > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO.pm:358 > STACK Bio::SeqIO::new > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO.pm:378 > STACK toplevel get_bioseq_tigr.pl:8 > > Could you please tell me if there is a problem with the parser or with the > input data format of Tigr? > > Thanks in advance > > > > > Matthieu CONTE > m_conte@hotmail.com > > _________________________________________________________________ > MSN Messenger : discutez en direct avec vos amis ! > http://www.msn.fr/msger/default.asp > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From kdj at sanger.ac.uk Tue Jan 27 06:57:26 2004 From: kdj at sanger.ac.uk (Keith James) Date: Tue Jan 27 07:03:53 2004 Subject: [Bioperl-l] Bio ::seqIO ::tigr In-Reply-To: References: Message-ID: >>>>> "matthieu" == matthieu CONTE writes: matthieu> I currently trying to use the Bio ::seqIO ::tigr module. matthieu> My objective is to download the whole rice genome form matthieu> Tigr ( adress below)and to integrate it in my BioSQL DB. matthieu> For this I am trying to convert the tigr format in swiss matthieu> format with the script below This looks like a mismatch between the version of your XML data and the DTD. However, it is hard to be sure without knowing the download dates of your data and DTD. TIGR change the DTD fairly regularly and although they aim to be backwards-compatible this does not always occur (e.g. adding new mandatory attributes or elements). I find it is good to download a new DTD each time, diff it against the previous one and then archive it if there are any changes. Looking at the their FTP site it seems that the XML files there have this element. Look at your file - does the ASSEMBLY element have a HEADER element with an AUTHOR_LIST element in it? Keith -- - Keith James Microarray Facility, Team 65 - - The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK - From khoueiry at ibsm.cnrs-mrs.fr Tue Jan 27 08:12:37 2004 From: khoueiry at ibsm.cnrs-mrs.fr (KHOUEIRY pierre) Date: Tue Jan 27 08:19:04 2004 Subject: [Bioperl-l] reducing time Message-ID: <401663C5.5020003@ibsm.cnrs-mrs.fr> Hi all, In my script, I make a treatment on a big number of fasta files *(same size)*. The problem is (with my exstimations) the total time will be at about 26 hours . In fact it tooks 951 seconds for 10 files. Is there any way to reduce time waist... Or is there a probleme in my code. I add that the script goes faster for the first 20 or 30 files then it slow down but still fix (tested on a big number of files without samll loop on sequences). The output file still empty at the begining till a number of files is being studied and then it stills like that until another series of files is treated. I think it's a buffer problem...! _Her's a bit of the code i use:_ while(my $file = readdir DH) { next if ($file =~ /^\./); my $stream = Bio::SeqIO->new(-file => " 'fasta'); while(my $one_seq = $stream->next_seq()) { $heatcount = 0; $nbhotspot = 0; $aacount = 0; $maxaacount = 0; $nbaamotif = 0; $aanb= 0; my $seq = $one_seq->seq(); /a for loop over each sequence goes here (a heavy one)/ $HSPercernt = $nbhotprot/$nbprot; print "$file\t\t\t"."$nbhotprot\t".substr(($HSPercernt*100),0,4)."\n"; print OUT "$file\t\t\t"."$nbhotprot\t\t\t".substr(($HSPercernt*100),0,4)."\n"; $nbprotanalysed ++; $HSPercernt = 0; $nbhotprot = 0; $i++; if($i%10==5){ my $endtime = time(); my $totaltime = $endtime-$inittime; print "the procedure took ---->", $totaltime,"seconds\n"; } }#End of reading directory while loop From pvh at egenetics.com Tue Jan 27 09:41:44 2004 From: pvh at egenetics.com (Peter van Heusden) Date: Tue Jan 27 09:48:15 2004 Subject: [Bioperl-l] 'Raw' archive of bioperl-guts mailing list? Message-ID: <401678A8.7010102@egenetics.com> Hi Is it possible to get a 'raw' archive of the bioperl-guts mailing list? I'm trying to retrieve some information from the cvs commit messages, and I'd like to process the messages which are now in the archive. Thanks, Peter From sebastien.frade at bayercropscience.com Tue Jan 27 09:42:14 2004 From: sebastien.frade at bayercropscience.com (sebastien.frade@bayercropscience.com) Date: Tue Jan 27 09:50:20 2004 Subject: [Bioperl-l] problem with pir sequence Message-ID: Hi, I'ma working with pir files, and i have a problem during reading file with bioperl. here is the code, use strict; use Bio::SeqIO; my $filename="deux.S64"; print new Bio::Tools::GuessSeqFormat( -file => $filename )->guess,"\n"; my $in = Bio::SeqIO->new(-file => $filename , '-format' => 'pir'); my $seq; while ($seq = $in->next_seq() ) { print "Sequence ",$seq->id," first 10 bases ",$seq->subseq(1,10),"\n"; } and here is the error message -------------------- WARNING --------------------- MSG: seq doesn't validate, mismatch is 1 --------------------------------------------------- ------------- EXCEPTION ------------- MSG: Attempting to set the sequence to [N;Alternatenames:albumin2SprecursorC;Species:BertholletiaexcelsaBrazilnutC;Date:21-Nov-1993#sequence_revision26-May-1995#text_change21-Jul-2000C;Accession:S14946;S14479;S06252;S21640;B25802R;GanderES;HolmstroemKO;dePaivaGR;deCastroLAB;CarneiroM;GrossideSaMFPlantMolBiol16437-4481991A;Title:Isolationcharacterizationandexpressionofagenecodingfora2SalbuminfromBertholletiaexcelsaBrazilnutA;Referencenumber:S14946;MUID:91370890;PMID:1840683A;Accession:S14946A;Status:preliminaryA;Moleculetype:DNAA;Residues:1-146 References: Message-ID: pir support is pretty minimal - you'll have to send a copy of the original seq file for someone to see if they can help. On Tue, 27 Jan 2004 sebastien.frade@bayercropscience.com wrote: > > > > > Hi, > > I'ma working with pir files, and i have a problem during reading file with > bioperl. > > here is the code, > > > > use strict; > > use Bio::SeqIO; > > my $filename="deux.S64"; > > print new Bio::Tools::GuessSeqFormat( -file => $filename )->guess,"\n"; > > > my $in = Bio::SeqIO->new(-file => $filename , '-format' => 'pir'); > my $seq; > > while ($seq = $in->next_seq() ) { > print "Sequence ",$seq->id," first 10 bases ",$seq->subseq(1,10),"\n"; > } > > > and here is the error message > > -------------------- WARNING --------------------- > MSG: seq doesn't validate, mismatch is 1 > --------------------------------------------------- > > ------------- EXCEPTION ------------- > MSG: Attempting to set the sequence to > [N;Alternatenames:albumin2SprecursorC;Species:BertholletiaexcelsaBrazilnutC;Date:21-Nov-1993#sequence_revision26-May-1995#text_change21-Jul-2000C;Accession:S14946;S14479;S06252;S21640;B25802R;GanderES;HolmstroemKO;dePaivaGR;deCastroLAB;CarneiroM;GrossideSaMFPlantMolBiol16437-4481991A;Title:Isolationcharacterizationandexpressionofagenecodingfora2SalbuminfromBertholletiaexcelsaBrazilnutA;Referencenumber:S14946;MUID:91370890;PMID:1840683A;Accession:S14946A;Status:preliminaryA;Moleculetype:DNAA;Residues:1-146 which does not look healthy > STACK Bio::PrimarySeq::seq /usr/local/lib/perl5/site_perl/5.8.0 > /Bio/PrimarySeq.pm:268 > STACK Bio::PrimarySeq::new /usr/local/lib/perl5/site_perl/5.8.0 > /Bio/PrimarySeq.pm:217 > STACK Bio::Seq::new /usr/local/lib/perl5/site_perl/5.8.0/Bio/Seq.pm:498 > STACK Bio::Seq::SeqFactory::create /usr/local/lib/perl5/site_perl/5.8.0 > /Bio/Seq/SeqFactory.pm:126 > STACK Bio::SeqIO::pir::next_seq /usr/local/lib/perl5/site_perl/5.8.0 > /Bio/SeqIO/pir.pm:122 > STACK toplevel pir.pl:15 > > > Is there a problem with my code ? > > Please help me!!! > > > > > > > > S?bastien Frade > BioInformatic Team > BAYER CropScience / BioScience > 4 rue Pierre FONTAINE > 91058 EVRY ? France > > tel: 33 (0) 1 69 47 61 52 > > fax: 33 (0) 1 69 47 61 42 > > mail: > sebastien.frade@bayercropscience.com > > http://bioinfo.evry.fr.bayercropscience > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From jason at cgt.duhs.duke.edu Tue Jan 27 09:51:55 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Jan 27 09:58:32 2004 Subject: [Bioperl-l] 'Raw' archive of bioperl-guts mailing list? In-Reply-To: <401678A8.7010102@egenetics.com> References: <401678A8.7010102@egenetics.com> Message-ID: There is a link for each month as a textfile here: http://portal.open-bio.org/pipermail/bioperl-guts-l/ If you are processing cvs commit messages makes more sense to go to the source rather than trusting the bioperl-guts messages... They mails are definitely not complete as there are various times when mails got held up or srv problems discarded some mails from commits. -jason On Tue, 27 Jan 2004, Peter van Heusden wrote: > Hi > > Is it possible to get a 'raw' archive of the bioperl-guts mailing list? > I'm trying to retrieve some information from the cvs commit messages, > and I'd like to process the messages which are now in the archive. > > Thanks, > Peter > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From sebastien.frade at bayercropscience.com Tue Jan 27 09:55:36 2004 From: sebastien.frade at bayercropscience.com (sebastien.frade@bayercropscience.com) Date: Tue Jan 27 10:03:51 2004 Subject: =?ISO-8859-1?Q?R=E9f=2E_=3A_Re=3A_[Bioperl-l]_problem_with_pir_sequence?= Message-ID: Here is the pir file I use. >P1;S14946 2S seed storage protein large chain - Brazil nut N;Alternate names: albumin 2S precursor C;Species: Bertholletia excelsa (Brazil nut) C;Date: 21-Nov-1993 #sequence_revision 26-May-1995 #text_change 21-Jul-2000 C;Accession: S14946; S14479; S06252; S21640; B25802 R;Gander, E.S.; Holmstroem, K.O.; de Paiva, G.R.; de Castro, L.A.B.; Carneiro, M.; Grossi de Sa, M.F. Plant Mol. Biol. 16, 437-448, 1991 A;Title: Isolation, characterization and expression of a gene coding for a 2S albumin from Bertholletia excelsa (Brazil nut). A;Reference number: S14946; MUID:91370890; PMID:1840683 A;Accession: S14946 A;Status: preliminary A;Molecule type: DNA A;Residues: 1-146 A;Cross-references: EMBL:X54490; NID:g17710; PIDN:CAA38362.1; PID:g17711 A;Note: the authors translated the codon CTT for residue 13 as Val and GTC for residue 14 as Leu R;Bassuener, R.; Schlesier, B. submitted to the EMBL Data Library, December 1990 A;Reference number: S14479 A;Accession: S14479 A;Status: preliminary A;Molecule type: DNA A;Residues: 1-146 A;Cross-references: EMBL:X57027; NID:g17714; PID:g17715 R;Altenbach, S.B.; Pearson, K.W.; Leung, F.W.; Sun, S.S.M. Plant Mol. Biol. 8, 239-250, 1987 A;Title: Cloning and sequence analysis of a cDNA encoding a Brazil nut protein exceptionally rich in methionine. A;Reference number: S06252 A;Accession: S06252 A;Status: not compared with conceptual translation A;Molecule type: mRNA A;Residues: 1-146 A;Experimental source: clone pHS-3 A;Note: part of this sequence, including the amino end of the large chain, was confirmed by protein sequencing R;Bassuener, R.; Schlesier, B. submitted to the EMBL Data Library, December 1990 A;Reference number: S21640 A;Accession: S21640 A;Status: preliminary A;Molecule type: DNA A;Residues: 1-146 A;Cross-references: EMBL:X57028; NID:g17716; PID:g17717 R;Ampe, C.; Van Damme, J.; de Castro, L.A.B.; Sampaio, M.J.A.M.; Van Montagu, M.; Vandekerckhove, J. Eur. J. Biochem. 159, 597-604, 1986 A;Title: The amino-acid sequence of the 2S sulphur-rich proteins from seeds of Brazil nut (Bertholletia excelsa H.B.K.). A;Reference number: A91173; MUID:87004679; PMID:3758080 A;Accession: B25802 A;Molecule type: protein A;Residues: 70-90,'E',92-121,'M',123-125,'L',127-142 C;Genetics: A;Introns: 60/3 C;Superfamily: wheat alpha-amylase inhibitor F;1-22/Domain: signal sequence #status predicted F;23-46/Domain: propeptide #status predicted F;47-69/Product: seed storage protein small chain #status predicted F;70-146/Product: seed storage protein large chain #status experimental MAKISVAAAALLVLMALGHATAFRATVTTTVVEEENQEECREQMQRQQMLSHCRMYMRQQ MEESPYQTMPRRGMEPHMSECCEQLEGMDESCRCEGLRMMMMRMQQEEMQPRGEQMRRMM RLAENIPSRCNLSPMRCPMGGSIAGF* S?bastien Frade BioInformatic Team BAYER CropScience / BioScience 4 rue Pierre FONTAINE 91058 EVRY ? France tel: 33 (0) 1 69 47 61 52 fax: 33 (0) 1 69 47 61 42 mail: sebastien.frade@bayercropscience.com http://bioinfo.evry.fr.bayercropscience Pour : sebastien.frade@bayercropscience.com cc : bioperl-l@bioperl.org Objet : Re: [Bioperl-l] problem with pir sequence bioperl-l-bounces@portal.open-bio. org 27/01/2004 15:51 pir support is pretty minimal - you'll have to send a copy of the original seq file for someone to see if they can help. On Tue, 27 Jan 2004 sebastien.frade@bayercropscience.com wrote: > > > > > Hi, > > I'ma working with pir files, and i have a problem during reading file with > bioperl. > > here is the code, > > > > use strict; > > use Bio::SeqIO; > > my $filename="deux.S64"; > > print new Bio::Tools::GuessSeqFormat( -file => $filename )->guess,"\n"; > > > my $in = Bio::SeqIO->new(-file => $filename , '-format' => 'pir'); > my $seq; > > while ($seq = $in->next_seq() ) { > print "Sequence ",$seq->id," first 10 bases ",$seq->subseq(1,10),"\n"; > } > > > and here is the error message > > -------------------- WARNING --------------------- > MSG: seq doesn't validate, mismatch is 1 > --------------------------------------------------- > > ------------- EXCEPTION ------------- > MSG: Attempting to set the sequence to > [N;Alternatenames:albumin2SprecursorC;Species:BertholletiaexcelsaBrazilnutC;Date:21-Nov-1993#sequence_revision26-May-1995#text_change21-Jul-2000C;Accession:S14946;S14479;S06252;S21640;B25802R;GanderES;HolmstroemKO;dePaivaGR;deCastroLAB;CarneiroM;GrossideSaMFPlantMolBiol16437-4481991A;Title:Isolationcharacterizationandexpressionofagenecodingfora2SalbuminfromBertholletiaexcelsaBrazilnutA;Referencenumber:S14946;MUID:91370890;PMID:1840683A;Accession:S14946A;Status:preliminaryA;Moleculetype:DNAA;Residues:1-146 which does not look healthy > STACK Bio::PrimarySeq::seq /usr/local/lib/perl5/site_perl/5.8.0 > /Bio/PrimarySeq.pm:268 > STACK Bio::PrimarySeq::new /usr/local/lib/perl5/site_perl/5.8.0 > /Bio/PrimarySeq.pm:217 > STACK Bio::Seq::new /usr/local/lib/perl5/site_perl/5.8.0/Bio/Seq.pm:498 > STACK Bio::Seq::SeqFactory::create /usr/local/lib/perl5/site_perl/5.8.0 > /Bio/Seq/SeqFactory.pm:126 > STACK Bio::SeqIO::pir::next_seq /usr/local/lib/perl5/site_perl/5.8.0 > /Bio/SeqIO/pir.pm:122 > STACK toplevel pir.pl:15 > > > Is there a problem with my code ? > > Please help me!!! > > > > > > > > S?bastien Frade > BioInformatic Team > BAYER CropScience / BioScience > 4 rue Pierre FONTAINE > 91058 EVRY ? France > > tel: 33 (0) 1 69 47 61 52 > > fax: 33 (0) 1 69 47 61 42 > > mail: > sebastien.frade@bayercropscience.com > > http://bioinfo.evry.fr.bayercropscience > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From MAILER-DAEMON at smtp.noos.fr Tue Jan 27 10:29:04 2004 From: MAILER-DAEMON at smtp.noos.fr (MAILER-DAEMON@smtp.noos.fr) Date: Tue Jan 27 10:35:35 2004 Subject: [Bioperl-l] failure notice Message-ID: <200401271535.i0RFZUEt019328@portal.open-bio.org> Hi. This is the qmail-send program at smtp.noos.fr. I'm afraid I wasn't able to deliver your message to the following addresses. This is a permanent error; I've given up. Sorry it didn't work out. : Sorry, no mailbox here by that name. (#5.1.1) --- Below this line is a copy of the message. 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[Bioperl-l] failure notice Message-ID: This is an info mail issued by the Bayer virus checking software: Prior to this message you received an e-mail where a virus has been detected and removed, details see below. The attachment is now empty. The sender has already been notified. Dies ist eine Info-Mail vom Bayer Virenscanner: Sie erhielten eine e-Mail, in der ein Virus entdeckt und entfernt wurde, Details siehe unten. Der Anhang ist nun leer. Der Absender wurde bereits benachrichtigt. Date: 01/27/2004 04:29:16 PM Subject: [Bioperl-l] failure notice Virus: WORM_MIMAIL.R File: text.zip From: bioperl-l-bounces@portal.open-bio.org To: bioperl-l@bioperl.org Action: Quarantined; Scanned by ScanMail for Lotus Notes 2.6 with scanengine 6.810-1005 and patternfile lpt$vpn.745 From heikki at nildram.co.uk Tue Jan 27 10:55:17 2004 From: heikki at nildram.co.uk (Heikki Lehvaslaiho) Date: Tue Jan 27 11:01:44 2004 Subject: [Bioperl-l] reducing time In-Reply-To: <401663C5.5020003@ibsm.cnrs-mrs.fr> References: <401663C5.5020003@ibsm.cnrs-mrs.fr> Message-ID: <200401271555.18222.heikki@nildram.co.uk> Pierre, I could not find anything wrong in your code. 95 seconds per file (you mean per sequence?) is really slow. The problem according my tests is your local system. Maybe you have too many files per directory? Not enough RAM? Maybe your subroutine is not optimal? Sporadic filling of the output file is normal behavour of the unix file system, so I do not think there is nothing wrong in that. It just shows that IO and/or CPU are very buzy. I tested your code by copying it into a file (rd.pl) and copying a half a dozen fasta files from BIOPERLROOT/t/data (alnfile.fasta amino.fa dna1.fa dna2.fa multi_1.fa multi_2.fa) into a subdirectory 'fasta' and ran it in my laptop: time perl rd.pl fasta The output from the time command was: 0.43user 0.02system 0:00.57elapsed 80%CPU (and time diff from code 0 sec.) Yours, -Heikki ################################### use Bio::SeqIO; opendir(DIR, shift ) || die "can't opendir : $!"; while (my $file = readdir DIR) { next if ($file =~ /^\./); print STDERR $file, "\n"; #next; my $stream = Bio::SeqIO->new(-file =>" 'fasta'); while (my $one_seq = $stream->next_seq()) { $inittime = time(); $heatcount = 0; $nbhotspot = 0; $aacount = 0; $maxaacount = 0; $nbaamotif = 0; $aanb= 0; my $seq = $one_seq->seq(); #/a for loop over each sequence goes here (a heavy one)/ $HSPercernt = 22;#$nbhotprot/$nbprot; print "$file\t\t\t"."$nbhotprot\t".substr(($HSPercernt*100),0,4)."\n"; print OUT "$file\t\t\t"."$nbhotprot\t\t\t".substr(($HSPercernt*100),0,4)."\n"; $nbprotanalysed ++; $HSPercernt = 0; $nbhotprot = 0; $i++; if ($i%10==5) { my $endtime = time(); my $totaltime = $endtime-$inittime; print "the procedure took ---->", $totaltime,"seconds\n"; } } } #End of reading directory while loop ################################### On Tuesday 27 Jan 2004 13:12, KHOUEIRY pierre wrote: > Hi all, > In my script, I make a treatment on a big number of fasta files *(same > size)*. The problem is (with my exstimations) the total time will be at > about 26 hours . In fact it tooks 951 seconds for 10 files. > Is there any way to reduce time waist... Or is there a probleme in my > code. I add that the script goes faster for the first 20 or 30 files > then it slow down but still fix (tested on a big number of files without > samll loop on sequences). The output file still empty at the begining > till a number of files is being studied and then it stills like that > until another series of files is treated. I think it's a buffer problem...! > > _Her's a bit of the code i use:_ > > while(my $file = readdir DH) > { > next if ($file =~ /^\./); > > my $stream = Bio::SeqIO->new(-file => > " 'fasta'); > > while(my $one_seq = $stream->next_seq()) > { > > $heatcount = 0; > $nbhotspot = 0; > $aacount = 0; > $maxaacount = 0; > $nbaamotif = 0; > $aanb= 0; > > my $seq = $one_seq->seq(); > > /a for loop over each sequence goes here (a heavy one)/ > $HSPercernt = $nbhotprot/$nbprot; > > print "$file\t\t\t"."$nbhotprot\t".substr(($HSPercernt*100),0,4)."\n"; > print OUT > "$file\t\t\t"."$nbhotprot\t\t\t".substr(($HSPercernt*100),0,4)."\n"; > > $nbprotanalysed ++; > $HSPercernt = 0; > $nbhotprot = 0; > $i++; > if($i%10==5){ > my $endtime = time(); > my $totaltime = $endtime-$inittime; > print "the procedure took ---->", $totaltime,"seconds\n"; > } > }#End of reading directory while loop > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From usergroup-help at mjolner.dk Tue Jan 27 11:21:21 2004 From: usergroup-help at mjolner.dk (usergroup-help@mjolner.dk) Date: Tue Jan 27 11:27:53 2004 Subject: [Bioperl-l] confirm subscribe to usergroup@mjolner.dk Message-ID: <1075220481.9311.ezmlm@mjolner.dk> Hi! This is the ezmlm program. I'm managing the usergroup@mjolner.dk mailing list. To confirm that you would like bioperl-l@bioperl.org added to the usergroup mailing list, please send an empty reply to this address: usergroup-sc.1075220481.pghpogbfgkgaofngfpae-bioperl-l=bioperl.org@mjolner.dk Usually, this happens when you just hit the "reply" button. If this does not work, simply copy the address and paste it into the "To:" field of a new message. This confirmation serves two purposes. First, it verifies that I am able to get mail through to you. Second, it protects you in case someone forges a subscription request in your name. --- Administrative commands for the usergroup list --- I can handle administrative requests automatically. Please DO NOT SEND THEM TO THE LIST ADDRESS! If you do, I will not see them and other subscribers will be annoyed. Instead, send your message to the correct command address: To subscribe to the list, send a message to: To remove your address from the list, send a message to: Send mail to the following for info and FAQ for this list: To get messages 123 through 145 (a maximum of 100 per request), mail: To get an index with subject and author for messages 123-456 , mail: They are always returned as sets of 100, max 2000 per request, so you'll actually get 100-499. To receive all messages with the same subject as message 12345, send an empty message to: The messages do not really need to be empty, but I will ignore their content. Only the ADDRESS you send to is important. You can start a subscription for an alternate address, for example "john@host.domain", just add a hyphen and your address (with '=' instead of '@') after the command word: To stop subscription for this address, mail: In both cases, I'll send a confirmation message to that address. When you receive it, simply reply to it to complete your subscription. If despite following these instructions, you do not get the desired results, please contact my owner at usergroup-owner@mjolner.dk. Please be patient, my owner is a lot slower than I am ;-) --- Enclosed is a copy of the request I received. Return-Path: Received: (qmail 9306 invoked by uid 10706); 27 Jan 2004 16:21:21 -0000 Received: from spamfilter.mjolner.dk (HELO spamfilter.mjolner.com) (10.0.0.81) by midgaard.mjolner.dk with SMTP; 27 Jan 2004 16:21:18 -0000 Received: from localhost (localhost [127.0.0.1]) by spamfilter.mjolner.com (Postfix) with ESMTP id E860428724 for ; Tue, 27 Jan 2004 17:31:08 +0100 (CET) Received: from spamfilter.mjolner.com ([127.0.0.1]) by localhost (blade.mjolner.com [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 08443-08 for ; Tue, 27 Jan 2004 17:31:08 +0100 (CET) Received: from bioperl.org (unknown [204.60.133.70]) by spamfilter.mjolner.com (Postfix) with ESMTP id ACF2428722 for ; Tue, 27 Jan 2004 17:31:07 +0100 (CET) From: bioperl-l@bioperl.org To: usergroup-subscribe@mjolner.com Subject: ***SPAM*** hi Date: Tue, 27 Jan 2004 11:20:50 -0500 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0005_44945239.81E56E97" X-Priority: 3 X-MSMail-Priority: Normal 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AAAAAAEAAQAAADgAAIAAAAAAAAAAAAAAAAAAAAEACQQAAFAAAACowAAAKAEAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAQAAAKAAAIB4AACAAAAAAAAAAAAAAAAAAAABAAkEAACQAAAA1MEAABQAAAAAAAAA AAAAAAEAMACwkAAAKAAAABAAAAAgAAAAAQAEAAAAAADAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AIAAAIAAAACAgACAAAAAgACAAICAAACAgIAAwMDAAAAA/wAA/wAAAP//AP8AAAD/AP8A//8AAP// /wAAAIiIiAAAAAAIh3d3eIAAAHj//4iHcAAAePeP//94AAB4/////3gAAHj3d3j/eAAAeP////94 AAB493d4/3gAAHj/////eAAAePd3j/94AAB4/////3gAAHj/////eAAAeH9/f394AACHc4eHh4AA AAezO3t3gAAAAAAAAIAAAPA/AADgBwAAwAcAAMADAADAAwAAwAMAAMADAADAAwAAwAMAAMADAADA AwAAwAMAAMADAADABwAA4AcAAP/fAADYkQAAAAABAAEAEBAQAAEABAAoAQAAAQAAAAAAAAAAAAAA AACQwgAAYMIAAAAAAAAAAAAAAAAAAJ3CAABwwgAAAAAAAAAAAAAAAAAAqsIAAHjCAAAAAAAAAAAA AAAAAAC1wgAAgMIAAAAAAAAAAAAAAAAAAMDCAACIwgAAAAAAAAAAAAAAAAAAAAAAAAAAAADKwgAA 2MIAAOjCAAAAAAAA9sIAAAAAAAAEwwAAAAAAAAzDAAAAAAAAcwAAgAAAAABLRVJORUwzMi5ETEwA QURWQVBJMzIuZGxsAE1TVkNSVC5kbGwAVVNFUjMyLmRsbABXUzJfMzIuZGxsAABMb2FkTGlicmFy eUEAAEdldFByb2NBZGRyZXNzAABFeGl0UHJvY2VzcwAAAFJlZ0Nsb3NlS2V5AAAAbWVtc2V0AAB3 c3ByaW50ZkEAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAFBLAQIUAAoAAAAAAJmCOzDKJx+eAFgAAABYAABUAAAAAAAAAAAAIAAAAAAA AAByZWFkbWUuaHRtICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAg ICAgICAgICAgICAgICAgICAgICAgICAgIC5leGVQSwUGAAAAAAEAAQCCAAAAclgAAAAA ------=_NextPart_000_0005_44945239.81E56E97-- From dag at bioteam.net Tue Jan 27 12:10:31 2004 From: dag at bioteam.net (Chris Dagdigian) Date: Tue Jan 27 12:32:23 2004 Subject: [Bioperl-l] 'Raw' archive of bioperl-guts mailing list? In-Reply-To: <401678A8.7010102@egenetics.com> Message-ID: Hello, You can get monthly raw archives from here: http://portal.open-bio.org/pipermail/bioperl-guts-l/ I may be able to tar them up for you to download if this suits your need. Regards, Chris On Tue, 27 Jan 2004, Peter van Heusden wrote: > Hi > > Is it possible to get a 'raw' archive of the bioperl-guts mailing list? > I'm trying to retrieve some information from the cvs commit messages, > and I'd like to process the messages which are now in the archive. > > Thanks, > Peter From hlapp at gmx.net Tue Jan 27 12:31:39 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue Jan 27 12:38:06 2004 Subject: [Bioperl-l] Bio ::seqIO ::tigr In-Reply-To: Message-ID: A question aside: why do you want to convert to swissprot in order to load into biosql? (load_seqdatabase.pl can use any SeqIO reader.) -hilmar On Tuesday, January 27, 2004, at 02:50 AM, matthieu CONTE wrote: > I currently trying to use the Bio ::seqIO ::tigr module. > My objective is to download the whole rice genome form Tigr ( adress > below)and to integrate it in my BioSQL DB. > For this I am trying to convert the tigr format in swiss format with > the script below > > > use Bio::SeqIO; > > my $in = Bio::SeqIO->new(-file > =>' =>'tigr'); > > my $out = Bio::SeqIO->new(-file => > '>/home/conte/pipeline_orthologues/data/orysa_swiss.txt' , > -format=>'swiss'); > > print $out $_ while <$in>; > > I obtain: > > ------------ EXCEPTION ------------- > MSG: [19]Required missing > STACK Bio::SeqIO::tigr::throw > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:1338 > STACK Bio::SeqIO::tigr::_process_header > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:700 > STACK Bio::SeqIO::tigr::_process_assembly > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:535 > STACK Bio::SeqIO::tigr::_process_tigr > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:453 > STACK Bio::SeqIO::tigr::_process > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:420 > STACK Bio::SeqIO::tigr::_initialize > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:90 > STACK Bio::SeqIO::new > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO.pm:358 > STACK Bio::SeqIO::new > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO.pm:378 > STACK toplevel get_bioseq_tigr.pl:8 > > Could you please tell me if there is a problem with the parser or with > the input data format of Tigr? > > Thanks in advance > > > > > Matthieu CONTE > m_conte@hotmail.com > > _________________________________________________________________ > MSN Messenger : discutez en direct avec vos amis ! > http://www.msn.fr/msger/default.asp > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From jaudall at iastate.edu Tue Jan 27 12:43:15 2004 From: jaudall at iastate.edu (Joshua A Udall) Date: Tue Jan 27 12:52:27 2004 Subject: [Bioperl-l] EST functional categories In-Reply-To: <30766.1075064249@www61.gmx.net> References: <6.0.1.1.2.20040122143719.01e2d918@jaudall.mail.iastate.edu> <30766.1075064249@www61.gmx.net> Message-ID: <6.0.1.1.2.20040127112248.01d56f40@jaudall.mail.iastate.edu> At 02:57 PM 1/25/2004, Eckhard Lehmann wrote: > > I'm working on an EST project. I'd like to use bioperl to identify > > putative functional categories of individual ESTs and eventually end up > > with those ubiquitous pie charts or histograms (using excel). I've seen > > that ontologies structures have been built into bioperl but there isn't > > much documentation (or I've overlooked it). I could use some help/example > >I am not quite sure about that - but isn't it better to do functional >analysis on contigs that are assembled of EST's, rather that individual EST's? Of course contigs, my mistake in the description. > > scripts to get started. I've blasted all my ESTs against nr. How do I > > take the best blast hit and look it it's functional category on > > GO/Interpro? > >In the EST project that I am working on - I have the impression yet, that >you can not pull out much usefull information of these short sequence parts. >When it comes to BLASTx for instance, you get many many different >confusing and >discusting non-informative hits. >With contigs you have mostly eliminated the redundancy and can do better >BLASTx. Functional analysis should then be possible by backtracking the EST >source information. sure, and even more confusing is that I'm working with a polyploid. You're right the contigs help a lot but assuming I want to use the best blast hit, how do I retrieve a GO object using that Arabidopsis gene id (from nr)? >I have done some stuff, but it is mainly database oriented (PostgreSQL, >PL/PgSQL) and has not much to do with BioPerl currently. Used only >BioPerl-DB to >load the EST sequences into a BioSQL setup along with contigs and things, and >now to fetch individual sequences into flat files sometimes. >However, I used Perl and GD::Graph for making pie charts and a web interface >to the database. > >Eckhard ;) > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l Joshua Udall Department of Ecology, Evolution, and Organismal Biology Iowa State University Ames, IA 50011 Ph: (515) 294-7098 Fax: (515) 294-1337 From ANTIGEN_EX-MAIL at nybg.org Tue Jan 27 13:50:21 2004 From: ANTIGEN_EX-MAIL at nybg.org (ANTIGEN_EX-MAIL) Date: Tue Jan 27 13:50:37 2004 Subject: [Bioperl-l] Antigen found FILE FILTER= *.zip file Message-ID: Antigen for Exchange found data.zip matching FILE FILTER= *.zip file filter. The file is currently Removed. The message, "Mail Transaction Failed", was sent from bioperl-l@bioperl.org and was discovered in IMC Queues\Inbound located at NYBG/NYBG-NT/EX-MAIL. From tewang at uci.edu Tue Jan 27 14:41:54 2004 From: tewang at uci.edu (Eric Wang) Date: Tue Jan 27 14:48:27 2004 Subject: [Bioperl-l] Popgene::Statistics Message-ID: <1075232514.smmsdV1.1.2@smtp.uci.edu> Dear all, I am a bit confused on the input format for the Bio::PopGen::Statistics class. It seems the IO will take CSV, and PrettyBase format. So does this mean the tests (Tajima_D, Fu_Li_D, etc) will compute the scores for heterozygote (diploid) dataset too? Also, it seems that we need to implement our own next_individual subroutine? is that the current status? Many thanks! Eric T. Wang Graduate Student University of California, Irvine Molecular biology, Genetics, and Biochemistry Bioinformatics Track tewang@uci.edu 949-824-1870 From donald.jackson at bms.com Tue Jan 27 15:28:11 2004 From: donald.jackson at bms.com (Donald G. Jackson) Date: Tue Jan 27 15:34:41 2004 Subject: [Bioperl-l] Question about using XML::Parser::PerlSAX for sequence parsing Message-ID: <4016C9DB.6090808@bms.com> Hi, I'm working on a SeqIO adapter for the NCBI TinySeq XML format and have a question about XML::Parser::PerlSAX. Currently, my parser goes through the whole XML file and stores the results in a stack. My next_seq() method pulls the next element off the stack, converts it to a Bio::Seq object, and returns it. This works, but I'd rather be able to step through the input XML one sequence at a time. I thought bioperl selected PerlSAX because it could do that, but I'm having trouble figuring out how. I looked at Bio::SeqIO::game, but that also loads all of the parsed data into memory. I'd like to implement something analagous to how Bio::SeqIO::fasta steps through an input file, though without having to get to such low-level methods. If anyone on the list has any suggestions, I'd be grateful! Thanks, Don Jackson BMS Bioinformatics PS - I'm putting together a test suite and hope to have the preliminary version of Bio::SeqIO::tinyseq checked into the cvs repository in the next day or so. From jason at cgt.duhs.duke.edu Tue Jan 27 18:25:59 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Jan 27 18:32:23 2004 Subject: [Bioperl-l] Popgene::Statistics In-Reply-To: <1075232514.smmsdV1.1.2@smtp.uci.edu> References: <1075232514.smmsdV1.1.2@smtp.uci.edu> Message-ID: On Tue, 27 Jan 2004, Eric Wang wrote: > Dear all, > > I am a bit confused on the input format for the Bio::PopGen::Statistics > > class. It seems the IO will take CSV, and PrettyBase format. > > So does this mean the tests (Tajima_D, Fu_Li_D, etc) will compute the > scores for heterozygote (diploid) dataset too? > Yeah the tests were initially written for dealing directly with output from the Coalescent simulations - forgot to add the part to deal with diploid pops. You have to convert the population to haploid first by making fake chromosomes - (This is only possible with new code I just committed) my $happop = $pop->haploid_population; my $D = Bio::PopGen::Statistics->tajima_D($happop); > Also, it seems that we need to implement our own next_individual > subroutine? is that the current status? Not really - only if you want to implement your own Bio::PopGen::IO parser... Where did you get the impression you need to implement next_individual yourself? Here is some basic code #!/usr/bin/perl -w use strict; use Bio::PopGen::IO; use Bio::PopGen::Statistics; my $in = Bio::PopGen::IO->new(-format => 'prettybase', -file => 'diploid.prettybase.txt'); my $pop = $in->next_population; my $happop = $pop->haploid_population; print Bio::PopGen::Statistics->tajima_D($happop),"\n"; Let me know if you have any more questions. --jason > > Many thanks! > > Eric T. Wang > Graduate Student > University of California, Irvine > Molecular biology, Genetics, and Biochemistry > Bioinformatics Track > tewang@uci.edu > 949-824-1870 > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From donald.jackson at bms.com Tue Jan 27 20:54:28 2004 From: donald.jackson at bms.com (Donald Jackson) Date: Tue Jan 27 21:00:55 2004 Subject: [Bioperl-l] Bio::SeqIO::tinyseq Message-ID: <5bb7a5bedc.5bedc5bb7a@bms.com> Hi, I've uploaded Bio::SeqIO::tinyseq, a SeqIO module for parsing the NCBI TinySeq XML format to the bioperl cvs repository. Currently, it only reads and writes 'fasta-like' information (accession, description, sequence, sequence type). The DTD supports additional info (such as organism/TaxID) which I'm working on adding to formats that support this info. Please let me know if you have questions, suggestions, and especially bugs... Don Jackson BMS Bioinformatics From MAILER-DAEMON at blort.org Tue Jan 27 23:37:43 2004 From: MAILER-DAEMON at blort.org (MAILER-DAEMON@blort.org) Date: Tue Jan 27 23:44:16 2004 Subject: [Bioperl-l] failure notice Message-ID: <200401280444.i0S4iCEs030442@portal.open-bio.org> Hi. This is the qmail-send program at blort.org. I'm afraid I wasn't able to deliver your message to the following addresses. This is a permanent error; I've given up. Sorry it didn't work out. : Sorry, no mailbox here by that name. vpopmail (#5.1.1) --- Below this line is a copy of the message. 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I'm trying to install bioperl to a local directory. [june@bg03n001e00]~/bioperl-1.4(4): make Make: line too long. Stop. [june@bg03n001e00]~/bioperl-1.4(7): uname -a OSF1 bg03n001e00.hpc.cmc.osaka-u.ac. V5.1 1885 alpha I'm not sure what other information I need to provide... Any suggestions very much appreciated. Thank you June From heikki at nildram.co.uk Wed Jan 28 02:58:02 2004 From: heikki at nildram.co.uk (Heikki Lehvaslaiho) Date: Wed Jan 28 03:04:31 2004 Subject: [Bioperl-l] Bio::SeqIO::tinyseq In-Reply-To: <5bb7a5bedc.5bedc5bb7a@bms.com> References: <5bb7a5bedc.5bedc5bb7a@bms.com> Message-ID: <200401280758.03040.heikki@nildram.co.uk> Donald, The best way to do this is to ignore the root level of the xml, use perl to parse entries out of it, and pass entry xml only to the parser. This keeps the memory usage down and you can parse as large file as you want. I've done it using XML::Twig in BIo::Variation::IO::xml, but the same can be applied to PerlSAX. sub next { my( $self ) = @_; local $/ = "\n"; return unless my $entry = $self->_readline; return unless $entry =~ /^\W*new; # create new parser object my $twig_handlers = {'seqDiff' => \&_seqDiff }; my $t = new XML::Twig ( TwigHandlers => $twig_handlers, KeepEncoding => 1 ); $t->parse($entry); return $seqdiff; } -Heikki On Wednesday 28 Jan 2004 01:54, Donald Jackson wrote: > Hi, > > I've uploaded Bio::SeqIO::tinyseq, a SeqIO module for parsing the NCBI > TinySeq XML format to the bioperl cvs repository. Currently, it only reads > and writes 'fasta-like' information (accession, description, sequence, > sequence type). The DTD supports additional info (such as organism/TaxID) > which I'm working on adding to formats that support this info. > > Please let me know if you have questions, suggestions, and especially > bugs... > > Don Jackson > BMS Bioinformatics > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From heikki at nildram.co.uk Wed Jan 28 02:58:02 2004 From: heikki at nildram.co.uk (Heikki Lehvaslaiho) Date: Wed Jan 28 03:04:34 2004 Subject: [Bioperl-l] Bio::SeqIO::tinyseq In-Reply-To: <5bb7a5bedc.5bedc5bb7a@bms.com> References: <5bb7a5bedc.5bedc5bb7a@bms.com> Message-ID: <200401280758.03040.heikki@nildram.co.uk> Donald, The best way to do this is to ignore the root level of the xml, use perl to parse entries out of it, and pass entry xml only to the parser. This keeps the memory usage down and you can parse as large file as you want. I've done it using XML::Twig in BIo::Variation::IO::xml, but the same can be applied to PerlSAX. sub next { my( $self ) = @_; local $/ = "\n"; return unless my $entry = $self->_readline; return unless $entry =~ /^\W*new; # create new parser object my $twig_handlers = {'seqDiff' => \&_seqDiff }; my $t = new XML::Twig ( TwigHandlers => $twig_handlers, KeepEncoding => 1 ); $t->parse($entry); return $seqdiff; } -Heikki On Wednesday 28 Jan 2004 01:54, Donald Jackson wrote: > Hi, > > I've uploaded Bio::SeqIO::tinyseq, a SeqIO module for parsing the NCBI > TinySeq XML format to the bioperl cvs repository. Currently, it only reads > and writes 'fasta-like' information (accession, description, sequence, > sequence type). The DTD supports additional info (such as organism/TaxID) > which I'm working on adding to formats that support this info. > > Please let me know if you have questions, suggestions, and especially > bugs... > > Don Jackson > BMS Bioinformatics > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From nautica21cccccc at hotmail.com Wed Jan 28 04:17:13 2004 From: nautica21cccccc at hotmail.com (gordon) Date: Wed Jan 28 04:26:25 2004 Subject: [Bioperl-l] Valium Online at Unbelievable Prices! -- timber racerx jamaica Message-ID: <1075281433-20743@excite.com> New OFFSHORE PHARMACY - Not a single medical question asked, guaranteed or it's free. Valium, Xanaxm, Soma, Zyban, Super V1agara, Pr0zac, etc. Lowest cost anywhere in the world. 128-bit encrypted site which means maximum confidentiality & no tracing. Executives, Doctor's & business people have been using our site for years & we are proud to present it to you. See what were all about today. http://castleh2opoloeclipseyoda.nepzzz.com/s95p/index.php?id=s95&c=pacers From m_conte at hotmail.com Wed Jan 28 05:07:28 2004 From: m_conte at hotmail.com (matthieu CONTE) Date: Wed Jan 28 05:13:57 2004 Subject: [Bioperl-l] Bio ::seqIO ::tigr Message-ID: Ok , I try directly with "load_seqdatabase.pl" but there is another problem..... [conte@bearn scripts]$ perl load_seqdatabase.pl -dbuser biosql -dbpass biosql -format tigr tigr /home/conte/pipeline_orthologues/data/orysa_tigr.txt Can't locate object method "get_BioDatabaseAdaptor" via package "Bio::DB::BioSQL::DBAdaptor" at load_seqdatabase.pl line 84. Indeed this method does not exist in Bio::DB::BioSQL::DBAdaptor.... Matthieu CONTE M. Sc. in Bioinformatics from SIB 00 33 06.68.90.28.70 m_conte@hotmail.com >From: Hilmar Lapp >To: "matthieu CONTE" >CC: bioperl-l@bioperl.org >Subject: Re: [Bioperl-l] Bio ::seqIO ::tigr Date: Tue, 27 Jan 2004 09:31:39 >-0800 > >A question aside: why do you want to convert to swissprot in order to load >into biosql? (load_seqdatabase.pl can use any SeqIO reader.) > > -hilmar > >On Tuesday, January 27, 2004, at 02:50 AM, matthieu CONTE wrote: > >>I currently trying to use the Bio ::seqIO ::tigr module. >>My objective is to download the whole rice genome form Tigr ( adress >>below)and to integrate it in my BioSQL DB. >>For this I am trying to convert the tigr format in swiss format with the >>script below >> >> >>use Bio::SeqIO; >> >>my $in = Bio::SeqIO->new(-file >>=>'>=>'tigr'); >> >>my $out = Bio::SeqIO->new(-file => >>'>/home/conte/pipeline_orthologues/data/orysa_swiss.txt' , >>-format=>'swiss'); >> >>print $out $_ while <$in>; >> >>I obtain: >> >>------------ EXCEPTION ------------- >>MSG: [19]Required missing >>STACK Bio::SeqIO::tigr::throw >>/usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:1338 >>STACK Bio::SeqIO::tigr::_process_header >>/usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:700 >>STACK Bio::SeqIO::tigr::_process_assembly >>/usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:535 >>STACK Bio::SeqIO::tigr::_process_tigr >>/usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:453 >>STACK Bio::SeqIO::tigr::_process >>/usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:420 >>STACK Bio::SeqIO::tigr::_initialize >>/usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:90 >>STACK Bio::SeqIO::new >>/usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO.pm:358 >>STACK Bio::SeqIO::new >>/usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO.pm:378 >>STACK toplevel get_bioseq_tigr.pl:8 >> >>Could you please tell me if there is a problem with the parser or with the >>input data format of Tigr? >> >>Thanks in advance >> >> >> >> >>Matthieu CONTE >>m_conte@hotmail.com >> >>_________________________________________________________________ >>MSN Messenger : discutez en direct avec vos amis ! >>http://www.msn.fr/msger/default.asp >> >>_______________________________________________ >>Bioperl-l mailing list >>Bioperl-l@portal.open-bio.org >>http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> >-- >------------------------------------------------------------- >Hilmar Lapp email: lapp at gnf.org >GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 >------------------------------------------------------------- > > _________________________________________________________________ MSN Messenger : discutez en direct avec vos amis ! http://www.msn.fr/msger/default.asp From Mailer-Daemon at fuse1.fusemail.net Wed Jan 28 05:50:04 2004 From: Mailer-Daemon at fuse1.fusemail.net (Mail Delivery System) Date: Wed Jan 28 05:56:29 2004 Subject: [Bioperl-l] Mail delivery failed: returning message to sender Message-ID: This message was created automatically by mail delivery software. A message that you sent could not be delivered to one or more of its recipients. This is a permanent error. The following address(es) failed: john@electricskeleton.net local delivery failed ------ This is a copy of the message, including all the headers. ------ Return-path: Received: from fusemail.com by fuse1.fusemail.net with smtp (FuseMail incSMTP) id 1AlnGl-0003k0-Kn for john@electricskeleton.net; Wed, 28 Jan 2004 04:50:03 -0600 Received: (qmail 49185 invoked from network); 28 Jan 2004 10:49:03 -0000 Received: from molmicro2.ucd.ie (HELO bioperl.org) (137.43.18.38) by lon-mail-1.gradwell.net with SMTP; 28 Jan 2004 10:49:03 -0000 From: bioperl-l@bioperl.org To: john@electricskeleton.net Subject: Mail Delivery System Date: Wed, 28 Jan 2004 10:45:00 -0800 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0005_7E5AB3EA.13FF5710" X-Priority: 3 X-MSMail-Priority: Normal Message-Id: This is a multi-part message in MIME format. ------=_NextPart_000_0005_7E5AB3EA.13FF5710 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit Mail transaction failed. 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Alert - ScanMail for Lotus Notes --> [Bioperl-l] Mail delivery failed: returning message to sender Message-ID: This is an info mail issued by the Bayer virus checking software: Prior to this message you received an e-mail where a virus has been detected and removed, details see below. The attachment is now empty. The sender has already been notified. Dies ist eine Info-Mail vom Bayer Virenscanner: Sie erhielten eine e-Mail, in der ein Virus entdeckt und entfernt wurde, Details siehe unten. Der Anhang ist nun leer. Der Absender wurde bereits benachrichtigt. Date: 01/28/2004 11:51:43 AM Subject: [Bioperl-l] Mail delivery failed: returning message to sender Virus: WORM_MIMAIL.R File: readme.zip From: bioperl-l-bounces@portal.open-bio.org To: bioperl-l@bioperl.org Action: Quarantined; Scanned by ScanMail for Lotus Notes 2.6 with scanengine 6.810-1005 and patternfile lpt$vpn.747 From dhoworth at mrc-lmb.cam.ac.uk Wed Jan 28 06:24:57 2004 From: dhoworth at mrc-lmb.cam.ac.uk (Dave Howorth) Date: Wed Jan 28 06:31:23 2004 Subject: [Bioperl-l] Bio::SeqIO::tinyseq In-Reply-To: <200401280758.03040.heikki@nildram.co.uk> References: <5bb7a5bedc.5bedc5bb7a@bms.com> <200401280758.03040.heikki@nildram.co.uk> Message-ID: <40179C09.50605@mrc-lmb.cam.ac.uk> Heikki Lehvaslaiho wrote: > The best way to do this is to ignore the root level of the xml, use perl to > parse entries out of it, and pass entry xml only to the parser. This keeps > the memory usage down and you can parse as large file as you want. Hmmm, it may be pragmatic but I'm sure there are other meanings of 'best'. By throwing away the root level you're losing any chance to validate the document or use other XML tools and you run the risk of making assumptions ... > local $/ = "\n"; ... There's no reason to expect there will ALWAYS be a newline following the tag in a valid XML file (suppose it's created by some XSLT tool that cares nothing about readability). You're making an assumption above and beyond the specification about how the XML is represented. Cheers, Dave From vsuni at email.com Wed Jan 28 07:02:28 2004 From: vsuni at email.com (vsuni@email.com) Date: Wed Jan 28 07:08:50 2004 Subject: [Bioperl-l] Re: test In-Reply-To: <20040128120219.D1B443E617@spf5.us4.outblaze.com> References: <20040128120219.D1B443E617@spf5.us4.outblaze.com> Message-ID: <20040128120228.18458.qmail@mta3-1.us4.outblaze.com> AUTO REPLY. THANK YOU FOR SENDING THE MAIL. I WILL TRY TO REPLY YOUR EMAIL AS SOON AS POSSIBLE. From Marc.Logghe at devgen.com Wed Jan 28 07:38:35 2004 From: Marc.Logghe at devgen.com (Marc Logghe) Date: Wed Jan 28 07:45:33 2004 Subject: [Bioperl-l] Bio ::seqIO ::tigr Message-ID: > -----Original Message----- > From: matthieu CONTE [mailto:m_conte@hotmail.com] > Sent: Wednesday, January 28, 2004 11:07 AM > To: hlapp@gmx.net; bioperl-l@bioperl.org > Subject: Re: [Bioperl-l] Bio ::seqIO ::tigr > > > Ok , I try directly with "load_seqdatabase.pl" but there is another > problem..... > > [conte@bearn scripts]$ perl load_seqdatabase.pl -dbuser > biosql -dbpass > biosql -format tigr tigr > /home/conte/pipeline_orthologues/data/orysa_tigr.txt > > Can't locate object method "get_BioDatabaseAdaptor" via package > "Bio::DB::BioSQL::DBAdaptor" at load_seqdatabase.pl line 84. > > Indeed this method does not exist in Bio::DB::BioSQL::DBAdaptor.... That is because you did not say which database to use. You should also pass the --driver argument, e.g. --driver Oracle or --driver mysql HTH, Marc From heikki at ebi.ac.uk Wed Jan 28 09:54:56 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Wed Jan 28 10:02:26 2004 Subject: [Bioperl-l] Bio::SeqIO::tinyseq In-Reply-To: <40179C09.50605@mrc-lmb.cam.ac.uk> References: <5bb7a5bedc.5bedc5bb7a@bms.com> <200401280758.03040.heikki@nildram.co.uk> <40179C09.50605@mrc-lmb.cam.ac.uk> Message-ID: <200401281454.56586.heikki@ebi.ac.uk> Dave, The more I use XML the more pragmatic I get. When things get tight, I've used perl directly to modify XML files; and gained 10x speed increase. Validation in most cases is not practical, so would not worry too much about about it, either. BTW, I am now convinced that structure definitions for any database-related format should be constructed from several definitions; in this case, one for top level and an other for the entry level. Thanks for pointing out that new line character in my code. -Heikki On Wednesday 28 Jan 2004 11:24, Dave Howorth wrote: > Heikki Lehvaslaiho wrote: > > The best way to do this is to ignore the root level of the xml, use perl > > to parse entries out of it, and pass entry xml only to the parser. This > > keeps the memory usage down and you can parse as large file as you want. > > Hmmm, it may be pragmatic but I'm sure there are other meanings of > 'best'. By throwing away the root level you're losing any chance to > validate the document or use other XML tools and you run the risk of > making assumptions ... > > > local $/ = "\n"; > > ... There's no reason to expect there will ALWAYS be a newline following > the tag in a valid XML file (suppose it's created by some XSLT tool that > cares nothing about readability). You're making an assumption above and > beyond the specification about how the XML is represented. > > Cheers, Dave > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From pvh at egenetics.com Wed Jan 28 10:01:28 2004 From: pvh at egenetics.com (Peter van Heusden) Date: Wed Jan 28 10:07:55 2004 Subject: [Bioperl-l] Bio::SeqIO::new possible wierdness Message-ID: <4017CEC8.4000608@egenetics.com> My review of the Bio::SeqIO::new method shows the following behaviour: Missing both ?file and ?fh arguments: falls back to using $ARGV[0] (the first command line argument) as sequence filename. If this fails, gives an exception about ?Unknown format?. -file argument (without ?fh argument): ? given, but file unreadable: throws exception ? undefined: reads $ARGV[0], as above. -fh argument (without ?file argument): ? given, but not a filehandle: gives exception ? given, but an invalid filehandle (not open): gives exception ? undefined: reads $ARGV[0], as above. -format argument: if the sequence file doesn?t correspond to the given format, some parsers give an error (e.g. EMBL), while others do not (GenBank), instead silently give wrong results. -format argument without ?file argument: Silently creates a SeqIO object which writes to STDOUT. I don't think that this $ARGV[0] shortcut should be in there - it causes unnecessary potential confusion. Imagine a situation where -fh or -file is specified (using a variable), but that variable somehow does not get defined. In that case, the $ARGV[0] fallback behaviour would be used, which might lead to a non-obvious error behaviour. I'd like to propose that either -file or -fh should be specified, otherwise an exception is thrown. While I'm about it, I'm thinking of migrating the exceptions to the new 'typed exceptions' that BioPerl now provides - is there any consensus on exception type names? Peter From donald.jackson at bms.com Wed Jan 28 11:04:42 2004 From: donald.jackson at bms.com (Donald G. Jackson) Date: Wed Jan 28 11:11:21 2004 Subject: [Bioperl-l] Bio::SeqIO::new possible wierdness In-Reply-To: <4017CEC8.4000608@egenetics.com> References: <4017CEC8.4000608@egenetics.com> Message-ID: <4017DD9A.4060405@bms.com> Personally, I like the fall-back but agree that $ARGV[0] shouldn't be it. I'd suggest STDIN - if somebody calls new without a file/handle I think they're more likely to be reading. OTOH, guessing format woud be tough. At the very least a warning would be appropriate, perhaps indicating the course of action. For xml handlers we can check the dtd and throw an error. I will modify my SeqIO::tinyseq::tinyseqHandler to do so. Don Jackson Peter van Heusden wrote: > My review of the Bio::SeqIO::new method shows the following behaviour: > > Missing both ?file and ?fh arguments: falls back to using $ARGV[0] > (the first command line argument) as sequence filename. If this fails, > gives an exception about ?Unknown format?. > -file argument (without ?fh argument): > ? given, but file unreadable: throws exception > ? undefined: reads $ARGV[0], as above. > -fh argument (without ?file argument): > ? given, but not a filehandle: gives exception > ? given, but an invalid filehandle (not open): gives exception > ? undefined: reads $ARGV[0], as above. > -format argument: if the sequence file doesn?t correspond to the given > format, some parsers give an error (e.g. EMBL), while others do not > (GenBank), instead silently give wrong results. > -format argument without ?file argument: Silently creates a SeqIO > object which writes to STDOUT. > > I don't think that this $ARGV[0] shortcut should be in there - it > causes unnecessary potential confusion. Imagine a situation where -fh > or -file is specified (using a variable), but that variable somehow > does not get defined. In that case, the $ARGV[0] fallback behaviour > would be used, which might lead to a non-obvious error behaviour. > > I'd like to propose that either -file or -fh should be specified, > otherwise an exception is thrown. While I'm about it, I'm thinking of > migrating the exceptions to the new 'typed exceptions' that BioPerl > now provides - is there any consensus on exception type names? > > Peter > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From andreas.bernauer at gmx.de Wed Jan 28 11:12:55 2004 From: andreas.bernauer at gmx.de (Andreas Bernauer) Date: Wed Jan 28 11:19:25 2004 Subject: [Bioperl-l] reducing time In-Reply-To: <200401271555.18222.heikki@nildram.co.uk> References: <401663C5.5020003@ibsm.cnrs-mrs.fr> <200401271555.18222.heikki@nildram.co.uk> Message-ID: <20040128161255.GA20680@hgt.mcb.uconn.edu> Heikki Lehvaslaiho wrote: > I could not find anything wrong in your code. 95 seconds per file (you mean > per sequence?) is really slow. The problem according my tests is your local > system. Maybe you have too many files per directory? I had this problem with too many files per directory. When I use more than about 2000 files or so in single directory, the access to a file slows down noticeably. There is nothing you can do about it on ext2 or ext3 file systems except of not using so many files in a single directory (as far as I know). Andreas. From dag at sonsorol.org Wed Jan 28 11:18:33 2004 From: dag at sonsorol.org (Chris Dagdigian) Date: Wed Jan 28 11:25:08 2004 Subject: [Bioperl-l] reducing time In-Reply-To: <20040128161255.GA20680@hgt.mcb.uconn.edu> References: <401663C5.5020003@ibsm.cnrs-mrs.fr> <200401271555.18222.heikki@nildram.co.uk> <20040128161255.GA20680@hgt.mcb.uconn.edu> Message-ID: <4017E0D9.5020103@sonsorol.org> Interestingly enough there is a thread on the bioclusters list today about dealing with filesystems and directories of large files. Here it is in the archives: https://bioinformatics.org/pipermail/bioclusters/2004-January/001404.html Tim Cutts also proposed an intersting perl hashing method that should handle up to "64 million files or so" -- this could be an option for people stuck with ext2 filesystems: https://bioinformatics.org/pipermail/bioclusters/2004-January/001408.html -Chris Andreas Bernauer wrote: > Heikki Lehvaslaiho wrote: > >>I could not find anything wrong in your code. 95 seconds per file (you mean >>per sequence?) is really slow. The problem according my tests is your local >>system. Maybe you have too many files per directory? > > > I had this problem with too many files per directory. When I use more > than about 2000 files or so in single directory, the access to a file > slows down noticeably. There is nothing you can do about it on ext2 > or ext3 file systems except of not using so many files in a single > directory (as far as I know). > > > Andreas. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Chris Dagdigian, Independent life science IT & informatics consulting Office: 617-666-6454, Mobile: 617-877-5498, Fax: 425-699-0193 PGP KeyID: 83D4310E Yahoo IM: craffi Web: http://bioteam.net From brian_osborne at cognia.com Wed Jan 28 11:31:17 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Wed Jan 28 11:38:05 2004 Subject: [Bioperl-l] Bio::SeqIO::new possible wierdness In-Reply-To: <4017CEC8.4000608@egenetics.com> Message-ID: Peter, -format argument: if the sequence file doesn't correspond to the given format, some parsers give an error (e.g. EMBL), while others do not (GenBank), instead silently give wrong results. This sounds much like Bug #1508, you might want to take a look: http://bugzilla.bioperl.org/show_bug.cgi?id=1508 Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Peter van Heusden Sent: Wednesday, January 28, 2004 10:01 AM To: bioperl-l@bioperl.org Subject: [Bioperl-l] Bio::SeqIO::new possible wierdness My review of the Bio::SeqIO::new method shows the following behaviour: Missing both -file and -fh arguments: falls back to using $ARGV[0] (the first command line argument) as sequence filename. If this fails, gives an exception about 'Unknown format'. -file argument (without -fh argument): ? given, but file unreadable: throws exception ? undefined: reads $ARGV[0], as above. -fh argument (without -file argument): ? given, but not a filehandle: gives exception ? given, but an invalid filehandle (not open): gives exception ? undefined: reads $ARGV[0], as above. -format argument: if the sequence file doesn't correspond to the given format, some parsers give an error (e.g. EMBL), while others do not (GenBank), instead silently give wrong results. -format argument without -file argument: Silently creates a SeqIO object which writes to STDOUT. I don't think that this $ARGV[0] shortcut should be in there - it causes unnecessary potential confusion. Imagine a situation where -fh or -file is specified (using a variable), but that variable somehow does not get defined. In that case, the $ARGV[0] fallback behaviour would be used, which might lead to a non-obvious error behaviour. I'd like to propose that either -file or -fh should be specified, otherwise an exception is thrown. While I'm about it, I'm thinking of migrating the exceptions to the new 'typed exceptions' that BioPerl now provides - is there any consensus on exception type names? Peter _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From hlapp at gmx.net Wed Jan 28 11:55:15 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed Jan 28 12:01:39 2004 Subject: [Bioperl-l] Bio ::seqIO ::tigr In-Reply-To: Message-ID: I suspect you have an old version of bioperl-db, or a version mix-up. You need to download and install the latest revision from CVS for bioperl-db. Note that if the root of the problem is with the pir parser then load_seqdatabase.pl will not cure it, as it just uses any Bio::SeqIO compliant parser to provide the input sequences. If the parser is broken then there won't be input ... It just saves you the round-trip (and possible errors associated with it) of going through swissprot format. -hilmar On Wednesday, January 28, 2004, at 02:07 AM, matthieu CONTE wrote: > Ok , I try directly with "load_seqdatabase.pl" but there is another > problem..... > > [conte@bearn scripts]$ perl load_seqdatabase.pl -dbuser biosql > -dbpass biosql -format tigr tigr > /home/conte/pipeline_orthologues/data/orysa_tigr.txt > > Can't locate object method "get_BioDatabaseAdaptor" via package > "Bio::DB::BioSQL::DBAdaptor" at load_seqdatabase.pl line 84. > > Indeed this method does not exist in Bio::DB::BioSQL::DBAdaptor.... > > > > > Matthieu CONTE > M. Sc. in Bioinformatics from SIB > > 00 33 06.68.90.28.70 > m_conte@hotmail.com > > > > > >> From: Hilmar Lapp >> To: "matthieu CONTE" >> CC: bioperl-l@bioperl.org >> Subject: Re: [Bioperl-l] Bio ::seqIO ::tigr Date: Tue, 27 Jan 2004 >> 09:31:39 -0800 >> >> A question aside: why do you want to convert to swissprot in order to >> load into biosql? (load_seqdatabase.pl can use any SeqIO reader.) >> >> -hilmar >> >> On Tuesday, January 27, 2004, at 02:50 AM, matthieu CONTE wrote: >> >>> I currently trying to use the Bio ::seqIO ::tigr module. >>> My objective is to download the whole rice genome form Tigr ( adress >>> below)and to integrate it in my BioSQL DB. >>> For this I am trying to convert the tigr format in swiss format with >>> the script below >>> >>> >>> use Bio::SeqIO; >>> >>> my $in = Bio::SeqIO->new(-file >>> =>'>> =>'tigr'); >>> >>> my $out = Bio::SeqIO->new(-file => >>> '>/home/conte/pipeline_orthologues/data/orysa_swiss.txt' , >>> -format=>'swiss'); >>> >>> print $out $_ while <$in>; >>> >>> I obtain: >>> >>> ------------ EXCEPTION ------------- >>> MSG: [19]Required missing >>> STACK Bio::SeqIO::tigr::throw >>> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:1338 >>> STACK Bio::SeqIO::tigr::_process_header >>> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:700 >>> STACK Bio::SeqIO::tigr::_process_assembly >>> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:535 >>> STACK Bio::SeqIO::tigr::_process_tigr >>> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:453 >>> STACK Bio::SeqIO::tigr::_process >>> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:420 >>> STACK Bio::SeqIO::tigr::_initialize >>> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:90 >>> STACK Bio::SeqIO::new >>> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO.pm:358 >>> STACK Bio::SeqIO::new >>> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO.pm:378 >>> STACK toplevel get_bioseq_tigr.pl:8 >>> >>> Could you please tell me if there is a problem with the parser or >>> with the input data format of Tigr? >>> >>> Thanks in advance >>> >>> >>> >>> >>> Matthieu CONTE >>> m_conte@hotmail.com >>> >>> _________________________________________________________________ >>> MSN Messenger : discutez en direct avec vos amis ! >>> http://www.msn.fr/msger/default.asp >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l@portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> -- >> ------------------------------------------------------------- >> Hilmar Lapp email: lapp at gnf.org >> GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 >> ------------------------------------------------------------- >> >> > > _________________________________________________________________ > MSN Messenger : discutez en direct avec vos amis ! > http://www.msn.fr/msger/default.asp > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From joel at nanovoid.com Wed Jan 28 12:02:39 2004 From: joel at nanovoid.com (Joel Dudley) Date: Wed Jan 28 12:09:01 2004 Subject: [Bioperl-l] Position Available: Bioinformatics Software Developer Message-ID: <4017EB2F.1030603@nanovoid.com> The Center for Functionaly Evolutionary Genomics at the Arizona BioDesign Institute is currently seeking software developers. Please refer to the official Human Resources posting for details (Note: the HR assigned position title is a misnomer): http://www.hr.asu.edu/vacancy_notice/vacancy_posting.asp?id=113788 Joel Dudley Faculty Research Associate Center for Evolutionary Functional Genomics Arizona Biodesign Institute @ Arizona State University P.S.: If open position postings such as this are not allowed by the etiquette of this list please inform me so that I do not make the same mistake in the future. This posting was sent to this list for the benefit of qualified list members that are currently seeking employment. From gdw1 at cornell.edu Wed Jan 28 12:30:16 2004 From: gdw1 at cornell.edu (Gregory Wilson) Date: Wed Jan 28 12:36:51 2004 Subject: [Bioperl-l] reducing time In-Reply-To: <4017E0D9.5020103@sonsorol.org> References: <401663C5.5020003@ibsm.cnrs-mrs.fr> <200401271555.18222.heikki@nildram.co.uk> <20040128161255.GA20680@hgt.mcb.uconn.edu> <4017E0D9.5020103@sonsorol.org> Message-ID: <1075311015.4121.5.camel@awn> There is a review of journaling filesystems at http://www.linux-mag.com/2002-10/jfs_01.html It is a little old now (Oct2002) but worth the read. Not to get into a FS war, but you could try ReiserFS. Specifically the quote: "ReiserFS is about eight to fifteen times faster than Ext2 at handling files smaller than 1K." More about reiserfs is at http://www.namesys.com/ Greg From heikki at nildram.co.uk Wed Jan 28 13:09:13 2004 From: heikki at nildram.co.uk (Heikki Lehvaslaiho) Date: Wed Jan 28 13:18:51 2004 Subject: Fwd: Re: [Bioperl-l] reducing time Message-ID: <200401281809.13423.heikki@nildram.co.uk> I got this earlier from Pierre. We can close the thread . -Heikki ---------- Forwarded Message ---------- Subject: Re: [Bioperl-l] reducing time Date: Tuesday 27 Jan 2004 16:12 From: KHOUEIRY pierre To: heikki@ebi.ac.uk I really appreciate ur interest heikki; In fact i modified my loops (these indicated bu heavy in the code) and I turn my script and it works good. it tooks 1.07 h now. in fact to telling u the reality i replace this loop (consisting of several loops) with the transliteration iperator tr///; And it works good now. thanks ------------------------------------------------------- -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From khoueiry at ibsm.cnrs-mrs.fr Wed Jan 28 13:38:39 2004 From: khoueiry at ibsm.cnrs-mrs.fr (KHOUEIRY pierre) Date: Wed Jan 28 13:45:01 2004 Subject: [Bioperl-l] reducing time Message-ID: <401801AF.3010104@ibsm.cnrs-mrs.fr> thank you all for your notes that I appreciate so much. In fact I resolved the problem concerning time reduction by replacing a big loop with the tr/// operator. But dealing with big and many files will be a big part of my work and everytime I have a problem. Right now per exemple, I'm runnig a perl script (look at the attachement). Here it's a little bit fast (i note that there is 1000 proteomes in the output directory), i mean by that at about 27 seconds/10 proteomes. I'm asking myself if it's the right and optimum way to do what the script shows. briefly, I search every proteome for the ID's I put in the table and I make a file... Any suggesting for that... Am'I on the right way for this. I think that runnig the table for every sequence is a hard way....!! From brian_osborne at cognia.com Wed Jan 28 13:51:16 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Wed Jan 28 13:57:59 2004 Subject: [Bioperl-l] installation trouble In-Reply-To: <000701c3e563$bdbaba00$7701a8c0@PHOENIX> Message-ID: June, One workaround that's been used is to fix this 'line too long' problem is to use the command 'make -i' instead of 'make'. This tells make to ignore errors, and this was on an Alpha, like you. More on the problem: http://bioperl.org/pipermail/bioperl-l/2002-August/009034.html Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of June Tantoolvesm Sent: Wednesday, January 28, 2004 12:58 AM To: bioperl-l@portal.open-bio.org Subject: [Bioperl-l] installation trouble Hello, I tried searching for help elsewhere but couldn't find anything...could someone please help? I'm trying to install bioperl to a local directory. [june@bg03n001e00]~/bioperl-1.4(4): make Make: line too long. Stop. [june@bg03n001e00]~/bioperl-1.4(7): uname -a OSF1 bg03n001e00.hpc.cmc.osaka-u.ac. V5.1 1885 alpha I'm not sure what other information I need to provide... Any suggestions very much appreciated. Thank you June _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From laurichj at bioinfo.ucr.edu Wed Jan 28 14:23:14 2004 From: laurichj at bioinfo.ucr.edu (Josh Lauricha) Date: Wed Jan 28 14:29:36 2004 Subject: [Bioperl-l] reducing time In-Reply-To: <1075311015.4121.5.camel@awn> References: <401663C5.5020003@ibsm.cnrs-mrs.fr> <200401271555.18222.heikki@nildram.co.uk> <20040128161255.GA20680@hgt.mcb.uconn.edu> <4017E0D9.5020103@sonsorol.org> <1075311015.4121.5.camel@awn> Message-ID: <20040128192314.GA2854@bioinfo.ucr.edu> On Wed 01/28/04 12:30, Gregory Wilson wrote: > Not to get into a FS war, but you could try ReiserFS. Specifically the > quote: "ReiserFS is about eight to fifteen times faster than Ext2 at > handling files smaller than 1K." More about reiserfs is at > http://www.namesys.com/ I've been using ReiserFS for quite some time and it really does handle very large directories of small files quite well... For instance: $ time find -type f | wc 28581 28581 389134 real 0m0.151s user 0m0.060s sys 0m0.100s and: $ time find -type f | wc 228648 228648 2312804 real 0m1.169s user 0m0.330s sys 0m0.910s In both cases, these are files with one protein in each, the first has 28k proteins, the second 228k (about 900MB). Of course, ls is going to take FOREVER on these, thats not because of the fs but rather because ls is sorting the list. Without the sorting: $ time ls -f -l >/dev/null real 0m3.961s user 0m2.530s sys 0m1.430s But, XFS and JFS will probably have similar performance. Anyhow, the perl hack would probably be simplest. -- ---------------------------- | Josh Lauricha | | laurichj@bioinfo.ucr.edu | | Bioinformatics, UCR | |--------------------------| From jason at cgt.duhs.duke.edu Wed Jan 28 14:32:24 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Jan 28 14:38:53 2004 Subject: [Bioperl-l] installation trouble In-Reply-To: References: Message-ID: Did you also install the latest ExtUtils::MakeMaker on your system - this is typically a problem with how the Makefile is generated by Perl and the number of files we have in our package. There are a couple of closed bug reports in bugzilla to this effect. -jason On Wed, 28 Jan 2004, Brian Osborne wrote: > June, > > One workaround that's been used is to fix this 'line too long' problem is to > use the command 'make -i' instead of 'make'. This tells make to ignore > errors, and this was on an Alpha, like you. > > More on the problem: > > http://bioperl.org/pipermail/bioperl-l/2002-August/009034.html > > > Brian O. > > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org > [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of June Tantoolvesm > Sent: Wednesday, January 28, 2004 12:58 AM > To: bioperl-l@portal.open-bio.org > Subject: [Bioperl-l] installation trouble > > Hello, > > I tried searching for help elsewhere but couldn't find anything...could > someone please help? I'm trying to install bioperl to a local directory. > > [june@bg03n001e00]~/bioperl-1.4(4): make > Make: line too long. Stop. > [june@bg03n001e00]~/bioperl-1.4(7): uname -a > OSF1 bg03n001e00.hpc.cmc.osaka-u.ac. V5.1 1885 alpha > > I'm not sure what other information I need to provide... > > Any suggestions very much appreciated. > > Thank you > June > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From jason at cgt.duhs.duke.edu Wed Jan 28 14:51:42 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Jan 28 14:58:05 2004 Subject: [Bioperl-l] Bio::SeqIO::new possible wierdness In-Reply-To: <4017DD9A.4060405@bms.com> References: <4017CEC8.4000608@egenetics.com> <4017DD9A.4060405@bms.com> Message-ID: On Wed, 28 Jan 2004, Donald G. Jackson wrote: > Personally, I like the fall-back but agree that $ARGV[0] shouldn't be it. > I'd suggest STDIN - if somebody calls new without a file/handle I think > they're more likely to be reading. OTOH, guessing format woud be tough. the guess format is trying to read off the top of the file I think - we support a 'peek' type of reading into the file, by having the _pushback functionality in Root::IO. I would like to see something like this go into Root:IO rather than in SeqIO - and have Root::IO give back a filename if it knows what it is. Also the Root::IO code could also do something like this: $file = "-" unless defined $file; open my $fh => $input or die $!; Which will then read from stdin if now filename is sent in - right now we don't really support that anymore because it was causing clog-ups in some of the DB::GFF code/tests I think. Maybe we localize this to 'FormattedReaderWriters' -- all the XXXIO(-format => 'XXX') modules so as to avoid the problems Lincoln saw. > At the very least a warning would be appropriate, perhaps indicating the > course of action. > > For xml handlers we can check the dtd and throw an error. I will modify > my SeqIO::tinyseq::tinyseqHandler to do so. > > Don Jackson > > > > Peter van Heusden wrote: > > > My review of the Bio::SeqIO::new method shows the following behaviour: > > > > Missing both file and fh arguments: falls back to using $ARGV[0] > > (the first command line argument) as sequence filename. If this fails, > > gives an exception about Unknown format. > > -file argument (without fh argument): > > given, but file unreadable: throws exception > > undefined: reads $ARGV[0], as above. > > -fh argument (without file argument): > > given, but not a filehandle: gives exception > > given, but an invalid filehandle (not open): gives exception > > undefined: reads $ARGV[0], as above. > > -format argument: if the sequence file doesnt correspond to the given > > format, some parsers give an error (e.g. EMBL), while others do not > > (GenBank), instead silently give wrong results. > > -format argument without file argument: Silently creates a SeqIO > > object which writes to STDOUT. > > > > I don't think that this $ARGV[0] shortcut should be in there - it > > causes unnecessary potential confusion. Imagine a situation where -fh > > or -file is specified (using a variable), but that variable somehow > > does not get defined. In that case, the $ARGV[0] fallback behaviour > > would be used, which might lead to a non-obvious error behaviour. > > > > I'd like to propose that either -file or -fh should be specified, > > otherwise an exception is thrown. While I'm about it, I'm thinking of > > migrating the exceptions to the new 'typed exceptions' that BioPerl > > now provides - is there any consensus on exception type names? > > > > Peter > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From Annie.Law at nrc-cnrc.gc.ca Wed Jan 28 15:42:47 2004 From: Annie.Law at nrc-cnrc.gc.ca (Law, Annie) Date: Wed Jan 28 15:49:13 2004 Subject: [Bioperl-l] Application using Bioperl Message-ID: <10C94843061E094A98C02EB77CFC328722FDF9@nrcmrdex1d.imsb.nrc.ca> Hi, I would appreciate help on the following. I would like to create a small application that would involve Excel XP on Windows 2000, and Bioperl and mysql on RedHat linux 9.0 The database will consist of clone IDs, accession numbers, and unigene IDs, and allow a user to add his own personal annotation as well. Later on, I would like to annotate with other information as well. I am trying to map things out and see if all of the parts in my application will fit together prior to doing too much developing. Basically my main concern now is to create the flow of information. There is the Excel workbook part and then there is the UNIX mysql database part. Writing a shell or perl script in the linux environment that will ftp files from unigene, locuslink Etc and then user bioperl to parse the data, Then use perl DBI to insert to information Also using perl DBI to upload information from the Excel sheet (user's personal annotation) Into the database. The part that I'm not too sure about is how to send the information from the Excel sheet to the database And how to grab the information from the database and update the Excel sheet. On top of that I am using two different operating systems. Are there some tools in VBA or in perl that I could use to build this bridge or I am using Excel since there are functions within Excel that are useful. Thanks for your help, Annie. From pvh at egenetics.com Wed Jan 28 15:45:29 2004 From: pvh at egenetics.com (Peter van Heusden) Date: Wed Jan 28 15:52:04 2004 Subject: [Bioperl-l] Bio::SeqIO::new possible wierdness In-Reply-To: References: <4017CEC8.4000608@egenetics.com> <4017DD9A.4060405@bms.com> Message-ID: <40181F69.8070109@egenetics.com> Jason Stajich wrote: >On Wed, 28 Jan 2004, Donald G. Jackson wrote: > > > >>Personally, I like the fall-back but agree that $ARGV[0] shouldn't be it. >>I'd suggest STDIN - if somebody calls new without a file/handle I think >>they're more likely to be reading. OTOH, guessing format woud be tough. >> >> > >the guess format is trying to read off the top of the file I think - we >support a 'peek' type of reading into the file, by having the _pushback >functionality in Root::IO. > >I would like to see something like this go into Root:IO rather than in >SeqIO - and have Root::IO give back a filename if it knows what it is. > >Also the Root::IO code could also do something like this: > $file = "-" unless defined $file; > open my $fh => $input or die $!; > >Which will then read from stdin if now filename is sent in - right now we >don't really support that anymore because it was causing clog-ups in some >of the DB::GFF code/tests I think. > >Maybe we localize this to 'FormattedReaderWriters' -- all the >XXXIO(-format => 'XXX') modules so as to avoid the problems Lincoln saw. > > > > Can you to where Lincoln "saw" this problem? The BioPerl mailing list archive is not searchable, and searching via Google doesn't turn anything up. Anyway, I'll look into Root::IO tomorrow and see what I come up with. Peter > > >>At the very least a warning would be appropriate, perhaps indicating the >>course of action. >> >>For xml handlers we can check the dtd and throw an error. I will modify >>my SeqIO::tinyseq::tinyseqHandler to do so. >> >>Don Jackson >> >> >> >>Peter van Heusden wrote: >> >> >> >>>My review of the Bio::SeqIO::new method shows the following behaviour: >>> >>>Missing both ?file and ?fh arguments: falls back to using $ARGV[0] >>>(the first command line argument) as sequence filename. If this fails, >>>gives an exception about ?Unknown format?. >>>-file argument (without ?fh argument): >>>? given, but file unreadable: throws exception >>>? undefined: reads $ARGV[0], as above. >>>-fh argument (without ?file argument): >>>? given, but not a filehandle: gives exception >>>? given, but an invalid filehandle (not open): gives exception >>>? undefined: reads $ARGV[0], as above. >>>-format argument: if the sequence file doesn?t correspond to the given >>>format, some parsers give an error (e.g. EMBL), while others do not >>>(GenBank), instead silently give wrong results. >>>-format argument without ?file argument: Silently creates a SeqIO >>>object which writes to STDOUT. >>> >>>I don't think that this $ARGV[0] shortcut should be in there - it >>>causes unnecessary potential confusion. Imagine a situation where -fh >>>or -file is specified (using a variable), but that variable somehow >>>does not get defined. In that case, the $ARGV[0] fallback behaviour >>>would be used, which might lead to a non-obvious error behaviour. >>> >>>I'd like to propose that either -file or -fh should be specified, >>>otherwise an exception is thrown. While I'm about it, I'm thinking of >>>migrating the exceptions to the new 'typed exceptions' that BioPerl >>>now provides - is there any consensus on exception type names? >>> >>>Peter >>>_______________________________________________ >>>Bioperl-l mailing list >>>Bioperl-l@portal.open-bio.org >>>http://portal.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >>> >>_______________________________________________ >>Bioperl-l mailing list >>Bioperl-l@portal.open-bio.org >>http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> >> > >-- >Jason Stajich >Duke University >jason at cgt.mc.duke.edu > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > From jason at cgt.duhs.duke.edu Wed Jan 28 16:33:45 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Jan 28 16:40:10 2004 Subject: [Bioperl-l] Bio::SeqIO::new possible wierdness In-Reply-To: <40181F69.8070109@egenetics.com> References: <4017CEC8.4000608@egenetics.com> <4017DD9A.4060405@bms.com> <40181F69.8070109@egenetics.com> Message-ID: The bioperl list is searchable - just not the bioperl-guts though - http://search.open-bio.org and/or google works fine for me This is the change Lincoln made though (cvs log on Bio/Root/IO.pm and found the last commit by lincoln). I had put the \*ARGV in there so that we could use the magic <> operator (allows STDIN or a list of files to all be used as transparent input). This caused some problems with tests in GFF, SeqFeature, or Registry. Here is his log message revision 1.50 date: 2003/11/21 03:03:38; author: lstein; state: Exp; lines: +2 -2 The following regression tests now pass: GFF, SeqFeature, Registry --jason jason@jason $ cvs diff -r 1.49 Bio/Root/IO.pm Index: Bio/Root/IO.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/Root/IO.pm,v retrieving revision 1.49 diff -r1.49 IO.pm 1c1 < # $Id: IO.pm,v 1.49 2003/10/28 21:58:54 jason Exp $ --- > # $Id: IO.pm,v 1.50 2003/11/21 03:03:38 lstein Exp $ 435c435 < my $fh = $self->_fh || \*ARGV; --- > my $fh = $self->_fh or return; On Wed, 28 Jan 2004, Peter van Heusden wrote: > Jason Stajich wrote: > > >On Wed, 28 Jan 2004, Donald G. Jackson wrote: > > > > > > > >>Personally, I like the fall-back but agree that $ARGV[0] shouldn't be it. > >>I'd suggest STDIN - if somebody calls new without a file/handle I think > >>they're more likely to be reading. OTOH, guessing format woud be tough. > >> > >> > > > >the guess format is trying to read off the top of the file I think - we > >support a 'peek' type of reading into the file, by having the _pushback > >functionality in Root::IO. > > > >I would like to see something like this go into Root:IO rather than in > >SeqIO - and have Root::IO give back a filename if it knows what it is. > > > >Also the Root::IO code could also do something like this: > > $file = "-" unless defined $file; > > open my $fh => $input or die $!; > > > >Which will then read from stdin if now filename is sent in - right now we > >don't really support that anymore because it was causing clog-ups in some > >of the DB::GFF code/tests I think. > > > >Maybe we localize this to 'FormattedReaderWriters' -- all the > >XXXIO(-format => 'XXX') modules so as to avoid the problems Lincoln saw. > > > > > > > > > Can you to where Lincoln "saw" this problem? The BioPerl mailing list > archive is not searchable, and searching via Google doesn't turn > anything up. > > Anyway, I'll look into Root::IO tomorrow and see what I come up with. > > Peter > > > > > > >>At the very least a warning would be appropriate, perhaps indicating the > >>course of action. > >> > >>For xml handlers we can check the dtd and throw an error. I will modify > >>my SeqIO::tinyseq::tinyseqHandler to do so. > >> > >>Don Jackson > >> > >> > >> > >>Peter van Heusden wrote: > >> > >> > >> > >>>My review of the Bio::SeqIO::new method shows the following behaviour: > >>> > >>>Missing both ?file and ?fh arguments: falls back to using $ARGV[0] > >>>(the first command line argument) as sequence filename. If this fails, > >>>gives an exception about ?Unknown format?. > >>>-file argument (without ?fh argument): > >>>? given, but file unreadable: throws exception > >>>? undefined: reads $ARGV[0], as above. > >>>-fh argument (without ?file argument): > >>>? given, but not a filehandle: gives exception > >>>? given, but an invalid filehandle (not open): gives exception > >>>? undefined: reads $ARGV[0], as above. > >>>-format argument: if the sequence file doesn?t correspond to the given > >>>format, some parsers give an error (e.g. EMBL), while others do not > >>>(GenBank), instead silently give wrong results. > >>>-format argument without ?file argument: Silently creates a SeqIO > >>>object which writes to STDOUT. > >>> > >>>I don't think that this $ARGV[0] shortcut should be in there - it > >>>causes unnecessary potential confusion. Imagine a situation where -fh > >>>or -file is specified (using a variable), but that variable somehow > >>>does not get defined. In that case, the $ARGV[0] fallback behaviour > >>>would be used, which might lead to a non-obvious error behaviour. > >>> > >>>I'd like to propose that either -file or -fh should be specified, > >>>otherwise an exception is thrown. While I'm about it, I'm thinking of > >>>migrating the exceptions to the new 'typed exceptions' that BioPerl > >>>now provides - is there any consensus on exception type names? > >>> > >>>Peter > >>>_______________________________________________ > >>>Bioperl-l mailing list > >>>Bioperl-l@portal.open-bio.org > >>>http://portal.open-bio.org/mailman/listinfo/bioperl-l > >>> > >>> > >>> > >>_______________________________________________ > >>Bioperl-l mailing list > >>Bioperl-l@portal.open-bio.org > >>http://portal.open-bio.org/mailman/listinfo/bioperl-l > >> > >> > >> > > > >-- > >Jason Stajich > >Duke University > >jason at cgt.mc.duke.edu > > > >_______________________________________________ > >Bioperl-l mailing list > >Bioperl-l@portal.open-bio.org > >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From fernan at iib.unsam.edu.ar Wed Jan 28 17:50:45 2004 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Wed Jan 28 17:57:36 2004 Subject: [Bioperl-l] more installation troubles on Alpha Message-ID: <20040128225045.GB2662@iib.unsam.edu.ar> Hi! I'm currently maintaing a port of bioperl on FreeBSD. I have just been informed that the port is failing to install on FreeBSD-alpha (I?ve only tested the port on i386). The complete log is at: http://bento.freebsd.org/errorlogs/alpha-4-latest/p5-bioperl-1.4.log However the informative line is: Not enough arguments for mkdir at ./Makefile.PL line 119, near "$dest_dir) " BEGIN not safe after errors--compilation aborted at ./Makefile.PL line 273. *** Error code 255 I'm interested to know if other people working on alphas have seen this problem. Also, I'm obviously interested in a solution :) Is this related to the 'Arg list too long' problem of a recent post? Thanks in advance, Fernan -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan From jason at cgt.duhs.duke.edu Wed Jan 28 19:31:53 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Jan 28 19:38:16 2004 Subject: [Bioperl-l] installation trouble In-Reply-To: References: Message-ID: I can replicate this problem with perl 5.6.0 and alpha/OSF1 and latest ExtUtils::MakeMaker so I would think someone need to re-file the bug report with Michael on rt.cpan.org for ExtUtils::MakeMaker... make -i doesn't really work either. This is a perl/system problem so we don't much control over it other than to start splitting bioperl into components which will generate a lot of headaches. You can work around it by expanding some of the system limits for shell length on the machine but this is less than ideal... -jason On Wed, 28 Jan 2004, Brian Osborne wrote: > June, > > One workaround that's been used is to fix this 'line too long' problem is to > use the command 'make -i' instead of 'make'. This tells make to ignore > errors, and this was on an Alpha, like you. > > More on the problem: > > http://bioperl.org/pipermail/bioperl-l/2002-August/009034.html > > > Brian O. > > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org > [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of June Tantoolvesm > Sent: Wednesday, January 28, 2004 12:58 AM > To: bioperl-l@portal.open-bio.org > Subject: [Bioperl-l] installation trouble > > Hello, > > I tried searching for help elsewhere but couldn't find anything...could > someone please help? I'm trying to install bioperl to a local directory. > > [june@bg03n001e00]~/bioperl-1.4(4): make > Make: line too long. Stop. > [june@bg03n001e00]~/bioperl-1.4(7): uname -a > OSF1 bg03n001e00.hpc.cmc.osaka-u.ac. V5.1 1885 alpha > > I'm not sure what other information I need to provide... > > Any suggestions very much appreciated. > > Thank you > June > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From brian_osborne at cognia.com Wed Jan 28 22:02:00 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Wed Jan 28 22:08:59 2004 Subject: [Bioperl-l] Bio::SeqIO::new possible wierdness In-Reply-To: Message-ID: Jason, I'm a bit suspicious of search.open-bio.org. I enter a term like 'Root' or 'GFF' and get back a dozen hits or so. It's inconceivable to me that there's only 12 messages in bioperl-l since 1999 containing the string 'GFF'. Something's wrong, either with the search or the display. And if there are no matches I see only a blank page, which is a bit inscrutable. Then if I select 'no restriction', which I guess means everything in the selectable list I don't see the Bioperl matches anymore, I just see a dozen or so Biojava matches. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Jason Stajich Sent: Wednesday, January 28, 2004 4:34 PM To: Peter van Heusden Cc: bioperl-l@bioperl.org Subject: Re: [Bioperl-l] Bio::SeqIO::new possible wierdness The bioperl list is searchable - just not the bioperl-guts though - http://search.open-bio.org and/or google works fine for me This is the change Lincoln made though (cvs log on Bio/Root/IO.pm and found the last commit by lincoln). I had put the \*ARGV in there so that we could use the magic <> operator (allows STDIN or a list of files to all be used as transparent input). This caused some problems with tests in GFF, SeqFeature, or Registry. Here is his log message revision 1.50 date: 2003/11/21 03:03:38; author: lstein; state: Exp; lines: +2 -2 The following regression tests now pass: GFF, SeqFeature, Registry --jason jason@jason $ cvs diff -r 1.49 Bio/Root/IO.pm Index: Bio/Root/IO.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/Root/IO.pm,v retrieving revision 1.49 diff -r1.49 IO.pm 1c1 < # $Id: IO.pm,v 1.49 2003/10/28 21:58:54 jason Exp $ --- > # $Id: IO.pm,v 1.50 2003/11/21 03:03:38 lstein Exp $ 435c435 < my $fh = $self->_fh || \*ARGV; --- > my $fh = $self->_fh or return; On Wed, 28 Jan 2004, Peter van Heusden wrote: > Jason Stajich wrote: > > >On Wed, 28 Jan 2004, Donald G. Jackson wrote: > > > > > > > >>Personally, I like the fall-back but agree that $ARGV[0] shouldn't be it. > >>I'd suggest STDIN - if somebody calls new without a file/handle I think > >>they're more likely to be reading. OTOH, guessing format woud be tough. > >> > >> > > > >the guess format is trying to read off the top of the file I think - we > >support a 'peek' type of reading into the file, by having the _pushback > >functionality in Root::IO. > > > >I would like to see something like this go into Root:IO rather than in > >SeqIO - and have Root::IO give back a filename if it knows what it is. > > > >Also the Root::IO code could also do something like this: > > $file = "-" unless defined $file; > > open my $fh => $input or die $!; > > > >Which will then read from stdin if now filename is sent in - right now we > >don't really support that anymore because it was causing clog-ups in some > >of the DB::GFF code/tests I think. > > > >Maybe we localize this to 'FormattedReaderWriters' -- all the > >XXXIO(-format => 'XXX') modules so as to avoid the problems Lincoln saw. > > > > > > > > > Can you to where Lincoln "saw" this problem? The BioPerl mailing list > archive is not searchable, and searching via Google doesn't turn > anything up. > > Anyway, I'll look into Root::IO tomorrow and see what I come up with. > > Peter > > > > > > >>At the very least a warning would be appropriate, perhaps indicating the > >>course of action. > >> > >>For xml handlers we can check the dtd and throw an error. I will modify > >>my SeqIO::tinyseq::tinyseqHandler to do so. > >> > >>Don Jackson > >> > >> > >> > >>Peter van Heusden wrote: > >> > >> > >> > >>>My review of the Bio::SeqIO::new method shows the following behaviour: > >>> > >>>Missing both ?file and ?fh arguments: falls back to using $ARGV[0] > >>>(the first command line argument) as sequence filename. If this fails, > >>>gives an exception about ?Unknown format?. > >>>-file argument (without ?fh argument): > >>>? given, but file unreadable: throws exception > >>>? undefined: reads $ARGV[0], as above. > >>>-fh argument (without ?file argument): > >>>? given, but not a filehandle: gives exception > >>>? given, but an invalid filehandle (not open): gives exception > >>>? undefined: reads $ARGV[0], as above. > >>>-format argument: if the sequence file doesn?t correspond to the given > >>>format, some parsers give an error (e.g. EMBL), while others do not > >>>(GenBank), instead silently give wrong results. > >>>-format argument without ?file argument: Silently creates a SeqIO > >>>object which writes to STDOUT. > >>> > >>>I don't think that this $ARGV[0] shortcut should be in there - it > >>>causes unnecessary potential confusion. Imagine a situation where -fh > >>>or -file is specified (using a variable), but that variable somehow > >>>does not get defined. In that case, the $ARGV[0] fallback behaviour > >>>would be used, which might lead to a non-obvious error behaviour. > >>> > >>>I'd like to propose that either -file or -fh should be specified, > >>>otherwise an exception is thrown. While I'm about it, I'm thinking of > >>>migrating the exceptions to the new 'typed exceptions' that BioPerl > >>>now provides - is there any consensus on exception type names? > >>> > >>>Peter > >>>_______________________________________________ > >>>Bioperl-l mailing list > >>>Bioperl-l@portal.open-bio.org > >>>http://portal.open-bio.org/mailman/listinfo/bioperl-l > >>> > >>> > >>> > >>_______________________________________________ > >>Bioperl-l mailing list > >>Bioperl-l@portal.open-bio.org > >>http://portal.open-bio.org/mailman/listinfo/bioperl-l > >> > >> > >> > > > >-- > >Jason Stajich > >Duke University > >jason at cgt.mc.duke.edu > > > >_______________________________________________ > >Bioperl-l mailing list > >Bioperl-l@portal.open-bio.org > >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From barry.moore at genetics.utah.edu Wed Jan 28 19:24:44 2004 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Thu Jan 29 00:00:14 2004 Subject: [Bioperl-l] Application using Bioperl In-Reply-To: <10C94843061E094A98C02EB77CFC328722FDF9@nrcmrdex1d.imsb.nrc.ca> References: <10C94843061E094A98C02EB77CFC328722FDF9@nrcmrdex1d.imsb.nrc.ca> Message-ID: <401852CC.8070404@genetics.utah.edu> Annie- You could keep everything on Linux by using OpenOffice Calc (or others) as a replacement for Excel. You can probably recreate most of the functionality of Excel's formulas etc. with perl if Calc doesn't do what you need, and just use Calc as a way to interface with your end user. Of course you lose the familiar interface of Excel for your end user if that is what they are used to. You could keep everything on Windows. Most of perl, MySQL and much of Bioperl will operate quite happily on recent versions of Windows. VB is able to interface with MySQL directly http://www.vbmysql.com/, and of course MS has it's own set of database applications that would link seamlessly with Excel (at a cost of course). Regardless of where your database is, if you plan to use perl as an interface with Excel search CPAN for Excel (http://search.cpan.org/search?query=Excel&mode=all) and you'll come up with quite a lot of modules related to Excel. In particular for the things you mentioned you might look at DBD::Excel , Spreadsheet::WriteExcel , SQL::Translator::Parser::Excel , Spreadsheet::WriteExcel::FromDB , DBIx::Dump . Barry Moore Law, Annie wrote: >Hi, > >I would appreciate help on the following. I would like to create a small >application that would involve Excel XP on >Windows 2000, and >Bioperl and mysql on RedHat linux 9.0 > >The database will consist of clone IDs, accession numbers, and unigene IDs, >and allow a user to >add his own personal annotation as well. Later on, I would like to annotate >with other information as well. > >I am trying to map things out and see if all of the parts in my application >will fit together prior to doing >too much developing. > >Basically my main concern now is to create the flow of information. >There is the Excel workbook part and then there is the UNIX mysql database >part. > >Writing a shell or perl script in the linux environment that will ftp files >from unigene, locuslink >Etc and then user bioperl to parse the data, >Then use perl DBI to insert to information > >Also using perl DBI to upload information from the Excel sheet (user's >personal annotation) >Into the database. > >The part that I'm not too sure about is how to send the information from the >Excel sheet to the database >And how to grab the information from the database and update the Excel >sheet. >On top of that I am using two different operating systems. > >Are there some tools in VBA or in perl that I could use to build this bridge >or > >I am using Excel since there are functions within Excel that are useful. > >Thanks for your help, >Annie. > > > > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > From hleonov at pob.huji.ac.il Wed Jan 28 04:00:55 2004 From: hleonov at pob.huji.ac.il (Hadas Leonov) Date: Thu Jan 29 00:00:44 2004 Subject: [Bioperl-l] 2 psi-blast questions Message-ID: <7B2B74D8-5170-11D8-A077-000A95BA144E@pob.huji.ac.il> Hi, I noticed that a psi-blast report only considers new hits if the 0.0 < E-value < 0.01 (?). Is there any possibility to change these parameters ? especially the 0.0 limit, cause large query sequences with 60% identity might still give an e value of 0.0, thereby causing me to miss them completely by the standard (and comfortable) method of going through a psi blast report: ... $result = $psi_report->round($iter); $newHits_ref = $result->newhits; HIT: while($hit = $result->nextSbjct) { my $hitName = $hit->name; $is_new = grep /\Q$hitName\E/, @{$newHits_ref}; unless ($is_new ) {next HIT;} #do something with the new hit } ... furthermore, the line : $hit = $result->nextSbjct sometimes causes the following error message to be displayed - -------------------- WARNING --------------------- MSG: Possible error (2) while parsing BLAST report! --------------------------------------------------- but i don't seem to find anything wrong with the actual parsing result. any ideas? Thanks, Hadas. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1160 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040128/51d8bd11/attachment.bin From john.herbert at clinical-pharmacology.oxford.ac.uk Wed Jan 28 10:25:33 2004 From: john.herbert at clinical-pharmacology.oxford.ac.uk (john herbert) Date: Thu Jan 29 00:01:08 2004 Subject: [Bioperl-l] BioPerl-run Primer3 trouble Message-ID: Hello All. Sorry if this is wrong place to ask this but here goes. I have the following code in a script: use strict; use Data::Dumper; use johnhutils; use IO::File; use Carp; use Getopt::Declare; use Bio::Tools::Run::Primer3; use Bio::SeqIO; my $results; # Setting up the enviroment, well theoretically. Which I am guessing tells BioPerl where the executable lives. $ENV{PRIMER3}="/usr/bin/"; my $seqio=Bio::SeqIO->new(-file=>'infile'); my $seq=$seqio->next_seq; my $primer3 = Bio::Tools::Run::Primer3->new(-seq=>$seq, -outfile=>"temp.out", -program => 'primer3_core' ); unless ($primer3->executable()) {print STDERR "primer3 can not be found. Is it installed?\n"; exit(-1)} This code then generates primer3 cannot be found Is it installed. However, if I combine the path and program, it runs at the command line. (/usr/bin/primer3_core) Would be gratefull if someone could point me to how I can get primer3 to run in my script. Thanks. ps (The administrator has apparently installed BioPerl-run) From june at ics.es.osaka-u.ac.jp Thu Jan 29 00:38:11 2004 From: june at ics.es.osaka-u.ac.jp (June Tantoolvesm) Date: Thu Jan 29 00:44:36 2004 Subject: [Bioperl-l] installation trouble In-Reply-To: Message-ID: <001801c3e62a$150a3030$7701a8c0@PHOENIX> Thank you for trying. It's too much headache for me, and you kind of lost me somewhere with the solution, so I left alpha/OSF1 and am befriending linux instead. Thanks anyhow, I really admire all the experts out there. June > -----Original Message----- > From: Jason Stajich > [mailto:jason@cgt.duhs.duke.edu] > Sent: Thursday, January 29, 2004 9:32 AM > To: Brian Osborne > Cc: June Tantoolvesm; bioperl-l@portal.open- > bio.org > Subject: RE: [Bioperl-l] installation trouble > > I can replicate this problem with perl 5.6.0 and > alpha/OSF1 and latest > ExtUtils::MakeMaker so I would think someone need > to re-file the bug > report with Michael on rt.cpan.org for > ExtUtils::MakeMaker... > > make -i doesn't really work either. > > This is a perl/system problem so we don't much > control over it other than > to start splitting bioperl into components which > will generate a lot of > headaches. > > You can work around it by expanding some of the > system limits for shell > length on the machine but this is less than > ideal... > > > -jason > > On Wed, 28 Jan 2004, Brian Osborne wrote: > > > June, > > > > One workaround that's been used is to fix this > 'line too long' problem is to > > use the command 'make -i' instead of 'make'. > This tells make to ignore > > errors, and this was on an Alpha, like you. > > > > More on the problem: > > > > http://bioperl.org/pipermail/bioperl-l/2002- > August/009034.html > > > > > > Brian O. > > > > -----Original Message----- > > From: bioperl-l-bounces@portal.open-bio.org > > [mailto:bioperl-l-bounces@portal.open-bio.org]On > Behalf Of June Tantoolvesm > > Sent: Wednesday, January 28, 2004 12:58 AM > > To: bioperl-l@portal.open-bio.org > > Subject: [Bioperl-l] installation trouble > > > > Hello, > > > > I tried searching for help elsewhere but > couldn't find anything...could > > someone please help? I'm trying to install > bioperl to a local directory. > > > > [june@bg03n001e00]~/bioperl-1.4(4): make > > Make: line too long. Stop. > > [june@bg03n001e00]~/bioperl-1.4(7): uname -a > > OSF1 bg03n001e00.hpc.cmc.osaka-u.ac. V5.1 1885 > alpha > > > > I'm not sure what other information I need to > provide... > > > > Any suggestions very much appreciated. > > > > Thank you > > June > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open- > bio.org/mailman/listinfo/bioperl-l > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open- > bio.org/mailman/listinfo/bioperl-l > > > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu From redwards at utmem.edu Thu Jan 29 01:14:35 2004 From: redwards at utmem.edu (Rob Edwards) Date: Thu Jan 29 01:20:56 2004 Subject: [Bioperl-l] BioPerl-run Primer3 trouble In-Reply-To: References: Message-ID: <68EB8DE4-5222-11D8-95E8-000A959E1622@utmem.edu> John, This is exactly the right place to ask the question. The problem is simple -- on your system primer3 is run as primer3_core, and in Bio::Tools::Run::Primer3 it is hard-coded (incorrectly) to be primer3 -- and simply bad coding on my behalf. I have put one fix in CVS, that appears to work for me, although I think the whole Primer3 code needs revisiting and cleaning up. If you can not install this send me an email and I will explain how to set this up to work correctly in one of your own directories. Rob On Jan 28, 2004, at 9:25 AM, john herbert wrote: > Hello All. > Sorry if this is wrong place to ask this but here goes. > > I have the following code in a script: > > > use strict; > use Data::Dumper; > use johnhutils; > use IO::File; > use Carp; > use Getopt::Declare; > use Bio::Tools::Run::Primer3; > > use Bio::SeqIO; > my $results; > # Setting up the enviroment, well theoretically. Which I am guessing > tells BioPerl where the executable lives. > $ENV{PRIMER3}="/usr/bin/"; > my $seqio=Bio::SeqIO->new(-file=>'infile'); > my $seq=$seqio->next_seq; > my $primer3 = Bio::Tools::Run::Primer3->new(-seq=>$seq, > -outfile=>"temp.out", -program => 'primer3_core' ); > > unless ($primer3->executable()) {print STDERR "primer3 can not be > found. Is it installed?\n"; exit(-1)} > > > This code then generates primer3 cannot be found Is it installed. > > However, if I combine the path and program, it runs at the command > line. (/usr/bin/primer3_core) > > Would be gratefull if someone could point me to how I can get primer3 > to run in my script. > > Thanks. > > ps (The administrator has apparently installed BioPerl-run) > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From pvh at egenetics.com Thu Jan 29 02:45:08 2004 From: pvh at egenetics.com (Peter van Heusden) Date: Thu Jan 29 02:51:34 2004 Subject: [Bioperl-l] Testing BioPerl objects for equality Message-ID: <4018BA04.6000708@egenetics.com> I've got an idea for testing where I'd like to 'round-trip' through SeqIO: read in from a file on disk, write out again with write_seq() and then read in the file written by write_seq() and compare the two sequence objects. If they aren't equal, it means we've got a problem. To make this work requires some kind of equals() method on Seq, SeqFeature, etc. This doesn't seem to be there at the moment - or am I missing something? Maybe there should probably be some kind of Bio::ComparableI interface which provides an equals() abstract method. Peter From birney at ebi.ac.uk Thu Jan 29 04:38:51 2004 From: birney at ebi.ac.uk (Ewan Birney) Date: Thu Jan 29 04:44:58 2004 Subject: [Bioperl-l] Testing BioPerl objects for equality In-Reply-To: <4018BA04.6000708@egenetics.com> Message-ID: On Thu, 29 Jan 2004, Peter van Heusden wrote: > I've got an idea for testing where I'd like to 'round-trip' through > SeqIO: read in from a file on disk, write out again with write_seq() and > then read in the file written by write_seq() and compare the two > sequence objects. If they aren't equal, it means we've got a problem. That sounds like a great idea... we've always had problems with diff'ing the files because of whitespace issues, but diff'ing the objects sounds great. > > To make this work requires some kind of equals() method on Seq, > SeqFeature, etc. This doesn't seem to be there at the moment - or am I > missing something? Maybe there should probably be some kind of > Bio::ComparableI interface which provides an equals() abstract method. > I would be ok with this, but I do note in passing that this precisely the sort of minature abstract interface that really has newbie's scratching their heads - - why did they do this? - is this interface important? - does this mean I can use '=' signs with objects? - do I need to make on of these to compare two objects? In the documentation to the interface can you give some reassurance that this is really just a little aide-memoire for the developers, and it is not that important or crucial, and certainly noone should be creating one of these beasts directly :) > Peter > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From ssi at telemednet.ru Thu Jan 29 06:07:21 2004 From: ssi at telemednet.ru (NTMail) Date: Thu Jan 29 06:09:54 2004 Subject: [Bioperl-l] Failed mail Message-ID: --------------------------------------------------------------------- Your message to mxs.valuehost.ru was rejected. I said: . And mxs.valuehost.ru responded with 554 mail server permanently rejected message (#5.3.0) --------------------------------------------------------------------- Your message follows: >Received: from [213.234.215.89] by ns.telemednet.ru (NTMail 3.03.0018/25.aaeo) with ESMTP id za409187 for ; Thu, 29 Jan 2004 13:46:19 +0300 >From: bioperl-l@bioperl.org >To: elena.koroleva@astonreal.com >Subject: hello >Date: Thu, 29 Jan 2004 13:44:41 +0300 >MIME-Version: 1.0 >Content-Type: multipart/mixed; > boundary="----=_NextPart_000_0003_33159E83.1BFD0B19" >X-Priority: 3 >X-MSMail-Priority: Normal >Message-Id: <10461941616393@telemednet.ru> > >This is a multi-part message in MIME format. > >------=_NextPart_000_0003_33159E83.1BFD0B19 >Content-Type: text/plain; > charset="Windows-1252" >Content-Transfer-Encoding: 7bit > > > > >------=_NextPart_000_0003_33159E83.1BFD0B19 >Content-Type: application/octet-stream; > name="message.scr" >Content-Transfer-Encoding: base64 >Content-Disposition: attachment; > filename="message.scr" > >TVqQAAMAAAAEAAAA//8AALgAAAAAAAAAQAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA >AAAAqAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA >AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAUEUA >AEwBAwAAAAAAAAAAAAAAAADgAA8BCwEHAABQAAAAEAAAAGAAAGC+AAAAcAAAAMAAAAAASgAAEAAA >AAIAAAQAAAAAAAAABAAAAAAAAAAA0AAAABAAAAAAAAACAAAAAAAQAAAQAAAAABAAABAAAAAAAAAQ >AAAAAAAAAAAAAADowQAAMAEAAADAAADoAQAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA >AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA >AAAAAAAAAAAAAAAAAAAAAABVUFgwAAAAAABgAAAAEAAAAAAAAAAEAAAAAAAAAAAAAAAAAACAAADg >VVBYMQAAAAAAUAAAAHAAAABQAAAABAAAAAAAAAAAAAAAAAAAQAAA4C5yc3JjAAAAABAAAADAAAAA >BAAAAFQAAAAAAAAAAAAAAAAAAEAAAMAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA >AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA >AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA >AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA >AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA >AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA >AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA >AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA >AAAAAAAAAAAAAAAAAAAAAAAAMS4yNABVUFghDAkCCUh+iY/UNhyBKZYAAFNOAAAAgAAAJgEAxe6H >ApIAUCZKAEAD/bJpmiwQBPQl6AEAS85pmm7ZH8gqwAO4sKimaZqmoJiQiICapmmaeHBoYFhQzWCf >aUgARAc4MDRN03QDKCQcGBDTLLvXCCMD+Cnw6E3TNE3g2NDIvLQ0TdM0rKSclIzONk3TiHxwaClv >XKbpmsEHVEwDRDiapmmaLCQcFAwEaZrObfwofwP07OSmaZqm3NTMyLyapmmatKykoJiQZ5umaYyA From Postmaster at immunbio.mpg.de Thu Jan 29 07:52:58 2004 From: Postmaster at immunbio.mpg.de (Postmaster@immunbio.mpg.de) Date: Thu Jan 29 07:59:26 2004 Subject: [Bioperl-l] Undeliverable Mail Message-ID: Bad address -- Error -- No such local user ========================= Start of returned 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Jackson) Date: Thu Jan 29 08:48:57 2004 Subject: [Bioperl-l] 2 psi-blast questions In-Reply-To: <7B2B74D8-5170-11D8-A077-000A95BA144E@pob.huji.ac.il> References: <7B2B74D8-5170-11D8-A077-000A95BA144E@pob.huji.ac.il> Message-ID: <40190DBD.8050602@bms.com> Hadas, the answer is 'yes and no'. You can set the -h value ($blaster->h()) to adjust the inclusion threshold for refining the scoring matrix. However, it only takes expect values - not identity/length - and the expect value can't go below zero. Lower e values are more significant; e=0 roughly means there isn't a snowball's chance in the netherworld of getting that hit by chance in a dataset the size of the one you searched. You can use the Bio::SearchIO::Blast parser's hit_filter and hsp_filter methods to pass in a coderef that rejects hits above/below a certain identity and length. If you do so, make sure you call identity on the HSP result objects, NOT the Hit objects as the identity numbers from Hit are inaccurate (a BLAST issue, not a SearchIO issue). I find that running PsiBlast takes some tweaking - adjusting the values for -e, -h, and -j (# rounds) so I build a good matrix and the search doesn't converge. Also look at -b and -v (# alignments/descriptions returned) to make sure you go deep enough into the results. Hope this helps, Don Jackson Hadas Leonov wrote: > Hi, > I noticed that a psi-blast report only considers new hits if the 0.0 < > E-value < 0.01 (?). > Is there any possibility to change these parameters ? especially the > 0.0 limit, cause large query sequences with 60% identity might still > give an e value of 0.0, thereby causing me to miss them completely by > the standard (and comfortable) method of going through a psi blast > report: > > ... > $result = $psi_report->round($iter); > $newHits_ref = $result->newhits; > HIT: while($hit = $result->nextSbjct) { > my $hitName = $hit->name; > $is_new = grep /\Q$hitName\E/, @{$newHits_ref}; > unless ($is_new ) {next HIT;} > #do something with the new hit > > } > ... > > furthermore, the line : $hit = $result->nextSbjct > sometimes causes the following error message to be displayed - > -------------------- WARNING --------------------- > MSG: Possible error (2) while parsing BLAST report! > --------------------------------------------------- > but i don't seem to find anything wrong with the actual parsing result. > > any ideas? > > Thanks, > Hadas. > >------------------------------------------------------------------------ > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > From hleonov at pob.huji.ac.il Thu Jan 29 09:06:17 2004 From: hleonov at pob.huji.ac.il (Hadas Leonov) Date: Thu Jan 29 09:13:17 2004 Subject: [Bioperl-l] 2 psi-blast questions In-Reply-To: <40190DBD.8050602@bms.com> References: <7B2B74D8-5170-11D8-A077-000A95BA144E@pob.huji.ac.il> <40190DBD.8050602@bms.com> Message-ID: <4E3E4F2F-5264-11D8-B5A6-000A95BA144E@pob.huji.ac.il> I wasn't clear enough :-) I don't need to change the identity\length parameters, I check them as I got over the report and decide which hit (hsp actually) is relevant for me. I know the e-value doesn't go below 0. the problem is that the psi-blast parser does not consider a hit as "new" if it's e-value is precisely 0.0 (or e-180 for that matter). I went around this problem in a different manner. I didn't quite get what the -h parameter does. what inclusion threshold is defined by it? -e is for changing the upper limit of the e-value, right? Thanks again, Hadas. On Jan 29, 2004, at 3:42 PM, Donald G. Jackson wrote: > Hadas, > > the answer is 'yes and no'. > > You can set the -h value ($blaster->h()) to adjust the inclusion > threshold for refining the scoring matrix. However, it only takes > expect values - not identity/length - and the expect value can't go > below zero. Lower e values are more significant; e=0 roughly means > there isn't a snowball's chance in the netherworld of getting that hit > by chance in a dataset the size of the one you searched. > You can use the Bio::SearchIO::Blast parser's hit_filter and > hsp_filter methods to pass in a coderef that rejects hits above/below > a certain identity and length. > If you do so, make sure you call identity on the HSP result objects, > NOT the Hit objects as the identity numbers from Hit are inaccurate (a > BLAST issue, not a SearchIO issue). > I find that running PsiBlast takes some tweaking - adjusting the > values for -e, -h, and -j (# rounds) so I build a good matrix and the > search doesn't converge. Also look at -b and -v (# > alignments/descriptions returned) to make sure you go deep enough into > the results. > > Hope this helps, > > Don Jackson > > Hadas Leonov wrote: > >> Hi, >> I noticed that a psi-blast report only considers new hits if the 0.0 >> < E-value < 0.01 (?). >> Is there any possibility to change these parameters ? especially the >> 0.0 limit, cause large query sequences with 60% identity might still >> give an e value of 0.0, thereby causing me to miss them completely by >> the standard (and comfortable) method of going through a psi blast >> report: >> >> ... >> $result = $psi_report->round($iter); >> $newHits_ref = $result->newhits; >> HIT: while($hit = $result->nextSbjct) { >> my $hitName = $hit->name; >> $is_new = grep /\Q$hitName\E/, @{$newHits_ref}; >> unless ($is_new ) {next HIT;} >> #do something with the new hit >> >> } >> ... >> >> furthermore, the line : $hit = $result->nextSbjct >> sometimes causes the following error message to be displayed - >> -------------------- WARNING --------------------- >> MSG: Possible error (2) while parsing BLAST report! >> --------------------------------------------------- >> but i don't seem to find anything wrong with the actual parsing >> result. >> >> any ideas? >> >> Thanks, >> Hadas. >> >> ---------------------------------------------------------------------- >> -- >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> > From iain.wallace at ucd.ie Thu Jan 29 09:09:50 2004 From: iain.wallace at ucd.ie (Iain Wallace) Date: Thu Jan 29 09:16:22 2004 Subject: [Bioperl-l] Rooting a tree Message-ID: <1075385390.4035.17.camel@bioinf10> Hi all, I am trying to root a tree so that the leaf distribution is balanced. I think the technical term is a "perfect binary tree". Basically it means that if I go down one level from the root, each of the two nodes contain half the number of leaves. If I go down another level each of the four nodes contain a quarter of the leaves. I am able to do this manually by creating an outgroup in the NJPlot program, so that visually it looks balanced, and then save the rooted tree. I tried to automate the process by using bioperl, and the reroot function at each internal node to find the best place to put the root node. This didn't work for me because, when I use the reroot function, I get 3 descendants instead of two. Does anyone know how to reroot the tree so that there is only two descendants? If anyone has any ideas about how i could accomplish this, i would really appreciate it.... Here is my code: #!/usr/bin/perl -w use strict; use Bio::TreeIO; use Bio::SeqIO; my $treefile=$ARGV[0]; my $treeio = new Bio::TreeIO( -file => $treefile) ; my $tree = $treeio->next_tree or die "No Tree\n"; my $rootnode = $tree->get_root_node(); my $total; my %data; for my $treenodes ( $tree->get_nodes) { undef %data; my %data; if (( !$treenodes->is_Leaf ) && ($treenodes!= $rootnode)) { #reroot tree print "rerooting\n"; $tree->reroot($treenodes); for my $node ( $tree->get_leaf_nodes ) { &inc_ancestor($node,\%data); # This assigns a count for the number of leaves each node has $total++; my $leafid=$node->internal_id; $data{$leafid}=1; } print "the descendents\n "; for my $descendentnode ( $treenodes->each_Descendent()){ my $leafid=$descendentnode->internal_id; print " There are ",$data{$leafid}," leaves here\n";; } $tree->reroot($rootnode); } } sub inc_ancestor { my $node = shift; my $data = shift; return unless defined $node && defined $node->ancestor; my $id = $node->ancestor->internal_id; $data->{$id}++; # This increments the count for the node.. &inc_ancestor($node->ancestor,$data); } From andreas.bernauer at gmx.de Thu Jan 29 12:22:03 2004 From: andreas.bernauer at gmx.de (Andreas Bernauer) Date: Thu Jan 29 12:28:30 2004 Subject: [Bioperl-l] 2 psi-blast questions In-Reply-To: <40190DBD.8050602@bms.com> References: <7B2B74D8-5170-11D8-A077-000A95BA144E@pob.huji.ac.il> <40190DBD.8050602@bms.com> Message-ID: <20040129172203.GA30781@hgt.mcb.uconn.edu> Donald G. Jackson wrote: > Hadas Leonov wrote: > >I noticed that a psi-blast report only considers new hits if the 0.0 < > >E-value < 0.01 (?). > >Is there any possibility to change these parameters ? especially the > >0.0 limit, cause large query sequences with 60% identity might still > >give an e value of 0.0, thereby causing me to miss them completely by > > You can set the -h value ($blaster->h()) to adjust the inclusion > threshold for refining the scoring matrix. However, it only takes > expect values - not identity/length - and the expect value can't go > below zero. I think he meant that evalues that are exactly zero get excluded, as the threshold is tested with a "lower than" (`<') instead of an "lower or equal than" (`<='). Andreas. From andreas.bernauer at gmx.de Thu Jan 29 12:25:56 2004 From: andreas.bernauer at gmx.de (Andreas Bernauer) Date: Thu Jan 29 12:32:22 2004 Subject: [Bioperl-l] reducing time In-Reply-To: <401801AF.3010104@ibsm.cnrs-mrs.fr> References: <401801AF.3010104@ibsm.cnrs-mrs.fr> Message-ID: <20040129172556.GB30781@hgt.mcb.uconn.edu> KHOUEIRY pierre wrote: > Right now per exemple, I'm runnig a perl script (look at the > attachement). There is no attachement. Andreas. From barry.moore at genetics.utah.edu Thu Jan 29 13:08:02 2004 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Thu Jan 29 13:14:29 2004 Subject: [Bioperl-l] 3-frame and 6-frame translation Message-ID: <40194C02.9050300@genetics.utah.edu> Last night I was looking at methods in various bioperl modules trying to come up to speed on the various ways to translate nt sequence in bioperl. I ran across two methods that, given a nt sequence (can't remember if they took a string or an object), would return (as an array or strings I think) either a 3-frame or 6-frame translation of the sequence. This morning I can't find the module where those are located again. I think the module might have had "utilities" in the path, but not sure. I know about the translate method of a PrimarySeq object and it's ability to specify frame, but still want to look more closely at the other mystery module that I have now lost. Does anyone know what I'm talking about, and where it is? This brings up a related question that had a similar post within the last 24 hours. My skill at searching the bioperl web site is terrible. I just use the http://search.open-bio.org/ search site, but the search results return almost (if not) exclusively postings to the bioperl list that are usually 3+ years old. I've tried just using Google limited to the bioperl domain with only moderately better success. The main thing that keeps me frustrated is that my searches never seem to descend into the module documentation where I might get a hit on a method description. Am I doing something wrong, or is this an intended limitation of searching bioperl? Barry Moore Dept. of Human Genetics University of Utah Salt Lake City, Utah From brian_osborne at cognia.com Thu Jan 29 13:28:49 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Thu Jan 29 13:35:57 2004 Subject: [Bioperl-l] 3-frame and 6-frame translation In-Reply-To: <40194C02.9050300@genetics.utah.edu> Message-ID: Barry, Bio::SeqUtils. # translate a sequence in all six frames @seqs = Bio::SeqUtils->translate_6frames($seq); Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Barry Moore Sent: Thursday, January 29, 2004 1:08 PM To: bioperl Subject: [Bioperl-l] 3-frame and 6-frame translation Last night I was looking at methods in various bioperl modules trying to come up to speed on the various ways to translate nt sequence in bioperl. I ran across two methods that, given a nt sequence (can't remember if they took a string or an object), would return (as an array or strings I think) either a 3-frame or 6-frame translation of the sequence. This morning I can't find the module where those are located again. I think the module might have had "utilities" in the path, but not sure. I know about the translate method of a PrimarySeq object and it's ability to specify frame, but still want to look more closely at the other mystery module that I have now lost. Does anyone know what I'm talking about, and where it is? This brings up a related question that had a similar post within the last 24 hours. My skill at searching the bioperl web site is terrible. I just use the http://search.open-bio.org/ search site, but the search results return almost (if not) exclusively postings to the bioperl list that are usually 3+ years old. I've tried just using Google limited to the bioperl domain with only moderately better success. The main thing that keeps me frustrated is that my searches never seem to descend into the module documentation where I might get a hit on a method description. Am I doing something wrong, or is this an intended limitation of searching bioperl? Barry Moore Dept. of Human Genetics University of Utah Salt Lake City, Utah _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From achnow at uymail.com Thu Jan 29 14:49:02 2004 From: achnow at uymail.com (achnow@uymail.com) Date: Thu Jan 29 15:09:58 2004 Subject: [Bioperl-l] Accept Electronic Checks Now! Message-ID: Dear Non Profit Organization, Do you need to accept Electronic Checks (ACH) through your website or business? If you have considered this or are just thinking about it. Boy, do we have what you need! 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This is the qmail-send program at mail.onmobile.com. I'm afraid I wasn't able to deliver your message to the following addresses. This is a permanent error; I've given up. Sorry it didn't work out. : Sorry, no mailbox here by that name. vpopmail (#5.1.1) --- Below this line is a copy of the message. 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The attachment is now empty. The sender has already been notified. Dies ist eine Info-Mail vom Bayer Virenscanner: Sie erhielten eine e-Mail, in der ein Virus entdeckt und entfernt wurde, Details siehe unten. Der Anhang ist nun leer. Der Absender wurde bereits benachrichtigt. Date: 01/30/2004 07:35:54 AM Subject: [Bioperl-l] failure notice Virus: WORM_MIMAIL.R File: text.zip From: bioperl-l-bounces@portal.open-bio.org To: bioperl-l@bioperl.org Action: Quarantined; Scanned by ScanMail for Lotus Notes 2.6 with scanengine 6.810-1005 and patternfile lpt$vpn.749 From immunoguest at hotmail.com Fri Jan 30 03:05:37 2004 From: immunoguest at hotmail.com (tai kwan do) Date: Fri Jan 30 03:11:56 2004 Subject: [Bioperl-l] Difference between Message-ID: Hello, Maybe someone could help me out with this problem, I've tried to email ncbi about this but they didn't bother answering. Basically, I'm seeing a difference in the data being output by stand-alone blast and online blast. The identities value are different between the xml output and the pairwise alignment output, even though I'm using the exact same input values. The other difference I see is in the query and hit sequences. I've included below the outputs using the same input parameters, is this normal behavior? gb|AE000111.1|AE000111 Escherichia coli K-12 MG1655 section 1 of 400 of the complete genome Length = 10596 Score = 589 bits (297), Expect = e-168 Identities = 315/324 (97%) Strand = Plus / Plus Query: 237 aggtaacggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgacagtg 296 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 237 aggtaacggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgacagtg 296 Query: 297 cgggcnnnnnnnnncgaccaaaggtaacgaggtaacaaccatgcgagtgttgaagttcgg 356 ||||| |||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 297 cgggctttttttttcgaccaaaggtaacgaggtaacaaccatgcgagtgttgaagttcgg 356 Query: 357 cggtacatcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaa 416 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 357 cggtacatcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaa 416 Query: 417 tgccaggcaggggcaggtggccaccgtcctctctgcccccgccaaaatcaccaaccacct 476 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 417 tgccaggcaggggcaggtggccaccgtcctctctgcccccgccaaaatcaccaaccacct 476 Query: 477 ggtggcgatgattgaaaaaaccattagcggccaggatgctttacccaatatcagcgatgc 536 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct: 477 ggtggcgatgattgaaaaaaccattagcggccaggatgctttacccaatatcagcgatgc 536 Query: 537 cgaacgtatttttgccgaactttt 560 |||||||||||||||||||||||| Sbjct: 537 cgaacgtatttttgccgaactttt 560 1 gi|1786181|gb|AE000111.1|AE000111 Escherichia coli K-12 MG1655 section 1 of 400 of the complete genome AE000111 10596 1 589.253 297 1.04898e-168 237 560 237 560 1 1 324 324 324 AGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT AGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Thanks in advance _________________________________________________________________ High-speed usersbe more efficient online with the new MSN Premium Internet Software. http://join.msn.com/?pgmarket=en-us&page=byoa/prem&ST=1 From postmaster at expasy-ng.isb-sib.ch Fri Jan 30 04:21:01 2004 From: postmaster at expasy-ng.isb-sib.ch (MailScanner) Date: Fri Jan 30 04:27:21 2004 Subject: [Bioperl-l] Warning: E-mail viruses detected Message-ID: <200401300921.i0U9L1EH015507@expasy-ng.isb-sib.ch> Our virus detector has just been triggered by a message you sent:- To: elisabeth.gasteiger@isb-sib.ch Subject: Hello Date: Fri Jan 30 10:21:01 2004 Any infected parts of the message (text.scr) have not been delivered. This message is simply to warn you that your computer system may have a virus present and should be checked. The virus detector said this about the message: Report: text.scr Found the W32/Mydoom.a@MM virus !!! Windows Screensavers are often used to hide viruses (text.scr) No programs allowed (text.scr) -- MailScanner Email Virus Scanner www.mailscanner.info Mailscanner thanks transtec Computers for their support From Mailer-Daemon at dkfz-heidelberg.de Fri Jan 30 05:52:16 2004 From: Mailer-Daemon at dkfz-heidelberg.de (Mailer-Daemon@dkfz-heidelberg.de) Date: Fri Jan 30 05:58:37 2004 Subject: [Bioperl-l] MAIL DELIVERY NOTIFICATION Message-ID: <200401301052.i0UAqGa19812@krebs.inet.dkfz-heidelberg.de> Dear Internet Email User, this is an automated mail delivery notification, because your email has not been delivered the usual way. Your mail was not deliverd for the following reason: Your mail contained an attachment with the filename extension scr Since such content may contain viruses or other dangerous code it was blocked by the firewall. Best regards, Your GeNUGate Mail Gateway ========================================================= ENVELOPE INFORMATION ========================================================= FROM = bioperl-l@bioperl.org RCPT = w.vonderlieth@dkfz.de ========================================================= HEADER INFORMATION ========================================================= Received: from bioperl.org (211.144.96.22) by (smtprelay) with ESMTP Fri Jan 30 11:52:03 2004. From: bioperl-l@bioperl.org To: w.vonderlieth@dkfz.de Subject: Mail Delivery System Date: Fri, 30 Jan 2004 18:53:41 +0800 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0008_DEE8190F.6382975A" X-Priority: 3 X-MSMail-Priority: Normal ========================================================= From donald.jackson at bms.com Fri Jan 30 08:41:38 2004 From: donald.jackson at bms.com (Donald G. Jackson) Date: Fri Jan 30 08:48:33 2004 Subject: [Bioperl-l] 2 psi-blast questions In-Reply-To: <20040129172203.GA30781@hgt.mcb.uconn.edu> References: <7B2B74D8-5170-11D8-A077-000A95BA144E@pob.huji.ac.il> <40190DBD.8050602@bms.com> <20040129172203.GA30781@hgt.mcb.uconn.edu> Message-ID: <401A5F12.8060204@bms.com> My apologies; I misunderstood the question. Don Jackson Andreas Bernauer wrote: >Donald G. Jackson wrote: > > >>Hadas Leonov wrote: >> >> >>>I noticed that a psi-blast report only considers new hits if the 0.0 < >>>E-value < 0.01 (?). >>>Is there any possibility to change these parameters ? especially the >>>0.0 limit, cause large query sequences with 60% identity might still >>>give an e value of 0.0, thereby causing me to miss them completely by >>> >>> >>You can set the -h value ($blaster->h()) to adjust the inclusion >>threshold for refining the scoring matrix. However, it only takes >>expect values - not identity/length - and the expect value can't go >>below zero. >> >> > >I think he meant that evalues that are exactly zero get excluded, as >the threshold is tested with a "lower than" (`<') instead of an "lower >or equal than" (`<='). > >Andreas. >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > From Mailer-Daemon at hawk.mail.pas.earthlink.net Fri Jan 30 09:01:27 2004 From: Mailer-Daemon at hawk.mail.pas.earthlink.net (Mail Delivery System) Date: Fri Jan 30 09:07:57 2004 Subject: [Bioperl-l] Mail delivery failed: returning message to sender Message-ID: This message was created automatically by mail delivery software (Exim). A message that you sent could not be delivered to one or more of its recipients. This is a permanent error. The following address(es) failed: 3dsudha_c2002@yahoo.com SMTP error from remote mailer after end of data: host mx2.mail.yahoo.com [64.156.215.6]: 554 delivery error: dd This user doesn't have a yahoo.com account (3dsudha_c2002@yahoo.com) [0] - mta227.mail.scd.yahoo.com ------ This is a copy of the message, including all the headers. ------ Return-path: Received: from h-64-105-20-14.dnvtco56.dynamic.covad.net ([64.105.20.14] helo=bioperl.org) by hawk.mail.pas.earthlink.net with esmtp (Exim 3.33 #1) id 1AmZD3-0002bS-00 for 3dsudha_c2002@yahoo.com; Fri, 30 Jan 2004 06:01:25 -0800 From: bioperl-l@bioperl.org To: 3dsudha_c2002@yahoo.com Subject: Hello Date: Fri, 30 Jan 2004 07:00:15 -0700 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0006_B689317E.8261FA1F" X-Priority: 3 X-MSMail-Priority: Normal Message-Id: This is a multi-part message in MIME format. ------=_NextPart_000_0006_B689317E.8261FA1F Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit '4Px7`QU fu P $Iv.Uf6 ۙ{x qd()n~b>2Wuѹys&?{799xF 7BE 5&-xh ->K'*T?Zjۧ A9jvi1Qy1Dv?/;kqV9lqbУs&m4}QN[vH3*( Fȴol,)Q]g8GHitè* Ug9ND"5VuƒQ8NSL uLʰؖ7*aDC#b[0&FF"ٛypEc|11ڠIi?#tRߌ^ ɺ*qu)}&-latݻkQ(HI wz0rעa";}촂,d Ը8Q~ao#:ri՗$6TivPnح ZKÌzCt^¸EB?bvQD(Jd/\bwN˿)9޵ǠL>xKU"s mghY]7(,`;|~9UhMJUvQDhABh?Ed)#XSKX 5 VE,cӈ<ؔd4C…Wp2auo܃Ջ58s6bv8M}a3;`8`6u AO(kȶi [Bioperl-l] Mail delivery failed: returning message to sender Message-ID: This is an info mail issued by the Bayer virus checking software: Prior to this message you received an e-mail where a virus has been detected and removed, details see below. The attachment is now empty. The sender has already been notified. Dies ist eine Info-Mail vom Bayer Virenscanner: Sie erhielten eine e-Mail, in der ein Virus entdeckt und entfernt wurde, Details siehe unten. Der Anhang ist nun leer. Der Absender wurde bereits benachrichtigt. Date: 01/30/2004 03:02:16 PM Subject: [Bioperl-l] Mail delivery failed: returning message to sender Virus: WORM_MYDOOM.A File: readme.zip From: bioperl-l-bounces@portal.open-bio.org To: bioperl-l@bioperl.org Action: Quarantined; Scanned by ScanMail for Lotus Notes 2.6 with scanengine 6.810-1005 and patternfile lpt$vpn.751 From jason at cgt.duhs.duke.edu Fri Jan 30 09:52:09 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Fri Jan 30 09:58:58 2004 Subject: [Bioperl-l] Bio::SeqIO::new possible wierdness In-Reply-To: References: Message-ID: I dunnno then - Chris has graciously set it up, either ht://dig is not doing its job very well or there something mis-configured. We Have tried to make the lists searchable at http://search.open-bio.org/ if it isn't working properly that is another issue. google + site:open-bio.org pipermail bioperl-l your-term also works pretty well. It really is a major job making sure all of the website/cvs/server components work correctly all the time. I wish there was a way to give Chris more of hand on these things, as he has a full-time consulting gig to keep him around in the first place. --jason On Wed, 28 Jan 2004, Brian Osborne wrote: > Jason, > > I'm a bit suspicious of search.open-bio.org. I enter a term like 'Root' or > 'GFF' and get back a dozen hits or so. It's inconceivable to me that there's > only 12 messages in bioperl-l since 1999 containing the string 'GFF'. > Something's wrong, either with the search or the display. And if there are > no matches I see only a blank page, which is a bit inscrutable. Then if I > select 'no restriction', which I guess means everything in the selectable > list I don't see the Bioperl matches anymore, I just see a dozen or so > Biojava matches. > > Brian O. > > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org > [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Jason Stajich > Sent: Wednesday, January 28, 2004 4:34 PM > To: Peter van Heusden > Cc: bioperl-l@bioperl.org > Subject: Re: [Bioperl-l] Bio::SeqIO::new possible wierdness > > The bioperl list is searchable - just not the bioperl-guts though - > http://search.open-bio.org > and/or google works fine for me > > > This is the change Lincoln made though (cvs log on Bio/Root/IO.pm > and found the last commit by lincoln). I had put the \*ARGV in there so > that we could use the magic <> operator (allows STDIN or a list of files > to all be used as transparent input). This caused some problems with > tests in GFF, SeqFeature, or Registry. > > Here is his log message > revision 1.50 > date: 2003/11/21 03:03:38; author: lstein; state: Exp; lines: +2 -2 > The following regression tests now pass: GFF, SeqFeature, Registry > > --jason > > jason@jason $ cvs diff -r 1.49 Bio/Root/IO.pm > Index: Bio/Root/IO.pm > =================================================================== > RCS file: /home/repository/bioperl/bioperl-live/Bio/Root/IO.pm,v > retrieving revision 1.49 > diff -r1.49 IO.pm > 1c1 > < # $Id: IO.pm,v 1.49 2003/10/28 21:58:54 jason Exp $ > --- > > # $Id: IO.pm,v 1.50 2003/11/21 03:03:38 lstein Exp $ > 435c435 > < my $fh = $self->_fh || \*ARGV; > --- > > my $fh = $self->_fh or return; > > > On Wed, 28 Jan 2004, Peter van Heusden wrote: > > > Jason Stajich wrote: > > > > >On Wed, 28 Jan 2004, Donald G. Jackson wrote: > > > > > > > > > > > >>Personally, I like the fall-back but agree that $ARGV[0] shouldn't be > it. > > >>I'd suggest STDIN - if somebody calls new without a file/handle I think > > >>they're more likely to be reading. OTOH, guessing format woud be tough. > > >> > > >> > > > > > >the guess format is trying to read off the top of the file I think - we > > >support a 'peek' type of reading into the file, by having the _pushback > > >functionality in Root::IO. > > > > > >I would like to see something like this go into Root:IO rather than in > > >SeqIO - and have Root::IO give back a filename if it knows what it is. > > > > > >Also the Root::IO code could also do something like this: > > > $file = "-" unless defined $file; > > > open my $fh => $input or die $!; > > > > > >Which will then read from stdin if now filename is sent in - right now we > > >don't really support that anymore because it was causing clog-ups in some > > >of the DB::GFF code/tests I think. > > > > > >Maybe we localize this to 'FormattedReaderWriters' -- all the > > >XXXIO(-format => 'XXX') modules so as to avoid the problems Lincoln saw. > > > > > > > > > > > > > > Can you to where Lincoln "saw" this problem? The BioPerl mailing list > > archive is not searchable, and searching via Google doesn't turn > > anything up. > > > > Anyway, I'll look into Root::IO tomorrow and see what I come up with. > > > > Peter > > > > > > > > > > >>At the very least a warning would be appropriate, perhaps indicating the > > >>course of action. > > >> > > >>For xml handlers we can check the dtd and throw an error. I will modify > > >>my SeqIO::tinyseq::tinyseqHandler to do so. > > >> > > >>Don Jackson > > >> > > >> > > >> > > >>Peter van Heusden wrote: > > >> > > >> > > >> > > >>>My review of the Bio::SeqIO::new method shows the following behaviour: > > >>> > > >>>Missing both ?file and ?fh arguments: falls back to using $ARGV[0] > > >>>(the first command line argument) as sequence filename. If this fails, > > >>>gives an exception about ?Unknown format?. > > >>>-file argument (without ?fh argument): > > >>>? given, but file unreadable: throws exception > > >>>? undefined: reads $ARGV[0], as above. > > >>>-fh argument (without ?file argument): > > >>>? given, but not a filehandle: gives exception > > >>>? given, but an invalid filehandle (not open): gives exception > > >>>? undefined: reads $ARGV[0], as above. > > >>>-format argument: if the sequence file doesn?t correspond to the given > > >>>format, some parsers give an error (e.g. EMBL), while others do not > > >>>(GenBank), instead silently give wrong results. > > >>>-format argument without ?file argument: Silently creates a SeqIO > > >>>object which writes to STDOUT. > > >>> > > >>>I don't think that this $ARGV[0] shortcut should be in there - it > > >>>causes unnecessary potential confusion. Imagine a situation where -fh > > >>>or -file is specified (using a variable), but that variable somehow > > >>>does not get defined. In that case, the $ARGV[0] fallback behaviour > > >>>would be used, which might lead to a non-obvious error behaviour. > > >>> > > >>>I'd like to propose that either -file or -fh should be specified, > > >>>otherwise an exception is thrown. While I'm about it, I'm thinking of > > >>>migrating the exceptions to the new 'typed exceptions' that BioPerl > > >>>now provides - is there any consensus on exception type names? > > >>> > > >>>Peter > > >>>_______________________________________________ > > >>>Bioperl-l mailing list > > >>>Bioperl-l@portal.open-bio.org > > >>>http://portal.open-bio.org/mailman/listinfo/bioperl-l > > >>> > > >>> > > >>> > > >>_______________________________________________ > > >>Bioperl-l mailing list > > >>Bioperl-l@portal.open-bio.org > > >>http://portal.open-bio.org/mailman/listinfo/bioperl-l > > >> > > >> > > >> > > > > > >-- > > >Jason Stajich > > >Duke University > > >jason at cgt.mc.duke.edu > > > > > >_______________________________________________ > > >Bioperl-l mailing list > > >Bioperl-l@portal.open-bio.org > > >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From dag at bioteam.net Fri Jan 30 09:43:51 2004 From: dag at bioteam.net (Chris Dagdigian) Date: Fri Jan 30 10:06:23 2004 Subject: [Bioperl-l] Bio::SeqIO::new possible wierdness In-Reply-To: Message-ID: We've tried over and over again to get good search going for open-bio.org. First we tried ht://dig and then I tried integrating it directly into the mailman archives (lots of python hacking). Nothing works well. htdig takes forever to run, eats disk space and still does not provide greate results. Right now google is probably best. we may want to discontinue all of our own search methods. Or we buy the google appliance thingie that is meant for corporate intranets :) -chris On Fri, 30 Jan 2004, Jason Stajich wrote: > I dunnno then - Chris has graciously set it up, either ht://dig is not > doing its job very well or there something mis-configured. We Have tried > to make the lists searchable at http://search.open-bio.org/ if it isn't > working properly that is another issue. google + > site:open-bio.org pipermail bioperl-l your-term > also works pretty well. > > It really is a major job making sure all of the website/cvs/server > components work correctly all the time. I wish there was a way to give > Chris more of hand on these things, as he has a full-time consulting gig > to keep him around in the first place. > > --jason > > On Wed, 28 Jan 2004, Brian Osborne wrote: > > > Jason, > > > > I'm a bit suspicious of search.open-bio.org. I enter a term like 'Root' or > > 'GFF' and get back a dozen hits or so. It's inconceivable to me that there's > > only 12 messages in bioperl-l since 1999 containing the string 'GFF'. > > Something's wrong, either with the search or the display. And if there are > > no matches I see only a blank page, which is a bit inscrutable. Then if I > > select 'no restriction', which I guess means everything in the selectable > > list I don't see the Bioperl matches anymore, I just see a dozen or so > > Biojava matches. > > > > Brian O. > > > > -----Original Message----- > > From: bioperl-l-bounces@portal.open-bio.org > > [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Jason Stajich > > Sent: Wednesday, January 28, 2004 4:34 PM > > To: Peter van Heusden > > Cc: bioperl-l@bioperl.org > > Subject: Re: [Bioperl-l] Bio::SeqIO::new possible wierdness > > > > The bioperl list is searchable - just not the bioperl-guts though - > > http://search.open-bio.org > > and/or google works fine for me > > > > > > This is the change Lincoln made though (cvs log on Bio/Root/IO.pm > > and found the last commit by lincoln). I had put the \*ARGV in there so > > that we could use the magic <> operator (allows STDIN or a list of files > > to all be used as transparent input). This caused some problems with > > tests in GFF, SeqFeature, or Registry. > > > > Here is his log message > > revision 1.50 > > date: 2003/11/21 03:03:38; author: lstein; state: Exp; lines: +2 -2 > > The following regression tests now pass: GFF, SeqFeature, Registry > > > > --jason > > > > jason@jason $ cvs diff -r 1.49 Bio/Root/IO.pm > > Index: Bio/Root/IO.pm > > =================================================================== > > RCS file: /home/repository/bioperl/bioperl-live/Bio/Root/IO.pm,v > > retrieving revision 1.49 > > diff -r1.49 IO.pm > > 1c1 > > < # $Id: IO.pm,v 1.49 2003/10/28 21:58:54 jason Exp $ > > --- > > > # $Id: IO.pm,v 1.50 2003/11/21 03:03:38 lstein Exp $ > > 435c435 > > < my $fh = $self->_fh || \*ARGV; > > --- > > > my $fh = $self->_fh or return; > > > > > > On Wed, 28 Jan 2004, Peter van Heusden wrote: > > > > > Jason Stajich wrote: > > > > > > >On Wed, 28 Jan 2004, Donald G. Jackson wrote: > > > > > > > > > > > > > > > >>Personally, I like the fall-back but agree that $ARGV[0] shouldn't be > > it. > > > >>I'd suggest STDIN - if somebody calls new without a file/handle I think > > > >>they're more likely to be reading. OTOH, guessing format woud be tough. > > > >> > > > >> > > > > > > > >the guess format is trying to read off the top of the file I think - we > > > >support a 'peek' type of reading into the file, by having the _pushback > > > >functionality in Root::IO. > > > > > > > >I would like to see something like this go into Root:IO rather than in > > > >SeqIO - and have Root::IO give back a filename if it knows what it is. > > > > > > > >Also the Root::IO code could also do something like this: > > > > $file = "-" unless defined $file; > > > > open my $fh => $input or die $!; > > > > > > > >Which will then read from stdin if now filename is sent in - right now we > > > >don't really support that anymore because it was causing clog-ups in some > > > >of the DB::GFF code/tests I think. > > > > > > > >Maybe we localize this to 'FormattedReaderWriters' -- all the > > > >XXXIO(-format => 'XXX') modules so as to avoid the problems Lincoln saw. > > > > > > > > > > > > > > > > > > > Can you to where Lincoln "saw" this problem? The BioPerl mailing list > > > archive is not searchable, and searching via Google doesn't turn > > > anything up. > > > > > > Anyway, I'll look into Root::IO tomorrow and see what I come up with. > > > > > > Peter > > > > > > > > > > > > > > >>At the very least a warning would be appropriate, perhaps indicating the > > > >>course of action. > > > >> > > > >>For xml handlers we can check the dtd and throw an error. I will modify > > > >>my SeqIO::tinyseq::tinyseqHandler to do so. > > > >> > > > >>Don Jackson > > > >> > > > >> > > > >> > > > >>Peter van Heusden wrote: > > > >> > > > >> > > > >> > > > >>>My review of the Bio::SeqIO::new method shows the following behaviour: > > > >>> > > > >>>Missing both ?file and ?fh arguments: falls back to using $ARGV[0] > > > >>>(the first command line argument) as sequence filename. If this fails, > > > >>>gives an exception about ?Unknown format?. > > > >>>-file argument (without ?fh argument): > > > >>>? given, but file unreadable: throws exception > > > >>>? undefined: reads $ARGV[0], as above. > > > >>>-fh argument (without ?file argument): > > > >>>? given, but not a filehandle: gives exception > > > >>>? given, but an invalid filehandle (not open): gives exception > > > >>>? undefined: reads $ARGV[0], as above. > > > >>>-format argument: if the sequence file doesn?t correspond to the given > > > >>>format, some parsers give an error (e.g. EMBL), while others do not > > > >>>(GenBank), instead silently give wrong results. > > > >>>-format argument without ?file argument: Silently creates a SeqIO > > > >>>object which writes to STDOUT. > > > >>> > > > >>>I don't think that this $ARGV[0] shortcut should be in there - it > > > >>>causes unnecessary potential confusion. Imagine a situation where -fh > > > >>>or -file is specified (using a variable), but that variable somehow > > > >>>does not get defined. In that case, the $ARGV[0] fallback behaviour > > > >>>would be used, which might lead to a non-obvious error behaviour. > > > >>> > > > >>>I'd like to propose that either -file or -fh should be specified, > > > >>>otherwise an exception is thrown. While I'm about it, I'm thinking of > > > >>>migrating the exceptions to the new 'typed exceptions' that BioPerl > > > >>>n