From ba6450 at wayne.edu Mon Dec 1 18:44:24 2008 From: ba6450 at wayne.edu (Munirul Islam) Date: Mon, 1 Dec 2008 18:44:24 -0500 Subject: [Bioperl-l] on FootPrinter Message-ID: <944e976e0812011544m4261f4d3yc05b3a2cb9c3de37@mail.gmail.com> Hi: We are trying to install FootPrinter on a linux machine. But we are getting errors. We also tried on MAC. Anyone here successfully installed it? I saw bioperl supports FootPrinter. http://search.cpan.org/~birney/bioperl-run-1.4/Bio/Tools/Run/FootPrinter.pm Your installation experience would definitely help us. Thank you. Munir Computer Science Wayne State University From anjan.purkayastha at gmail.com Mon Dec 1 17:05:16 2008 From: anjan.purkayastha at gmail.com (ANJAN PURKAYASTHA) Date: Mon, 1 Dec 2008 17:05:16 -0500 Subject: [Bioperl-l] problem with bp_genbank2gff3.pl Message-ID: hi, i copied and pasted the genbank2gff3.pls script into a file /usr/bin/bp_genbank2gff3.pl and tried running it. error message: Can't locate object method "FT_SO_map" via package "Bio::SeqFeature::Tools::TypeMapper" at /usr/bin/bp_genbank2gff3.pl line 285. any idea how i get to the map FT_SO_map method? thanks, anjan -- ============================= anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 From cain.cshl at gmail.com Mon Dec 1 22:14:18 2008 From: cain.cshl at gmail.com (Scott Cain) Date: Mon, 1 Dec 2008 22:14:18 -0500 Subject: [Bioperl-l] problem with bp_genbank2gff3.pl In-Reply-To: References: Message-ID: <536f21b00812011914t778e95ecjf52a0e8e7c652ee7@mail.gmail.com> Hello Anjan, Did you install BioPerl? If so, what version? You shouldn't really need to copy and paste bp_genbank2gff3.pl; it should just be there. The error message you got implies that BioPerl isn't installed or isn't installed correctly. Scott On Mon, Dec 1, 2008 at 5:05 PM, ANJAN PURKAYASTHA wrote: > hi, > i copied and pasted the genbank2gff3.pls script into a file > /usr/bin/bp_genbank2gff3.pl and tried running it. > error message: > Can't locate object method "FT_SO_map" via package > "Bio::SeqFeature::Tools::TypeMapper" at /usr/bin/bp_genbank2gff3.pl line > 285. > > any idea how i get to the map FT_SO_map method? > thanks, > anjan > > -- > ============================= > anjan purkayastha, phd > bioinformatics analyst > whitehead institute for biomedical research > nine cambridge center > cambridge, ma 02142 > > purkayas [at] wi [dot] mit [dot] edu > 703.740.6939 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From heikki at sanbi.ac.za Mon Dec 1 23:45:47 2008 From: heikki at sanbi.ac.za (Heikki Lehvaslaiho) Date: Tue, 2 Dec 2008 06:45:47 +0200 Subject: [Bioperl-l] reorgansing tests by group Message-ID: I just had a go at reorganising some tests by group in bioperl-live. Seems to work like charm. The work flow is: 1. mkdir group 2. svn move test.t. group More instructions are in: http://www.bioperl.org/wiki/Talk:Release_1.6#Test_suite The more I think about this the better I like it. By reorganising tests, we can see what kind of groups were have in Bio name space. Moving tests around is cheap and easy and does not affect code at all. We can experiment to our harts content. Unless I have done some big boo-boo and someone yells at me, I am going to go on reorganising test (when I've got time later this week). -Heikki From hlapp at gmx.net Tue Dec 2 00:09:55 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 2 Dec 2008 00:09:55 -0500 Subject: [Bioperl-l] reorgansing tests by group In-Reply-To: References: Message-ID: <72AAEC8C-138C-4053-82A0-3E7207C4F8F3@gmx.net> On Dec 1, 2008, at 11:45 PM, Heikki Lehvaslaiho wrote: > The work flow is: > > 1. mkdir group Doesn't that need to be 1. svn mkdir group or otherwise svn add the directory afterwards? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From neetisomaiya at gmail.com Tue Dec 2 00:54:14 2008 From: neetisomaiya at gmail.com (neeti somaiya) Date: Tue, 2 Dec 2008 11:24:14 +0530 Subject: [Bioperl-l] Problem in OMIM parser Message-ID: <764978cf0812012154t7f247a45haf23be4dc53cd21a@mail.gmail.com> Hi, I am downloading the OMIM genemap file from here : ftp://ftp.ncbi.nih.gov/repository/OMIM/ I was using the OMIMparser all these days to parse the genemap and omim.txt files and get the relevant data, and it was working perfect, but today suddenly I got an exception at the following line of my code : my $omim_parser = Bio::Phenotype::OMIM::OMIMparser->new(-genemap => $genemap,-omimtext => $omimtext); The exception I got was : ------------- EXCEPTION ------------- MSG: Gene map file "genemap" is not in the expected format STACK Bio::Phenotype::OMIM::OMIMparser::_read_genemap /root/BiologicalDatabases/OMIM/OMIMparser.pm:881 STACK Bio::Phenotype::OMIM::OMIMparser::genemap_file_name /root/BiologicalDatabases/OMIM/OMIMparser.pm:408 STACK Bio::Phenotype::OMIM::OMIMparser::new /root/BiologicalDatabases/OMIM/OMIMparser.pm:224 STACK main::main parseOmimData.pl:56 STACK toplevel parseOmimData.pl:39 -------------------------------------- Please suggest what I can do now. -- -Neeti Even my blood says, B positive From heikki.lehvaslaiho at gmail.com Tue Dec 2 01:05:15 2008 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Tue, 2 Dec 2008 08:05:15 +0200 Subject: [Bioperl-l] reorgansing tests by group In-Reply-To: <72AAEC8C-138C-4053-82A0-3E7207C4F8F3@gmx.net> References: <72AAEC8C-138C-4053-82A0-3E7207C4F8F3@gmx.net> Message-ID: Yes, forgot that! The directory needs to be added to the repository: 1. mkdir group 2. svn add group 3. svn move test1.t. group 4. svn move test2.t. group 5. ... -Heikki 2008/12/2 Hilmar Lapp : > > On Dec 1, 2008, at 11:45 PM, Heikki Lehvaslaiho wrote: > >> The work flow is: >> >> 1. mkdir group > > > Doesn't that need to be > > 1. svn mkdir group > > or otherwise svn add the directory afterwards? > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- -Heikki Heikki Lehvaslaiho - heikki lehvaslaiho gmail com http://kapkaupunki.blogspot.com/ From cjfields at illinois.edu Tue Dec 2 08:37:44 2008 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 2 Dec 2008 07:37:44 -0600 Subject: [Bioperl-l] reorgansing tests by group In-Reply-To: References: <72AAEC8C-138C-4053-82A0-3E7207C4F8F3@gmx.net> Message-ID: <6B22EAB9-3228-437B-889E-3323A3655505@illinois.edu> Wow, I go to sleep and the tests are almost reorganized. Thanks Heikki! The only (very small) caveat I find to using recursive tests is any additional non-test files we add, including data for tests in the / data directory, must not end with *.t, otherwise the build file will try to run it and bomb. There was one file I changed to .tt which is now passed over. If needed we can move over to an autogenerated file which explicitly lists the tests to run (this would likely be at a later point). On a related point, what does everyone think of moving BioPerlTest to core so the other distributions can use it? I think it is worth doing eventually, but it could possibly wait until 1.6.x or 1.7. I have tested it out and it works but needs some dependency issues ironed out. chris On Dec 2, 2008, at 12:05 AM, Heikki Lehvaslaiho wrote: > Yes, forgot that! The directory needs to be added to the repository: > > 1. mkdir group > 2. svn add group > 3. svn move test1.t. group > 4. svn move test2.t. group > 5. ... > > > -Heikki > > 2008/12/2 Hilmar Lapp : >> >> On Dec 1, 2008, at 11:45 PM, Heikki Lehvaslaiho wrote: >> >>> The work flow is: >>> >>> 1. mkdir group >> >> >> Doesn't that need to be >> >> 1. svn mkdir group >> >> or otherwise svn add the directory afterwards? >> >> -hilmar >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >> =========================================================== >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > -Heikki > Heikki Lehvaslaiho - heikki lehvaslaiho gmail com > http://kapkaupunki.blogspot.com/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From lincoln.stein at gmail.com Tue Dec 2 10:49:45 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 2 Dec 2008 10:49:45 -0500 Subject: [Bioperl-l] [Gmod-gbrowse] bioperl-live & annotator plugin In-Reply-To: <4935551B.9060101@molgen.mpg.de> References: <4935551B.9060101@molgen.mpg.de> Message-ID: <6dce9a0b0812020749g4d78db54w173429d9b8ea58db@mail.gmail.com> Hi Sean, Did your plugin break when you upgraded to GBrowse 1.7, or when you upgraded bioperl? Knowing this will help me figure out where to look for the problem. It frankly looks like a database problem in the sense that the xyplot glyph is trying to render 100 features rather than a feature with 100 parts. Are you sure this step is correct? $feature_list->add_type($matrix=>{glyph => 'xyplot', > graph_type => 'boxes', > scale => 'auto', > height => 40, > bump => 0, > min_score=>0, > max_score=>$maxscore, > key => "$matrix affinities ($maxscore)", > fgcolor => $COLORS[$i % @COLORS], > bgcolor => $COLORS[$i % @COLORS], > }); It seems to me you intend to add the $feature, not the $matrix variable. Lincoln On Tue, Dec 2, 2008 at 10:32 AM, Sean O'Keeffe wrote: > Hi all, > I'm experiencing a little issue when upgrading to the latest bioperl-live > build. > We needed the new glyph libraries as older versions can't display wiggle > density plots and also experience versioning issues for Gbrowse 1.7. > On upgrading to the latest nightly build, all seemed fine until we tried > our TF affinity annotator plugin. > The plugin basically generates GFF output of a selected matrix binding to > the sequence of the current window, and displays the score values as an > xyplot. > We've never had any real issues 'til the new libraries were loaded. I tried > switching the old xyplot.pm with the new one but to no avail. > I've attached 2 images old and new of the generated output, plus some code > and feature file output. > Any insight would be great, > > Sean. > > +++++++++++++++++++++++++++++++++++++++++++++++++++ > > the code of interest in the plugin > > ...... > my $i = 0; > my (@features,$feature,$start,$end,$score,$maxscore,$strand); > $feature_list = Bio::Graphics::FeatureFile->new(); > > foreach $matrix (@matrices){ > $maxscore=0; > # Usually the track is created first but here we want the maxscore passed > to > # the track so we process the features first and create the track after. > foreach $_ (@result){ > next if (/\#/); > next unless (/$matrix/); > @features = split("\t", $_); > > $start=$features[3];$end=$features[4];$score=$features[5];$strand=$features[6]; > if ($score>$maxscore) { > $maxscore=$score; > } > # Fill the feature list with features > $feature = Bio::Graphics::Feature->new(-start=>$abs_start + $start, > -stop=>$abs_start + $end, > -score=>$score, > -strand=>$strand, > -ref=>$ref, > -name=>$matrix, > -type=>'region', > -source=>'ANNOTATE'); > $feature_list->add_feature($feature,$matrix); > } > # Create the track and add features > $feature_list->add_type($matrix=>{glyph => 'xyplot', > graph_type => 'boxes', > scale => 'auto', > height => 40, > bump => 0, > min_score=>0, > max_score=>$maxscore, > key => "$matrix affinities ($maxscore)", > fgcolor => $COLORS[$i % @COLORS], > bgcolor => $COLORS[$i % @COLORS], > }); > $i++; > } > return $feature_list; > ......... > > +++++++++++++++++++++++++++++++++++++++++++ > > the feature file which is passed to the plugin > > #command_line= /project/gbrowse/Pipeline/Annotation/ANNOTATE_v2.07 -s > /project/general/tmp/TIwySJV5kx --pscm /project/general/tmp/FkztCDpBvb -name > SRF_C -a -g 0.5 -t 0 -R 200 -S 100 -p 1.0 > segment ANNOTATE region 1 200 0.000103017 + . > matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200 > segment ANNOTATE region 101 300 0.000101877 + . > matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200 > segment ANNOTATE region 201 400 6.76318e-05 + . > matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200 > segment ANNOTATE region 301 500 7.0194e-05 + . > matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200 > segment ANNOTATE region 401 600 3.36309e-05 + . > matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200 > segment ANNOTATE region 501 700 7.15977e-05 + . > matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200 > segment ANNOTATE region 601 800 0.000639066 + . > matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200 > segment ANNOTATE region 701 900 0.000589631 + . > matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200 > segment ANNOTATE region 801 1000 0.000580096 + . > matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200 > segment ANNOTATE region 901 1100 0.00139282 + . > matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200 > ... > > > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse at lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Stacey Quinn Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 USA (516) 367-8380 Assistant: Sandra Michelsen From lincoln.stein at gmail.com Tue Dec 2 10:51:06 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 2 Dec 2008 10:51:06 -0500 Subject: [Bioperl-l] [Gmod-gbrowse] bioperl-live & annotator plugin In-Reply-To: <6dce9a0b0812020749g4d78db54w173429d9b8ea58db@mail.gmail.com> References: <4935551B.9060101@molgen.mpg.de> <6dce9a0b0812020749g4d78db54w173429d9b8ea58db@mail.gmail.com> Message-ID: <6dce9a0b0812020751x2ee9dd69q718570315b79ebce@mail.gmail.com> I take it back. You should add the matrix in add_type(), assuming that $matrix is some sort of descriptive term. Lincoln On Tue, Dec 2, 2008 at 10:49 AM, Lincoln Stein wrote: > Hi Sean, > > Did your plugin break when you upgraded to GBrowse 1.7, or when you > upgraded bioperl? Knowing this will help me figure out where to look for the > problem. It frankly looks like a database problem in the sense that the > xyplot glyph is trying to render 100 features rather than a feature with 100 > parts. > > Are you sure this step is correct? > > $feature_list->add_type($matrix=>{glyph => 'xyplot', >> graph_type => 'boxes', >> scale => 'auto', >> height => 40, >> bump => 0, >> min_score=>0, >> max_score=>$maxscore, >> key => "$matrix affinities ($maxscore)", >> fgcolor => $COLORS[$i % @COLORS], >> bgcolor => $COLORS[$i % @COLORS], >> }); > > > It seems to me you intend to add the $feature, not the $matrix variable. > > Lincoln > > On Tue, Dec 2, 2008 at 10:32 AM, Sean O'Keeffe wrote: > >> Hi all, >> I'm experiencing a little issue when upgrading to the latest bioperl-live >> build. >> We needed the new glyph libraries as older versions can't display wiggle >> density plots and also experience versioning issues for Gbrowse 1.7. >> On upgrading to the latest nightly build, all seemed fine until we tried >> our TF affinity annotator plugin. >> The plugin basically generates GFF output of a selected matrix binding to >> the sequence of the current window, and displays the score values as an >> xyplot. >> We've never had any real issues 'til the new libraries were loaded. I >> tried switching the old xyplot.pm with the new one but to no avail. >> I've attached 2 images old and new of the generated output, plus some code >> and feature file output. >> Any insight would be great, >> >> Sean. >> >> +++++++++++++++++++++++++++++++++++++++++++++++++++ >> >> the code of interest in the plugin >> >> ...... >> my $i = 0; >> my (@features,$feature,$start,$end,$score,$maxscore,$strand); >> $feature_list = Bio::Graphics::FeatureFile->new(); >> >> foreach $matrix (@matrices){ >> $maxscore=0; >> # Usually the track is created first but here we want the maxscore >> passed to >> # the track so we process the features first and create the track after. >> foreach $_ (@result){ >> next if (/\#/); >> next unless (/$matrix/); >> @features = split("\t", $_); >> >> $start=$features[3];$end=$features[4];$score=$features[5];$strand=$features[6]; >> if ($score>$maxscore) { >> $maxscore=$score; >> } >> # Fill the feature list with features >> $feature = Bio::Graphics::Feature->new(-start=>$abs_start + $start, >> -stop=>$abs_start + $end, >> -score=>$score, >> -strand=>$strand, >> -ref=>$ref, >> -name=>$matrix, >> -type=>'region', >> -source=>'ANNOTATE'); >> $feature_list->add_feature($feature,$matrix); >> } >> # Create the track and add features >> $feature_list->add_type($matrix=>{glyph => 'xyplot', >> graph_type => 'boxes', >> scale => 'auto', >> height => 40, >> bump => 0, >> min_score=>0, >> max_score=>$maxscore, >> key => "$matrix affinities ($maxscore)", >> fgcolor => $COLORS[$i % @COLORS], >> bgcolor => $COLORS[$i % @COLORS], >> }); >> $i++; >> } >> return $feature_list; >> ......... >> >> +++++++++++++++++++++++++++++++++++++++++++ >> >> the feature file which is passed to the plugin >> >> #command_line= /project/gbrowse/Pipeline/Annotation/ANNOTATE_v2.07 -s >> /project/general/tmp/TIwySJV5kx --pscm /project/general/tmp/FkztCDpBvb -name >> SRF_C -a -g 0.5 -t 0 -R 200 -S 100 -p 1.0 >> segment ANNOTATE region 1 200 0.000103017 + . >> matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200 >> segment ANNOTATE region 101 300 0.000101877 + . >> matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200 >> segment ANNOTATE region 201 400 6.76318e-05 + . >> matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200 >> segment ANNOTATE region 301 500 7.0194e-05 + . >> matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200 >> segment ANNOTATE region 401 600 3.36309e-05 + . >> matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200 >> segment ANNOTATE region 501 700 7.15977e-05 + . >> matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200 >> segment ANNOTATE region 601 800 0.000639066 + . >> matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200 >> segment ANNOTATE region 701 900 0.000589631 + . >> matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200 >> segment ANNOTATE region 801 1000 0.000580096 + . >> matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200 >> segment ANNOTATE region 901 1100 0.00139282 + . >> matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200 >> ... >> >> >> >> >> ------------------------------------------------------------------------- >> This SF.Net email is sponsored by the Moblin Your Move Developer's >> challenge >> Build the coolest Linux based applications with Moblin SDK & win great >> prizes >> Grand prize is a trip for two to an Open Source event anywhere in the >> world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse at lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> >> > > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Stacey Quinn > > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 USA > (516) 367-8380 > Assistant: Sandra Michelsen > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Stacey Quinn Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 USA (516) 367-8380 Assistant: Sandra Michelsen From lincoln.stein at gmail.com Tue Dec 2 11:51:39 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 2 Dec 2008 11:51:39 -0500 Subject: [Bioperl-l] [Gmod-gbrowse] Bioperl 1.6 and Bio::Graphics In-Reply-To: <510199F3-D209-45E9-A03C-5F49E849F44A@illinois.edu> References: <2E7089AA-50C0-45E9-A9E6-F80BD9876B99@illinois.edu> <536f21b00811261037s4cc34377u6c45c9aef89159b2@mail.gmail.com> <510199F3-D209-45E9-A03C-5F49E849F44A@illinois.edu> Message-ID: <6dce9a0b0812020851s2b2a8f54ibd7f47910f2e0afe@mail.gmail.com> Hi Chris, I am supportive of splitting out Bio::Graphics, but not the Bio::DB::* modules before the 1.6 release. The only dependency issue is the module Bio::Graphics::FeatureBase, which is a lightweight hash-based Bio::SeqFeatureI module that is shared between Bio::Graphics::Feature and Bio::DB::SeqFeature. It should be renamed and kept in the main bioperl distribution. Will it confuse people if I rename this module Bio::SeqFeature::Lite? Lincoln On Wed, Nov 26, 2008 at 3:25 PM, Chris Fields wrote: > > On Nov 26, 2008, at 12:37 PM, Scott Cain wrote: > > Hi Chris, >> >> While the decision ultimately rests with Lincoln (as, presumably, will >> most of the work :-) I'm not sure I agree that the split needs to >> happen before the 1.6 release. Consider the case where GBrowse 1.70 >> requires a newer version of Bio::Graphics than is available in >> BioPerl. We would put a version requirement in the Makefile.PL for >> Bio::Graphics::Panel to be some number greater than the current >> BioPerl release and put it on cpan. Users would then do the cpan >> shell shuffle, and get the right version of Bio::Graphics, and if they >> don't already have BioPerl, they'll get that too (with an older >> version of Bio::Graphics that will be immediately overwritten). Is >> there a flaw (or horrible user experience) in my thinking? >> >> Scott >> > > Sorry Scott, forgot to mention it wouldn't just be Bio::Graphics. Lincoln > also mentioned Bio::DB::GFF and Bio::DB::SeqFeature::Store (basically > anything Gbrowse-related) would be included, so maybe bio-gbrowse or similar > would be a better name. > > If you like we could postpone a split (less work for the release). A split > bio-gbrowse release would just overwrite the older modules as you mention. > However, I plan on having regular point releases to CPAN; how do we want to > handle Gbrowse-related bug fixes in a point release down the road, after a > Bio::Graphics split? > > Do we stop Bio::Graphics fixes at a certain point after a post-1.6 split so > an installation script always finds the latest Bio::Graphics::Panel? Or do > we want to merge those fixes into the point release regardless, just in > case? > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Stacey Quinn Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 USA (516) 367-8380 Assistant: Sandra Michelsen From cjfields at illinois.edu Tue Dec 2 12:07:43 2008 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 2 Dec 2008 11:07:43 -0600 Subject: [Bioperl-l] [Gmod-gbrowse] Bioperl 1.6 and Bio::Graphics In-Reply-To: <6dce9a0b0812020851s2b2a8f54ibd7f47910f2e0afe@mail.gmail.com> References: <2E7089AA-50C0-45E9-A9E6-F80BD9876B99@illinois.edu> <536f21b00811261037s4cc34377u6c45c9aef89159b2@mail.gmail.com> <510199F3-D209-45E9-A03C-5F49E849F44A@illinois.edu> <6dce9a0b0812020851s2b2a8f54ibd7f47910f2e0afe@mail.gmail.com> Message-ID: <79F44969-E938-4647-9086-55DFD3AB1FD8@illinois.edu> Lincoln, > Hi Chris, > > I am supportive of splitting out Bio::Graphics, but not the > Bio::DB::* modules before the 1.6 release. The only dependency issue > is the module Bio::Graphics::FeatureBase, which is a lightweight > hash-based Bio::SeqFeatureI module that is shared between > Bio::Graphics::Feature and Bio::DB::SeqFeature. It should be renamed > and kept in the main bioperl distribution. Okay, we can do that. Would you want that to be under bio-graphics in subversion, or should we think ahead a bit in case other Gbrowse- dependent modules migrate there and call it something else? > Will it confuse people if I rename this module Bio::SeqFeature::Lite? Bio::SeqFeature::Lite works for me. I can't see that causing too many problems as long as Gbrowse installation always picks the latest dev or CPAN release based on the version (though I don't know if there are any documentation fixes we need to take care of, maybe on the wiki). chris > Lincoln > > On Wed, Nov 26, 2008 at 3:25 PM, Chris Fields > wrote: > > On Nov 26, 2008, at 12:37 PM, Scott Cain wrote: > > Hi Chris, > > While the decision ultimately rests with Lincoln (as, presumably, will > most of the work :-) I'm not sure I agree that the split needs to > happen before the 1.6 release. Consider the case where GBrowse 1.70 > requires a newer version of Bio::Graphics than is available in > BioPerl. We would put a version requirement in the Makefile.PL for > Bio::Graphics::Panel to be some number greater than the current > BioPerl release and put it on cpan. Users would then do the cpan > shell shuffle, and get the right version of Bio::Graphics, and if they > don't already have BioPerl, they'll get that too (with an older > version of Bio::Graphics that will be immediately overwritten). Is > there a flaw (or horrible user experience) in my thinking? > > Scott > > Sorry Scott, forgot to mention it wouldn't just be Bio::Graphics. > Lincoln also mentioned Bio::DB::GFF and Bio::DB::SeqFeature::Store > (basically anything Gbrowse-related) would be included, so maybe bio- > gbrowse or similar would be a better name. > > If you like we could postpone a split (less work for the release). > A split bio-gbrowse release would just overwrite the older modules > as you mention. However, I plan on having regular point releases to > CPAN; how do we want to handle Gbrowse-related bug fixes in a point > release down the road, after a Bio::Graphics split? > > Do we stop Bio::Graphics fixes at a certain point after a post-1.6 > split so an installation script always finds the latest > Bio::Graphics::Panel? Or do we want to merge those fixes into the > point release regardless, just in case? > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Stacey Quinn > > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 USA > (516) 367-8380 > Assistant: Sandra Michelsen From assiatu_barrie at yahoo.com Tue Dec 2 12:40:31 2008 From: assiatu_barrie at yahoo.com (Assiatu Barrie) Date: Tue, 2 Dec 2008 09:40:31 -0800 (PST) Subject: [Bioperl-l] Fw: Help with installation Message-ID: <20871.38071.qm@web82201.mail.mud.yahoo.com> Assiatu Barrie Dept. of Biology Univ of TX, Arlington Arlington, TX 76019 abarrie at uta.edu assiatu_barrie at yahoo.com www.uta.edu --- On Tue, 12/2/08, Assiatu Barrie wrote: From: Assiatu Barrie Subject: Help with installation To: bioperl-l at biolperl.org Date: Tuesday, December 2, 2008, 11:36 AM Hello My name is Assiatu Barrie, a grad student from UTA.? I am trying to download bioperl on my mac os laptop but unsuccessful, please help.? I keep getting an error message regarding Make not been installed.? I tried installing Build.pl, but not successful.? I am very very new to perl so I will really appreciate the help.? Thank you Assiatu Barrie Dept. of Biology Univ of TX, Arlington Arlington, TX 76019 abarrie at uta.edu assiatu_barrie at yahoo.com www.uta.edu From Kevin.M.Brown at asu.edu Tue Dec 2 12:35:06 2008 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Tue, 2 Dec 2008 10:35:06 -0700 Subject: [Bioperl-l] on FootPrinter In-Reply-To: <944e976e0812011544m4261f4d3yc05b3a2cb9c3de37@mail.gmail.com> References: <944e976e0812011544m4261f4d3yc05b3a2cb9c3de37@mail.gmail.com> Message-ID: <1A4207F8295607498283FE9E93B775B4058B2684@EX02.asurite.ad.asu.edu> Try installing a more recent version of BioPerl by following the directions at http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Munirul Islam > Sent: Monday, December 01, 2008 4:44 PM > To: bioperl-l at lists.open-bio.org; Zachary Papper > Subject: [Bioperl-l] on FootPrinter > > Hi: > > We are trying to install FootPrinter on a linux machine. > But we are getting errors. We also tried on MAC. Anyone here > successfully > installed it? > > I saw bioperl supports FootPrinter. > http://search.cpan.org/~birney/bioperl-run-1.4/Bio/Tools/Run/F > ootPrinter.pm > > Your installation experience would definitely help us. > > Thank you. > Munir > Computer Science > Wayne State University > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Tue Dec 2 18:03:21 2008 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 2 Dec 2008 17:03:21 -0600 Subject: [Bioperl-l] PullHSP bug Message-ID: Sendu, I found a silent bug while fixing some issues with SimpleAlign which are causing blast_pull tests to fail (HSP-related). It appears that the query sequence ID is not being caught, causing LocatableSeq::get_nse() to throw an exception within SimpleAlign when using PullHSPI::get_aln. It appears that the hit seq ID is caught properly, though (hence the oddness). All other SearchIO.t tests pass. Could you look into this? ... ok 165 ok 166 ok 167 ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Attribute id not set STACK: Error::throw STACK: Bio::Root::Root::throw /Users/cjfields/bioperl/bioperl-live/ blib/lib/Bio/Root/Root.pm:357 STACK: Bio::LocatableSeq::get_nse /Users/cjfields/bioperl/bioperl-live/ blib/lib/Bio/LocatableSeq.pm:301 STACK: Bio::SimpleAlign::add_seq /Users/cjfields/bioperl/bioperl-live/ blib/lib/Bio/SimpleAlign.pm:293 STACK: Bio::Search::HSP::PullHSPI::get_aln /Users/cjfields/bioperl/ bioperl-live/blib/lib/Bio/Search/HSP/PullHSPI.pm:471 STACK: t/SearchIO/blast_pull.t:237 ----------------------------------------------------------- # Looks like you planned 287 tests but only ran 167. # Looks like your test died just after 167. Dubious, test returned 255 (wstat 65280, 0xff00) Failed 120/287 subtests Test Summary Report ------------------- t/SearchIO/blast_pull.t (Wstat: 65280 Tests: 167 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 287 tests but ran 167. Files=1, Tests=167, 1 wallclock secs ( 0.04 usr 0.01 sys + 0.34 cusr 0.04 csys = 0.43 CPU) Result: FAIL Failed 1/1 test programs. 0/167 subtests failed. From cjfields at illinois.edu Tue Dec 2 21:40:32 2008 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 2 Dec 2008 20:40:32 -0600 Subject: [Bioperl-l] PullHSP bug In-Reply-To: <4935D1F1.1050304@sendu.me.uk> References: <4935D1F1.1050304@sendu.me.uk> Message-ID: <1D8F1862-46F3-45FB-AEDC-A4E9BC8FDC9D@illinois.edu> On Dec 2, 2008, at 6:25 PM, Sendu Bala wrote: > Chris Fields wrote: >> Sendu, >> I found a silent bug while fixing some issues with SimpleAlign >> which are causing blast_pull tests to fail (HSP-related). It >> appears that the query sequence ID is not being caught > > I don't see this as a bug of PullHSPI. The blastn report being > parsed in that failing test has no query sequence id, so obviously > PullHSPI can't give an ID to the query sequence it creates. It appears the problem boils down to a small inconsistency with the way blank IDs are handled between the two BLAST parsers. The regular blast parser explicitly sets this to '', while blast_pull leaves it undef. When one constructs a LocatableSeq w/o an ID it dies, but '' works, hence the problem. I don't think using '' is a real solution though (seems like something added to silence errors). The short and easy fix is either having get_nse() or blast_pull fall back to '', but both are technically wrong as there isn't a true ID. Ideas? Maybe a fallback 'unknown' ID (which seems to be used as a ). > Why does SimpleAlign now fall over when an added sequence has no id? > I'd suggest the old behaviour be retained... I don't think going back to the old behavior would be the correct thing to do. When adding seqs to a SimpleAlign, the NSE is used to index sequences and check for conflicts. The index was previously built from scratch (didn't use LocatableSeq::get_nse) but was recalled using get_nse, which is inconsistent. If get_nse changes slightly, such as optionally adding the version to remain consistent with Pfam/ Rfam, this suddenly breaks. That behavior is now fixed to always use get_nse regardless. Coming up with a fix for the ID so indexing works correctly would be a better solution. chris From bix at sendu.me.uk Tue Dec 2 19:25:21 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 03 Dec 2008 00:25:21 +0000 Subject: [Bioperl-l] PullHSP bug In-Reply-To: References: Message-ID: <4935D1F1.1050304@sendu.me.uk> Chris Fields wrote: > Sendu, > > I found a silent bug while fixing some issues with SimpleAlign which are > causing blast_pull tests to fail (HSP-related). It appears that the > query sequence ID is not being caught I don't see this as a bug of PullHSPI. The blastn report being parsed in that failing test has no query sequence id, so obviously PullHSPI can't give an ID to the query sequence it creates. Why does SimpleAlign now fall over when an added sequence has no id? I'd suggest the old behaviour be retained... From cjfields at illinois.edu Wed Dec 3 10:06:06 2008 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 3 Dec 2008 09:06:06 -0600 Subject: [Bioperl-l] PullHSP bug In-Reply-To: <49366FB6.30301@sendu.me.uk> References: <4935D1F1.1050304@sendu.me.uk> <1D8F1862-46F3-45FB-AEDC-A4E9BC8FDC9D@illinois.edu> <49366FB6.30301@sendu.me.uk> Message-ID: <957E01D2-15D5-4FBC-8882-139D21C2BF31@illinois.edu> On Dec 3, 2008, at 5:38 AM, Sendu Bala wrote: > Chris Fields wrote: >> The short and easy fix is either having get_nse() or blast_pull >> fall back to '', but both are technically wrong as there isn't a >> true ID. Ideas? Maybe a fallback 'unknown' ID (which seems to be >> used as a ). ...fallback in some cases (Can tell I was getting tired). > I'd say for now at least the fix would be to alter get_nse() to fall > back to ''. You don't want the work-around code duplicated in > multiple places. Indeed, the normal blast parser should be altered > to return undef as well. That solution requires get_nse to silently convert this; the exception is raised b/c the N/S-E is used for indexing (so lack of any one of those may result in indexing issues, such as replacing sequences with same ID but no S-E, etc.). > Then if a more desirable solution is thought of in the future, > there's just one place to implement it: in get_nse(). We don't want the exception turned off unless it is explicitly known the sequence instance lacks any or all of the N/S-E, such as in this case. Setting an explicit LocatableSeq flag for such instances (force_nse), then having get_nse() DTRT internally would be easy to implement. Odd, list mail hasn't been coming through (bioperl-gut either). I'll post something to support. chris From maj at fortinbras.us Wed Dec 3 10:23:32 2008 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 3 Dec 2008 10:23:32 -0500 Subject: [Bioperl-l] global verbosity Message-ID: <47A4C981089F42718A6644540AB23117@NewLife> I was looking for a way to set verbosity globally (but not for debugging), so that all subsequently created objects would be absolutely quiet. I found $Bio::Root::Root:VERBOSITY, but saw that it didn't matter to downstream objects when it was changed. Digging in to the issue, found that global verbosity can't really be set, though one can access the value of $VERBOSITY with Bio::Root::Root::verbose(). http://bugzilla.open-bio.org/show_bug.cgi?id=2696 has a patch + .t to Root.pm that I think solves the issue, allowing getting and setting of global verbosity, so that the global value now propagates to new objects. There is a stickier issue (example using Bio::Seq and Bio::Seq->primary_seq() in the .t file), in which setting an object's verbosity post-construction does not propagate to sub-objects contained in the object, so that one might not get what one expects. cheers MAJ From maj at fortinbras.us Wed Dec 3 11:32:12 2008 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 3 Dec 2008 11:32:12 -0500 Subject: [Bioperl-l] Fw: Help with installation In-Reply-To: <20871.38071.qm@web82201.mail.mud.yahoo.com> Message-ID: <4FCA0CBD70784B939ECAF1F212D44B65@NewLife> Assiatu- You may find the fink installer helpful- see http://www.bioperl.org/wiki/Getting_BioPerl#MacOS_X_using_fink cheers MAJ From heikki.lehvaslaiho at gmail.com Wed Dec 3 13:23:28 2008 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Wed, 3 Dec 2008 20:23:28 +0200 Subject: [Bioperl-l] reorgansing tests by group In-Reply-To: <6B22EAB9-3228-437B-889E-3323A3655505@illinois.edu> References: <72AAEC8C-138C-4053-82A0-3E7207C4F8F3@gmx.net> <6B22EAB9-3228-437B-889E-3323A3655505@illinois.edu> Message-ID: 2008/12/2 Chris Fields : > Wow, I go to sleep and the tests are almost reorganized. Thanks Heikki! > > The only (very small) caveat I find to using recursive tests is any > additional non-test files we add, including data for tests in the /data > directory, must not end with *.t, otherwise the build file will try to run > it and bomb. There was one file I changed to .tt which is now passed over. > If needed we can move over to an autogenerated file which explicitly lists > the tests to run (this would likely be at a later point). Chris, I'll try to do the rests very soon now. Do not touch the t directory until I've committed by reorganisations! > On a related point, what does everyone think of moving BioPerlTest to core > so the other distributions can use it? I think it is worth doing > eventually, but it could possibly wait until 1.6.x or 1.7. I have tested it > out and it works but needs some dependency issues ironed out. Moving to core would be a good thing. Do it. -Heikki > chris > > On Dec 2, 2008, at 12:05 AM, Heikki Lehvaslaiho wrote: > >> Yes, forgot that! The directory needs to be added to the repository: >> >> 1. mkdir group >> 2. svn add group >> 3. svn move test1.t. group >> 4. svn move test2.t. group >> 5. ... >> >> >> -Heikki >> >> 2008/12/2 Hilmar Lapp : >>> >>> On Dec 1, 2008, at 11:45 PM, Heikki Lehvaslaiho wrote: >>> >>>> The work flow is: >>>> >>>> 1. mkdir group >>> >>> >>> Doesn't that need to be >>> >>> 1. svn mkdir group >>> >>> or otherwise svn add the directory afterwards? >>> >>> -hilmar >>> -- >>> =========================================================== >>> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >>> =========================================================== >>> >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> >> >> -- >> -Heikki >> Heikki Lehvaslaiho - heikki lehvaslaiho gmail com >> http://kapkaupunki.blogspot.com/ >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- -Heikki Heikki Lehvaslaiho - heikki lehvaslaiho gmail com http://kapkaupunki.blogspot.com/ From paolo.pavan at tecnoparco.org Wed Dec 3 13:21:50 2008 From: paolo.pavan at tecnoparco.org (Paolo Pavan) Date: Wed, 3 Dec 2008 19:21:50 +0100 Subject: [Bioperl-l] About graphic rendering Message-ID: <56be91b60812031021k741d4638o15dcade5dcceb0e0@mail.gmail.com> Hi everybody, I've a question about a Bio::Graphics rendering. I would like to display a blast HSP on a track but I would like to draw the "tails" of my mapping sequence that don't match the subject. So I instantiate these 3 object that represent all the three segments I want to display: my $feature = Bio::SeqFeature::Generic->new( -display_name =>$sequence_to_map->display_id, -start =>$hsp->sbjct->start, -end =>$hsp->sbjct->end, ); my $feature_pre = Bio::SeqFeature::Generic->new( -start =>($hsp->sbjct->start - $hsp->query->start), -end =>$hsp->sbjct->start-1 ); my $feature_post = Bio::SeqFeature::Generic->new( -start => $hsp->sbjct->end+1, -end => $hsp->sbjct->end + $sequence_to_map->length - $hsp->query->end ); now I have to add these features to my $track in a manner that the $feature_pre and $feature_post paint or color in a different way than $feature but align horizontally. I tried with: $feature->add_sub_SeqFeature($feature_pre, 'EXPAND'); $feature->add_sub_SeqFeature($feature_post, 'EXPAND'); $track->add_feature($feature); This does not work, because the features spread vertically, and more I cannot change the glyph because seems to be a track property, not a feature one. Any idea? Thank you for your help, Paolo From cjfields at illinois.edu Wed Dec 3 14:53:31 2008 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 3 Dec 2008 13:53:31 -0600 Subject: [Bioperl-l] reorgansing tests by group In-Reply-To: References: <72AAEC8C-138C-4053-82A0-3E7207C4F8F3@gmx.net> <6B22EAB9-3228-437B-889E-3323A3655505@illinois.edu> Message-ID: <845A46AD-7B28-4EB1-ABB5-63A8FA21099A@illinois.edu> On Dec 3, 2008, at 12:23 PM, Heikki Lehvaslaiho wrote: > 2008/12/2 Chris Fields : >> Wow, I go to sleep and the tests are almost reorganized. Thanks >> Heikki! >> >> The only (very small) caveat I find to using recursive tests is any >> additional non-test files we add, including data for tests in the / >> data >> directory, must not end with *.t, otherwise the build file will try >> to run >> it and bomb. There was one file I changed to .tt which is now >> passed over. >> If needed we can move over to an autogenerated file which >> explicitly lists >> the tests to run (this would likely be at a later point). > > Chris, > > I'll try to do the rests very soon now. Do not touch the t directory > until I've committed by reorganisations! Okay. I moved Tools already but I'll leave everything else. >> On a related point, what does everyone think of moving BioPerlTest >> to core >> so the other distributions can use it? I think it is worth doing >> eventually, but it could possibly wait until 1.6.x or 1.7. I have >> tested it >> out and it works but needs some dependency issues ironed out. > > Moving to core would be a good thing. Do it. > > > -Heikki That'll be next then. -c From cjfields at illinois.edu Wed Dec 3 15:03:27 2008 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 3 Dec 2008 14:03:27 -0600 Subject: [Bioperl-l] reorgansing tests by group In-Reply-To: References: <72AAEC8C-138C-4053-82A0-3E7207C4F8F3@gmx.net> <6B22EAB9-3228-437B-889E-3323A3655505@illinois.edu> Message-ID: <9C6F2A11-D4D5-49BF-8ECE-5E0235C3F4F9@illinois.edu> On Dec 3, 2008, at 12:23 PM, Heikki Lehvaslaiho wrote: > 2008/12/2 Chris Fields : >> Wow, I go to sleep and the tests are almost reorganized. Thanks >> Heikki! >> >> The only (very small) caveat I find to using recursive tests is any >> additional non-test files we add, including data for tests in the / >> data >> directory, must not end with *.t, otherwise the build file will try >> to run >> it and bomb. There was one file I changed to .tt which is now >> passed over. >> If needed we can move over to an autogenerated file which >> explicitly lists >> the tests to run (this would likely be at a later point). > > Chris, > > I'll try to do the rests very soon now. Do not touch the t directory > until I've committed by reorganisations! > >> On a related point, what does everyone think of moving BioPerlTest >> to core >> so the other distributions can use it? I think it is worth doing >> eventually, but it could possibly wait until 1.6.x or 1.7. I have >> tested it >> out and it works but needs some dependency issues ironed out. > > Moving to core would be a good thing. Do it. > > > -Heikki ...also, just to note, the mail lists appear to be acting up (support has been notified). My commits last night are here: http://lists.open-bio.org/pipermail/bioperl-guts-l/2008-December/date.html chris From bix at sendu.me.uk Wed Dec 3 06:38:30 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 03 Dec 2008 11:38:30 +0000 Subject: [Bioperl-l] PullHSP bug In-Reply-To: <1D8F1862-46F3-45FB-AEDC-A4E9BC8FDC9D@illinois.edu> References: <4935D1F1.1050304@sendu.me.uk> <1D8F1862-46F3-45FB-AEDC-A4E9BC8FDC9D@illinois.edu> Message-ID: <49366FB6.30301@sendu.me.uk> Chris Fields wrote: > The short and easy fix is either having get_nse() or blast_pull fall > back to '', but both are technically wrong as there isn't a true ID. > Ideas? Maybe a fallback 'unknown' ID (which seems to be used as a ). I'd say for now at least the fix would be to alter get_nse() to fall back to ''. You don't want the work-around code duplicated in multiple places. Indeed, the normal blast parser should be altered to return undef as well. Then if a more desirable solution is thought of in the future, there's just one place to implement it: in get_nse(). From heikki.lehvaslaiho at gmail.com Wed Dec 3 16:48:06 2008 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Wed, 3 Dec 2008 23:48:06 +0200 Subject: [Bioperl-l] reorgansing tests by group In-Reply-To: <9C6F2A11-D4D5-49BF-8ECE-5E0235C3F4F9@illinois.edu> References: <72AAEC8C-138C-4053-82A0-3E7207C4F8F3@gmx.net> <6B22EAB9-3228-437B-889E-3323A3655505@illinois.edu> <9C6F2A11-D4D5-49BF-8ECE-5E0235C3F4F9@illinois.edu> Message-ID: 2008/12/3 Chris Fields : > > On Dec 3, 2008, at 12:23 PM, Heikki Lehvaslaiho wrote: > >> 2008/12/2 Chris Fields : >>> >>> Wow, I go to sleep and the tests are almost reorganized. Thanks Heikki! I jsut had long flight that gave me time to think this through! Now they are done! The ones on the top level are deprecated, unfinished or can be left there (Perl.t & PodSyntax.t). I moved some tests from t/Tools into t/SeqTools. All of them give additional functionality to Sequence objects and are not parsers like tests in t/Tools directory. The exceptions in current t/Tools are Analysis subdirectory tests. I would have pulled them and t/Tools/Run/RemoteBlast.t into t/WebAnalysis.t I committed all in one go. I suspect that the mail generated is too long (like in your case) and does not get sent. -Heikki >>> The only (very small) caveat I find to using recursive tests is any >>> additional non-test files we add, including data for tests in the /data >>> directory, must not end with *.t, otherwise the build file will try to >>> run >>> it and bomb. There was one file I changed to .tt which is now passed >>> over. >>> If needed we can move over to an autogenerated file which explicitly >>> lists >>> the tests to run (this would likely be at a later point). >> >> Chris, >> >> I'll try to do the rests very soon now. Do not touch the t directory >> until I've committed by reorganisations! >> >>> On a related point, what does everyone think of moving BioPerlTest to >>> core >>> so the other distributions can use it? I think it is worth doing >>> eventually, but it could possibly wait until 1.6.x or 1.7. I have tested >>> it >>> out and it works but needs some dependency issues ironed out. >> >> Moving to core would be a good thing. Do it. >> >> >> -Heikki > > ...also, just to note, the mail lists appear to be acting up (support has > been notified). My commits last night are here: > > http://lists.open-bio.org/pipermail/bioperl-guts-l/2008-December/date.html > > chris > > From cjfields at illinois.edu Wed Dec 3 22:39:13 2008 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 3 Dec 2008 21:39:13 -0600 Subject: [Bioperl-l] reorgansing tests by group In-Reply-To: References: <72AAEC8C-138C-4053-82A0-3E7207C4F8F3@gmx.net> <6B22EAB9-3228-437B-889E-3323A3655505@illinois.edu> <9C6F2A11-D4D5-49BF-8ECE-5E0235C3F4F9@illinois.edu> Message-ID: <00B3B97E-F784-4128-9497-1F466CDBBA4C@illinois.edu> You rock! (And consequently must be very tired). I'll try moving BioPerlTest into Bio::Root::Test (might be tricky)... chris On Dec 3, 2008, at 3:48 PM, Heikki Lehvaslaiho wrote: > 2008/12/3 Chris Fields : >> >> On Dec 3, 2008, at 12:23 PM, Heikki Lehvaslaiho wrote: >> >>> 2008/12/2 Chris Fields : >>>> >>>> Wow, I go to sleep and the tests are almost reorganized. Thanks >>>> Heikki! > > I jsut had long flight that gave me time to think this through! > > Now they are done! The ones on the top level are deprecated, > unfinished or can be left there (Perl.t & PodSyntax.t). > > I moved some tests from t/Tools into t/SeqTools. All of them give > additional functionality to Sequence objects and are not parsers like > tests in t/Tools directory. The exceptions in current t/Tools > are Analysis subdirectory tests. I would have pulled them and > t/Tools/Run/RemoteBlast.t into t/WebAnalysis.t > > > I committed all in one go. I suspect that the mail generated is too > long (like in your case) and does not get sent. > > -Heikki > > > >>>> The only (very small) caveat I find to using recursive tests is any >>>> additional non-test files we add, including data for tests in >>>> the /data >>>> directory, must not end with *.t, otherwise the build file will >>>> try to >>>> run >>>> it and bomb. There was one file I changed to .tt which is now >>>> passed >>>> over. >>>> If needed we can move over to an autogenerated file which >>>> explicitly >>>> lists >>>> the tests to run (this would likely be at a later point). >>> >>> Chris, >>> >>> I'll try to do the rests very soon now. Do not touch the t directory >>> until I've committed by reorganisations! >>> >>>> On a related point, what does everyone think of moving >>>> BioPerlTest to >>>> core >>>> so the other distributions can use it? I think it is worth doing >>>> eventually, but it could possibly wait until 1.6.x or 1.7. I >>>> have tested >>>> it >>>> out and it works but needs some dependency issues ironed out. >>> >>> Moving to core would be a good thing. Do it. >>> >>> >>> -Heikki >> >> ...also, just to note, the mail lists appear to be acting up >> (support has >> been notified). My commits last night are here: >> >> http://lists.open-bio.org/pipermail/bioperl-guts-l/2008-December/date.html >> >> chris >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cain.cshl at gmail.com Wed Dec 3 23:33:11 2008 From: cain.cshl at gmail.com (Scott Cain) Date: Wed, 3 Dec 2008 23:33:11 -0500 Subject: [Bioperl-l] Fw: Help with installation In-Reply-To: <4FCA0CBD70784B939ECAF1F212D44B65@NewLife> References: <20871.38071.qm@web82201.mail.mud.yahoo.com> <4FCA0CBD70784B939ECAF1F212D44B65@NewLife> Message-ID: <536f21b00812032033g30d6e8fcs7a19925f5df1df63@mail.gmail.com> And if you haven't done so already, you almost certainly want to install the Mac OS X developer's tools, which are on the OS installer DVD. Scott On Wed, Dec 3, 2008 at 11:32 AM, Mark A. Jensen wrote: > Assiatu- > You may find the fink installer helpful- see > http://www.bioperl.org/wiki/Getting_BioPerl#MacOS_X_using_fink > cheers MAJ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From hlapp at gmx.net Thu Dec 4 10:09:27 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 4 Dec 2008 10:09:27 -0500 Subject: [Bioperl-l] global verbosity In-Reply-To: <47A4C981089F42718A6644540AB23117@NewLife> References: <47A4C981089F42718A6644540AB23117@NewLife> Message-ID: <310BAD14-D050-438D-BCDC-5C700E10CF6E@gmx.net> On Dec 3, 2008, at 10:23 AM, Mark A. Jensen wrote: > I found $Bio::Root::Root:VERBOSITY, but saw that it didn't matter to > downstream objects when it was changed. Interesting, but I agree. > Digging in to the issue, found that global verbosity can't really be > set, though one can access the value of $VERBOSITY with > Bio::Root::Root::verbose(). One can of course set $Bio::Root::Root::VERBOSITY. > http://bugzilla.open-bio.org/show_bug.cgi?id=2696 > has a patch + .t to Root.pm that I > think solves the issue, allowing getting and setting of global > verbosity, so that the global value now propagates to new objects. I guess the simple fix would have been if (defined $value || ! defined $self->{'_root_verbose'}) { - $self->{'_root_verbose'} = $value || 0; + $self->{'_root_verbose'} = $value || $VERBOSITY || 0; } But I like your patch in that it enables a static method call to set the global default. Except the line + $self->{'_root_verbose'} = $VERBOSITY; + # now look for flag and update if nec... Doesn't that override any previously set value to the global default? I.e., I don't think the above would pass $seq->verbose(1); ok ($seq->verbose(), 1); Or am I missing something? > > > There is a stickier issue (example using Bio::Seq and > Bio::Seq->primary_seq() in the .t file), in which > setting an object's verbosity post-construction does not propagate to > sub-objects contained in the object, so that one might not get what > one expects. I think the run-time changing for an object not propagating to sub- objects is expected behavior. It would also be very difficult to solve this cleanly, as you would either have to expect derived objects to override some method to inject their own sub-objects into the chain, or you would need base objects to have knowledge about what their derivatives do. For our records I responded that to the patch as well. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Thu Dec 4 10:12:38 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 4 Dec 2008 10:12:38 -0500 Subject: [Bioperl-l] PullHSP bug In-Reply-To: <1D8F1862-46F3-45FB-AEDC-A4E9BC8FDC9D@illinois.edu> References: <4935D1F1.1050304@sendu.me.uk> <1D8F1862-46F3-45FB-AEDC-A4E9BC8FDC9D@illinois.edu> Message-ID: <06A26DF4-54C6-4A69-817E-28C83EB18B53@gmx.net> On Dec 2, 2008, at 9:40 PM, Chris Fields wrote: > It appears the problem boils down to a small inconsistency with the > way blank IDs are handled between the two BLAST parsers. The > regular blast parser explicitly sets this to '', while blast_pull > leaves it undef. When one constructs a LocatableSeq w/o an ID it > dies, but '' works, hence the problem. I don't think using '' is a > real solution though (seems like something added to silence errors). I agree. Using '' where a value is expected is an ugly kludge. Is it possible to fix this? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From bix at sendu.me.uk Thu Dec 4 10:41:59 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Thu, 04 Dec 2008 15:41:59 +0000 Subject: [Bioperl-l] global verbosity In-Reply-To: <47A4C981089F42718A6644540AB23117@NewLife> References: <47A4C981089F42718A6644540AB23117@NewLife> Message-ID: <4937FA47.3050801@sendu.me.uk> Mark A. Jensen wrote: > I was looking for a way to set verbosity globally (but not for > debugging), so that all subsequently created objects would be > absolutely quiet. I didn't look at your solution yet, but it might be instructive to read the previous discussion on this topic: http://thread.gmane.org/gmane.comp.lang.perl.bio.general/12130/focus=12156 It looks like I decided against implementing my own idea there, but if whatever you have in mind is similar and/or takes into account the issues raised... From maj at fortinbras.us Thu Dec 4 10:37:19 2008 From: maj at fortinbras.us (Mark A. Jensen) Date: Thu, 4 Dec 2008 10:37:19 -0500 Subject: [Bioperl-l] global verbosity In-Reply-To: <310BAD14-D050-438D-BCDC-5C700E10CF6E@gmx.net> References: <47A4C981089F42718A6644540AB23117@NewLife> <310BAD14-D050-438D-BCDC-5C700E10CF6E@gmx.net> Message-ID: ----- Original Message ----- From: "Hilmar Lapp" To: "Mark A. Jensen" Cc: Sent: Thursday, December 04, 2008 10:09 AM Subject: Re: [Bioperl-l] global verbosity ... > But I like your patch in that it enables a static method call to set the > global default. [thanks!] Except the line > > + $self->{'_root_verbose'} = $VERBOSITY; > + # now look for flag and update if nec... > > Doesn't that override any previously set value to the global default? I.e., I > don't think the above would pass > > $seq->verbose(1); > ok ($seq->verbose(), 1); > > Or am I missing something? Maybe the patch is confusing-- that line is in the Root constructor, not in verbose(), so this should be the first verbosity the object sees. Clearly, would be naughty in the verbose method. The rest of the patch is in verbose(). (Now am I missing sth?) > >> >> >> There is a stickier issue (example using Bio::Seq and >> Bio::Seq->primary_seq() in the .t file), in which >> setting an object's verbosity post-construction does not propagate to >> sub-objects contained in the object, so that one might not get what >> one expects. > > I think the run-time changing for an object not propagating to sub- objects is > expected behavior. It would also be very difficult to solve this cleanly, as > you would either have to expect derived objects to override some method to > inject their own sub-objects into the chain, or you would need base objects > to have knowledge about what their derivatives do. I agree. As I commented at the patch, I do think that certain properties (not nec. methods or subobjects) should be passed down to naturally derived objects if the referring object desires is (e.g., a LocatableSeq slice should probably have the same primary id as the original sequence). I took a stab at this in Bug #2673. > > For our records I responded that to the patch as well. > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== cheers - MAJ From paolo.pavan at tecnoparco.org Thu Dec 4 10:54:48 2008 From: paolo.pavan at tecnoparco.org (Paolo Pavan) Date: Thu, 4 Dec 2008 16:54:48 +0100 Subject: [Bioperl-l] About graphic rendering In-Reply-To: <56be91b60812031021k741d4638o15dcade5dcceb0e0@mail.gmail.com> References: <56be91b60812031021k741d4638o15dcade5dcceb0e0@mail.gmail.com> Message-ID: <56be91b60812040754y67c6a54fy9e7d354f8ae98dfd@mail.gmail.com> Hi everybody, I've a question about a Bio::Graphics rendering. I would like to display a blast HSP on a track but I would like to draw the "tails" of my mapping sequence that don't match the subject. So I instantiate these 3 object that represent all the three segments I want to display: my $feature = Bio::SeqFeature::Generic->new( -display_name =>$sequence_to_map->display_id, -start =>$hsp->sbjct->start, -end =>$hsp->sbjct->end, ); my $feature_pre = Bio::SeqFeature::Generic->new( -start =>($hsp->sbjct->start - $hsp->query->start), -end =>$hsp->sbjct->start-1 ); my $feature_post = Bio::SeqFeature::Generic->new( -start => $hsp->sbjct->end+1, -end => $hsp->sbjct->end + $sequence_to_map->length - $hsp->query->end ); now I have to add these features to my $track in a manner that the $feature_pre and $feature_post paint or color in a different way than $feature but align horizontally. I tried with: $feature->add_sub_SeqFeature($feature_pre, 'EXPAND'); $feature->add_sub_SeqFeature($feature_post, 'EXPAND'); $track->add_feature($feature); This does not work, because the features spread vertically, and more I cannot change the glyph because seems to be a track property, not a feature one. Any idea? Thank you for your help, Paolo Ps: I send this twice because it seems it didn't work the first time. I apologize. From maj at fortinbras.us Thu Dec 4 11:01:44 2008 From: maj at fortinbras.us (Mark A. Jensen) Date: Thu, 4 Dec 2008 11:01:44 -0500 Subject: [Bioperl-l] global verbosity In-Reply-To: <4937FA47.3050801@sendu.me.uk> References: <47A4C981089F42718A6644540AB23117@NewLife> <4937FA47.3050801@sendu.me.uk> Message-ID: <7E745F39A16C46B895F7385F65FF8B5C@NewLife> [from the gmane link: > Hilmar Lapp wrote: >> Well, the rule would be: >> >> 1) if a local (instance) verbosity has been set, use it >> 2) otherwise, if a global (class, static) verbosity has been set, >> use it >> 3) otherwise, use a default value. >> >> This would mean indeed that if you changed verbosity for a specific >> instance it will be unaffected by global changes of the verbosity level. ] I believe the solution follows those rules to the letter. The option for setting verbosity as an arg in the constructor remains, and while the global $VERBOSITY is used as the default for instances, this variable itself has a default (0), which I think handles rule 3. The patch allows the instance verbosity to be undefined, and remain so, falling through to the global if the getter is called before the setter. This and the global set method (which obviates a need to know the global symbol) may be the under-the-hood advantages here, though Hilmar's solution is elegant and small. ----- Original Message ----- From: "Sendu Bala" To: "Mark A. Jensen" Cc: Sent: Thursday, December 04, 2008 10:41 AM Subject: Re: [Bioperl-l] global verbosity > Mark A. Jensen wrote: >> I was looking for a way to set verbosity globally (but not for >> debugging), so that all subsequently created objects would be >> absolutely quiet. > > I didn't look at your solution yet, but it might be instructive to read the > previous discussion on this topic: > http://thread.gmane.org/gmane.comp.lang.perl.bio.general/12130/focus=12156 > > It looks like I decided against implementing my own idea there, but if > whatever you have in mind is similar and/or takes into account the issues > raised... > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From hlapp at gmx.net Thu Dec 4 11:24:41 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 4 Dec 2008 11:24:41 -0500 Subject: [Bioperl-l] global verbosity In-Reply-To: References: <47A4C981089F42718A6644540AB23117@NewLife> <310BAD14-D050-438D-BCDC-5C700E10CF6E@gmx.net> Message-ID: <42587E3F-4638-47E7-A3DF-F0135D0CB2C2@gmx.net> On Dec 4, 2008, at 10:37 AM, Mark A. Jensen wrote: >> >> Doesn't that override any previously set value to the global >> default? I.e., I don't think the above would pass >> >> $seq->verbose(1); >> ok ($seq->verbose(), 1); >> >> Or am I missing something? > > Maybe the patch is confusing-- that line is in the Root constructor, > not in verbose() Ah - so that's what I was missing. Makes sense then. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From lincoln.stein at gmail.com Thu Dec 4 11:30:11 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Thu, 4 Dec 2008 11:30:11 -0500 Subject: [Bioperl-l] About graphic rendering In-Reply-To: <56be91b60812031021k741d4638o15dcade5dcceb0e0@mail.gmail.com> References: <56be91b60812031021k741d4638o15dcade5dcceb0e0@mail.gmail.com> Message-ID: <6dce9a0b0812040830p266af928jcb55734bbf4afa3d@mail.gmail.com> Which glyph are you using to display these features? You may wish to set the bump property to zero so that the features don't spread out vertically; this happens automatically with some of the glyphs such as "heterogeneous_segment" Lincoln On Wed, Dec 3, 2008 at 1:21 PM, Paolo Pavan wrote: > Hi everybody, > I've a question about a Bio::Graphics rendering. I would like to display a > blast HSP on a track but I would like to draw the "tails" of my mapping > sequence that don't match the subject. So I instantiate these 3 object that > represent all the three segments I want to display: > > my $feature = Bio::SeqFeature::Generic->new( > -display_name > =>$sequence_to_map->display_id, > -start =>$hsp->sbjct->start, > -end =>$hsp->sbjct->end, > ); > my $feature_pre = Bio::SeqFeature::Generic->new( > -start =>($hsp->sbjct->start - > $hsp->query->start), > -end =>$hsp->sbjct->start-1 > ); > my $feature_post = Bio::SeqFeature::Generic->new( > -start => $hsp->sbjct->end+1, > -end => $hsp->sbjct->end + > $sequence_to_map->length - $hsp->query->end > ); > > now I have to add these features to my $track in a manner that the > $feature_pre and $feature_post paint or color in a different way than > $feature but align horizontally. > I tried with: > > $feature->add_sub_SeqFeature($feature_pre, 'EXPAND'); > $feature->add_sub_SeqFeature($feature_post, 'EXPAND'); > > $track->add_feature($feature); > > This does not work, because the features spread vertically, and more I > cannot change the glyph because seems to be a track property, not a feature > one. > Any idea? > > Thank you for your help, > Paolo > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Stacey Quinn Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 USA (516) 367-8380 Assistant: Sandra Michelsen From cjfields at illinois.edu Thu Dec 4 11:49:05 2008 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 4 Dec 2008 10:49:05 -0600 Subject: [Bioperl-l] PullHSP bug In-Reply-To: <06A26DF4-54C6-4A69-817E-28C83EB18B53@gmx.net> References: <4935D1F1.1050304@sendu.me.uk> <1D8F1862-46F3-45FB-AEDC-A4E9BC8FDC9D@illinois.edu> <06A26DF4-54C6-4A69-817E-28C83EB18B53@gmx.net> Message-ID: <273E85C3-4057-47EB-A615-77AB2FA86F06@illinois.edu> On Dec 4, 2008, at 9:12 AM, Hilmar Lapp wrote: > > On Dec 2, 2008, at 9:40 PM, Chris Fields wrote: > >> It appears the problem boils down to a small inconsistency with the >> way blank IDs are handled between the two BLAST parsers. The >> regular blast parser explicitly sets this to '', while blast_pull >> leaves it undef. When one constructs a LocatableSeq w/o an ID it >> dies, but '' works, hence the problem. I don't think using '' is a >> real solution though (seems like something added to silence errors). > > > I agree. Using '' where a value is expected is an ugly kludge. Is it > possible to fix this? > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== It's fixed. I added a force_nse() flag to LocatableSeq which sets per- instance and allows get_nse to make an NSE under circumstances where the seq ID is undefined. LocatableSeqs which lack an ID but have the flag explicitly get something like '/$start-$end' instead of throwing an exception (the default). The flag is off by default, so you will still get an exception in case leaving off the ID was unintentional (didn't want any silent bugs sneaking through). This solution may not be optimal. The NSE is currently used for indexing LocatableSeqs and checking for possible collisions in SimpleAlign. One gets a warning in the latter case ("Replacing one sequence [$nse]"), so maybe that's enough. chris From paolo.pavan at tecnoparco.org Thu Dec 4 13:07:49 2008 From: paolo.pavan at tecnoparco.org (Paolo Pavan) Date: Thu, 4 Dec 2008 19:07:49 +0100 Subject: [Bioperl-l] About graphic rendering In-Reply-To: <6dce9a0b0812040830p266af928jcb55734bbf4afa3d@mail.gmail.com> References: <56be91b60812031021k741d4638o15dcade5dcceb0e0@mail.gmail.com> <6dce9a0b0812040830p266af928jcb55734bbf4afa3d@mail.gmail.com> Message-ID: <56be91b60812041007x7d150b27i4354db3d54eec361@mail.gmail.com> Hi Lincoln, thank you for your answer. It actually seems that I don't have a glyph called "heterogeneous_segment", maybe is it a BioPerl version problem? I have 1.5.2 installed. ( MSG: The requested glyph class, ``heterogeneous_segment'' is not available: Can't locate Bio/Graphics/Glyph/heterogeneous_segment.pm in @INC ... ) However, I could even use a generic glyph if I can change the color of the external features. I tried to use a bump = 0 but this cause to collapse more segments I would like to add. This is the graphic initialization part of the code: my $axis = Bio::SeqFeature::Generic-> new( -start => 0, -end => $database_seq->length ); my $panel = Bio::Graphics::Panel->new ( -length => $database_seq->length, -width => $graphic_length, -pad_left => 10, -pad_right => 10 ); $panel->add_track( $axis, -glyph =>'arrow', -tick =>2, -fgcolor=>'black', -double =>1 ); my $track = $panel->add_track( -glyph => 'generic', -label => 1, -bgcolor =>'blue', #-bump =>1 ); Maybe isn't clear the idea of the final picture I would like to obtain? Thank you again. 2008/12/4 Lincoln Stein > Which glyph are you using to display these features? You may wish to set > the bump property to zero so that the features don't spread out vertically; > this happens automatically with some of the glyphs such as > "heterogeneous_segment" > > Lincoln > > On Wed, Dec 3, 2008 at 1:21 PM, Paolo Pavan wrote: > >> Hi everybody, >> I've a question about a Bio::Graphics rendering. I would like to display a >> blast HSP on a track but I would like to draw the "tails" of my mapping >> sequence that don't match the subject. So I instantiate these 3 object >> that >> represent all the three segments I want to display: >> >> my $feature = Bio::SeqFeature::Generic->new( >> -display_name >> =>$sequence_to_map->display_id, >> -start =>$hsp->sbjct->start, >> -end =>$hsp->sbjct->end, >> ); >> my $feature_pre = Bio::SeqFeature::Generic->new( >> -start =>($hsp->sbjct->start - >> $hsp->query->start), >> -end =>$hsp->sbjct->start-1 >> ); >> my $feature_post = Bio::SeqFeature::Generic->new( >> -start => $hsp->sbjct->end+1, >> -end => $hsp->sbjct->end + >> $sequence_to_map->length - $hsp->query->end >> ); >> >> now I have to add these features to my $track in a manner that the >> $feature_pre and $feature_post paint or color in a different way than >> $feature but align horizontally. >> I tried with: >> >> $feature->add_sub_SeqFeature($feature_pre, 'EXPAND'); >> $feature->add_sub_SeqFeature($feature_post, 'EXPAND'); >> >> $track->add_feature($feature); >> >> This does not work, because the features spread vertically, and more I >> cannot change the glyph because seems to be a track property, not a >> feature >> one. >> Any idea? >> >> Thank you for your help, >> Paolo >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Stacey Quinn > > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 USA > (516) 367-8380 > Assistant: Sandra Michelsen > From lincoln.stein at gmail.com Thu Dec 4 13:11:52 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Thu, 4 Dec 2008 13:11:52 -0500 Subject: [Bioperl-l] About graphic rendering In-Reply-To: <56be91b60812041007x7d150b27i4354db3d54eec361@mail.gmail.com> References: <56be91b60812031021k741d4638o15dcade5dcceb0e0@mail.gmail.com> <6dce9a0b0812040830p266af928jcb55734bbf4afa3d@mail.gmail.com> <56be91b60812041007x7d150b27i4354db3d54eec361@mail.gmail.com> Message-ID: <6dce9a0b0812041011o27729143x2cddc46d089a17da@mail.gmail.com> My mistake. The glyph is named "heterogeneous_segments" with an "s" Lincoln On Thu, Dec 4, 2008 at 1:07 PM, Paolo Pavan wrote: > Hi Lincoln, thank you for your answer. > It actually seems that I don't have a glyph called "heterogeneous_segment", > maybe is it a BioPerl version problem? I have 1.5.2 installed. > ( MSG: The requested glyph class, ``heterogeneous_segment'' is not > available: Can't locate Bio/Graphics/Glyph/heterogeneous_segment.pm in > @INC ... ) > > However, I could even use a generic glyph if I can change the color of the > external features. I tried to use a bump = 0 but this cause to collapse more > segments I would like to add. > This is the graphic initialization part of the code: > > my $axis = Bio::SeqFeature::Generic-> new( > -start => 0, > -end => $database_seq->length > ); > > my $panel = Bio::Graphics::Panel->new ( > -length => $database_seq->length, > -width => $graphic_length, > -pad_left => 10, > -pad_right => 10 > ); > > $panel->add_track( $axis, > -glyph =>'arrow', > -tick =>2, > -fgcolor=>'black', > -double =>1 > ); > my $track = $panel->add_track( > -glyph => 'generic', > -label => 1, > -bgcolor =>'blue', > #-bump =>1 > ); > > Maybe isn't clear the idea of the final picture I would like to obtain? > > Thank you again. > > 2008/12/4 Lincoln Stein > > Which glyph are you using to display these features? You may wish to set >> the bump property to zero so that the features don't spread out vertically; >> this happens automatically with some of the glyphs such as >> "heterogeneous_segment" >> >> Lincoln >> >> On Wed, Dec 3, 2008 at 1:21 PM, Paolo Pavan wrote: >> >>> Hi everybody, >>> I've a question about a Bio::Graphics rendering. I would like to display >>> a >>> blast HSP on a track but I would like to draw the "tails" of my mapping >>> sequence that don't match the subject. So I instantiate these 3 object >>> that >>> represent all the three segments I want to display: >>> >>> my $feature = Bio::SeqFeature::Generic->new( >>> -display_name >>> =>$sequence_to_map->display_id, >>> -start =>$hsp->sbjct->start, >>> -end =>$hsp->sbjct->end, >>> ); >>> my $feature_pre = Bio::SeqFeature::Generic->new( >>> -start =>($hsp->sbjct->start - >>> $hsp->query->start), >>> -end =>$hsp->sbjct->start-1 >>> ); >>> my $feature_post = Bio::SeqFeature::Generic->new( >>> -start => $hsp->sbjct->end+1, >>> -end => $hsp->sbjct->end + >>> $sequence_to_map->length - $hsp->query->end >>> ); >>> >>> now I have to add these features to my $track in a manner that the >>> $feature_pre and $feature_post paint or color in a different way than >>> $feature but align horizontally. >>> I tried with: >>> >>> $feature->add_sub_SeqFeature($feature_pre, 'EXPAND'); >>> $feature->add_sub_SeqFeature($feature_post, 'EXPAND'); >>> >>> $track->add_feature($feature); >>> >>> This does not work, because the features spread vertically, and more I >>> cannot change the glyph because seems to be a track property, not a >>> feature >>> one. >>> Any idea? >>> >>> Thank you for your help, >>> Paolo >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> >> >> -- >> Lincoln D. Stein >> >> Ontario Institute for Cancer Research >> 101 College St., Suite 800 >> Toronto, ON, Canada M5G0A3 >> 416 673-8514 >> Assistant: Stacey Quinn >> >> Cold Spring Harbor Laboratory >> 1 Bungtown Road >> Cold Spring Harbor, NY 11724 USA >> (516) 367-8380 >> Assistant: Sandra Michelsen >> > > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Stacey Quinn Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 USA (516) 367-8380 Assistant: Sandra Michelsen From maj at fortinbras.us Thu Dec 4 14:06:51 2008 From: maj at fortinbras.us (Mark A. Jensen) Date: Thu, 4 Dec 2008 14:06:51 -0500 Subject: [Bioperl-l] global verbosity In-Reply-To: <42587E3F-4638-47E7-A3DF-F0135D0CB2C2@gmx.net> References: <47A4C981089F42718A6644540AB23117@NewLife><310BAD14-D050-438D-BCDC-5C700E10CF6E@gmx.net> <42587E3F-4638-47E7-A3DF-F0135D0CB2C2@gmx.net> Message-ID: <1B4ABCFA1F2F4284B4EDAC51DF950E4D@NewLife> Although-- if that line is left out of the constructor, then I think the object's v. can be left undefined and verbose() will fall through to the global value without setting the instance, as advertised above--- ----- Original Message ----- From: "Hilmar Lapp" To: "Mark A. Jensen" Cc: Sent: Thursday, December 04, 2008 11:24 AM Subject: Re: [Bioperl-l] global verbosity > > On Dec 4, 2008, at 10:37 AM, Mark A. Jensen wrote: > >>> >>> Doesn't that override any previously set value to the global default? >>> I.e., I don't think the above would pass >>> >>> $seq->verbose(1); >>> ok ($seq->verbose(), 1); >>> >>> Or am I missing something? >> >> Maybe the patch is confusing-- that line is in the Root constructor, not in >> verbose() > > > Ah - so that's what I was missing. Makes sense then. > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From gundalav at gmail.com Fri Dec 5 05:55:15 2008 From: gundalav at gmail.com (Gundala Viswanath) Date: Fri, 5 Dec 2008 19:55:15 +0900 Subject: [Bioperl-l] Getting Genomic Position of Genes using BioPerl Message-ID: <73f827b50812050255j3ef91674uc48b2a5b900f2cd5@mail.gmail.com> Dear All, Is there a way we can get the genomic position of a gene from any species, using BioPerl? For example given such genes names, we want to know the chromosomes, strand, start_pos, end_pos: C53H9.2 (C. Elegans) CBG22213 (C Brigs) cr01.sctg20.wum.79 (C. Reria) ENSG00000064655 (H. Sapiens) YGL099W (S. Cerevisieae) I am thinking if there already exist any module to do such task. Regards, G. Viswanath From paolo.pavan at tecnoparco.org Fri Dec 5 07:41:52 2008 From: paolo.pavan at tecnoparco.org (Paolo Pavan) Date: Fri, 5 Dec 2008 13:41:52 +0100 Subject: [Bioperl-l] About graphic rendering In-Reply-To: <6dce9a0b0812041011o27729143x2cddc46d089a17da@mail.gmail.com> References: <56be91b60812031021k741d4638o15dcade5dcceb0e0@mail.gmail.com> <6dce9a0b0812040830p266af928jcb55734bbf4afa3d@mail.gmail.com> <56be91b60812041007x7d150b27i4354db3d54eec361@mail.gmail.com> <6dce9a0b0812041011o27729143x2cddc46d089a17da@mail.gmail.com> Message-ID: <56be91b60812050441r9ab81d2xb9ed73f8f198b149@mail.gmail.com> Thank you very much Lincoln, this is what I was searching for, but I realize I'm a little confused still. Now what I've got is my $feature that paints subtle and my $pre_ and $post_ that paint like a solid line, the best would be exactly the contrary. I was giong deeper with the bioperl modules documentation page for heterogeneous_segmentsand I found that there is a way to change the color of a subfeature setting the property named -{source}_color => $color but I don't understand what is "source". Maybe the confusion comes from the fact I haven't understood the way of each feature inherit its own Glyph (because they paint differently, they must have their own glyph, isn't it?). Please can you explain how this happens and how I can set the properties for each segment? What are the others glyphs behave the same way of "graded_segments" (bump = 0) ? Thank you again, your help is much appreciated, Paolo 2008/12/4 Lincoln Stein > My mistake. The glyph is named "heterogeneous_segments" with an "s" > > Lincoln > > > On Thu, Dec 4, 2008 at 1:07 PM, Paolo Pavan wrote: > >> Hi Lincoln, thank you for your answer. >> It actually seems that I don't have a glyph called >> "heterogeneous_segment", maybe is it a BioPerl version problem? I have 1.5.2 >> installed. >> ( MSG: The requested glyph class, ``heterogeneous_segment'' is not >> available: Can't locate Bio/Graphics/Glyph/heterogeneous_segment.pm in >> @INC ... ) >> >> However, I could even use a generic glyph if I can change the color of the >> external features. I tried to use a bump = 0 but this cause to collapse more >> segments I would like to add. >> This is the graphic initialization part of the code: >> >> my $axis = Bio::SeqFeature::Generic-> new( >> -start => 0, >> -end => $database_seq->length >> ); >> >> my $panel = Bio::Graphics::Panel->new ( >> -length => $database_seq->length, >> -width => $graphic_length, >> -pad_left => 10, >> -pad_right => 10 >> ); >> >> $panel->add_track( $axis, >> -glyph =>'arrow', >> -tick =>2, >> -fgcolor=>'black', >> -double =>1 >> ); >> my $track = $panel->add_track( >> -glyph => 'generic', >> -label => 1, >> -bgcolor =>'blue', >> #-bump =>1 >> ); >> >> Maybe isn't clear the idea of the final picture I would like to obtain? >> >> Thank you again. >> >> 2008/12/4 Lincoln Stein >> >> Which glyph are you using to display these features? You may wish to set >>> the bump property to zero so that the features don't spread out vertically; >>> this happens automatically with some of the glyphs such as >>> "heterogeneous_segment" >>> >>> Lincoln >>> >>> On Wed, Dec 3, 2008 at 1:21 PM, Paolo Pavan wrote: >>> >>>> Hi everybody, >>>> I've a question about a Bio::Graphics rendering. I would like to display >>>> a >>>> blast HSP on a track but I would like to draw the "tails" of my mapping >>>> sequence that don't match the subject. So I instantiate these 3 object >>>> that >>>> represent all the three segments I want to display: >>>> >>>> my $feature = Bio::SeqFeature::Generic->new( >>>> -display_name >>>> =>$sequence_to_map->display_id, >>>> -start =>$hsp->sbjct->start, >>>> -end =>$hsp->sbjct->end, >>>> ); >>>> my $feature_pre = Bio::SeqFeature::Generic->new( >>>> -start =>($hsp->sbjct->start - >>>> $hsp->query->start), >>>> -end =>$hsp->sbjct->start-1 >>>> ); >>>> my $feature_post = Bio::SeqFeature::Generic->new( >>>> -start => $hsp->sbjct->end+1, >>>> -end => $hsp->sbjct->end + >>>> $sequence_to_map->length - $hsp->query->end >>>> ); >>>> >>>> now I have to add these features to my $track in a manner that the >>>> $feature_pre and $feature_post paint or color in a different way than >>>> $feature but align horizontally. >>>> I tried with: >>>> >>>> $feature->add_sub_SeqFeature($feature_pre, 'EXPAND'); >>>> $feature->add_sub_SeqFeature($feature_post, 'EXPAND'); >>>> >>>> $track->add_feature($feature); >>>> >>>> This does not work, because the features spread vertically, and more I >>>> cannot change the glyph because seems to be a track property, not a >>>> feature >>>> one. >>>> Any idea? >>>> >>>> Thank you for your help, >>>> Paolo >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> >>> >>> -- >>> Lincoln D. Stein >>> >>> Ontario Institute for Cancer Research >>> 101 College St., Suite 800 >>> Toronto, ON, Canada M5G0A3 >>> 416 673-8514 >>> Assistant: Stacey Quinn >>> >>> Cold Spring Harbor Laboratory >>> 1 Bungtown Road >>> Cold Spring Harbor, NY 11724 USA >>> (516) 367-8380 >>> Assistant: Sandra Michelsen >>> >> >> > > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Stacey Quinn > > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 USA > (516) 367-8380 > Assistant: Sandra Michelsen > From sdavis2 at mail.nih.gov Fri Dec 5 07:47:57 2008 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Fri, 5 Dec 2008 07:47:57 -0500 Subject: [Bioperl-l] Getting Genomic Position of Genes using BioPerl In-Reply-To: <73f827b50812050255j3ef91674uc48b2a5b900f2cd5@mail.gmail.com> References: <73f827b50812050255j3ef91674uc48b2a5b900f2cd5@mail.gmail.com> Message-ID: <264855a00812050447v6ff7df8du36b8fb82dcb7567e@mail.gmail.com> On Fri, Dec 5, 2008 at 5:55 AM, Gundala Viswanath wrote: > Dear All, > > Is there a way we can get the genomic position > of a gene from any species, using BioPerl? > > For example given such genes names, we want to > know the chromosomes, strand, start_pos, end_pos: > > C53H9.2 (C. Elegans) > CBG22213 (C Brigs) > cr01.sctg20.wum.79 (C. Reria) > ENSG00000064655 (H. Sapiens) > YGL099W (S. Cerevisieae) > > I am thinking if there already exist > any module to do such task. You might want to look at the Ensembl perl api (and perhaps the mart api, also). Sean From lincoln.stein at gmail.com Fri Dec 5 09:41:00 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Fri, 5 Dec 2008 09:41:00 -0500 Subject: [Bioperl-l] About graphic rendering In-Reply-To: <56be91b60812050441r9ab81d2xb9ed73f8f198b149@mail.gmail.com> References: <56be91b60812031021k741d4638o15dcade5dcceb0e0@mail.gmail.com> <6dce9a0b0812040830p266af928jcb55734bbf4afa3d@mail.gmail.com> <56be91b60812041007x7d150b27i4354db3d54eec361@mail.gmail.com> <6dce9a0b0812041011o27729143x2cddc46d089a17da@mail.gmail.com> <56be91b60812050441r9ab81d2xb9ed73f8f198b149@mail.gmail.com> Message-ID: <6dce9a0b0812050641s6dab79dfu8281e68b57bd8420@mail.gmail.com> Hi Paolo, When you create each subfeature, assign it a unique source_tag, for example use "extent" for the left and right extents of the feature, and "aligned" for the part that aligns.. Then specify the color of each type of subfeature this way: -extent_color => 'grey', -aligned_color => 'black' Lincoln On Fri, Dec 5, 2008 at 7:41 AM, Paolo Pavan wrote: > Thank you very much Lincoln, this is what I was searching for, but I > realize I'm a little confused still. > Now what I've got is my $feature that paints subtle and my $pre_ and $post_ > that paint like a solid line, the best would be exactly the contrary. > I was giong deeper with the bioperl modules documentation page for > heterogeneous_segmentsand I found that there is a way to change the color of a subfeature setting > the property named -{source}_color => $color > but I don't understand what is "source". > Maybe the confusion comes from the fact I haven't understood the way of > each feature inherit its own Glyph (because they paint differently, they > must have their own glyph, isn't it?). Please can you explain how this > happens and how I can set the properties for each segment? > What are the others glyphs behave the same way of "graded_segments" (bump = > 0) ? > > Thank you again, your help is much appreciated, > Paolo > > > > 2008/12/4 Lincoln Stein > >> My mistake. The glyph is named "heterogeneous_segments" with an "s" >> >> Lincoln >> >> >> On Thu, Dec 4, 2008 at 1:07 PM, Paolo Pavan wrote: >> >>> Hi Lincoln, thank you for your answer. >>> It actually seems that I don't have a glyph called >>> "heterogeneous_segment", maybe is it a BioPerl version problem? I have 1.5.2 >>> installed. >>> ( MSG: The requested glyph class, ``heterogeneous_segment'' is not >>> available: Can't locate Bio/Graphics/Glyph/heterogeneous_segment.pm in >>> @INC ... ) >>> >>> However, I could even use a generic glyph if I can change the color of >>> the external features. I tried to use a bump = 0 but this cause to collapse >>> more segments I would like to add. >>> This is the graphic initialization part of the code: >>> >>> my $axis = Bio::SeqFeature::Generic-> new( >>> -start => 0, >>> -end => $database_seq->length >>> ); >>> >>> my $panel = Bio::Graphics::Panel->new ( >>> -length => $database_seq->length, >>> -width => $graphic_length, >>> -pad_left => 10, >>> -pad_right => 10 >>> ); >>> >>> $panel->add_track( $axis, >>> -glyph =>'arrow', >>> -tick =>2, >>> -fgcolor=>'black', >>> -double =>1 >>> ); >>> my $track = $panel->add_track( >>> -glyph => 'generic', >>> -label => 1, >>> -bgcolor =>'blue', >>> #-bump =>1 >>> ); >>> >>> Maybe isn't clear the idea of the final picture I would like to obtain? >>> >>> Thank you again. >>> >>> 2008/12/4 Lincoln Stein >>> >>> Which glyph are you using to display these features? You may wish to set >>>> the bump property to zero so that the features don't spread out vertically; >>>> this happens automatically with some of the glyphs such as >>>> "heterogeneous_segment" >>>> >>>> Lincoln >>>> >>>> On Wed, Dec 3, 2008 at 1:21 PM, Paolo Pavan >>> > wrote: >>>> >>>>> Hi everybody, >>>>> I've a question about a Bio::Graphics rendering. I would like to >>>>> display a >>>>> blast HSP on a track but I would like to draw the "tails" of my mapping >>>>> sequence that don't match the subject. So I instantiate these 3 object >>>>> that >>>>> represent all the three segments I want to display: >>>>> >>>>> my $feature = Bio::SeqFeature::Generic->new( >>>>> -display_name >>>>> =>$sequence_to_map->display_id, >>>>> -start =>$hsp->sbjct->start, >>>>> -end =>$hsp->sbjct->end, >>>>> ); >>>>> my $feature_pre = Bio::SeqFeature::Generic->new( >>>>> -start =>($hsp->sbjct->start >>>>> - >>>>> $hsp->query->start), >>>>> -end =>$hsp->sbjct->start-1 >>>>> ); >>>>> my $feature_post = Bio::SeqFeature::Generic->new( >>>>> -start => >>>>> $hsp->sbjct->end+1, >>>>> -end => $hsp->sbjct->end + >>>>> $sequence_to_map->length - $hsp->query->end >>>>> ); >>>>> >>>>> now I have to add these features to my $track in a manner that the >>>>> $feature_pre and $feature_post paint or color in a different way than >>>>> $feature but align horizontally. >>>>> I tried with: >>>>> >>>>> $feature->add_sub_SeqFeature($feature_pre, 'EXPAND'); >>>>> $feature->add_sub_SeqFeature($feature_post, 'EXPAND'); >>>>> >>>>> $track->add_feature($feature); >>>>> >>>>> This does not work, because the features spread vertically, and more I >>>>> cannot change the glyph because seems to be a track property, not a >>>>> feature >>>>> one. >>>>> Any idea? >>>>> >>>>> Thank you for your help, >>>>> Paolo >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> >>>> >>>> >>>> -- >>>> Lincoln D. Stein >>>> >>>> Ontario Institute for Cancer Research >>>> 101 College St., Suite 800 >>>> Toronto, ON, Canada M5G0A3 >>>> 416 673-8514 >>>> Assistant: Stacey Quinn >>>> >>>> Cold Spring Harbor Laboratory >>>> 1 Bungtown Road >>>> Cold Spring Harbor, NY 11724 USA >>>> (516) 367-8380 >>>> Assistant: Sandra Michelsen >>>> >>> >>> >> >> >> -- >> Lincoln D. Stein >> >> Ontario Institute for Cancer Research >> 101 College St., Suite 800 >> Toronto, ON, Canada M5G0A3 >> 416 673-8514 >> Assistant: Stacey Quinn >> >> Cold Spring Harbor Laboratory >> 1 Bungtown Road >> Cold Spring Harbor, NY 11724 USA >> (516) 367-8380 >> Assistant: Sandra Michelsen >> > > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Stacey Quinn Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 USA (516) 367-8380 Assistant: Sandra Michelsen From bosborne11 at verizon.net Fri Dec 5 08:51:00 2008 From: bosborne11 at verizon.net (Brian Osborne) Date: Fri, 05 Dec 2008 08:51:00 -0500 Subject: [Bioperl-l] Getting Genomic Position of Genes using BioPerl In-Reply-To: <264855a00812050447v6ff7df8du36b8fb82dcb7567e@mail.gmail.com> References: <73f827b50812050255j3ef91674uc48b2a5b900f2cd5@mail.gmail.com> <264855a00812050447v6ff7df8du36b8fb82dcb7567e@mail.gmail.com> Message-ID: Gundala, There's an introduction to some of these approaches, including the ENSEMBL API, at: http://www.bioperl.org/wiki/HOWTO:Getting_Genomic_Sequences Brian O. On Dec 5, 2008, at 7:47 AM, Sean Davis wrote: > On Fri, Dec 5, 2008 at 5:55 AM, Gundala Viswanath > wrote: >> Dear All, >> >> Is there a way we can get the genomic position >> of a gene from any species, using BioPerl? >> >> For example given such genes names, we want to >> know the chromosomes, strand, start_pos, end_pos: >> >> C53H9.2 (C. Elegans) >> CBG22213 (C Brigs) >> cr01.sctg20.wum.79 (C. Reria) >> ENSG00000064655 (H. Sapiens) >> YGL099W (S. Cerevisieae) >> >> I am thinking if there already exist >> any module to do such task. > > You might want to look at the Ensembl perl api (and perhaps the mart > api, also). > > Sean > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From maj at fortinbras.us Sat Dec 6 01:20:11 2008 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 6 Dec 2008 01:20:11 -0500 Subject: [Bioperl-l] Problem in OMIM parser In-Reply-To: <764978cf0812012154t7f247a45haf23be4dc53cd21a@mail.gmail.com> Message-ID: <8501BB9BBEBF40148C79563C246A8029@NewLife> Hi Neeti - I looked at the source, and found that that exception is thrown when there are not exactly 18 fields ( separated by 17 "|" symbols ) on a genemap file line. The Bioperl tests ran fine for OMIMparser on the test data file. I had a hunch, so I removed the final linebreak from the test file; that is, from this... . . . 1.132|12|2|97|1p35.1|P28|P|Inner dynein arm, clamydomonas, ...[\n] 1.133|6|10|98|1p35|BAI2|P|Brain-specific angiongenesis inhibi...[\n] 1.134|8|21|91|1p35|EBVS1|P|Epstein-Barr virus integration sit...[\n] 1.135|3|21|93|1p35|G1P3, IFI616|C|Interferon, alpha-inducibl...[\n] [EOF] to this... . . . 1.132|12|2|97|1p35.1|P28|P|Inner dynein arm, clamydomonas, ...[\n] 1.133|6|10|98|1p35|BAI2|P|Brain-specific angiongenesis inhibi...[\n] 1.134|8|21|91|1p35|EBVS1|P|Epstein-Barr virus integration sit...[\n] 1.135|3|21|93|1p35|G1P3, IFI616|C|Interferon, alpha-inducibl...[EOF] and ran the test again. Immediately, I got ** ok 1 - use Bio::Phenotype::OMIM::OMIMparser; ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Gene map file "t\data\omim_genemap_test" is not in the expected format STACK: Error::throw STACK: Bio::Root::Root::throw c:/Perl/site/lib/Bio/Root/Root.pm:374 STACK: Bio::Phenotype::OMIM::OMIMparser::_read_genemap c:/Perl/site/lib/Bio/Phen otype/OMIM/OMIMparser.pm:883 STACK: Bio::Phenotype::OMIM::OMIMparser::genemap_file_name c:/Perl/site/lib/Bio/ Phenotype/OMIM/OMIMparser.pm:408 STACK: Bio::Phenotype::OMIM::OMIMparser::new c:/Perl/site/lib/Bio/Phenotype/OMIM /OMIMparser.pm:224 STACK: t/Phenotype/OMIMparser.t:16 ----------------------------------------------------------- # Looks like you planned 174 tests but only ran 1. # Looks like your test died just after 1. ** just your exception. So you might begin by making sure you're not chopping the final newline character from your input files, or visiting those files to make sure there is a linebreak after the final line. Hope this a start. cheers MAJ From David.Messina at sbc.su.se Sat Dec 6 06:04:11 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Sat, 6 Dec 2008 12:04:11 +0100 Subject: [Bioperl-l] Problem in OMIM parser In-Reply-To: <8501BB9BBEBF40148C79563C246A8029@NewLife> References: <764978cf0812012154t7f247a45haf23be4dc53cd21a@mail.gmail.com> <8501BB9BBEBF40148C79563C246A8029@NewLife> Message-ID: <628aabb70812060304w685fe27ak68017e6b69b60036@mail.gmail.com> Nice detective work, Mark! I improved the error message to suggest the linebreak as possibly the problem. I also added a test that makes sure the exception is thrown when there's a missing linebreak. Dave From maj at fortinbras.us Sat Dec 6 12:50:20 2008 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 6 Dec 2008 12:50:20 -0500 Subject: [Bioperl-l] Problem in OMIM parser In-Reply-To: <628aabb70812060304w685fe27ak68017e6b69b60036@mail.gmail.com> References: <764978cf0812012154t7f247a45haf23be4dc53cd21a@mail.gmail.com><8501BB9BBEBF40148C79563C246A8029@NewLife> <628aabb70812060304w685fe27ak68017e6b69b60036@mail.gmail.com> Message-ID: Dave- with developer response time like this, why doesn't everyone use Bioperl?- cheers-MAJ ----- Original Message ----- From: "Dave Messina" To: "Mark A. Jensen" Cc: Sent: Saturday, December 06, 2008 6:04 AM Subject: Re: [Bioperl-l] Problem in OMIM parser > Nice detective work, Mark! > I improved the error message to suggest the linebreak as possibly the > problem. > > I also added a test that makes sure the exception is thrown when there's a > missing linebreak. > > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Sat Dec 6 14:01:01 2008 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 6 Dec 2008 13:01:01 -0600 Subject: [Bioperl-l] Windows, Perl, and BioPerl Message-ID: <0B5AF275-8442-4AC2-9A72-AC659A4E97B4@illinois.edu> Just to keep those Windows users out there informed (from alias's journal at use.perl.org): http://use.perl.org/~Alias/journal/38036 The key sentence: 'Commencing this month, Microsoft will be providing every CPAN author with free access to a centrally-hosted virtual machine environment containing every major version of Windows.' Windows XP Professional Windows Server 2003 32-bit Windows Server 2003 64-bit Windows Vista Ultimate Windows Server 2008 32-bit Windows Server 2008 64-bit So, anyone wanting to take advantage of this (per BioPerl or Gbrowse)? chris From hlapp at gmx.net Sat Dec 6 14:28:04 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 6 Dec 2008 14:28:04 -0500 Subject: [Bioperl-l] Problem in OMIM parser In-Reply-To: References: <764978cf0812012154t7f247a45haf23be4dc53cd21a@mail.gmail.com><8501BB9BBEBF40148C79563C246A8029@NewLife> <628aabb70812060304w685fe27ak68017e6b69b60036@mail.gmail.com> Message-ID: On Dec 6, 2008, at 12:50 PM, Mark A. Jensen wrote: > Dave- with developer response time like this, why doesn't everyone > use Bioperl?- > cheers-MAJ You mean to imply that there are people who don't? ;) -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From kpclancy at hotmail.com Sat Dec 6 18:57:58 2008 From: kpclancy at hotmail.com (Kevin Clancy) Date: Sat, 6 Dec 2008 16:57:58 -0700 Subject: [Bioperl-l] Windows, Perl, and BioPerl In-Reply-To: <0B5AF275-8442-4AC2-9A72-AC659A4E97B4@illinois.edu> References: <0B5AF275-8442-4AC2-9A72-AC659A4E97B4@illinois.edu> Message-ID: What projects would be suitable for folk in Windows world? I've been using basic BioPerl on Windows since the late 90s. I haven't tried GBrowse on Windows - is there reason to believe it won't work? Thanks kevin > From: cjfields at illinois.edu > To: bioperl-l at lists.open-bio.org > Date: Sat, 6 Dec 2008 13:01:01 -0600 > Subject: [Bioperl-l] Windows, Perl, and BioPerl > > Just to keep those Windows users out there informed (from alias's > journal at use.perl.org): > > http://use.perl.org/~Alias/journal/38036 > > The key sentence: > > 'Commencing this month, Microsoft will be providing every CPAN author > with free access to a centrally-hosted virtual machine environment > containing every major version of Windows.' > > Windows XP Professional > Windows Server 2003 32-bit > Windows Server 2003 64-bit > Windows Vista Ultimate > Windows Server 2008 32-bit > Windows Server 2008 64-bit > > So, anyone wanting to take advantage of this (per BioPerl or Gbrowse)? > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Sat Dec 6 22:26:35 2008 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 6 Dec 2008 21:26:35 -0600 Subject: [Bioperl-l] Windows, Perl, and BioPerl In-Reply-To: References: <0B5AF275-8442-4AC2-9A72-AC659A4E97B4@illinois.edu> Message-ID: <471701B8-623A-4CEC-81EA-BAD79F9CB3A2@illinois.edu> One of the most common problems with some perl modules is cross- platform compilation of XS-based modules containing C/C++ code. So maybe testing bioperl-ext? Or the proposed biolib initiative (www.biolib.open-bio.org ), which aims to create swig-based bindings for the various Bio* languages? We have also run into problems in the past with bioperl-db and Windows. We have also had OS-dependent issues pop up now and then, so I think it's a good thing (and I'm primarily using OS X/Linux now). chris On Dec 6, 2008, at 5:57 PM, Kevin Clancy wrote: > What projects would be suitable for folk in Windows world? I've been > using basic BioPerl on Windows since the late 90s. I haven't tried > GBrowse on Windows - is there reason to believe it won't work? > Thanks > kevin > >> From: cjfields at illinois.edu >> To: bioperl-l at lists.open-bio.org >> Date: Sat, 6 Dec 2008 13:01:01 -0600 >> Subject: [Bioperl-l] Windows, Perl, and BioPerl >> >> Just to keep those Windows users out there informed (from alias's >> journal at use.perl.org): >> >> http://use.perl.org/~Alias/journal/38036 >> >> The key sentence: >> >> 'Commencing this month, Microsoft will be providing every CPAN author >> with free access to a centrally-hosted virtual machine environment >> containing every major version of Windows.' >> >> Windows XP Professional >> Windows Server 2003 32-bit >> Windows Server 2003 64-bit >> Windows Vista Ultimate >> Windows Server 2008 32-bit >> Windows Server 2008 64-bit >> >> So, anyone wanting to take advantage of this (per BioPerl or >> Gbrowse)? >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From David.Messina at sbc.su.se Sun Dec 7 04:56:48 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Sun, 7 Dec 2008 10:56:48 +0100 Subject: [Bioperl-l] Problem in OMIM parser In-Reply-To: References: <764978cf0812012154t7f247a45haf23be4dc53cd21a@mail.gmail.com> <8501BB9BBEBF40148C79563C246A8029@NewLife> <628aabb70812060304w685fe27ak68017e6b69b60036@mail.gmail.com> Message-ID: <628aabb70812070156r8820de8je0612e6ea83c7732@mail.gmail.com> On Sat, Dec 6, 2008 at 20:28, Hilmar Lapp wrote: > > On Dec 6, 2008, at 12:50 PM, Mark A. Jensen wrote: > > Dave- with developer response time like this, why doesn't everyone use >> Bioperl?- >> cheers-MAJ >> > > You mean to imply that there are people who don't? ;) And ye shall know them by their code. :) D From neetisomaiya at gmail.com Mon Dec 8 06:06:36 2008 From: neetisomaiya at gmail.com (neeti somaiya) Date: Mon, 8 Dec 2008 16:36:36 +0530 Subject: [Bioperl-l] Problem in OMIM parser In-Reply-To: <8501BB9BBEBF40148C79563C246A8029@NewLife> References: <764978cf0812012154t7f247a45haf23be4dc53cd21a@mail.gmail.com> <8501BB9BBEBF40148C79563C246A8029@NewLife> Message-ID: <764978cf0812080306g2374b8c7gff1b455f5a9dafbe@mail.gmail.com> Hey, I ran my parser again today, with no changes what so ever (I did not check for the line break or anything), and it ran fine. ~Neeti. On Sat, Dec 6, 2008 at 11:50 AM, Mark A. Jensen wrote: > Hi Neeti - > > I looked at the source, and found that that exception is thrown > when there are not exactly 18 fields ( separated by 17 "|" symbols ) > on a genemap file line. The Bioperl tests ran fine for OMIMparser > on the test data file. I had a hunch, so I removed the final linebreak > from the test file; that is, from this... > . > . > . > 1.132|12|2|97|1p35.1|P28|P|Inner dynein arm, clamydomonas, ...[\n] > 1.133|6|10|98|1p35|BAI2|P|Brain-specific angiongenesis inhibi...[\n] > 1.134|8|21|91|1p35|EBVS1|P|Epstein-Barr virus integration sit...[\n] > 1.135|3|21|93|1p35|G1P3, IFI616|C|Interferon, alpha-inducibl...[\n] > [EOF] > > to this... > . > . > . > 1.132|12|2|97|1p35.1|P28|P|Inner dynein arm, clamydomonas, ...[\n] > 1.133|6|10|98|1p35|BAI2|P|Brain-specific angiongenesis inhibi...[\n] > 1.134|8|21|91|1p35|EBVS1|P|Epstein-Barr virus integration sit...[\n] > 1.135|3|21|93|1p35|G1P3, IFI616|C|Interferon, alpha-inducibl...[EOF] > > and ran the test again. Immediately, I got > > ** > ok 1 - use Bio::Phenotype::OMIM::OMIMparser; > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Gene map file "t\data\omim_genemap_test" is not in the expected format > STACK: Error::throw > STACK: Bio::Root::Root::throw c:/Perl/site/lib/Bio/Root/Root.pm:374 > STACK: Bio::Phenotype::OMIM::OMIMparser::_read_genemap > c:/Perl/site/lib/Bio/Phen > otype/OMIM/OMIMparser.pm:883 > STACK: Bio::Phenotype::OMIM::OMIMparser::genemap_file_name > c:/Perl/site/lib/Bio/ > Phenotype/OMIM/OMIMparser.pm:408 > STACK: Bio::Phenotype::OMIM::OMIMparser::new > c:/Perl/site/lib/Bio/Phenotype/OMIM > /OMIMparser.pm:224 > STACK: t/Phenotype/OMIMparser.t:16 > ----------------------------------------------------------- > # Looks like you planned 174 tests but only ran 1. > # Looks like your test died just after 1. > ** > > just your exception. So you might begin by making sure you're not chopping > the final > newline character from your input files, or visiting those files to make > sure there is > a linebreak after the final line. > > Hope this a start. > cheers MAJ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- -Neeti Even my blood says, B positive From Samantha.Thompson at greenbiologics.com Mon Dec 8 09:34:29 2008 From: Samantha.Thompson at greenbiologics.com (Samantha Thompson) Date: Mon, 8 Dec 2008 14:34:29 -0000 Subject: [Bioperl-l] Processing seq in Bio::Seq objects References: <764978cf0812012154t7f247a45haf23be4dc53cd21a@mail.gmail.com><8501BB9BBEBF40148C79563C246A8029@NewLife><628aabb70812060304w685fe27ak68017e6b69b60036@mail.gmail.com> <628aabb70812070156r8820de8je0612e6ea83c7732@mail.gmail.com> Message-ID: Hi, I'm trying to find out if Bio::Seq or related has any built in routines for telling me things like how many of each of Gs Ts Cs and As (plus others) there are in a submitted DNA sequence. I'm writing a few little programs that do simple things like primer temperature calculation so something like GC content is good to know. Just thought I'd ask before writing the routines in Perl from scratch. Also, I'm implementing a lot of the web interface stuff to my bioperl (and other) routines using the Catalyst MVC framework modules in Perl. Just wondering what web frameworks any of you recommend if you're producing stuff that's available to others online. I'm currently making a bit of a mini local/proprietry strain and sequence database which I'm finding incorporating snippets of BioPerl more and more useful as I go along. Thanks, Sam -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Dave Messina Sent: 07 December 2008 09:57 To: Hilmar Lapp Cc: bioperl-l at lists.open-bio.org; Mark A. Jensen Subject: Re: [Bioperl-l] Problem in OMIM parser On Sat, Dec 6, 2008 at 20:28, Hilmar Lapp wrote: > > On Dec 6, 2008, at 12:50 PM, Mark A. Jensen wrote: > > Dave- with developer response time like this, why doesn't everyone use >> Bioperl?- >> cheers-MAJ >> > > You mean to imply that there are people who don't? ;) And ye shall know them by their code. :) D _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From cain.cshl at gmail.com Mon Dec 8 09:55:01 2008 From: cain.cshl at gmail.com (Scott Cain) Date: Mon, 8 Dec 2008 09:55:01 -0500 Subject: [Bioperl-l] Windows, Perl, and BioPerl In-Reply-To: <471701B8-623A-4CEC-81EA-BAD79F9CB3A2@illinois.edu> References: <0B5AF275-8442-4AC2-9A72-AC659A4E97B4@illinois.edu> <471701B8-623A-4CEC-81EA-BAD79F9CB3A2@illinois.edu> Message-ID: <536f21b00812080655i1cc83434vef2919b5dfac23f4@mail.gmail.com> That and the fact that it appears to be Strawberry Perl that will be on the machines. Strawberry Perl is a completely free implementation of perl for Windows (as opposed to ActiveState perl, which is only free as in beer I believe). However, every time I've tried to run GBrowse with Strawberry Perl I've run into road blocks, so maybe it has matured enough to try again. At least it will be easy to do with these free VMs. Scott On Sat, Dec 6, 2008 at 10:26 PM, Chris Fields wrote: > One of the most common problems with some perl modules is cross-platform > compilation of XS-based modules containing C/C++ code. So maybe testing > bioperl-ext? Or the proposed biolib initiative (www.biolib.open-bio.org), > which aims to create swig-based bindings for the various Bio* languages? > > We have also run into problems in the past with bioperl-db and Windows. We > have also had OS-dependent issues pop up now and then, so I think it's a > good thing (and I'm primarily using OS X/Linux now). > > chris > > On Dec 6, 2008, at 5:57 PM, Kevin Clancy wrote: > >> What projects would be suitable for folk in Windows world? I've been using >> basic BioPerl on Windows since the late 90s. I haven't tried GBrowse on >> Windows - is there reason to believe it won't work? >> Thanks >> kevin >> >>> From: cjfields at illinois.edu >>> To: bioperl-l at lists.open-bio.org >>> Date: Sat, 6 Dec 2008 13:01:01 -0600 >>> Subject: [Bioperl-l] Windows, Perl, and BioPerl >>> >>> Just to keep those Windows users out there informed (from alias's >>> journal at use.perl.org): >>> >>> http://use.perl.org/~Alias/journal/38036 >>> >>> The key sentence: >>> >>> 'Commencing this month, Microsoft will be providing every CPAN author >>> with free access to a centrally-hosted virtual machine environment >>> containing every major version of Windows.' >>> >>> Windows XP Professional >>> Windows Server 2003 32-bit >>> Windows Server 2003 64-bit >>> Windows Vista Ultimate >>> Windows Server 2008 32-bit >>> Windows Server 2008 64-bit >>> >>> So, anyone wanting to take advantage of this (per BioPerl or Gbrowse)? >>> >>> chris >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From cjfields at illinois.edu Mon Dec 8 10:02:27 2008 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 8 Dec 2008 09:02:27 -0600 Subject: [Bioperl-l] Windows, Perl, and BioPerl In-Reply-To: <536f21b00812080655i1cc83434vef2919b5dfac23f4@mail.gmail.com> References: <0B5AF275-8442-4AC2-9A72-AC659A4E97B4@illinois.edu> <471701B8-623A-4CEC-81EA-BAD79F9CB3A2@illinois.edu> <536f21b00812080655i1cc83434vef2919b5dfac23f4@mail.gmail.com> Message-ID: <139602D9-32AE-41A3-BB49-09CAB35B4DC4@illinois.edu> I believe Strawberry Perl aims to have a native Perl which allows direct links to CPAN (i.e. no intermediate PPM; it would be like running perl on other OS's). ActivePerl already has a semblance of that (I tried it out with the last ActivePerl), but I don't think it's fully supported yet and I believe it installs to a separate directory. Might be nice to work out what the roadblocks are; would they be in bioperl? chris On Dec 8, 2008, at 8:55 AM, Scott Cain wrote: > That and the fact that it appears to be Strawberry Perl that will be > on the machines. Strawberry Perl is a completely free implementation > of perl for Windows (as opposed to ActiveState perl, which is only > free as in beer I believe). However, every time I've tried to run > GBrowse with Strawberry Perl I've run into road blocks, so maybe it > has matured enough to try again. At least it will be easy to do with > these free VMs. > > Scott > > > On Sat, Dec 6, 2008 at 10:26 PM, Chris Fields > wrote: >> One of the most common problems with some perl modules is cross- >> platform >> compilation of XS-based modules containing C/C++ code. So maybe >> testing >> bioperl-ext? Or the proposed biolib initiative (www.biolib.open-bio.org >> ), >> which aims to create swig-based bindings for the various Bio* >> languages? >> >> We have also run into problems in the past with bioperl-db and >> Windows. We >> have also had OS-dependent issues pop up now and then, so I think >> it's a >> good thing (and I'm primarily using OS X/Linux now). >> >> chris >> >> On Dec 6, 2008, at 5:57 PM, Kevin Clancy wrote: >> >>> What projects would be suitable for folk in Windows world? I've >>> been using >>> basic BioPerl on Windows since the late 90s. I haven't tried >>> GBrowse on >>> Windows - is there reason to believe it won't work? >>> Thanks >>> kevin >>> >>>> From: cjfields at illinois.edu >>>> To: bioperl-l at lists.open-bio.org >>>> Date: Sat, 6 Dec 2008 13:01:01 -0600 >>>> Subject: [Bioperl-l] Windows, Perl, and BioPerl >>>> >>>> Just to keep those Windows users out there informed (from alias's >>>> journal at use.perl.org): >>>> >>>> http://use.perl.org/~Alias/journal/38036 >>>> >>>> The key sentence: >>>> >>>> 'Commencing this month, Microsoft will be providing every CPAN >>>> author >>>> with free access to a centrally-hosted virtual machine environment >>>> containing every major version of Windows.' >>>> >>>> Windows XP Professional >>>> Windows Server 2003 32-bit >>>> Windows Server 2003 64-bit >>>> Windows Vista Ultimate >>>> Windows Server 2008 32-bit >>>> Windows Server 2008 64-bit >>>> >>>> So, anyone wanting to take advantage of this (per BioPerl or >>>> Gbrowse)? >>>> >>>> chris >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cain.cshl at gmail.com Mon Dec 8 10:10:25 2008 From: cain.cshl at gmail.com (Scott Cain) Date: Mon, 8 Dec 2008 10:10:25 -0500 Subject: [Bioperl-l] Windows, Perl, and BioPerl In-Reply-To: <139602D9-32AE-41A3-BB49-09CAB35B4DC4@illinois.edu> References: <0B5AF275-8442-4AC2-9A72-AC659A4E97B4@illinois.edu> <471701B8-623A-4CEC-81EA-BAD79F9CB3A2@illinois.edu> <536f21b00812080655i1cc83434vef2919b5dfac23f4@mail.gmail.com> <139602D9-32AE-41A3-BB49-09CAB35B4DC4@illinois.edu> Message-ID: <536f21b00812080710g27822c34q8290c1654edada34@mail.gmail.com> I don't recall what roadblocks there were--just that it was frustrating. I guess we'll all find out when the machines are available (the announcement was just that there would be machines available "soon"). Scott On Mon, Dec 8, 2008 at 10:02 AM, Chris Fields wrote: > I believe Strawberry Perl aims to have a native Perl which allows direct > links to CPAN (i.e. no intermediate PPM; it would be like running perl on > other OS's). ActivePerl already has a semblance of that (I tried it out > with the last ActivePerl), but I don't think it's fully supported yet and I > believe it installs to a separate directory. > > Might be nice to work out what the roadblocks are; would they be in bioperl? > > chris > > On Dec 8, 2008, at 8:55 AM, Scott Cain wrote: > >> That and the fact that it appears to be Strawberry Perl that will be >> on the machines. Strawberry Perl is a completely free implementation >> of perl for Windows (as opposed to ActiveState perl, which is only >> free as in beer I believe). However, every time I've tried to run >> GBrowse with Strawberry Perl I've run into road blocks, so maybe it >> has matured enough to try again. At least it will be easy to do with >> these free VMs. >> >> Scott >> >> >> On Sat, Dec 6, 2008 at 10:26 PM, Chris Fields >> wrote: >>> >>> One of the most common problems with some perl modules is cross-platform >>> compilation of XS-based modules containing C/C++ code. So maybe testing >>> bioperl-ext? Or the proposed biolib initiative >>> (www.biolib.open-bio.org), >>> which aims to create swig-based bindings for the various Bio* languages? >>> >>> We have also run into problems in the past with bioperl-db and Windows. >>> We >>> have also had OS-dependent issues pop up now and then, so I think it's a >>> good thing (and I'm primarily using OS X/Linux now). >>> >>> chris >>> >>> On Dec 6, 2008, at 5:57 PM, Kevin Clancy wrote: >>> >>>> What projects would be suitable for folk in Windows world? I've been >>>> using >>>> basic BioPerl on Windows since the late 90s. I haven't tried GBrowse on >>>> Windows - is there reason to believe it won't work? >>>> Thanks >>>> kevin >>>> >>>>> From: cjfields at illinois.edu >>>>> To: bioperl-l at lists.open-bio.org >>>>> Date: Sat, 6 Dec 2008 13:01:01 -0600 >>>>> Subject: [Bioperl-l] Windows, Perl, and BioPerl >>>>> >>>>> Just to keep those Windows users out there informed (from alias's >>>>> journal at use.perl.org): >>>>> >>>>> http://use.perl.org/~Alias/journal/38036 >>>>> >>>>> The key sentence: >>>>> >>>>> 'Commencing this month, Microsoft will be providing every CPAN author >>>>> with free access to a centrally-hosted virtual machine environment >>>>> containing every major version of Windows.' >>>>> >>>>> Windows XP Professional >>>>> Windows Server 2003 32-bit >>>>> Windows Server 2003 64-bit >>>>> Windows Vista Ultimate >>>>> Windows Server 2008 32-bit >>>>> Windows Server 2008 64-bit >>>>> >>>>> So, anyone wanting to take advantage of this (per BioPerl or Gbrowse)? >>>>> >>>>> chris >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From Samantha.Thompson at greenbiologics.com Mon Dec 8 10:35:42 2008 From: Samantha.Thompson at greenbiologics.com (Samantha Thompson) Date: Mon, 8 Dec 2008 15:35:42 -0000 Subject: [Bioperl-l] Processing seq in Bio::Seq objects References: <764978cf0812012154t7f247a45haf23be4dc53cd21a@mail.gmail.com><8501BB9BBEBF40148C79563C246A8029@NewLife><628aabb70812060304w685fe27ak68017e6b69b60036@mail.gmail.com> <628aabb70812070156r8820de8je0612e6ea83c7732@mail.gmail.com> <493D3598.2030201@cam.ac.uk> Message-ID: Hi, Thanks for this. However, I think it's common for molecular biologists I work with in the lab to use primer calculation formulae that are different/simpler than those often recommended by things like Primer3 and sigma's ordering website. Typically, we use a formula from Maniartis et al (I think a different author in later editions), Molecular Cloning. So I thought I'd work up a calculator based on this. I'll also take a look at the SeqStats module thanks for your help :) Sam -----Original Message----- From: Roy Chaudhuri [mailto:rrc22 at cam.ac.uk] Sent: 08 December 2008 14:56 To: Samantha Thompson Cc: bioperl-l List Subject: Re: [Bioperl-l] Processing seq in Bio::Seq objects Hi Sam. For nucleotide counts look at Bio::Tools::SeqStats. However, there is already code for calculating primer melting temperatures in BioPerl, in Bio::SeqFeature::Primer. Roy. -- Dr. Roy Chaudhuri Department of Veterinary Medicine University of Cambridge, U.K. Samantha Thompson wrote: > Hi, > > I'm trying to find out if Bio::Seq or related has any built in routines > for telling me things like how many of each of Gs Ts Cs and As (plus > others) there are in a submitted DNA sequence. I'm writing a few little > programs that do simple things like primer temperature calculation so > something like GC content is good to know. Just thought I'd ask before > writing the routines in Perl from scratch. > Also, I'm implementing a lot of the web interface stuff to my bioperl > (and other) routines using the Catalyst MVC framework modules in Perl. > Just wondering what web frameworks any of you recommend if you're > producing stuff that's available to others online. I'm currently making > a bit of a mini local/proprietry strain and sequence database which I'm > finding incorporating snippets of BioPerl more and more useful as I go > along. > > Thanks, > > Sam > > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Dave Messina > Sent: 07 December 2008 09:57 > To: Hilmar Lapp > Cc: bioperl-l at lists.open-bio.org; Mark A. Jensen > Subject: Re: [Bioperl-l] Problem in OMIM parser > > On Sat, Dec 6, 2008 at 20:28, Hilmar Lapp wrote: > >> On Dec 6, 2008, at 12:50 PM, Mark A. Jensen wrote: >> >> Dave- with developer response time like this, why doesn't everyone > use >>> Bioperl?- >>> cheers-MAJ >>> >> You mean to imply that there are people who don't? ;) > > > > And ye shall know them by their code. :) > > D > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From roy.chaudhuri at gmail.com Mon Dec 8 10:18:58 2008 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Mon, 08 Dec 2008 15:18:58 +0000 Subject: [Bioperl-l] Processing seq in Bio::Seq objects In-Reply-To: References: <764978cf0812012154t7f247a45haf23be4dc53cd21a@mail.gmail.com><8501BB9BBEBF40148C79563C246A8029@NewLife><628aabb70812060304w685fe27ak68017e6b69b60036@mail.gmail.com> <628aabb70812070156r8820de8je0612e6ea83c7732@mail.gmail.com> Message-ID: <493D3AE2.2080808@gmail.com> Hi Sam. For nucleotide counts look at Bio::Tools::SeqStats. However, there is already code for calculating primer melting temperatures in BioPerl, in Bio::SeqFeature::Primer. Roy. -- Dr. Roy Chaudhuri Department of Veterinary Medicine University of Cambridge, U.K. Samantha Thompson wrote: > Hi, > > I'm trying to find out if Bio::Seq or related has any built in routines > for telling me things like how many of each of Gs Ts Cs and As (plus > others) there are in a submitted DNA sequence. I'm writing a few little > programs that do simple things like primer temperature calculation so > something like GC content is good to know. Just thought I'd ask before > writing the routines in Perl from scratch. > Also, I'm implementing a lot of the web interface stuff to my bioperl > (and other) routines using the Catalyst MVC framework modules in Perl. > Just wondering what web frameworks any of you recommend if you're > producing stuff that's available to others online. I'm currently making > a bit of a mini local/proprietry strain and sequence database which I'm > finding incorporating snippets of BioPerl more and more useful as I go > along. > > Thanks, > > Sam > > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Dave Messina > Sent: 07 December 2008 09:57 > To: Hilmar Lapp > Cc: bioperl-l at lists.open-bio.org; Mark A. Jensen > Subject: Re: [Bioperl-l] Problem in OMIM parser > > On Sat, Dec 6, 2008 at 20:28, Hilmar Lapp wrote: > >> On Dec 6, 2008, at 12:50 PM, Mark A. Jensen wrote: >> >> Dave- with developer response time like this, why doesn't everyone > use >>> Bioperl?- >>> cheers-MAJ >>> >> You mean to imply that there are people who don't? ;) > > > > And ye shall know them by their code. :) > > D > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From roy.chaudhuri at gmail.com Mon Dec 8 10:47:18 2008 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Mon, 08 Dec 2008 15:47:18 +0000 Subject: [Bioperl-l] Processing seq in Bio::Seq objects In-Reply-To: References: <764978cf0812012154t7f247a45haf23be4dc53cd21a@mail.gmail.com><8501BB9BBEBF40148C79563C246A8029@NewLife><628aabb70812060304w685fe27ak68017e6b69b60036@mail.gmail.com> <628aabb70812070156r8820de8je0612e6ea83c7732@mail.gmail.com> <493D3598.2030201@cam.ac.uk> Message-ID: <493D4186.3030502@gmail.com> I think the method you are referring to is available in the Tm_estimate method of Bio::SeqFeature::Primer3. That is the old method that was used for Tm calculation in BioPerl before the more accurate thermodynamic calculation was implemented: http://bioperl.org/pipermail/bioperl-l/2004-February/014905.html Roy. Samantha Thompson wrote: > Hi, > Thanks for this. > However, I think it's common for molecular biologists I work with in the > lab to use primer calculation formulae that are different/simpler than > those often recommended by things like Primer3 and sigma's ordering > website. Typically, we use a formula from Maniartis et al (I think a > different author in later editions), Molecular Cloning. So I thought I'd > work up a calculator based on this. > I'll also take a look at the SeqStats module thanks for your help :) > > Sam > > -----Original Message----- > From: Roy Chaudhuri [mailto:rrc22 at cam.ac.uk] > Sent: 08 December 2008 14:56 > To: Samantha Thompson > Cc: bioperl-l List > Subject: Re: [Bioperl-l] Processing seq in Bio::Seq objects > > Hi Sam. > > For nucleotide counts look at Bio::Tools::SeqStats. However, there is > already code for calculating primer melting temperatures in BioPerl, in > Bio::SeqFeature::Primer. > > Roy. > > -- > Dr. Roy Chaudhuri > Department of Veterinary Medicine > University of Cambridge, U.K. > > > Samantha Thompson wrote: >> Hi, >> >> I'm trying to find out if Bio::Seq or related has any built in > routines >> for telling me things like how many of each of Gs Ts Cs and As (plus >> others) there are in a submitted DNA sequence. I'm writing a few > little >> programs that do simple things like primer temperature calculation so >> something like GC content is good to know. Just thought I'd ask before >> writing the routines in Perl from scratch. >> Also, I'm implementing a lot of the web interface stuff to my bioperl >> (and other) routines using the Catalyst MVC framework modules in Perl. >> Just wondering what web frameworks any of you recommend if you're >> producing stuff that's available to others online. I'm currently > making >> a bit of a mini local/proprietry strain and sequence database which > I'm >> finding incorporating snippets of BioPerl more and more useful as I go >> along. >> >> Thanks, >> >> Sam >> >> -----Original Message----- >> From: bioperl-l-bounces at lists.open-bio.org >> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Dave > Messina >> Sent: 07 December 2008 09:57 >> To: Hilmar Lapp >> Cc: bioperl-l at lists.open-bio.org; Mark A. Jensen >> Subject: Re: [Bioperl-l] Problem in OMIM parser >> >> On Sat, Dec 6, 2008 at 20:28, Hilmar Lapp wrote: >> >>> On Dec 6, 2008, at 12:50 PM, Mark A. Jensen wrote: >>> >>> Dave- with developer response time like this, why doesn't everyone >> use >>>> Bioperl?- >>>> cheers-MAJ >>>> >>> You mean to imply that there are people who don't? ;) >> >> >> And ye shall know them by their code. :) >> >> D >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From Samantha.Thompson at greenbiologics.com Mon Dec 8 10:59:55 2008 From: Samantha.Thompson at greenbiologics.com (Samantha Thompson) Date: Mon, 8 Dec 2008 15:59:55 -0000 Subject: [Bioperl-l] Degenerate primer calculation Message-ID: Hi, I also have another similar sequence analysis/primer problem. What I'd like to do is produce degenerate primers from amino acid sequences. What I did initially was take the codon usage table and rewrite it in a hash in perl in the form of degenerate codon usage e.g Lysine/K would be AAR, its reverse complement would be YTT. So my form then takes an amino acid sequence (derived as a consensus from multiple the alignment of homologous proteins) and converts them into degenerate codons and then that degenerate primer (actually several primers synthesised with different bases pooled together), in order to search for homologues to the protein in unsequenced organisms. I would like to improve this by being able to take a consensus described more in the form of a Prosite motif (I think thats the right one) such as [TS]YW[RKSD] and then develop a degenerate nucleotide sequence corresponding to this. So I'm wondering if bioperl contains anything like this (both prosite motif format parsing and degenerate code from multiple alignments or such a motif), or if I need to write this myself (which I want to if it doesn't exist already). Thanks again, Sam From bix at sendu.me.uk Mon Dec 8 10:57:37 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 08 Dec 2008 15:57:37 +0000 Subject: [Bioperl-l] Moving ModuleBuildBioperl and BioperlTest to Bio::Root Message-ID: <493D43F1.8010903@sendu.me.uk> It's been suggested by others and has annoyed me since the 1.5.2 release, so I've now made the appropriate changes to ModuleBuildBioperl and BioperlTest to make them part of the core package to be installed as the new modules Bio::Root::Build and Bio::Root::Test. t/lib/Test/Warn/Bioperl.pm also becomes Bio::Root::TestWarn. This then allows all other bioperl packages like bioperl-run etc. to just use those modules (since they already depend on Bio::Root::Root in core package, these modules must have been installed), rather than the current situation of having the build and test modules duplicated in each package, which isn't so nice maintenance-wise. The main change needed is changing all the test scripts (again) to use the new module name, but that's trivial and can be automated. (I'll do it, it would only take a few seconds) Before I go ahead and commit, please feedback with any concerns or suggestions. I don't anticipate this being contentious, so I'll probably commit later today or tomorrow. From cjfields at illinois.edu Mon Dec 8 11:41:04 2008 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 8 Dec 2008 10:41:04 -0600 Subject: [Bioperl-l] Degenerate primer calculation In-Reply-To: References: Message-ID: <0F8B16D2-8DFC-4EC5-B99B-74A91C92B1B8@illinois.edu> On Dec 8, 2008, at 9:59 AM, Samantha Thompson wrote: > Hi, > > I also have another similar sequence analysis/primer problem. > > What I'd like to do is produce degenerate primers from amino acid > sequences. > > What I did initially was take the codon usage table and rewrite it > in a > hash in perl in the form of degenerate codon usage e.g Lysine/K > would be > AAR, its reverse complement would be YTT. So my form then takes an > amino > acid sequence (derived as a consensus from multiple the alignment of > homologous proteins) and converts them into degenerate codons and then > that degenerate primer (actually several primers synthesised with > different bases pooled together), in order to search for homologues to > the protein in unsequenced organisms. > > I would like to improve this by being able to take a consensus > described > more in the form of a Prosite motif (I think thats the right one) such > as [TS]YW[RKSD] and then develop a degenerate nucleotide sequence > corresponding to this. > > So I'm wondering if bioperl contains anything like this (both prosite > motif format parsing and degenerate code from multiple alignments or > such a motif), or if I need to write this myself (which I want to if > it > doesn't exist already). > > Thanks again, > > Sam Bio::Tools::CodonTable reverse translates, but I don't think it accepts patterns. Maybe a pipeline including Bio::Tools::SeqPattern? Might be an interesting programming challenge if it isn't already set up for that. chris From cjfields at illinois.edu Mon Dec 8 11:46:04 2008 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 8 Dec 2008 10:46:04 -0600 Subject: [Bioperl-l] Moving ModuleBuildBioperl and BioperlTest to Bio::Root In-Reply-To: <493D43F1.8010903@sendu.me.uk> References: <493D43F1.8010903@sendu.me.uk> Message-ID: <7228F4CD-81F9-41AB-BE09-90DAB021590C@illinois.edu> On Dec 8, 2008, at 9:57 AM, Sendu Bala wrote: > It's been suggested by others and has annoyed me since the 1.5.2 > release, so I've now made the appropriate changes to > ModuleBuildBioperl and BioperlTest to make them part of the core > package to be installed as the new modules Bio::Root::Build and > Bio::Root::Test. t/lib/Test/Warn/Bioperl.pm also becomes > Bio::Root::TestWarn. Yay! One small bit: Should we make that Bio::Root::Test::Warn (in case we wanted to extend with other Test-related modules)? > This then allows all other bioperl packages like bioperl-run etc. to > just use those modules (since they already depend on Bio::Root::Root > in core package, these modules must have been installed), rather > than the current situation of having the build and test modules > duplicated in each package, which isn't so nice maintenance-wise. > > The main change needed is changing all the test scripts (again) to > use the new module name, but that's trivial and can be automated. > (I'll do it, it would only take a few seconds) > > > Before I go ahead and commit, please feedback with any concerns or > suggestions. I don't anticipate this being contentious, so I'll > probably commit later today or tomorrow. Works for me. I tried this out but ran into small problems with lack of Test::Warn with one module using warning_like and didn't have time to debug it; it was a simple 'use lib' issue though. chris From bix at sendu.me.uk Mon Dec 8 13:31:45 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 08 Dec 2008 18:31:45 +0000 Subject: [Bioperl-l] Moving ModuleBuildBioperl and BioperlTest to Bio::Root In-Reply-To: <7228F4CD-81F9-41AB-BE09-90DAB021590C@illinois.edu> References: <493D43F1.8010903@sendu.me.uk> <7228F4CD-81F9-41AB-BE09-90DAB021590C@illinois.edu> Message-ID: <493D6811.5050302@sendu.me.uk> Chris Fields wrote: > > On Dec 8, 2008, at 9:57 AM, Sendu Bala wrote: > >> It's been suggested by others and has annoyed me since the 1.5.2 >> release, so I've now made the appropriate changes to >> ModuleBuildBioperl and BioperlTest to make them part of the core >> package to be installed as the new modules Bio::Root::Build and >> Bio::Root::Test. t/lib/Test/Warn/Bioperl.pm also becomes >> Bio::Root::TestWarn. > > Yay! One small bit: Should we make that Bio::Root::Test::Warn (in case > we wanted to extend with other Test-related modules)? Now done, and I followed this suggestion. > Works for me. I tried this out but ran into small problems with lack of > Test::Warn with one module using warning_like and didn't have time to > debug it; it was a simple 'use lib' issue though. I didn't see any issues; let me know. BTW, thanks to all those involved in sorting the test scripts into subdirs. I ran the whole test suite for the first time in ages and it's very nice to have everything neatly organised. From cjfields at illinois.edu Mon Dec 8 13:50:34 2008 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 8 Dec 2008 12:50:34 -0600 Subject: [Bioperl-l] Moving ModuleBuildBioperl and BioperlTest to Bio::Root In-Reply-To: <493D6811.5050302@sendu.me.uk> References: <493D43F1.8010903@sendu.me.uk> <7228F4CD-81F9-41AB-BE09-90DAB021590C@illinois.edu> <493D6811.5050302@sendu.me.uk> Message-ID: On Dec 8, 2008, at 12:31 PM, Sendu Bala wrote: > Chris Fields wrote: >> On Dec 8, 2008, at 9:57 AM, Sendu Bala wrote: >>> It's been suggested by others and has annoyed me since the 1.5.2 >>> release, so I've now made the appropriate changes to >>> ModuleBuildBioperl and BioperlTest to make them part of the core >>> package to be installed as the new modules Bio::Root::Build and >>> Bio::Root::Test. t/lib/Test/Warn/Bioperl.pm also becomes >>> Bio::Root::TestWarn. >> Yay! One small bit: Should we make that Bio::Root::Test::Warn (in >> case we wanted to extend with other Test-related modules)? > > Now done, and I followed this suggestion. > > >> Works for me. I tried this out but ran into small problems with >> lack of Test::Warn with one module using warning_like and didn't >> have time to debug it; it was a simple 'use lib' issue though. > > I didn't see any issues; let me know. > > > BTW, thanks to all those involved in sorting the test scripts into > subdirs. I ran the whole test suite for the first time in ages and > it's very nice to have everything neatly organised. np. A few still remain to be split up (Annotation, FeatureIO, and others) but it's a fantastic start. Major kudos to Heikki and Dave for this! chris From cjfields at illinois.edu Mon Dec 8 14:12:24 2008 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 8 Dec 2008 13:12:24 -0600 Subject: [Bioperl-l] Moving ModuleBuildBioperl and BioperlTest to Bio::Root In-Reply-To: <96651D1D-63C9-48B2-89C6-E8409B4D5D63@verizon.net> References: <493D43F1.8010903@sendu.me.uk> <7228F4CD-81F9-41AB-BE09-90DAB021590C@illinois.edu> <493D6811.5050302@sendu.me.uk> <96651D1D-63C9-48B2-89C6-E8409B4D5D63@verizon.net> Message-ID: <79780F73-23C8-4033-8EC9-47C510E30D52@illinois.edu> Sorry! Should have added you in there as well; my bad! chris On Dec 8, 2008, at 1:10 PM, Brian Osborne wrote: > Hey! What about the guy who split the these monstrous *.t files into > smaller scripts in the first place? > > One guess as to who that was, years ago. > > ;-) > > > > > On Dec 8, 2008, at 1:50 PM, Chris Fields wrote: > >>> BTW, thanks to all those involved in sorting the test scripts into >>> subdirs. I ran the whole test suite for the first time in ages and >>> it's very nice to have everything neatly organised. >> >> np. A few still remain to be split up (Annotation, FeatureIO, and >> others) but it's a fantastic start. Major kudos to Heikki and Dave >> for this! > From cjfields at illinois.edu Mon Dec 8 14:35:45 2008 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 8 Dec 2008 13:35:45 -0600 Subject: [Bioperl-l] Release AUTHORS file Message-ID: All, Anyone who has donated code to the project should ensure they are in the AUTHORS file and that any information already present is correct (ie. email, modules, etc.). For those w/o dev access let me know by direct email and I will add your names in. chris From bosborne11 at verizon.net Mon Dec 8 14:10:26 2008 From: bosborne11 at verizon.net (Brian Osborne) Date: Mon, 8 Dec 2008 14:10:26 -0500 Subject: [Bioperl-l] Moving ModuleBuildBioperl and BioperlTest to Bio::Root In-Reply-To: References: <493D43F1.8010903@sendu.me.uk> <7228F4CD-81F9-41AB-BE09-90DAB021590C@illinois.edu> <493D6811.5050302@sendu.me.uk> Message-ID: <96651D1D-63C9-48B2-89C6-E8409B4D5D63@verizon.net> Hey! What about the guy who split the these monstrous *.t files into smaller scripts in the first place? One guess as to who that was, years ago. ;-) On Dec 8, 2008, at 1:50 PM, Chris Fields wrote: >> BTW, thanks to all those involved in sorting the test scripts into >> subdirs. I ran the whole test suite for the first time in ages and >> it's very nice to have everything neatly organised. > > np. A few still remain to be split up (Annotation, FeatureIO, and > others) but it's a fantastic start. Major kudos to Heikki and Dave > for this! From huihui at webmail.hzau.edu.cn Mon Dec 8 22:12:57 2008 From: huihui at webmail.hzau.edu.cn (Gao Chunhui) Date: Tue, 9 Dec 2008 11:12:57 +0800 Subject: [Bioperl-l] How to retrieve fulltext in pdf using BioPerl Message-ID: <5b2271350812081912m458b24c5g5cf920f47965e1c8@mail.gmail.com> Hi, all Does anyone have a script could fetch PDF for a PubMed ID using bioperl module? I want to do this job but the instruction of "Bio::DB::Biblio::pdf" is hard to follow. I searched the wiki site for a reference with no useful information either. If somebody knows the right way, please tell me. Thank you in advance. Best wishes. yours, spring Gao From cjfields at illinois.edu Tue Dec 9 00:00:24 2008 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 8 Dec 2008 23:00:24 -0600 Subject: [Bioperl-l] DEPRECATED list Message-ID: <40D71863-8964-4CFA-BF2F-39B6DED11BC9@illinois.edu> The following modules are slated to be removed for the 1.6 release: Version Version Deprecated Modules Deprecated Removed Comment -------------------------------------------------------------------------------- Bio::Tools::RestrictionEnzyme 1.5 1.6 use Bio::Restriction Bio::Tools::BPlite 1.5 1.6 use Bio::SearchIO Bio::Tools::BPpsilite 1.5 1.6 use Bio::SearchIO Bio::Tools::BPbl2seq 1.5 1.6 use Bio::SearchIO Bio::Ontology::SimpleGOEngine 1.5.1 1.6 use Bio::Ontology::OBOEngine Bio::Factory::ResultFactoryI 1.5.2 1.6 Superseded by Bio::Factory::ObjectFactory Bio::Factory::HitFactoryI 1.5.2 1.6 Superseded by Bio::Factory::ObjectFactory Bio::Graph 1.5.2 1.6 Superseded by bioperl- network Bio::Tools::WebBlat 1.5.2 1.6 Requested that this not be maintained Bio::DB::XEMBL 1.5.2 1.6 Service no longer available; use DBFetch Bio::DB::XEMBLService 1.5.2 1.6 Service no longer available; use DBFetch The following are to be added to the deprecation list: Bio::Tools::RNAMotif 1.5.2 1.7 Superseded by Bio::SearchIO::rnamotif Bio::Tools::Infernal 1.5.2 1.7 Superseded by Bio::SearchIO::infernal Bio::Tools::ERPIN 1.5.2 1.7 Superseded by Bio::SearchIO::erpin Were there any others we should recommend? I noticed Bio::Species isn't on the list for 1.7. I also suggest Bio::Search::BlastUtils (it is the same as Bio::Search::SearchUtils, but older). chris From hartzell at alerce.com Mon Dec 8 23:54:52 2008 From: hartzell at alerce.com (George Hartzell) Date: Mon, 8 Dec 2008 20:54:52 -0800 Subject: [Bioperl-l] How to retrieve fulltext in pdf using BioPerl In-Reply-To: <5b2271350812081912m458b24c5g5cf920f47965e1c8@mail.gmail.com> References: <5b2271350812081912m458b24c5g5cf920f47965e1c8@mail.gmail.com> Message-ID: <18749.64028.455450.237990@almost.alerce.com> Gao Chunhui writes: > Hi, all > Does anyone have a script could fetch PDF for a PubMed ID using > bioperl module? > I want to do this job but the instruction of > "Bio::DB::Biblio::pdf" is hard to follow. I searched the wiki site > for a reference with no useful information either. > If somebody knows the right way, please tell me. > > Thank you in advance. > Best wishes. > yours, spring Gao Hmmm, I thought that this mightwork (based on the cpan docs), but #!/usr/bin/perl use strict; use warnings; use Bio::Biblio; my $biblio = Bio::Biblio->new( -access => 'pdf'); $biblio = $biblio->find( 14726805 ); my $pdf = $biblio->pdf(); open PDF, ">foo.pdf" or die "Unable to open foo.pdf\n"; print PDF $pdf; close PDF or die "Unable to close foo.pdf\n"; exit(0); it turns out that when I try to run it I don't have a pdf.pm. A bit of digging makes it look like it's been removed somewhere between CPAN version and the tip of the tree. I'll leave it up to others who are more current to let you know if there's a newer way to do things. g. From bosborne11 at verizon.net Mon Dec 8 23:47:21 2008 From: bosborne11 at verizon.net (Brian Osborne) Date: Mon, 08 Dec 2008 23:47:21 -0500 Subject: [Bioperl-l] Degenerate primer calculation In-Reply-To: References: Message-ID: Sam, There's reverse_translate_all() in Bio::Tools::CodonTable, and there's also expand() in Bio::Tools::SeqPattern, this should be able to take any degenerate nucleotide symbol and give the you [GATC], I think. You could use both of these. It seems that what's missing is a method that parses the Prosite-style motif, and you would have to supply that and any code that could transform the various data structures that are created. Interesting problem. If you do create code to do this please provide it to Bioperl as a script or as methods, this would be _very_ useful. Brian O. On Dec 8, 2008, at 10:59 AM, Samantha Thompson wrote: > Hi, > > > > I also have another similar sequence analysis/primer problem. > > What I'd like to do is produce degenerate primers from amino acid > sequences. > > What I did initially was take the codon usage table and rewrite it > in a > hash in perl in the form of degenerate codon usage e.g Lysine/K > would be > AAR, its reverse complement would be YTT. So my form then takes an > amino > acid sequence (derived as a consensus from multiple the alignment of > homologous proteins) and converts them into degenerate codons and then > that degenerate primer (actually several primers synthesised with > different bases pooled together), in order to search for homologues to > the protein in unsequenced organisms. > > I would like to improve this by being able to take a consensus > described > more in the form of a Prosite motif (I think thats the right one) such > as [TS]YW[RKSD] and then develop a degenerate nucleotide sequence > corresponding to this. > > So I'm wondering if bioperl contains anything like this (both prosite > motif format parsing and degenerate code from multiple alignments or > such a motif), or if I need to write this myself (which I want to if > it > doesn't exist already). > > > > Thanks again, > > > > Sam > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Tue Dec 9 00:54:28 2008 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 8 Dec 2008 23:54:28 -0600 Subject: [Bioperl-l] Degenerate primer calculation In-Reply-To: References: Message-ID: <5CB199C2-9A62-41CA-BA94-1D51C181C632@illinois.edu> An aside, but Higher Order Perl describes some nice memory-efficient ways to achieve this (using an iterator or a stream IIRC). Might be worth investigating. chris On Dec 8, 2008, at 10:47 PM, Brian Osborne wrote: > Sam, > > There's reverse_translate_all() in Bio::Tools::CodonTable, and > there's also expand() in Bio::Tools::SeqPattern, this should be able > to take any degenerate nucleotide symbol and give the you [GATC], I > think. You could use both of these. It seems that what's missing is > a method that parses the Prosite-style motif, and you would have to > supply that and any code that could transform the various data > structures that are created. Interesting problem. > > If you do create code to do this please provide it to Bioperl as a > script or as methods, this would be _very_ useful. > > Brian O. > > > On Dec 8, 2008, at 10:59 AM, Samantha Thompson wrote: > >> Hi, >> >> >> >> I also have another similar sequence analysis/primer problem. >> >> What I'd like to do is produce degenerate primers from amino acid >> sequences. >> >> What I did initially was take the codon usage table and rewrite it >> in a >> hash in perl in the form of degenerate codon usage e.g Lysine/K >> would be >> AAR, its reverse complement would be YTT. So my form then takes an >> amino >> acid sequence (derived as a consensus from multiple the alignment of >> homologous proteins) and converts them into degenerate codons and >> then >> that degenerate primer (actually several primers synthesised with >> different bases pooled together), in order to search for homologues >> to >> the protein in unsequenced organisms. >> >> I would like to improve this by being able to take a consensus >> described >> more in the form of a Prosite motif (I think thats the right one) >> such >> as [TS]YW[RKSD] and then develop a degenerate nucleotide sequence >> corresponding to this. >> >> So I'm wondering if bioperl contains anything like this (both prosite >> motif format parsing and degenerate code from multiple alignments or >> such a motif), or if I need to write this myself (which I want to >> if it >> doesn't exist already). >> >> >> >> Thanks again, >> >> >> >> Sam >> >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From limericksean at gmail.com Tue Dec 9 12:24:38 2008 From: limericksean at gmail.com (Sean O'Keeffe) Date: Tue, 9 Dec 2008 18:24:38 +0100 Subject: [Bioperl-l] bioperl-live install issue on unix Message-ID: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> Hi all, I've just downloaded bioperl-live with svn. All fine. Tried doing a local install in a personal module area like so: 'cd /home/okeeffe/bioperl-live; perl Build.PL --install_base /home/okeeffe/bioperl; ./Build install' and got the following error at the install stage: ... Manifying /home/okeeffe/bioperl/lib/perl5/Bio/WebAgent.pm Unlinking /usr/local/lib/perl5/site_perl/5.8.7/Bio/WebAgent.pm (shadowing?) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! WARNING: WARNING: Failed chmod(438, /usr/local/lib/perl5/site_perl/5.8.7/Bio/WebAgent.pm): Operation not permitted !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ERROR: Cannot unlink '/usr/local/lib/perl5/site_perl/5.8.7/Bio/WebAgent.pm': Permission denied !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! What is shadowing? Why is it trying to unlink a system-wide perl module? Perl is v5.8.7 Thanks, Sean. From cjfields at illinois.edu Tue Dec 9 12:40:57 2008 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 9 Dec 2008 11:40:57 -0600 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> References: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> Message-ID: <96731226-A2E2-4BFB-A214-79E82C1FA5A1@illinois.edu> Very odd, haven't tried --install_base so it may be related to that. I would file this as a bug until we can work it out. chris On Dec 9, 2008, at 11:24 AM, Sean O'Keeffe wrote: > Hi all, > > I've just downloaded bioperl-live with svn. All fine. > Tried doing a local install in a personal module area like so: > > 'cd /home/okeeffe/bioperl-live; perl Build.PL --install_base > /home/okeeffe/bioperl; ./Build install' > > and got the following error at the install stage: > ... > Manifying /home/okeeffe/bioperl/lib/perl5/Bio/WebAgent.pm > Unlinking /usr/local/lib/perl5/site_perl/5.8.7/Bio/WebAgent.pm > (shadowing?) > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > WARNING: WARNING: Failed chmod(438, > /usr/local/lib/perl5/site_perl/5.8.7/Bio/WebAgent.pm): Operation not > permitted > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Cannot unlink > '/usr/local/lib/perl5/site_perl/5.8.7/Bio/WebAgent.pm': Permission > denied > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > > > What is shadowing? Why is it trying to unlink a system-wide perl > module? > Perl is v5.8.7 > Thanks, > Sean. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From Kevin.M.Brown at asu.edu Tue Dec 9 12:31:18 2008 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Tue, 9 Dec 2008 10:31:18 -0700 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> References: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> Message-ID: <1A4207F8295607498283FE9E93B775B40593146B@EX02.asurite.ad.asu.edu> It's trying to unlink the installed Bio::Perl module (notice the path to the module ends with Bio/module_name.pm) and failing as you don't have permission to delete files from /usr/local/lib/perl5/site_perl/5.8.7/ as that is a system directory and generally reserved for root to write to. > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Sean O'Keeffe > Sent: Tuesday, December 09, 2008 10:25 AM > To: bioperl-l at portal.open-bio.org > Subject: [Bioperl-l] bioperl-live install issue on unix > > Hi all, > > I've just downloaded bioperl-live with svn. All fine. > Tried doing a local install in a personal module area like so: > > 'cd /home/okeeffe/bioperl-live; perl Build.PL --install_base > /home/okeeffe/bioperl; ./Build install' > > and got the following error at the install stage: > ... > Manifying /home/okeeffe/bioperl/lib/perl5/Bio/WebAgent.pm > Unlinking > /usr/local/lib/perl5/site_perl/5.8.7/Bio/WebAgent.pm (shadowing?) > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > !!!!!!!!!! > WARNING: WARNING: Failed chmod(438, > /usr/local/lib/perl5/site_perl/5.8.7/Bio/WebAgent.pm): Operation not > permitted > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > !!!!!!!!!! > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > !!!!!!!!!! > ERROR: Cannot unlink > '/usr/local/lib/perl5/site_perl/5.8.7/Bio/WebAgent.pm': Permission > denied > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > !!!!!!!!!! > > > What is shadowing? Why is it trying to unlink a system-wide > perl module? > Perl is v5.8.7 > Thanks, > Sean. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From bix at sendu.me.uk Tue Dec 9 13:12:31 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 09 Dec 2008 18:12:31 +0000 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> References: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> Message-ID: <493EB50F.7090608@sendu.me.uk> Sean O'Keeffe wrote: > Hi all, > > I've just downloaded bioperl-live with svn. All fine. > Tried doing a local install in a personal module area like so: > > 'cd /home/okeeffe/bioperl-live; perl Build.PL --install_base > /home/okeeffe/bioperl; ./Build install' > > and got the following error at the install stage: > ... > Manifying /home/okeeffe/bioperl/lib/perl5/Bio/WebAgent.pm > Unlinking /usr/local/lib/perl5/site_perl/5.8.7/Bio/WebAgent.pm (shadowing?) > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > WARNING: WARNING: Failed chmod(438, > /usr/local/lib/perl5/site_perl/5.8.7/Bio/WebAgent.pm): Operation not > permitted > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Cannot unlink > '/usr/local/lib/perl5/site_perl/5.8.7/Bio/WebAgent.pm': Permission > denied > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > > > What is shadowing? Why is it trying to unlink a system-wide perl module? > Perl is v5.8.7 You have your CPAN configured to uninstall old modules before installing new ones. Try: > cpan cpan> o conf mbuild_install_arg "" cpan> o conf commit From limericksean at gmail.com Tue Dec 9 14:08:25 2008 From: limericksean at gmail.com (Sean O'Keeffe) Date: Tue, 9 Dec 2008 20:08:25 +0100 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: <493EB50F.7090608@sendu.me.uk> References: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> <493EB50F.7090608@sendu.me.uk> Message-ID: <462784640812091108j3745d8a6hac6579560a515430@mail.gmail.com> Hi Sendu, Tried your suggestion to no avail. Same error. Sean. 2008/12/9 Sendu Bala : > Sean O'Keeffe wrote: >> >> Hi all, >> >> I've just downloaded bioperl-live with svn. All fine. >> Tried doing a local install in a personal module area like so: >> >> 'cd /home/okeeffe/bioperl-live; perl Build.PL --install_base >> /home/okeeffe/bioperl; ./Build install' >> >> and got the following error at the install stage: >> ... >> Manifying /home/okeeffe/bioperl/lib/perl5/Bio/WebAgent.pm >> Unlinking /usr/local/lib/perl5/site_perl/5.8.7/Bio/WebAgent.pm >> (shadowing?) >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> WARNING: WARNING: Failed chmod(438, >> /usr/local/lib/perl5/site_perl/5.8.7/Bio/WebAgent.pm): Operation not >> permitted >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> ERROR: Cannot unlink >> '/usr/local/lib/perl5/site_perl/5.8.7/Bio/WebAgent.pm': Permission >> denied >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> >> >> What is shadowing? Why is it trying to unlink a system-wide perl module? >> Perl is v5.8.7 > > You have your CPAN configured to uninstall old modules before installing new > ones. Try: > >> cpan > cpan> o conf mbuild_install_arg "" > cpan> o conf commit > > From bix at sendu.me.uk Tue Dec 9 14:20:36 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 09 Dec 2008 19:20:36 +0000 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: <462784640812091108j3745d8a6hac6579560a515430@mail.gmail.com> References: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> <493EB50F.7090608@sendu.me.uk> <462784640812091108j3745d8a6hac6579560a515430@mail.gmail.com> Message-ID: <493EC504.10604@sendu.me.uk> Sean O'Keeffe wrote: > Hi Sendu, > Tried your suggestion to no avail. Same error. Check all your CPAN settings (o conf) and make sure you don't have any uninstall settings anywhere else. None of the mbuild* options should have 'uninst' in them for starters, and clean up the make* options as well just in case. > 2008/12/9 Sendu Bala : >> You have your CPAN configured to uninstall old modules before installing new >> ones. Try: >> >>> cpan >> cpan> o conf mbuild_install_arg "" >> cpan> o conf commit From jason at bioperl.org Tue Dec 9 14:23:27 2008 From: jason at bioperl.org (Jason Stajich) Date: Tue, 9 Dec 2008 11:23:27 -0800 Subject: [Bioperl-l] Fwd: purge method of Bio::Align::AlignI References: <411981270812091046r1908f353nb198b8468d5dd154@mail.gmail.com> Message-ID: Laura - please ask these questions on the mailing list in the future so that others can benefit from the Q&A (and others can 'Answer'). It is indeed implemented in Bio::SimpleAlign - which is what you get back when you read in an alignment with Bio::AlignIO. Bio::Align::AlignI is just an interface and not intended to be used directly. -jason Begin forwarded message: > From: "Laura Wegener Parfrey" > Date: December 9, 2008 10:46:19 AM PST > To: jason at bioperl.org > Subject: purge method of Bio::Align::AlignI > Reply-To: lwegener at nsm.umass.edu > > I want to remove sequences that are similar to each other from an > alignment. I would like to use Bio::Align::AlignI 'purge' , but it > is not > implemented. > > Is 'purge' implemented anywhere to do this? Or are there alternative > methods? > Thank you, > Laura > > -- > Laura Wegener Parfrey > Program in Organismic and Evolutionary Biology > University of Massachusetts > 611 N. Pleasant Street > Amherst, MA 01003 Jason Stajich jason at bioperl.org From limericksean at gmail.com Tue Dec 9 14:27:49 2008 From: limericksean at gmail.com (Sean O'Keeffe) Date: Tue, 9 Dec 2008 20:27:49 +0100 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: <493EC504.10604@sendu.me.uk> References: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> <493EB50F.7090608@sendu.me.uk> <462784640812091108j3745d8a6hac6579560a515430@mail.gmail.com> <493EC504.10604@sendu.me.uk> Message-ID: <462784640812091127w25aa272em7bee17c99b3d4fea@mail.gmail.com> seems fine to me? cpan[1]> o conf $CPAN::Config options from '/home/okeeffe/.cpan/CPAN/MyConfig.pm': commit [Commit changes to disk] defaults [Reload defaults from disk] help [Short help about 'o conf' usage] init [Interactive setting of all options] applypatch undef auto_commit [0] build_cache [10] build_dir [/home/okeeffe/.cpan/build] build_dir_reuse undef build_requires_install_policy undef bzip2 undef cache_metadata [1] check_sigs undef colorize_debug undef colorize_output undef colorize_print undef colorize_warn undef commandnumber_in_prompt [1] commands_quote undef cpan_home [/home/okeeffe/.cpan] curl undef dontload_hash dontload_list undef ftp [/usr/bin/ftp] ftp_passive [1] ftp_proxy [] getcwd [cwd] gpg [] gzip [/bin/gzip] histfile [/home/okeeffe/.cpan/histfile] histsize [100] http_proxy [] inactivity_timeout [0] index_expire [1] inhibit_startup_message [0] keep_source_where [/home/okeeffe/.cpan/sources] load_module_verbosity undef lynx [/usr/bin/lynx] make [/usr/bin/make] make_arg [] make_install_arg [] make_install_make_command [/usr/bin/make] makepl_arg [LIB=/home/okeeffe/bioperl] mbuild_arg [] mbuild_install_arg [] mbuild_install_build_command [./Build] mbuildpl_arg [] ncftp [] ncftpget [] no_proxy [] pager [/bin/less -isRR] password undef patch undef prefer_installer undef prefs_dir undef prerequisites_policy [ask] proxy_pass undef proxy_user undef randomize_urllist undef scan_cache [atstart] shell [/bin/bash] show_unparsable_versions undef show_upload_date undef show_zero_versions undef tar [/bin/tar] tar_verbosity undef term_is_latin [1] term_ornaments [1] test_report undef unzip [/usr/bin/unzip] urllist 0 [ftp://ftp.cs.tu-berlin.de/pub/lang/perl/CPAN/] 1 [ftp://ftp.fu-berlin.de/unix/languages/perl/] 2 [ftp://ftp.gwdg.de/pub/languages/perl/CPAN/] use_sqlite [0] username undef wait_list undef wget [/usr/bin/wget] yaml_load_code undef yaml_module undef 2008/12/9 Sendu Bala : > Sean O'Keeffe wrote: >> >> Hi Sendu, >> Tried your suggestion to no avail. Same error. > > Check all your CPAN settings (o conf) and make sure you don't have any > uninstall settings anywhere else. None of the mbuild* options should have > 'uninst' in them for starters, and clean up the make* options as well just > in case. > > >> 2008/12/9 Sendu Bala : >>> >>> You have your CPAN configured to uninstall old modules before installing >>> new >>> ones. Try: >>> >>>> cpan >>> >>> cpan> o conf mbuild_install_arg "" >>> cpan> o conf commit > > From Samantha.Thompson at greenbiologics.com Tue Dec 9 14:34:56 2008 From: Samantha.Thompson at greenbiologics.com (Samantha Thompson) Date: Tue, 9 Dec 2008 19:34:56 -0000 Subject: [Bioperl-l] blast module errors with web app Message-ID: Hi, I seem to be able to get stand alone blast to run ok, using a script like the one in the Beginner's HowTo ... But when running it embedded in my web app I get the following errors/exceptions: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: blastall call crashed: -1 /usr/bin/blastall -d "/src/GBLCCDB16s" -i /tmp/FxXS98W1H0 -o /tmp/6gp_EnCnsu -p blastn STACK: Error::throw STACK: Bio::Root::Root::throw /usr/lib/perl5/vendor_perl/5.10.0/Bio/Root/Root.pm:359 STACK: Bio::Tools::Run::StandAloneBlast::_runblast /usr/lib/perl5/vendor_perl/5.10.0/Bio/Tools/Run/StandAloneBlast.pm:813 STACK: Bio::Tools::Run::StandAloneBlast::_generic_local_blast /usr/lib/perl5/vendor_perl/5.10.0/Bio/Tools/Run/StandAloneBlast.pm:760 STACK: Bio::Tools::Run::StandAloneBlast::blastall /usr/lib/perl5/vendor_perl/5.10.0/Bio/Tools/Run/StandAloneBlast.pm:570 This comes from the stack trace of my Catalyst web app.... I wonder if these particular exceptions mean anything to anyone. Does BLAST not like the database have folder names in it? Maybe theres a problem with the tmp folder not existing as part of my web app. Maybe I need to explicitly define the -i and -o parameters... Thanks, Sam From maj at fortinbras.us Tue Dec 9 14:37:35 2008 From: maj at fortinbras.us (Mark A. Jensen) Date: Tue, 9 Dec 2008 14:37:35 -0500 Subject: [Bioperl-l] Fwd: purge method of Bio::Align::AlignI In-Reply-To: Message-ID: So Laura, you would do $alnio = new Bio::AlignIO(-file='myalign.fas', -format='fasta') # or whatever format you please $aln = $alnio->next_aln; # this gives you your myalign.fas in $aln, a Bio::SimpleAlign object # then do $purged_ones = $aln->purge(0.75); cheers MAJ From bix at sendu.me.uk Tue Dec 9 14:46:56 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 09 Dec 2008 19:46:56 +0000 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: <462784640812091127w25aa272em7bee17c99b3d4fea@mail.gmail.com> References: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> <493EB50F.7090608@sendu.me.uk> <462784640812091108j3745d8a6hac6579560a515430@mail.gmail.com> <493EC504.10604@sendu.me.uk> <462784640812091127w25aa272em7bee17c99b3d4fea@mail.gmail.com> Message-ID: <493ECB30.9080506@sendu.me.uk> Sean O'Keeffe wrote: > seems fine to me? Yeah, seems fine. And, I wasn't paying attention to what you're doing, so I don't think CPAN settings matter in this situation anyway. Unless you're supplying uninst=1 to Build in some other way, what you see shouldn't be happening. Check if you have a $ENV{HOME}/.modulebuildrc file (actually, do a locate for all instances of .modulebuildrc), and delete (or edit out uninst from) it. And/or do ./Build install --uninst=0 Failing that, try installing the latest Module::Build and have another go. From MEC at stowers-institute.org Tue Dec 9 15:07:22 2008 From: MEC at stowers-institute.org (Cook, Malcolm) Date: Tue, 9 Dec 2008 14:07:22 -0600 Subject: [Bioperl-l] blast module errors with web app In-Reply-To: References: Message-ID: perhaps your environment underl Catalyst server is incomplete.... do this interactively: > env | grep -i blast do you see any blast related environment variables? are they set in the Catalyst server process? Just thinkin... Malcolm Cook > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Samantha Thompson > Sent: Tuesday, December 09, 2008 1:35 PM > To: bioperl-l List > Subject: [Bioperl-l] blast module errors with web app > > Hi, > > > > I seem to be able to get stand alone blast to run ok, using a > script like the one in the Beginner's HowTo ... > > But when running it embedded in my web app I get the following > errors/exceptions: > > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: blastall call crashed: -1 /usr/bin/blastall -d "/src/GBLCCDB16s" > -i /tmp/FxXS98W1H0 -o /tmp/6gp_EnCnsu -p blastn > > > > STACK: Error::throw > > STACK: Bio::Root::Root::throw > /usr/lib/perl5/vendor_perl/5.10.0/Bio/Root/Root.pm:359 > > STACK: Bio::Tools::Run::StandAloneBlast::_runblast > /usr/lib/perl5/vendor_perl/5.10.0/Bio/Tools/Run/StandAloneBlast.pm:813 > > STACK: Bio::Tools::Run::StandAloneBlast::_generic_local_blast > /usr/lib/perl5/vendor_perl/5.10.0/Bio/Tools/Run/StandAloneBlast.pm:760 > > STACK: Bio::Tools::Run::StandAloneBlast::blastall > /usr/lib/perl5/vendor_perl/5.10.0/Bio/Tools/Run/StandAloneBlast.pm:570 > > > > This comes from the stack trace of my Catalyst web app.... > > I wonder if these particular exceptions mean anything to > anyone. Does BLAST not like the database have folder names in > it? Maybe theres a problem with the tmp folder not existing > as part of my web app. Maybe I need to explicitly define the > -i and -o parameters... > > > > Thanks, > > > > Sam > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From Samantha.Thompson at greenbiologics.com Tue Dec 9 15:24:31 2008 From: Samantha.Thompson at greenbiologics.com (Samantha Thompson) Date: Tue, 9 Dec 2008 20:24:31 -0000 Subject: [Bioperl-l] blast module errors with web app References: Message-ID: Hi, I tried this env grep, theres nothing in my env variables with regards to blast... With the blast executables I gunzip'd them from ncbi and cp'd the executables from the blast/bin directory of the distribution to my own /usr/bin ... When I run blastall from the command line anywhere it works fine... when I run it in a normal perl script it works (in that the test script tells me the number of hits on the command line) .... but when I run it from within the Catalyst app it throws those exceptions... it may be because it's trying to create that tmp directory when it runs and isn't able to... I'm not sure how I would set those in Catalyst, but thats kind of veering away from BioPerl into Catalyst.. I will try a few more things.... Thanks, Sam -----Original Message----- From: Cook, Malcolm [mailto:MEC at stowers-institute.org] Sent: 09 December 2008 20:07 To: Samantha Thompson; 'bioperl-l List' Subject: RE: blast module errors with web app perhaps your environment underl Catalyst server is incomplete.... do this interactively: > env | grep -i blast do you see any blast related environment variables? are they set in the Catalyst server process? Just thinkin... Malcolm Cook > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Samantha Thompson > Sent: Tuesday, December 09, 2008 1:35 PM > To: bioperl-l List > Subject: [Bioperl-l] blast module errors with web app > > Hi, > > > > I seem to be able to get stand alone blast to run ok, using a > script like the one in the Beginner's HowTo ... > > But when running it embedded in my web app I get the following > errors/exceptions: > > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: blastall call crashed: -1 /usr/bin/blastall -d "/src/GBLCCDB16s" > -i /tmp/FxXS98W1H0 -o /tmp/6gp_EnCnsu -p blastn > > > > STACK: Error::throw > > STACK: Bio::Root::Root::throw > /usr/lib/perl5/vendor_perl/5.10.0/Bio/Root/Root.pm:359 > > STACK: Bio::Tools::Run::StandAloneBlast::_runblast > /usr/lib/perl5/vendor_perl/5.10.0/Bio/Tools/Run/StandAloneBlast.pm:813 > > STACK: Bio::Tools::Run::StandAloneBlast::_generic_local_blast > /usr/lib/perl5/vendor_perl/5.10.0/Bio/Tools/Run/StandAloneBlast.pm:760 > > STACK: Bio::Tools::Run::StandAloneBlast::blastall > /usr/lib/perl5/vendor_perl/5.10.0/Bio/Tools/Run/StandAloneBlast.pm:570 > > > > This comes from the stack trace of my Catalyst web app.... > > I wonder if these particular exceptions mean anything to > anyone. Does BLAST not like the database have folder names in > it? Maybe theres a problem with the tmp folder not existing > as part of my web app. Maybe I need to explicitly define the > -i and -o parameters... > > > > Thanks, > > > > Sam > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From Samantha.Thompson at greenbiologics.com Tue Dec 9 15:42:18 2008 From: Samantha.Thompson at greenbiologics.com (Samantha Thompson) Date: Tue, 9 Dec 2008 20:42:18 -0000 Subject: [Bioperl-l] FW: blast module errors with web app Message-ID: OK Something interesting did happen.. I think this is probably a Catalyst issue rather than a BioPerl one. It still throws the exceptions... but it actually produces a blast report (so runs the program and the results are produced)... I will have a go at trying to figure out what the Catalyst stack trace errors mean. Sam -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Samantha Thompson Sent: 09 December 2008 20:25 To: bioperl-l List Subject: Re: [Bioperl-l] blast module errors with web app Hi, I tried this env grep, theres nothing in my env variables with regards to blast... With the blast executables I gunzip'd them from ncbi and cp'd the executables from the blast/bin directory of the distribution to my own /usr/bin ... When I run blastall from the command line anywhere it works fine... when I run it in a normal perl script it works (in that the test script tells me the number of hits on the command line) .... but when I run it from within the Catalyst app it throws those exceptions... it may be because it's trying to create that tmp directory when it runs and isn't able to... I'm not sure how I would set those in Catalyst, but thats kind of veering away from BioPerl into Catalyst.. I will try a few more things.... Thanks, Sam -----Original Message----- From: Cook, Malcolm [mailto:MEC at stowers-institute.org] Sent: 09 December 2008 20:07 To: Samantha Thompson; 'bioperl-l List' Subject: RE: blast module errors with web app perhaps your environment underl Catalyst server is incomplete.... do this interactively: > env | grep -i blast do you see any blast related environment variables? are they set in the Catalyst server process? Just thinkin... Malcolm Cook > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Samantha Thompson > Sent: Tuesday, December 09, 2008 1:35 PM > To: bioperl-l List > Subject: [Bioperl-l] blast module errors with web app > > Hi, > > > > I seem to be able to get stand alone blast to run ok, using a > script like the one in the Beginner's HowTo ... > > But when running it embedded in my web app I get the following > errors/exceptions: > > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: blastall call crashed: -1 /usr/bin/blastall -d "/src/GBLCCDB16s" > -i /tmp/FxXS98W1H0 -o /tmp/6gp_EnCnsu -p blastn > > > > STACK: Error::throw > > STACK: Bio::Root::Root::throw > /usr/lib/perl5/vendor_perl/5.10.0/Bio/Root/Root.pm:359 > > STACK: Bio::Tools::Run::StandAloneBlast::_runblast > /usr/lib/perl5/vendor_perl/5.10.0/Bio/Tools/Run/StandAloneBlast.pm:813 > > STACK: Bio::Tools::Run::StandAloneBlast::_generic_local_blast > /usr/lib/perl5/vendor_perl/5.10.0/Bio/Tools/Run/StandAloneBlast.pm:760 > > STACK: Bio::Tools::Run::StandAloneBlast::blastall > /usr/lib/perl5/vendor_perl/5.10.0/Bio/Tools/Run/StandAloneBlast.pm:570 > > > > This comes from the stack trace of my Catalyst web app.... > > I wonder if these particular exceptions mean anything to > anyone. Does BLAST not like the database have folder names in > it? Maybe theres a problem with the tmp folder not existing > as part of my web app. Maybe I need to explicitly define the > -i and -o parameters... > > > > Thanks, > > > > Sam > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Tue Dec 9 17:27:46 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 09 Dec 2008 22:27:46 +0000 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: <462784640812091212p33a0014bgeddac47dae880092@mail.gmail.com> References: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> <493EB50F.7090608@sendu.me.uk> <462784640812091108j3745d8a6hac6579560a515430@mail.gmail.com> <493EC504.10604@sendu.me.uk> <462784640812091127w25aa272em7bee17c99b3d4fea@mail.gmail.com> <493ECB30.9080506@sendu.me.uk> <462784640812091202n27c5cd5djcfb9abbacb9aef44@mail.gmail.com> <462784640812091212p33a0014bgeddac47dae880092@mail.gmail.com> Message-ID: <493EF0E2.3050607@sendu.me.uk> Sean O'Keeffe wrote: > I give up. Module::Build can't be installed with CPAN without su access. You should be able to. If you have problems doing even that, you might want to ask on the CPAN/ M::B mailing list. In the mean time, just add the checkout directory to your PERL5LIB for an easy way to 'install'. From cjfields at illinois.edu Tue Dec 9 20:12:09 2008 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 9 Dec 2008 19:12:09 -0600 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: <493EF0E2.3050607@sendu.me.uk> References: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> <493EB50F.7090608@sendu.me.uk> <462784640812091108j3745d8a6hac6579560a515430@mail.gmail.com> <493EC504.10604@sendu.me.uk> <462784640812091127w25aa272em7bee17c99b3d4fea@mail.gmail.com> <493ECB30.9080506@sendu.me.uk> <462784640812091202n27c5cd5djcfb9abbacb9aef44@mail.gmail.com> <462784640812091212p33a0014bgeddac47dae880092@mail.gmail.com> <493EF0E2.3050607@sendu.me.uk> Message-ID: On Dec 9, 2008, at 4:27 PM, Sendu Bala wrote: > Sean O'Keeffe wrote: >> I give up. Module::Build can't be installed with CPAN without su >> access. > > You should be able to. If you have problems doing even that, you > might want to ask on the CPAN/ M::B mailing list. > > In the mean time, just add the checkout directory to your PERL5LIB > for an easy way to 'install'. Sean, you should file this as a bug just in case (with us). It may very well be a Module::Build issue in the end, but it definitely shouldn't fall through the cracks if it's possibly ours. chris From cjfields at illinois.edu Wed Dec 10 00:44:54 2008 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 9 Dec 2008 23:44:54 -0600 Subject: [Bioperl-l] DEPRECATED list In-Reply-To: <40D71863-8964-4CFA-BF2F-39B6DED11BC9@illinois.edu> References: <40D71863-8964-4CFA-BF2F-39B6DED11BC9@illinois.edu> Message-ID: One last day to respond; I'll start removing the modules scheduled below tomorrow (already have removed their dependencies from Build.PL). chris On Dec 8, 2008, at 11:00 PM, Chris Fields wrote: > The following modules are slated to be removed for the 1.6 release: > > Version Version > Deprecated Modules Deprecated Removed Comment > -------------------------------------------------------------------------------- > Bio::Tools::RestrictionEnzyme 1.5 1.6 use Bio::Restriction > Bio::Tools::BPlite 1.5 1.6 use Bio::SearchIO > Bio::Tools::BPpsilite 1.5 1.6 use Bio::SearchIO > Bio::Tools::BPbl2seq 1.5 1.6 use Bio::SearchIO > Bio::Ontology::SimpleGOEngine 1.5.1 1.6 use > Bio::Ontology::OBOEngine > Bio::Factory::ResultFactoryI 1.5.2 1.6 Superseded by > Bio::Factory::ObjectFactory > Bio::Factory::HitFactoryI 1.5.2 1.6 Superseded by > Bio::Factory::ObjectFactory > Bio::Graph 1.5.2 1.6 Superseded by bioperl- > network > Bio::Tools::WebBlat 1.5.2 1.6 Requested that this > not be maintained > Bio::DB::XEMBL 1.5.2 1.6 Service no longer > available; use DBFetch > Bio::DB::XEMBLService 1.5.2 1.6 Service no longer > available; use DBFetch > > The following are to be added to the deprecation list: > > Bio::Tools::RNAMotif 1.5.2 1.7 Superseded by > Bio::SearchIO::rnamotif > Bio::Tools::Infernal 1.5.2 1.7 Superseded by > Bio::SearchIO::infernal > Bio::Tools::ERPIN 1.5.2 1.7 Superseded by > Bio::SearchIO::erpin > > Were there any others we should recommend? I noticed Bio::Species > isn't on the list for 1.7. I also suggest Bio::Search::BlastUtils > (it is the same as Bio::Search::SearchUtils, but older). > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From gundalav at gmail.com Wed Dec 10 01:40:00 2008 From: gundalav at gmail.com (Gundala Viswanath) Date: Wed, 10 Dec 2008 15:40:00 +0900 Subject: [Bioperl-l] Conversion of Wormbase Gene ID into Ensembl Gene ID with BioPerl Message-ID: <73f827b50812092240o4472a203ucf1c54a8e5fd7a07@mail.gmail.com> Dear all, I want to convert Wormbase Gene Id such as these: WBGene00004094 WBGene00018862 WBGene00011061 into Ensemblized ID. I can't seem to find such a method in Ensembl API. At the end of the day, I just want to extract the position of these genes from Ensembl database via the API. - Gundala Viswanath Jakarta - Indonesia From limericksean at gmail.com Wed Dec 10 05:27:54 2008 From: limericksean at gmail.com (Sean O'Keeffe) Date: Wed, 10 Dec 2008 11:27:54 +0100 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: References: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> <493EB50F.7090608@sendu.me.uk> <462784640812091108j3745d8a6hac6579560a515430@mail.gmail.com> <493EC504.10604@sendu.me.uk> <462784640812091127w25aa272em7bee17c99b3d4fea@mail.gmail.com> <493ECB30.9080506@sendu.me.uk> <462784640812091202n27c5cd5djcfb9abbacb9aef44@mail.gmail.com> <462784640812091212p33a0014bgeddac47dae880092@mail.gmail.com> <493EF0E2.3050607@sendu.me.uk> Message-ID: <462784640812100227m2c84a83dm527f61ea90625e29@mail.gmail.com> ok i've committed this to bugzilla. in the meantime, i'd like to keep plugging away at this end & so would like to resolve the module::build issue. whats the solution to installing this in non-system wide area for starters? sean. 2008/12/10 Chris Fields : > On Dec 9, 2008, at 4:27 PM, Sendu Bala wrote: > >> Sean O'Keeffe wrote: >>> >>> I give up. Module::Build can't be installed with CPAN without su access. >> >> You should be able to. If you have problems doing even that, you might >> want to ask on the CPAN/ M::B mailing list. >> >> In the mean time, just add the checkout directory to your PERL5LIB for an >> easy way to 'install'. > > Sean, you should file this as a bug just in case (with us). It may very > well be a Module::Build issue in the end, but it definitely shouldn't fall > through the cracks if it's possibly ours. > > chris > > From limericksean at gmail.com Wed Dec 10 05:37:56 2008 From: limericksean at gmail.com (Sean O'Keeffe) Date: Wed, 10 Dec 2008 11:37:56 +0100 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: References: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> <493EB50F.7090608@sendu.me.uk> <462784640812091108j3745d8a6hac6579560a515430@mail.gmail.com> <493EC504.10604@sendu.me.uk> <462784640812091127w25aa272em7bee17c99b3d4fea@mail.gmail.com> <493ECB30.9080506@sendu.me.uk> <462784640812091202n27c5cd5djcfb9abbacb9aef44@mail.gmail.com> <462784640812091212p33a0014bgeddac47dae880092@mail.gmail.com> <493EF0E2.3050607@sendu.me.uk> Message-ID: <462784640812100237p5a921b86u4c15ab05bf228fbf@mail.gmail.com> Ok so just now i decided to wipe .cpan from my home directory and do a fresh install and reload > cpan cpan> install CPAN even this returns the following: are my settings totally off the wall here? Running make install Prepending /home/okeeffe/.cpan/build/CPAN-1.9301-wnpJfD/blib/arch /home/okeeffe/.cpan/build/CPAN-1.9301-wnpJfD/blib/lib to PERL5LIB for 'install' !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ERROR: Can't create '/usr/local/bin' Do not have write permissions on '/usr/local/bin' !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! at -e line 1 make: *** [pure_perl_install] Error 9 ANDK/CPAN-1.9301.tar.gz /usr/bin/make install -- NOT OK ---- are my settings totally off the wall here? sean. 2008/12/10 Chris Fields : > On Dec 9, 2008, at 4:27 PM, Sendu Bala wrote: > >> Sean O'Keeffe wrote: >>> >>> I give up. Module::Build can't be installed with CPAN without su access. >> >> You should be able to. If you have problems doing even that, you might >> want to ask on the CPAN/ M::B mailing list. >> >> In the mean time, just add the checkout directory to your PERL5LIB for an >> easy way to 'install'. > > Sean, you should file this as a bug just in case (with us). It may very > well be a Module::Build issue in the end, but it definitely shouldn't fall > through the cracks if it's possibly ours. > > chris > > From dhoworth at mrc-lmb.cam.ac.uk Wed Dec 10 06:06:45 2008 From: dhoworth at mrc-lmb.cam.ac.uk (Dave Howorth) Date: Wed, 10 Dec 2008 11:06:45 +0000 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: <462784640812100237p5a921b86u4c15ab05bf228fbf@mail.gmail.com> References: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> <493EB50F.7090608@sendu.me.uk> <462784640812091108j3745d8a6hac6579560a515430@mail.gmail.com> <493EC504.10604@sendu.me.uk> <462784640812091127w25aa272em7bee17c99b3d4fea@mail.gmail.com> <493ECB30.9080506@sendu.me.uk> <462784640812091202n27c5cd5djcfb9abbacb9aef44@mail.gmail.com> <462784640812091212p33a0014bgeddac47dae880092@mail.gmail.com> <493EF0E2.3050607@sendu.me.uk> <462784640812100237p5a921b86u4c15ab05bf228fbf@mail.gmail.com> Message-ID: <493FA2C5.3080506@mrc-lmb.cam.ac.uk> Sean O'Keeffe wrote: > Ok so just now i decided to wipe .cpan from my home directory and do a > fresh install and reload > >> cpan > cpan> install CPAN > > even this returns the following: > are my settings totally off the wall here? > > Running make install > Prepending /home/okeeffe/.cpan/build/CPAN-1.9301-wnpJfD/blib/arch > /home/okeeffe/.cpan/build/CPAN-1.9301-wnpJfD/blib/lib to PERL5LIB for > 'install' > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > ERROR: Can't create '/usr/local/bin' > Do not have write permissions on '/usr/local/bin' > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! I had something similar when setting up a personal cpan recently. In my case the problem turned out to be the config settings for 'makepl_arg' and 'mbuildpl_arg'. I hacked them blindly and I don't know whether what I have now is 'correct' but it appears to work: 'makepl_arg' => q[LIB=~/perl/lib INSTALLMAN1DIR=~/perl/man/man1 INSTALLMAN3DIR=~/perl/man/man3 INSTALLARCHLIB=~/perl/lib INSTALLSCRIPT=~/perl/bin INSTALLBIN=~/perl/bin INSTALLSITEMAN1DIR=~/perl/man/man1 INSTALLSITEMAN3DIR=~/perl/man/man3 INSTALLSITEARCH=~/perl/lib INSTALLSITELIB=~/perl/lib INSTALLSITEBIN=~/perl/bin], 'mbuildpl_arg' => q[--lib=~/perl/lib --installman1dir=~/perl/man/man1 --installman3dir=~/perl/man/man3 --installarchlib=~/perl/lib --installscript=~/perl/bin --installbin=~/perl/bin --installsiteman1dir=~/perl/man/man1 --installsiteman3dir=~/perl/man/man3 --installsitearch=~/perl/lib --installsitelib=~/perl/lib --installsitebin=~/perl/bin], No idea whether it's related to your problem, but you might want to check that what you have makes sense to you. Cheers, Dave From whs at ebi.ac.uk Wed Dec 10 06:43:35 2008 From: whs at ebi.ac.uk (William Spooner) Date: Wed, 10 Dec 2008 11:43:35 +0000 Subject: [Bioperl-l] Conversion of Wormbase Gene ID into Ensembl Gene ID with BioPerl In-Reply-To: <73f827b50812092240o4472a203ucf1c54a8e5fd7a07@mail.gmail.com> References: <73f827b50812092240o4472a203ucf1c54a8e5fd7a07@mail.gmail.com> Message-ID: On 10 Dec 2008, at 06:40, Gundala Viswanath wrote: > Dear all, > > I want to convert Wormbase Gene Id such as these: > WBGene00004094 WBGene00018862 WBGene00011061 > > into Ensemblized ID. > > I can't seem to find such a method in Ensembl API. > > At the end of the day, I just want to extract the position > of these genes from Ensembl database via the API. > > - Gundala Viswanath > Jakarta - Indonesia > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Hi Gundala, The Ensembl C. elegans database is a mirror of wormbase's, so a good place to look is WormMart. See, for example, this query; http://biomart.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=WS190&ATTRIBUTES=wormbase_gene.default.attributes.gene |wormbase_gene.default.attributes.public_name| wormbase_gene .default .attributes .sequence_name &FILTERS =wormbase_gene.default.filters.species_selection."Caenorhabditis elegans"| wormbase_gene .default.filters.gene."WBGene00004094,WBGene00018862,WBGene00011061"| wormbase_gene .default.filters.identity_status."Live"&VISIBLEPANEL=resultspanel For details on how to do this programatically, see the 'Perl' button on the mart interface. All the best, Will --- William Spooner Visiting Scientist whs at ebi.ac.uk From David.Messina at sbc.su.se Wed Dec 10 07:36:46 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 10 Dec 2008 13:36:46 +0100 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: <493FA2C5.3080506@mrc-lmb.cam.ac.uk> References: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> <493EC504.10604@sendu.me.uk> <462784640812091127w25aa272em7bee17c99b3d4fea@mail.gmail.com> <493ECB30.9080506@sendu.me.uk> <462784640812091202n27c5cd5djcfb9abbacb9aef44@mail.gmail.com> <462784640812091212p33a0014bgeddac47dae880092@mail.gmail.com> <493EF0E2.3050607@sendu.me.uk> <462784640812100237p5a921b86u4c15ab05bf228fbf@mail.gmail.com> <493FA2C5.3080506@mrc-lmb.cam.ac.uk> Message-ID: <628aabb70812100436t15dac8fag35d90b7aa39d6a94@mail.gmail.com> Following on to what Dave H. said, cpan itself needs to know that you want to install in a personal module area; it, too, defaults to the system location. >From the CPAN man page: 5) I am not root, how can I install a module in a personal directory? You will most probably like something like this: o conf makepl_arg "LIB=~/myperl/lib \ INSTALLMAN1DIR=~/myperl/man/man1 \ INSTALLMAN3DIR=~/myperl/man/man3" install Sybase::Sybperl You can make this setting permanent like all "o conf" settings with "o conf commit". You will have to add ~/myperl/man to the MANPATH environment variable and also tell your perl programs to look into ~/myperl/lib, e.g. by including use lib "$ENV{HOME}/myperl/lib"; or setting the PERL5LIB environment variable. Another thing you should bear in mind is that the UNINST parameter should never be set if you are not root. So, now that you've wiped your cpan configuration parameters, you need to set some new ones, even before you update CPAN. Actually, the advice on the BioPerl Installation page is better than the above. Do the following: % cpan cpan>o conf makepl_arg PREFIX=/home/users/dag/My_Local_Perl_Modules cpan>o conf mbuildpl_arg "--prefix /home/users/dag/My_Local_Perl_Modules" cpan>o conf commit Here's the whole section of the installation instructions that deal with personal installations: http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_IN_A_PERSONAL_MODULE_AREA By the way, just a bit below that section are the instructions on how to set your PERL5LIB environmental variable. Dave From limericksean at gmail.com Wed Dec 10 07:40:35 2008 From: limericksean at gmail.com (Sean O'Keeffe) Date: Wed, 10 Dec 2008 13:40:35 +0100 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: <628aabb70812100436t15dac8fag35d90b7aa39d6a94@mail.gmail.com> References: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> <462784640812091127w25aa272em7bee17c99b3d4fea@mail.gmail.com> <493ECB30.9080506@sendu.me.uk> <462784640812091202n27c5cd5djcfb9abbacb9aef44@mail.gmail.com> <462784640812091212p33a0014bgeddac47dae880092@mail.gmail.com> <493EF0E2.3050607@sendu.me.uk> <462784640812100237p5a921b86u4c15ab05bf228fbf@mail.gmail.com> <493FA2C5.3080506@mrc-lmb.cam.ac.uk> <628aabb70812100436t15dac8fag35d90b7aa39d6a94@mail.gmail.com> Message-ID: <462784640812100440q3caf1f6duf0b29b59a0066158@mail.gmail.com> ok will try this out. thanks all so far. 2008/12/10 Dave Messina : > Following on to what Dave H. said, cpan itself needs to know that you want > to install in a personal module area; it, too, defaults to the system > location. > > From the CPAN man page: > 5) I am not root, how can I install a module in a personal directory? > > You will most probably like something like this: > > o conf makepl_arg "LIB=~/myperl/lib \ > INSTALLMAN1DIR=~/myperl/man/man1 \ > INSTALLMAN3DIR=~/myperl/man/man3" > install Sybase::Sybperl > > You can make this setting permanent like all "o conf" settings > with "o conf commit". > > You will have to add ~/myperl/man to the MANPATH environment > variable and also tell your perl programs to look into > ~/myperl/lib, e.g. by including > > use lib "$ENV{HOME}/myperl/lib"; > > or setting the PERL5LIB environment variable. > > Another thing you should bear in mind is that the UNINST > parameter should never be set if you are not root. > > > So, now that you've wiped your cpan configuration parameters, you need to > set some new ones, even before you update CPAN. > > Actually, the advice on the BioPerl Installation page is better than the > above. Do the following: > > % cpan > cpan>o conf makepl_arg PREFIX=/home/users/dag/My_Local_Perl_Modules > cpan>o conf mbuildpl_arg "--prefix /home/users/dag/My_Local_Perl_Modules" > cpan>o conf commit > > > Here's the whole section of the installation instructions that deal with > personal installations: > http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_IN_A_PERSONAL_MODULE_AREA > > By the way, just a bit below that section are the instructions on how to set > your PERL5LIB environmental variable. > > > Dave > > From limericksean at gmail.com Wed Dec 10 07:56:57 2008 From: limericksean at gmail.com (Sean O'Keeffe) Date: Wed, 10 Dec 2008 13:56:57 +0100 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: <628aabb70812100436t15dac8fag35d90b7aa39d6a94@mail.gmail.com> References: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> <462784640812091127w25aa272em7bee17c99b3d4fea@mail.gmail.com> <493ECB30.9080506@sendu.me.uk> <462784640812091202n27c5cd5djcfb9abbacb9aef44@mail.gmail.com> <462784640812091212p33a0014bgeddac47dae880092@mail.gmail.com> <493EF0E2.3050607@sendu.me.uk> <462784640812100237p5a921b86u4c15ab05bf228fbf@mail.gmail.com> <493FA2C5.3080506@mrc-lmb.cam.ac.uk> <628aabb70812100436t15dac8fag35d90b7aa39d6a94@mail.gmail.com> Message-ID: <462784640812100456u4b200dbciea08a13ecfaedfc3@mail.gmail.com> Ok I tried setting the cpan make and build directives as follows: > perl -e shell -MCPAN CPAN: File::HomeDir loaded ok (v0.66) cpan shell -- CPAN exploration and modules installation (v1.9205) ReadLine support enabled cpan[1]> o conf makepl_arg PREFIX=/home/okeeffe/perllib makepl_arg [PREFIX=/home/okeeffe/perllib] Please use 'o conf commit' to make the config permanent! cpan[2]> o conf mbuildpl_arg "--prefix /home/okeeffe/perllib" mbuildpl_arg [--prefix /home/okeeffe/perllib] Please use 'o conf commit' to make the config permanent! However, commit failed: cpan[3]> o conf commit Catching error: "/usr/local/lib/perl5/5.8.7/CPAN/Config.pm is not writable at /usr/local/lib/perl5/5.8.7/CPAN/HandleConfig.pm line 286\cJ\cICPAN::HandleConfig::commit('CPAN::HandleConfig', 'args', 'ARRAY(0x667060)') called at /usr/local/lib/perl5/5.8.7/CPAN/HandleConfig.pm line 128\cJ\cICPAN::HandleConfig::edit('CPAN::HandleConfig', 'commit') called at /usr/local/lib/perl5/5.8.7/CPAN.pm line 2029\cJ\cICPAN::Shell::o('CPAN::Shell', 'conf', 'commit') called at /usr/local/lib/perl5/5.8.7/CPAN.pm line 274\cJ\cIeval {...} called at /usr/local/lib/perl5/5.8.7/CPAN.pm line 274\cJ\cICPAN::shell() called at -e line 1\cJ" at /usr/local/lib/perl5/5.8.7/CPAN.pm line 281 CPAN::shell() called at -e line 1 2008/12/10 Dave Messina : > Following on to what Dave H. said, cpan itself needs to know that you want > to install in a personal module area; it, too, defaults to the system > location. > > From the CPAN man page: > 5) I am not root, how can I install a module in a personal directory? > > You will most probably like something like this: > > o conf makepl_arg "LIB=~/myperl/lib \ > INSTALLMAN1DIR=~/myperl/man/man1 \ > INSTALLMAN3DIR=~/myperl/man/man3" > install Sybase::Sybperl > > You can make this setting permanent like all "o conf" settings > with "o conf commit". > > You will have to add ~/myperl/man to the MANPATH environment > variable and also tell your perl programs to look into > ~/myperl/lib, e.g. by including > > use lib "$ENV{HOME}/myperl/lib"; > > or setting the PERL5LIB environment variable. > > Another thing you should bear in mind is that the UNINST > parameter should never be set if you are not root. > > > So, now that you've wiped your cpan configuration parameters, you need to > set some new ones, even before you update CPAN. > > Actually, the advice on the BioPerl Installation page is better than the > above. Do the following: > > % cpan > cpan>o conf makepl_arg PREFIX=/home/users/dag/My_Local_Perl_Modules > cpan>o conf mbuildpl_arg "--prefix /home/users/dag/My_Local_Perl_Modules" > cpan>o conf commit > > > Here's the whole section of the installation instructions that deal with > personal installations: > http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_IN_A_PERSONAL_MODULE_AREA > > By the way, just a bit below that section are the instructions on how to set > your PERL5LIB environmental variable. > > > Dave > > From David.Messina at sbc.su.se Wed Dec 10 08:16:34 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 10 Dec 2008 14:16:34 +0100 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: <462784640812100456u4b200dbciea08a13ecfaedfc3@mail.gmail.com> References: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> <493ECB30.9080506@sendu.me.uk> <462784640812091202n27c5cd5djcfb9abbacb9aef44@mail.gmail.com> <462784640812091212p33a0014bgeddac47dae880092@mail.gmail.com> <493EF0E2.3050607@sendu.me.uk> <462784640812100237p5a921b86u4c15ab05bf228fbf@mail.gmail.com> <493FA2C5.3080506@mrc-lmb.cam.ac.uk> <628aabb70812100436t15dac8fag35d90b7aa39d6a94@mail.gmail.com> <462784640812100456u4b200dbciea08a13ecfaedfc3@mail.gmail.com> Message-ID: <628aabb70812100516k47d0628dl463d2786aec1e8cc@mail.gmail.com> Try quitting out of the cpan shell and checking if it's written stuff to your ~/.cpan directory. I'm betting that when you wiped out your .cpan directory, it had to read the defaults from the system location. But it should, after that first time, have written a new .cpan directory in your home dir for you. Start up cpan again and list your configuration with 'o conf'. Read carefully the first lines printed after you do the 'o conf' command -- it should tell you where it's reading your configuration information from. It should say something like: cpan> o conf $CPAN::Config options from '/home/okeefe/.cpan/CPAN/MyConfig.pm': If that's okay, then check carefully the following values -- all of your cpan-related configuration parameters should point to your ~/.cpan directory. build_dir [/home/okeefe/.cpan/build] cpan_home [/home/okeefe/.cpan] histfile [/home/okeefe/.cpan/histfile] keep_source_where [/home/okeefe/.cpan/sources] prefs_dir [/home/okeefe/.cpan/prefs] If any of those aren't correct, try changing one of them and then doing 'o conf commit'. Until you can get that to work, nothing in cpan is going to work for you. If those are all correct, then set the make and build params as mentioned before and try 'o conf commit' on those. D From limericksean at gmail.com Wed Dec 10 09:31:41 2008 From: limericksean at gmail.com (Sean O'Keeffe) Date: Wed, 10 Dec 2008 15:31:41 +0100 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: <628aabb70812100516k47d0628dl463d2786aec1e8cc@mail.gmail.com> References: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> <462784640812091202n27c5cd5djcfb9abbacb9aef44@mail.gmail.com> <462784640812091212p33a0014bgeddac47dae880092@mail.gmail.com> <493EF0E2.3050607@sendu.me.uk> <462784640812100237p5a921b86u4c15ab05bf228fbf@mail.gmail.com> <493FA2C5.3080506@mrc-lmb.cam.ac.uk> <628aabb70812100436t15dac8fag35d90b7aa39d6a94@mail.gmail.com> <462784640812100456u4b200dbciea08a13ecfaedfc3@mail.gmail.com> <628aabb70812100516k47d0628dl463d2786aec1e8cc@mail.gmail.com> Message-ID: <462784640812100631g13f2230cw8ce048ce36a0c954@mail.gmail.com> > o conf $CPAN::Config options from '/usr/local/lib/perl5/5.8.7/CPAN/Config.pm': ... So how to change this is the key? 2008/12/10 Dave Messina : > Try quitting out of the cpan shell and checking if it's written stuff to > your ~/.cpan directory. I'm betting that when you wiped out your .cpan > directory, it had to read the defaults from the system location. But it > should, after that first time, have written a new .cpan directory in your > home dir for you. > > Start up cpan again and list your configuration with 'o conf'. > > Read carefully the first lines printed after you do the 'o conf' command -- > it should tell you where it's reading your configuration information from. > > It should say something like: > cpan> o conf > $CPAN::Config options from '/home/okeefe/.cpan/CPAN/MyConfig.pm': > > If that's okay, then check carefully the following values -- all of your > cpan-related configuration parameters should point to your ~/.cpan > directory. > > build_dir [/home/okeefe/.cpan/build] > cpan_home [/home/okeefe/.cpan] > histfile [/home/okeefe/.cpan/histfile] > keep_source_where [/home/okeefe/.cpan/sources] > prefs_dir [/home/okeefe/.cpan/prefs] > > > If any of those aren't correct, try changing one of them and then doing 'o > conf commit'. Until you can get that to work, nothing in cpan is going to > work for you. > > If those are all correct, then set the make and build params as mentioned > before and try 'o conf commit' on those. > > > D > > From David.Messina at sbc.su.se Wed Dec 10 09:38:55 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 10 Dec 2008 15:38:55 +0100 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: <462784640812100631g13f2230cw8ce048ce36a0c954@mail.gmail.com> References: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> <462784640812091212p33a0014bgeddac47dae880092@mail.gmail.com> <493EF0E2.3050607@sendu.me.uk> <462784640812100237p5a921b86u4c15ab05bf228fbf@mail.gmail.com> <493FA2C5.3080506@mrc-lmb.cam.ac.uk> <628aabb70812100436t15dac8fag35d90b7aa39d6a94@mail.gmail.com> <462784640812100456u4b200dbciea08a13ecfaedfc3@mail.gmail.com> <628aabb70812100516k47d0628dl463d2786aec1e8cc@mail.gmail.com> <462784640812100631g13f2230cw8ce048ce36a0c954@mail.gmail.com> Message-ID: <628aabb70812100638m49b62e10p4c72b79af241284d@mail.gmail.com> On Wed, Dec 10, 2008 at 15:31, Sean O'Keeffe wrote: > > o conf > $CPAN::Config options from '/usr/local/lib/perl5/5.8.7/CPAN/Config.pm': > ... > > So how to change this is the key? Did you try quitting out of the cpan shell and seeing if it wrote you a new ~/.cpan directory? If that didn't happen, start up the cpan shell again and type 'o conf init'. Taking the defaults for now should be fine. That should force it to make your personal ~/.cpan. Remember to 'o conf commit' after answering all the config stuff. D From limericksean at gmail.com Wed Dec 10 09:43:51 2008 From: limericksean at gmail.com (Sean O'Keeffe) Date: Wed, 10 Dec 2008 15:43:51 +0100 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: <628aabb70812100638m49b62e10p4c72b79af241284d@mail.gmail.com> References: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> <493EF0E2.3050607@sendu.me.uk> <462784640812100237p5a921b86u4c15ab05bf228fbf@mail.gmail.com> <493FA2C5.3080506@mrc-lmb.cam.ac.uk> <628aabb70812100436t15dac8fag35d90b7aa39d6a94@mail.gmail.com> <462784640812100456u4b200dbciea08a13ecfaedfc3@mail.gmail.com> <628aabb70812100516k47d0628dl463d2786aec1e8cc@mail.gmail.com> <462784640812100631g13f2230cw8ce048ce36a0c954@mail.gmail.com> <628aabb70812100638m49b62e10p4c72b79af241284d@mail.gmail.com> Message-ID: <462784640812100643o15785a53w670dca7095ad1297@mail.gmail.com> ok that's done it dave, thanks. right i'll start from the top again and let you know how she goes. cheers. 2008/12/10 Dave Messina : > > > On Wed, Dec 10, 2008 at 15:31, Sean O'Keeffe wrote: >> >> > o conf >> $CPAN::Config options from '/usr/local/lib/perl5/5.8.7/CPAN/Config.pm': >> ... >> >> So how to change this is the key? > > Did you try quitting out of the cpan shell and seeing if it wrote you a new > ~/.cpan directory? > > If that didn't happen, start up the cpan shell again and type 'o conf init'. > Taking the defaults for now should be fine. That should force it to make > your personal ~/.cpan. > > > Remember to 'o conf commit' after answering all the config stuff. > > D > > > From limericksean at gmail.com Wed Dec 10 11:10:24 2008 From: limericksean at gmail.com (Sean O'Keeffe) Date: Wed, 10 Dec 2008 17:10:24 +0100 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: <462784640812100643o15785a53w670dca7095ad1297@mail.gmail.com> References: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> <462784640812100237p5a921b86u4c15ab05bf228fbf@mail.gmail.com> <493FA2C5.3080506@mrc-lmb.cam.ac.uk> <628aabb70812100436t15dac8fag35d90b7aa39d6a94@mail.gmail.com> <462784640812100456u4b200dbciea08a13ecfaedfc3@mail.gmail.com> <628aabb70812100516k47d0628dl463d2786aec1e8cc@mail.gmail.com> <462784640812100631g13f2230cw8ce048ce36a0c954@mail.gmail.com> <628aabb70812100638m49b62e10p4c72b79af241284d@mail.gmail.com> <462784640812100643o15785a53w670dca7095ad1297@mail.gmail.com> Message-ID: <462784640812100810i61752edbw3d0e41787af19b84@mail.gmail.com> at the risk of sounding idiotic, i've realised that the issue may have been of my own making. i had ssh'd to another server and hadn't thought about it when starting the install. i just assumed i was in my /home/dir but was only virtually there. exiting from this, everything went smooth. apologies for all hassles caused. my only other question is where has Bio::Graphics gone from the bioperl checkout on svn? sean. 2008/12/10 Sean O'Keeffe : > ok that's done it dave, thanks. > right i'll start from the top again and let you know how she goes. > > cheers. > > 2008/12/10 Dave Messina : >> >> >> On Wed, Dec 10, 2008 at 15:31, Sean O'Keeffe wrote: >>> >>> > o conf >>> $CPAN::Config options from '/usr/local/lib/perl5/5.8.7/CPAN/Config.pm': >>> ... >>> >>> So how to change this is the key? >> >> Did you try quitting out of the cpan shell and seeing if it wrote you a new >> ~/.cpan directory? >> >> If that didn't happen, start up the cpan shell again and type 'o conf init'. >> Taking the defaults for now should be fine. That should force it to make >> your personal ~/.cpan. >> >> >> Remember to 'o conf commit' after answering all the config stuff. >> >> D >> >> >> > From cjfields at illinois.edu Wed Dec 10 11:40:59 2008 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 10 Dec 2008 10:40:59 -0600 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: <462784640812100810i61752edbw3d0e41787af19b84@mail.gmail.com> References: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> <462784640812100237p5a921b86u4c15ab05bf228fbf@mail.gmail.com> <493FA2C5.3080506@mrc-lmb.cam.ac.uk> <628aabb70812100436t15dac8fag35d90b7aa39d6a94@mail.gmail.com> <462784640812100456u4b200dbciea08a13ecfaedfc3@mail.gmail.com> <628aabb70812100516k47d0628dl463d2786aec1e8cc@mail.gmail.com> <462784640812100631g13f2230cw8ce048ce36a0c954@mail.gmail.com> <628aabb70812100638m49b62e10p4c72b79af241284d@mail.gmail.com> <462784640812100643o15785a53w670dca7095ad1297@mail.gmail.com> <462784640812100810i61752edbw3d0e41787af19b84@mail.gmail.com> Message-ID: <013CAA83-FA66-4FB7-8975-22BF336DBF3E@illinois.edu> On Dec 10, 2008, at 10:10 AM, Sean O'Keeffe wrote: > at the risk of sounding idiotic, i've realised that the issue may have > been of my own making. > i had ssh'd to another server and hadn't thought about it when > starting the install. > i just assumed i was in my /home/dir but was only virtually there. > exiting from this, everything went smooth. apologies for all hassles > caused. > > my only other question is where has Bio::Graphics gone from the > bioperl checkout on svn? > > sean. Bio::Graphics is now separate from BioPerl as of 1.6. It will be a separate installation via CPAN, see: http://search.cpan.org/~lds/Bio-Graphics-1.8/ Note the bioperl README. I am hoping to install a hook into Build.PL to post-install this or any any other split-off modules in the future, but we may just have a Bundle package to do this instead. One of the remaining decisions for 1.6... chris From maj at fortinbras.us Wed Dec 10 11:36:27 2008 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 10 Dec 2008 11:36:27 -0500 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: <462784640812100810i61752edbw3d0e41787af19b84@mail.gmail.com> Message-ID: <43877789791543CFBCDE98E50D23D214@NewLife> Sean- I learned a lot watching this saga unfold. Hold your head high- cheers MAJ From David.Messina at sbc.su.se Wed Dec 10 11:53:41 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 10 Dec 2008 17:53:41 +0100 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: <462784640812100810i61752edbw3d0e41787af19b84@mail.gmail.com> References: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> <462784640812100237p5a921b86u4c15ab05bf228fbf@mail.gmail.com> <493FA2C5.3080506@mrc-lmb.cam.ac.uk> <628aabb70812100436t15dac8fag35d90b7aa39d6a94@mail.gmail.com> <462784640812100456u4b200dbciea08a13ecfaedfc3@mail.gmail.com> <628aabb70812100516k47d0628dl463d2786aec1e8cc@mail.gmail.com> <462784640812100631g13f2230cw8ce048ce36a0c954@mail.gmail.com> <628aabb70812100638m49b62e10p4c72b79af241284d@mail.gmail.com> <462784640812100643o15785a53w670dca7095ad1297@mail.gmail.com> <462784640812100810i61752edbw3d0e41787af19b84@mail.gmail.com> Message-ID: <628aabb70812100853p41e4b0fare4ad663e2a556b17@mail.gmail.com> Hi Sean, Great, glad you were able to get it to work. As of a few days ago, Bio::Graphics is now distributed separately via CPAN, so you can get it that way. One warning: given its dependence on GD, which requires the C library gd, which has dependencies of its own, Bio::Graphics can be non-trivial to install on some systems. If you aren't able to get it installed in the straightforward way via CPAN, It's important to read the (plentiful) documentation that comes with it. Dave From limericksean at gmail.com Wed Dec 10 12:27:19 2008 From: limericksean at gmail.com (Sean O'Keeffe) Date: Wed, 10 Dec 2008 18:27:19 +0100 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: <013CAA83-FA66-4FB7-8975-22BF336DBF3E@illinois.edu> References: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com> <493FA2C5.3080506@mrc-lmb.cam.ac.uk> <628aabb70812100436t15dac8fag35d90b7aa39d6a94@mail.gmail.com> <462784640812100456u4b200dbciea08a13ecfaedfc3@mail.gmail.com> <628aabb70812100516k47d0628dl463d2786aec1e8cc@mail.gmail.com> <462784640812100631g13f2230cw8ce048ce36a0c954@mail.gmail.com> <628aabb70812100638m49b62e10p4c72b79af241284d@mail.gmail.com> <462784640812100643o15785a53w670dca7095ad1297@mail.gmail.com> <462784640812100810i61752edbw3d0e41787af19b84@mail.gmail.com> <013CAA83-FA66-4FB7-8975-22BF336DBF3E@illinois.edu> Message-ID: <462784640812100927h4e3a1dcbq7ff695ab43782b71@mail.gmail.com> ok. well to cut a long story short, the reason for my initial bioperl installation was it was a gbrowse requirement for me. upgrading gbrowse (>1.69) returned Bio::Graphics compatibility issues for me which were previously resolved by updating bioperl-live. i had assumed (i know never assume) the graphics were, amongst other things, the important part. so now i'll hit the Bio::Graphics trail and see what happens., or wait 'til the 1.6 release. ok well cheers folks (for now). 2008/12/10 Chris Fields : > On Dec 10, 2008, at 10:10 AM, Sean O'Keeffe wrote: > >> at the risk of sounding idiotic, i've realised that the issue may have >> been of my own making. >> i had ssh'd to another server and hadn't thought about it when >> starting the install. >> i just assumed i was in my /home/dir but was only virtually there. >> exiting from this, everything went smooth. apologies for all hassles >> caused. >> >> my only other question is where has Bio::Graphics gone from the >> bioperl checkout on svn? >> >> sean. > > Bio::Graphics is now separate from BioPerl as of 1.6. It will be a separate > installation via CPAN, see: > > http://search.cpan.org/~lds/Bio-Graphics-1.8/ > > Note the bioperl README. > > I am hoping to install a hook into Build.PL to post-install this or any any > other split-off modules in the future, but we may just have a Bundle package > to do this instead. One of the remaining decisions for 1.6... > > chris > From David.Messina at sbc.su.se Wed Dec 10 12:43:53 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 10 Dec 2008 18:43:53 +0100 Subject: [Bioperl-l] Build.PL, 'requires', 'recommends', and optional modules Message-ID: <628aabb70812100943q74f80973g7c17f4a49a834b6f@mail.gmail.com> Hey everyone, So in testing the latest bioperl-live, I noticed that there's a new dependency for Microarray::Tools::ReseqChip, namely Statistics::Frequency. I seem to remember at some point during the Build process, I would get prompted if I want to install optional modules, but I wasn't, and poking around in the Module::Build docs I couldn't find the details. Since, according to the docs for Microarray::Tools::ReseqChip indicate it relies on Statistics::Frequency, I think S::F should go in the 'requires' block in Build.PL, right? And wouldn't that also be true for the other external dependencies of M::T::ReseqChip, Spreadsheet::ParseExcel and Spreadsheet::WriteExcel? Or do all three of those go in 'recommends'? Whether 'requires' or 'recommends', could someone refresh my memory on how this works, and in what way one gets prompted for uninstalled modules? Thanks, Dave (By the way, I know that this module was just added and so all of the twiddly setup stuff might not have been done quite yet. I'm not complaining -- this just triggered my curiosity about how this works...) From Kevin.M.Brown at asu.edu Wed Dec 10 12:38:49 2008 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Wed, 10 Dec 2008 10:38:49 -0700 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: <462784640812100927h4e3a1dcbq7ff695ab43782b71@mail.gmail.com> References: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com><493FA2C5.3080506@mrc-lmb.cam.ac.uk><628aabb70812100436t15dac8fag35d90b7aa39d6a94@mail.gmail.com><462784640812100456u4b200dbciea08a13ecfaedfc3@mail.gmail.com><628aabb70812100516k47d0628dl463d2786aec1e8cc@mail.gmail.com><462784640812100631g13f2230cw8ce048ce36a0c954@mail.gmail.com><628aabb70812100638m49b62e10p4c72b79af241284d@mail.gmail.com><462784640812100643o15785a53w670dca7095ad1297@mail.gmail.com><462784640812100810i61752edbw3d0e41787af19b84@mail.gmail.com><013CAA83-FA66-4FB7-8975-22BF336DBF3E@illinois.edu> <462784640812100927h4e3a1dcbq7ff695ab43782b71@mail.gmail.com> Message-ID: <1A4207F8295607498283FE9E93B775B4059316BF@EX02.asurite.ad.asu.edu> IIRC, Bio::Graphics was split off because of the fact that Gbrowse depends on it. So, as a convenience to them (so they don't have to wait on a full release of Bio::Perl) it was split off. > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Sean O'Keeffe > Sent: Wednesday, December 10, 2008 10:27 AM > To: Chris Fields > Cc: bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] bioperl-live install issue on unix > > ok. well to cut a long story short, the reason for my initial bioperl > installation was it was a gbrowse requirement for me. > upgrading gbrowse (>1.69) returned Bio::Graphics compatibility issues > for me which were previously resolved by updating bioperl-live. > i had assumed (i know never assume) the graphics were, amongst other > things, the important part. > so now i'll hit the Bio::Graphics trail and see what happens., or wait > 'til the 1.6 release. > > ok well cheers folks (for now). > > 2008/12/10 Chris Fields : > > On Dec 10, 2008, at 10:10 AM, Sean O'Keeffe wrote: > > > >> at the risk of sounding idiotic, i've realised that the > issue may have > >> been of my own making. > >> i had ssh'd to another server and hadn't thought about it when > >> starting the install. > >> i just assumed i was in my /home/dir but was only virtually there. > >> exiting from this, everything went smooth. apologies for > all hassles > >> caused. > >> > >> my only other question is where has Bio::Graphics gone from the > >> bioperl checkout on svn? > >> > >> sean. > > > > Bio::Graphics is now separate from BioPerl as of 1.6. It > will be a separate > > installation via CPAN, see: > > > > http://search.cpan.org/~lds/Bio-Graphics-1.8/ > > > > Note the bioperl README. > > > > I am hoping to install a hook into Build.PL to post-install > this or any any > > other split-off modules in the future, but we may just have > a Bundle package > > to do this instead. One of the remaining decisions for 1.6... > > > > chris > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From Kevin.M.Brown at asu.edu Wed Dec 10 12:38:49 2008 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Wed, 10 Dec 2008 10:38:49 -0700 Subject: [Bioperl-l] bioperl-live install issue on unix In-Reply-To: <462784640812100927h4e3a1dcbq7ff695ab43782b71@mail.gmail.com> References: <462784640812090924h5b458b5aw54e0e3901929f48e@mail.gmail.com><493FA2C5.3080506@mrc-lmb.cam.ac.uk><628aabb70812100436t15dac8fag35d90b7aa39d6a94@mail.gmail.com><462784640812100456u4b200dbciea08a13ecfaedfc3@mail.gmail.com><628aabb70812100516k47d0628dl463d2786aec1e8cc@mail.gmail.com><462784640812100631g13f2230cw8ce048ce36a0c954@mail.gmail.com><628aabb70812100638m49b62e10p4c72b79af241284d@mail.gmail.com><462784640812100643o15785a53w670dca7095ad1297@mail.gmail.com><462784640812100810i61752edbw3d0e41787af19b84@mail.gmail.com><013CAA83-FA66-4FB7-8975-22BF336DBF3E@illinois.edu> <462784640812100927h4e3a1dcbq7ff695ab43782b71@mail.gmail.com> Message-ID: <1A4207F8295607498283FE9E93B775B4059316BF@EX02.asurite.ad.asu.edu> IIRC, Bio::Graphics was split off because of the fact that Gbrowse depends on it. So, as a convenience to them (so they don't have to wait on a full release of Bio::Perl) it was split off. > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Sean O'Keeffe > Sent: Wednesday, December 10, 2008 10:27 AM > To: Chris Fields > Cc: bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] bioperl-live install issue on unix > > ok. well to cut a long story short, the reason for my initial bioperl > installation was it was a gbrowse requirement for me. > upgrading gbrowse (>1.69) returned Bio::Graphics compatibility issues > for me which were previously resolved by updating bioperl-live. > i had assumed (i know never assume) the graphics were, amongst other > things, the important part. > so now i'll hit the Bio::Graphics trail and see what happens., or wait > 'til the 1.6 release. > > ok well cheers folks (for now). > > 2008/12/10 Chris Fields : > > On Dec 10, 2008, at 10:10 AM, Sean O'Keeffe wrote: > > > >> at the risk of sounding idiotic, i've realised that the > issue may have > >> been of my own making. > >> i had ssh'd to another server and hadn't thought about it when > >> starting the install. > >> i just assumed i was in my /home/dir but was only virtually there. > >> exiting from this, everything went smooth. apologies for > all hassles > >> caused. > >> > >> my only other question is where has Bio::Graphics gone from the > >> bioperl checkout on svn? > >> > >> sean. > > > > Bio::Graphics is now separate from BioPerl as of 1.6. It > will be a separate > > installation via CPAN, see: > > > > http://search.cpan.org/~lds/Bio-Graphics-1.8/ > > > > Note the bioperl README. > > > > I am hoping to install a hook into Build.PL to post-install > this or any any > > other split-off modules in the future, but we may just have > a Bundle package > > to do this instead. One of the remaining decisions for 1.6... > > > > chris > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Wed Dec 10 13:23:48 2008 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 10 Dec 2008 12:23:48 -0600 Subject: [Bioperl-l] Build.PL, 'requires', 'recommends', and optional modules In-Reply-To: <628aabb70812100943q74f80973g7c17f4a49a834b6f@mail.gmail.com> References: <628aabb70812100943q74f80973g7c17f4a49a834b6f@mail.gmail.com> Message-ID: On Dec 10, 2008, at 11:43 AM, Dave Messina wrote: > Hey everyone, > So in testing the latest bioperl-live, I noticed that there's a new > dependency for Microarray::Tools::ReseqChip, namely > Statistics::Frequency. > > I seem to remember at some point during the Build process, I would get > prompted if I want to install optional modules, but I wasn't, and > poking > around in the Module::Build docs I couldn't find the details. > > Since, according to the docs for Microarray::Tools::ReseqChip > indicate it > relies on Statistics::Frequency, I think S::F should go in the > 'requires' > block in Build.PL, right? > > And wouldn't that also be true for the other external dependencies of > M::T::ReseqChip, Spreadsheet::ParseExcel and Spreadsheet::WriteExcel? > > Or do all three of those go in 'recommends'? Sorry, been caught up with non-bioperl-related work. I'm able to get back to it a bit more this week now. You definitely want 'Recommends'; this module isn't required for core functionality. > Whether 'requires' or 'recommends', could someone refresh my memory > on how > this works, and in what way one gets prompted for uninstalled modules? > > > Thanks, > Dave > > > (By the way, I know that this module was just added and so all of the > twiddly setup stuff might not have been done quite yet. I'm not > complaining > -- this just triggered my curiosity about how this works...) Literally just added in. I'm still working out semantics on these modules off-list with Marian (trying to remove the Statistics::Frequency dep), but if you want you can go ahead and add in the additional dependencies and I'll correct it later. I'll post something to the list in a second which I hope will help clarify some things I think all the devs (not just core) expect. chris From jason at bioperl.org Wed Dec 10 13:42:47 2008 From: jason at bioperl.org (Jason Stajich) Date: Wed, 10 Dec 2008 10:42:47 -0800 Subject: [Bioperl-l] Fwd: [Bioperl-guts-l] [15134] bioperl-live/trunk/Bio/Microarray/Tools: use superclasses initialization and argument processing/ attribute setting as suggested in styleguide References: <200812101410.mBAEALFw011802@dev.open-bio.org> Message-ID: Since we've started discussing the idea of starting to move things out into smaller packages, does it make sense to move this Bio::Microarray into its own package before it gets bigger? What about the old bioperl- microarray stuff from Allen Day? I also know that as we haven't branched for 1.6 Chris we'll have to make some decisions about new code going in before then? Not trying to stifle any of the development with extra work but trying to see if we should start to make some logical slices of packages? -jason Begin forwarded message: > From: Marian Thieme > Date: December 10, 2008 6:10:21 AM PST > To: bioperl-guts-l at bioperl.org > Subject: [Bioperl-guts-l] [15134] bioperl-live/trunk/Bio/Microarray/ > Tools: use superclasses initialization and argument processing/ > attribute setting as suggested in styleguide > > Revision: 15134 > Author: thm09830 > Date: 2008-12-10 09:10:21 -0500 (Wed, 10 Dec 2008) > > Log Message: > ----------- > use superclasses initialization and argument processing/attribute > setting as suggested in styleguide > > Modified Paths: > -------------- > bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm > bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm > > Modified: bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm > =================================================================== > --- bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm > 2008-12-10 12:51:47 UTC (rev 15133) > +++ bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm > 2008-12-10 14:10:21 UTC (rev 15134) > @@ -78,12 +78,13 @@ > > sub new { > > - my ($class, $file_name) = @_; > - my $self = $class->SUPER::new(); > + my ($class, @args) = @_; > + my $self = $class->SUPER::new(@args); > + my ($file_name)=$self->_rearrange([qw(AFFY_DESIGN_FILENAME)], > @args); > + > $self->{_frags_hash}=undef; > $self->{_oligos2calc_hash}=undef; > $self->throw("Must provide filename as first argument !") unless > $file_name; > - > > my %max_ins_hash=(); > $self->{_frags_hash}=$self- > >_parse_Affy_mtDNA_design_annotation_file($file_name); > > Modified: bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm > =================================================================== > --- bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm 2008-12-10 > 12:51:47 UTC (rev 15133) > +++ bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm 2008-12-10 > 14:10:21 UTC (rev 15134) > @@ -194,8 +194,11 @@ > > sub new { > > - my ($class, $design_file_name, $format, $refseq_max_ins_hash, > $refseq) = @_; > - my $self = $class->SUPER::new(); > + #my ($class, $design_file_name, $format, $refseq_max_ins_hash, > $refseq) = @_; > + my ($class, @args) = @_; > + my $self = $class->SUPER::new(@args); > + my ($design_file_name, $format, $refseq_max_ins_hash, $refseq)= > $self->_rearrange([qw(AFFY_DESIGN_FILENAME FORMAT_OF_DESIGN_FILE > MAX_INSERTION_HASH_REFERENCE REFERENCE_SEQUENCE)], @args); > + > $self->{_frags_hash}=undef; > $self->{_max_ins_hash}=undef; > $self->{_refseq}=undef; > > > _______________________________________________ > Bioperl-guts-l mailing list > Bioperl-guts-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l Jason Stajich jason at bioperl.org From cjfields at illinois.edu Wed Dec 10 13:47:34 2008 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 10 Dec 2008 12:47:34 -0600 Subject: [Bioperl-l] For the 1.6 release... Message-ID: <34BA7B99-BB11-4325-9B66-F8690CF3227C@illinois.edu> All, Just to note for anyone not subscribed to the dev list, I haven't created a branch or tagged anything for 1.6 yet, but will probably do so in the next week. We are seeing some very promising code from new devs. However, we don't want subtle bugs sneaking in with rushed code at the last minute. This means: 1) Any new modules and functionality trying to make it into the initial 1.6 release at the last minute still need to pass *all* tests, not just the ones in a particular test file. 2) Be prepared to ->support<- your code/modules (and it's current design, flowers/warts and all). This code will go out to a LOT of users. As noted previously, API changes that break code or tests will NOT be allowed in this release series. If you think there is a design flaw: take a deep breath. There is no need to rush. See #3 below. 3) We intend on having regular point releases (about every 3-4 months) for bug fixes and some added functionality (as long as it does not change the API and can be supported). If your module's or code's API is in a state that may change, please consider waiting until a later point release. 1.6 has been a long time coming. We made the point early on for this release that the focus was primarily to be on bug fixes; enhancements would only be included if they come with and can pass all new and current tests. chris From cjfields at illinois.edu Wed Dec 10 13:59:41 2008 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 10 Dec 2008 12:59:41 -0600 Subject: [Bioperl-l] Fwd: [Bioperl-guts-l] [15134] bioperl-live/trunk/Bio/Microarray/Tools: use superclasses initialization and argument processing/ attribute setting as suggested in styleguide In-Reply-To: References: <200812101410.mBAEALFw011802@dev.open-bio.org> Message-ID: <1952AD80-A0E9-4183-AFF0-4D0064F57584@illinois.edu> Sounds like a good idea, with one caveat: Allen had pretty much given up on bioperl-microarray last I heard (last significant commits were ~6 yrs ago). It would be nice to revive with this theme in mind, though maybe bioperl-expression would be better (could focus on other expression-related issues along with microarray data). Marian, what do you think? chris P.S. An aside: I'm planning on running lots of Illumina data myself and have been thinking about making a BioC-BioPerl bridge, then seeing how it fits into a bioperl-microarray. Just need a working perl-R interface (NOT RSPerl). On Dec 10, 2008, at 12:42 PM, Jason Stajich wrote: > Since we've started discussing the idea of starting to move things > out into smaller packages, does it make sense to move this > Bio::Microarray into its own package before it gets bigger? What > about the old bioperl-microarray stuff from Allen Day? > > I also know that as we haven't branched for 1.6 Chris we'll have to > make some decisions about new code going in before then? > > Not trying to stifle any of the development with extra work but > trying to see if we should start to make some logical slices of > packages? > > -jason > > Begin forwarded message: > >> From: Marian Thieme >> Date: December 10, 2008 6:10:21 AM PST >> To: bioperl-guts-l at bioperl.org >> Subject: [Bioperl-guts-l] [15134] bioperl-live/trunk/Bio/Microarray/ >> Tools: use superclasses initialization and argument processing/ >> attribute setting as suggested in styleguide >> >> Revision: 15134 >> Author: thm09830 >> Date: 2008-12-10 09:10:21 -0500 (Wed, 10 Dec 2008) >> >> Log Message: >> ----------- >> use superclasses initialization and argument processing/attribute >> setting as suggested in styleguide >> >> Modified Paths: >> -------------- >> bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >> bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm >> >> Modified: bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >> =================================================================== >> --- bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >> 2008-12-10 12:51:47 UTC (rev 15133) >> +++ bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >> 2008-12-10 14:10:21 UTC (rev 15134) >> @@ -78,12 +78,13 @@ >> >> sub new { >> >> - my ($class, $file_name) = @_; >> - my $self = $class->SUPER::new(); >> + my ($class, @args) = @_; >> + my $self = $class->SUPER::new(@args); >> + my ($file_name)=$self->_rearrange([qw(AFFY_DESIGN_FILENAME)], >> @args); >> + >> $self->{_frags_hash}=undef; >> $self->{_oligos2calc_hash}=undef; >> $self->throw("Must provide filename as first argument !") unless >> $file_name; >> - >> >> my %max_ins_hash=(); >> $self->{_frags_hash}=$self- >> >_parse_Affy_mtDNA_design_annotation_file($file_name); >> >> Modified: bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm >> =================================================================== >> --- bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm 2008-12-10 >> 12:51:47 UTC (rev 15133) >> +++ bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm 2008-12-10 >> 14:10:21 UTC (rev 15134) >> @@ -194,8 +194,11 @@ >> >> sub new { >> >> - my ($class, $design_file_name, $format, $refseq_max_ins_hash, >> $refseq) = @_; >> - my $self = $class->SUPER::new(); >> + #my ($class, $design_file_name, $format, $refseq_max_ins_hash, >> $refseq) = @_; >> + my ($class, @args) = @_; >> + my $self = $class->SUPER::new(@args); >> + my ($design_file_name, $format, $refseq_max_ins_hash, $refseq)= >> $self->_rearrange([qw(AFFY_DESIGN_FILENAME FORMAT_OF_DESIGN_FILE >> MAX_INSERTION_HASH_REFERENCE REFERENCE_SEQUENCE)], @args); >> + >> $self->{_frags_hash}=undef; >> $self->{_max_ins_hash}=undef; >> $self->{_refseq}=undef; >> >> >> _______________________________________________ >> Bioperl-guts-l mailing list >> Bioperl-guts-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l > > Jason Stajich > jason at bioperl.org > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cain.cshl at gmail.com Wed Dec 10 14:27:46 2008 From: cain.cshl at gmail.com (Scott Cain) Date: Wed, 10 Dec 2008 14:27:46 -0500 Subject: [Bioperl-l] For the 1.6 release... In-Reply-To: <34BA7B99-BB11-4325-9B66-F8690CF3227C@illinois.edu> References: <34BA7B99-BB11-4325-9B66-F8690CF3227C@illinois.edu> Message-ID: <536f21b00812101127p32d71f1fwa47d05425a4211d8@mail.gmail.com> Hi Chris, Count me as one who is rushing to get newish code ready. I hope to have Bio::DB::SeqFeature::Store::DBI::Pg ready to go by tomorrow. Scott On Wed, Dec 10, 2008 at 1:47 PM, Chris Fields wrote: > All, > > Just to note for anyone not subscribed to the dev list, I haven't created a > branch or tagged anything for 1.6 yet, but will probably do so in the next > week. > > We are seeing some very promising code from new devs. However, we don't > want subtle bugs sneaking in with rushed code at the last minute. This > means: > > 1) Any new modules and functionality trying to make it into the initial 1.6 > release at the last minute still need to pass *all* tests, not just the ones > in a particular test file. > > 2) Be prepared to ->support<- your code/modules (and it's current design, > flowers/warts and all). This code will go out to a LOT of users. As noted > previously, API changes that break code or tests will NOT be allowed in this > release series. If you think there is a design flaw: take a deep breath. > There is no need to rush. See #3 below. > > 3) We intend on having regular point releases (about every 3-4 months) for > bug fixes and some added functionality (as long as it does not change the > API and can be supported). If your module's or code's API is in a state > that may change, please consider waiting until a later point release. > > 1.6 has been a long time coming. We made the point early on for this > release that the focus was primarily to be on bug fixes; enhancements would > only be included if they come with and can pass all new and current tests. > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From cjfields at illinois.edu Wed Dec 10 14:47:30 2008 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 10 Dec 2008 13:47:30 -0600 Subject: [Bioperl-l] For the 1.6 release... In-Reply-To: <536f21b00812101127p32d71f1fwa47d05425a4211d8@mail.gmail.com> References: <34BA7B99-BB11-4325-9B66-F8690CF3227C@illinois.edu> <536f21b00812101127p32d71f1fwa47d05425a4211d8@mail.gmail.com> Message-ID: <08489666-EA04-44AE-A2A6-BC3A2FC3084D@illinois.edu> Works for me. I'll post a bit ahead of time before I tag 1.6. chris On Dec 10, 2008, at 1:27 PM, Scott Cain wrote: > Hi Chris, > > Count me as one who is rushing to get newish code ready. I hope to > have Bio::DB::SeqFeature::Store::DBI::Pg ready to go by tomorrow. > > Scott > > > On Wed, Dec 10, 2008 at 1:47 PM, Chris Fields > wrote: >> All, >> >> Just to note for anyone not subscribed to the dev list, I haven't >> created a >> branch or tagged anything for 1.6 yet, but will probably do so in >> the next >> week. >> >> We are seeing some very promising code from new devs. However, we >> don't >> want subtle bugs sneaking in with rushed code at the last minute. >> This >> means: >> >> 1) Any new modules and functionality trying to make it into the >> initial 1.6 >> release at the last minute still need to pass *all* tests, not just >> the ones >> in a particular test file. >> >> 2) Be prepared to ->support<- your code/modules (and it's current >> design, >> flowers/warts and all). This code will go out to a LOT of users. >> As noted >> previously, API changes that break code or tests will NOT be >> allowed in this >> release series. If you think there is a design flaw: take a deep >> breath. >> There is no need to rush. See #3 below. >> >> 3) We intend on having regular point releases (about every 3-4 >> months) for >> bug fixes and some added functionality (as long as it does not >> change the >> API and can be supported). If your module's or code's API is in a >> state >> that may change, please consider waiting until a later point release. >> >> 1.6 has been a long time coming. We made the point early on for this >> release that the focus was primarily to be on bug fixes; >> enhancements would >> only be included if they come with and can pass all new and current >> tests. >> >> chris >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Wed Dec 10 15:27:34 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 10 Dec 2008 20:27:34 +0000 Subject: [Bioperl-l] For the 1.6 release... In-Reply-To: <34BA7B99-BB11-4325-9B66-F8690CF3227C@illinois.edu> References: <34BA7B99-BB11-4325-9B66-F8690CF3227C@illinois.edu> Message-ID: <49402636.9000803@sendu.me.uk> Chris Fields wrote: > Just to note for anyone not subscribed to the dev list, The what now? > We are seeing some very promising code from new devs. However, we don't > want subtle bugs sneaking in with rushed code at the last minute. This > means: > > 1) Any new modules and functionality trying to make it into the initial > 1.6 release at the last minute still need to pass *all* tests, not just > the ones in a particular test file. Yuh, I have a bunch of modules that need committing, just need to write the test scripts. Can you give me some idea when you plan to tag 1.6 so I can give myself a deadline to get that done? Cheers, Sendu. From David.Messina at sbc.su.se Wed Dec 10 15:34:21 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 10 Dec 2008 21:34:21 +0100 Subject: [Bioperl-l] Build.PL, 'requires', 'recommends', and optional modules In-Reply-To: References: <628aabb70812100943q74f80973g7c17f4a49a834b6f@mail.gmail.com> Message-ID: <628aabb70812101234t6f0ed1f8x22b525664bcd9deb@mail.gmail.com> > > Sorry, been caught up with non-bioperl-related work. The nerve! > You definitely want 'Recommends'; this module isn't required for core > functionality. > OK, thanks. > Literally just added in. I'm still working out semantics on these modules > off-list with Marian (trying to remove the Statistics::Frequency dep), but > if you want you can go ahead and add in the additional dependencies and I'll > correct it later. > Nope, no need for me to jump in here before you guys are done -- I'm happy to wait. D From bix at sendu.me.uk Wed Dec 10 15:42:38 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 10 Dec 2008 20:42:38 +0000 Subject: [Bioperl-l] Build.PL, 'requires', 'recommends', and optional modules In-Reply-To: <628aabb70812100943q74f80973g7c17f4a49a834b6f@mail.gmail.com> References: <628aabb70812100943q74f80973g7c17f4a49a834b6f@mail.gmail.com> Message-ID: <494029BE.4060403@sendu.me.uk> Dave Messina wrote: > Hey everyone, > So in testing the latest bioperl-live, I noticed that there's a new > dependency for Microarray::Tools::ReseqChip, namely Statistics::Frequency. > > I seem to remember at some point during the Build process, I would get > prompted if I want to install optional modules, but I wasn't, and poking > around in the Module::Build docs I couldn't find the details. Module::Build doesn't have that (installation) functionality. But see below. > Since, according to the docs for Microarray::Tools::ReseqChip indicate it > relies on Statistics::Frequency, I think S::F should go in the 'requires' > block in Build.PL, right? > > And wouldn't that also be true for the other external dependencies of > M::T::ReseqChip, Spreadsheet::ParseExcel and Spreadsheet::WriteExcel? > > Or do all three of those go in 'recommends'? Recommends. The idea being, with BioPerl currently being as monolithic as it is, not all users are going to want to use all modules within it. We don't want to complicate their installation by having tons of external dependencies if they never even use the BioPerl modules that cause those deps. Not everyone will use B::M::T::ReseqChip, so we don't force them to install S::F - we only recommend they do. BioPerl installation now happens through Bio::Root::Build, which is a subclass of Module::Build that lets users make an informed choice about what to install. It has a system that detects missing deps, installs them if they're required, and asks the user if they want to install any of the recommended deps. Importantly, when it asks it explains what BioPerl module(s) need that dep, hence the 'informed' choice. Hope that's clearer (does this need explanation on the wiki somewhere, do I need to add POD docs to B::R::Build?), Sendu. From cjfields at illinois.edu Wed Dec 10 15:48:11 2008 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 10 Dec 2008 14:48:11 -0600 Subject: [Bioperl-l] For the 1.6 release... In-Reply-To: <49402636.9000803@sendu.me.uk> References: <34BA7B99-BB11-4325-9B66-F8690CF3227C@illinois.edu> <49402636.9000803@sendu.me.uk> Message-ID: On Dec 10, 2008, at 2:27 PM, Sendu Bala wrote: > Chris Fields wrote: >> Just to note for anyone not subscribed to the dev list, > > The what now? bioperl-guts-l. Not leaving anyone out of the loop. ;> >> We are seeing some very promising code from new devs. However, we >> don't want subtle bugs sneaking in with rushed code at the last >> minute. This means: >> 1) Any new modules and functionality trying to make it into the >> initial 1.6 release at the last minute still need to pass *all* >> tests, not just the ones in a particular test file. > > Yuh, I have a bunch of modules that need committing, just need to > write the test scripts. Can you give me some idea when you plan to > tag 1.6 so I can give myself a deadline to get that done? > > > Cheers, > Sendu. Middle next week sound good? Gives me more time to write up some tests myself. chris From bix at sendu.me.uk Wed Dec 10 15:50:20 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 10 Dec 2008 20:50:20 +0000 Subject: [Bioperl-l] For the 1.6 release... In-Reply-To: References: <34BA7B99-BB11-4325-9B66-F8690CF3227C@illinois.edu> <49402636.9000803@sendu.me.uk> Message-ID: <49402B8C.6060903@sendu.me.uk> Chris Fields wrote: > On Dec 10, 2008, at 2:27 PM, Sendu Bala wrote: >> Yuh, I have a bunch of modules that need committing, just need to >> write the test scripts. Can you give me some idea when you plan to tag >> 1.6 so I can give myself a deadline to get that done? > > Middle next week sound good? Gives me more time to write up some tests > myself. That's great, thanks. I'll try to get them done this week in any case. From cjfields at illinois.edu Wed Dec 10 15:52:24 2008 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 10 Dec 2008 14:52:24 -0600 Subject: [Bioperl-l] Build.PL, 'requires', 'recommends', and optional modules In-Reply-To: <494029BE.4060403@sendu.me.uk> References: <628aabb70812100943q74f80973g7c17f4a49a834b6f@mail.gmail.com> <494029BE.4060403@sendu.me.uk> Message-ID: On Dec 10, 2008, at 2:42 PM, Sendu Bala wrote: ... > BioPerl installation now happens through Bio::Root::Build, which is > a subclass of Module::Build that lets users make an informed choice > about what to install. It has a system that detects missing deps, > installs them if they're required, and asks the user if they want to > install any of the recommended deps. Importantly, when it asks it > explains what BioPerl module(s) need that dep, hence the 'informed' > choice. > > Hope that's clearer (does this need explanation on the wiki > somewhere, do I need to add POD docs to B::R::Build?), > Sendu. Maybe. It's not critical for release, and it is fairly specific for developers. This will definitley become more important when we split up things after 1.6 is out (e.g. every split should migrate to using Bio::Root::Build). chris From David.Messina at sbc.su.se Wed Dec 10 16:03:36 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 10 Dec 2008 22:03:36 +0100 Subject: [Bioperl-l] Build.PL, 'requires', 'recommends', and optional modules In-Reply-To: References: <628aabb70812100943q74f80973g7c17f4a49a834b6f@mail.gmail.com> <494029BE.4060403@sendu.me.uk> Message-ID: <628aabb70812101303k747a7a82q74c743aaaa8124fe@mail.gmail.com> Thanks, Sendu -- that's the info I needed. From lorigardnerwilson at earthlink.net Wed Dec 10 14:00:07 2008 From: lorigardnerwilson at earthlink.net (Lori G. Wilson) Date: Wed, 10 Dec 2008 11:00:07 -0800 Subject: [Bioperl-l] Trying to install bioPerl-db on Windows XP Message-ID: <494011B7.3020306@earthlink.net> I believe I have run all the prerequistes and am now attempting: build test I have attached a screen shot of the errors I'm getting. The only error seems to be: Can't locate object method "new" via package "Bio::DB::DBI::Oracle" (perhaps you forgot to load "Bio::DB::DBI::oracle"?) at ...\blib\lib/Bio/DB/SimpleDBContext.pm line 368. My SimpleDBContext.pm is attached. Line 368 is: $self->{'dbi'} = $dbimod->new(-dbcontext => $self); What do you suggest? Thank you, Lori 510-685-6571 -------------- next part -------------- A non-text attachment was scrubbed... Name: bioperl-dbError.jpg Type: image/jpeg Size: 119011 bytes Desc: not available URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: SimpleDBContext.pm URL: From lorigardnerwilson at earthlink.net Wed Dec 10 15:06:07 2008 From: lorigardnerwilson at earthlink.net (Lori G. Wilson) Date: Wed, 10 Dec 2008 12:06:07 -0800 Subject: [Bioperl-l] Trying to install bioPerl-db on Windows XP In-Reply-To: <494011B7.3020306@earthlink.net> References: <494011B7.3020306@earthlink.net> Message-ID: <4940212F.4070305@earthlink.net> Hello, I solved my previous problem (the driver was "Oracle" not "oracle"), but I hit another snag (see attached). How do these parameters: { 'port' => '1521', 'schema_sql' => ['../biosql-schema/sql/biosqldb-mysql.sql'], 'dbname' => 'biolori', 'host' => 'Shanie', 'database' => 'biosql', 'password' => 'password', 'user' => 'biolori at pennant', 'driver' => 'Oracle', } relate to the following excerpt from my TNSNames.ora file? PENNANT = (DESCRIPTION = (ADDRESS = (PROTOCOL = TCP)(HOST = Shanie)(PORT = 1521)) (CONNECT_DATA = (SERVER = DEDICATED) (SERVICE_NAME = pennant.Shanie) ) ) Thanks again, Lori Lori G. Wilson wrote: > I believe I have run all the prerequistes and am now attempting: > > build test > > I have attached a screen shot of the errors I'm getting. The only > error seems to be: > > Can't locate object method "new" via package "Bio::DB::DBI::Oracle" > (perhaps you forgot to load "Bio::DB::DBI::oracle"?) at > ...\blib\lib/Bio/DB/SimpleDBContext.pm line 368. > My SimpleDBContext.pm is attached. Line 368 is: > > $self->{'dbi'} = $dbimod->new(-dbcontext => $self); > > What do you suggest? > > Thank you, > > Lori > 510-685-6571 -------------- next part -------------- A non-text attachment was scrubbed... Name: bioperl-dbError2.jpg Type: image/jpeg Size: 319277 bytes Desc: not available URL: From Marian.thieme at klinik.uni-regensburg.de Thu Dec 11 05:12:42 2008 From: Marian.thieme at klinik.uni-regensburg.de (Marian thieme) Date: Thu, 11 Dec 2008 11:12:42 +0100 Subject: [Bioperl-l] Fwd: [Bioperl-guts-l] [15134] bioperl-live/trunk/Bio/Microarray/Tools: use superclasses initialization and argument processing/ attribute setting as suggested in styleguide In-Reply-To: <1952AD80-A0E9-4183-AFF0-4D0064F57584@illinois.edu> References: <200812101410.mBAEALFw011802@dev.open-bio.org> <1952AD80-A0E9-4183-AFF0-4D0064F57584@illinois.edu> Message-ID: <4940F5AA020000C50007741D@gwsmtp2.uni-regensburg.de> I also had the impression that "it" was discouraged to use bioperl for microarray processing. As I know from my colleagues and also I did to good extemt) people use R (especially Bioconductor) for most of the issues concerning microarrays. (there are so many supoorted microarray designs, preprocessing and normalization tools, and complete packages to perform differential expression analysis). At least for the expression chips but also for genotyping/SNP chips I think R/BioC is method of choice. Probably for the resequencing chips they are not that well supported, because its only a minority that uses this kind of chips. Therefore I think ReseqChip has its right to exist, even though it would reach more people if it would a R/BioC package. (Moreover I believe that this kind of chips wont have broader interest, because second generation sequencing methods will probably be more appropriate in the next few years) So to cut a long story short, I find Chris' idea of bridging bioperl to BioC (or vice versa) very good: Dont compete against R/BioC, but make it easier to use both together. marian Marian Thieme Institute of Functional Genomics University Regensburg Josef Engert Str. 9 93053 Regensburg Germany P: 0049 (0)941 943 1584 F: 0049 (0)941 943 5020 E: marian.thieme at klinik.uni-regensburg.de W: http://www-cgi.uni-regensburg.de/Klinik/FunktionelleGenomik >>> Chris Fields 12/10/2008 7:59 PM >>> Sounds like a good idea, with one caveat: Allen had pretty much given up on bioperl-microarray last I heard (last significant commits were ~6 yrs ago). It would be nice to revive with this theme in mind, though maybe bioperl-expression would be better (could focus on other expression-related issues along with microarray data). Marian, what do you think? chris P.S. An aside: I'm planning on running lots of Illumina data myself and have been thinking about making a BioC-BioPerl bridge, then seeing how it fits into a bioperl-microarray. Just need a working perl-R interface (NOT RSPerl). On Dec 10, 2008, at 12:42 PM, Jason Stajich wrote: > Since we've started discussing the idea of starting to move things > out into smaller packages, does it make sense to move this > Bio::Microarray into its own package before it gets bigger? What > about the old bioperl-microarray stuff from Allen Day? > > I also know that as we haven't branched for 1.6 Chris we'll have to > make some decisions about new code going in before then? > > Not trying to stifle any of the development with extra work but > trying to see if we should start to make some logical slices of > packages? > > -jason > > Begin forwarded message: > >> From: Marian Thieme >> Date: December 10, 2008 6:10:21 AM PST >> To: bioperl-guts-l at bioperl.org >> Subject: [Bioperl-guts-l] [15134] bioperl-live/trunk/Bio/Microarray/ >> Tools: use superclasses initialization and argument processing/ >> attribute setting as suggested in styleguide >> >> Revision: 15134 >> Author: thm09830 >> Date: 2008-12-10 09:10:21 -0500 (Wed, 10 Dec 2008) >> >> Log Message: >> ----------- >> use superclasses initialization and argument processing/attribute >> setting as suggested in styleguide >> >> Modified Paths: >> -------------- >> bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >> bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm >> >> Modified: bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >> =================================================================== >> --- bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >> 2008-12-10 12:51:47 UTC (rev 15133) >> +++ bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >> 2008-12-10 14:10:21 UTC (rev 15134) >> @@ -78,12 +78,13 @@ >> >> sub new { >> >> - my ($class, $file_name) = @_; >> - my $self = $class->SUPER::new(); >> + my ($class, @args) = @_; >> + my $self = $class->SUPER::new(@args); >> + my ($file_name)=$self->_rearrange([qw(AFFY_DESIGN_FILENAME)], >> @args); >> + >> $self->{_frags_hash}=undef; >> $self->{_oligos2calc_hash}=undef; >> $self->throw("Must provide filename as first argument !") unless >> $file_name; >> - >> >> my %max_ins_hash=(); >> $self->{_frags_hash}=$self- >> >_parse_Affy_mtDNA_design_annotation_file($file_name); >> >> Modified: bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm >> =================================================================== >> --- bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm 2008-12-10 >> 12:51:47 UTC (rev 15133) >> +++ bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm 2008-12-10 >> 14:10:21 UTC (rev 15134) >> @@ -194,8 +194,11 @@ >> >> sub new { >> >> - my ($class, $design_file_name, $format, $refseq_max_ins_hash, >> $refseq) = @_; >> - my $self = $class->SUPER::new(); >> + #my ($class, $design_file_name, $format, $refseq_max_ins_hash, >> $refseq) = @_; >> + my ($class, @args) = @_; >> + my $self = $class->SUPER::new(@args); >> + my ($design_file_name, $format, $refseq_max_ins_hash, $refseq)= >> $self->_rearrange([qw(AFFY_DESIGN_FILENAME FORMAT_OF_DESIGN_FILE >> MAX_INSERTION_HASH_REFERENCE REFERENCE_SEQUENCE)], @args); >> + >> $self->{_frags_hash}=undef; >> $self->{_max_ins_hash}=undef; >> $self->{_refseq}=undef; >> >> >> _______________________________________________ >> Bioperl-guts-l mailing list >> Bioperl-guts-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l > > Jason Stajich > jason at bioperl.org > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From hlapp at gmx.net Thu Dec 11 09:55:12 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 11 Dec 2008 09:55:12 -0500 Subject: [Bioperl-l] Trying to install bioPerl-db on Windows XP In-Reply-To: <4940212F.4070305@earthlink.net> References: <494011B7.3020306@earthlink.net> <4940212F.4070305@earthlink.net> Message-ID: <915B3B21-3E9F-4FCA-9B1A-E5FE374D0D28@gmx.net> For Oracle, the dbname parameter should be what you would otherwise use as SID (usually that's also the ORACLE_SID environment variable, and depending on the Oracle version TWO_TASK needs to be set too if the database is on a remote host). Note that if you have a tnsnames.ora file that has the SID defined then you shouldn't need to duplicate the respective parameters here. For example, in your case you shouldn't need to have port and host set (you could just comment them out). There is much more documentation for the individual parameters in DBHarness.conf.example. Looking at which, I realize that it says host is mandatory, which is wrong. (In fact, for MySQL and PostgreSQL, leaving host undef versus setting it to localhost is not the same.) Let me know if that will solve the problem. -hilmar On Dec 10, 2008, at 3:06 PM, Lori G. Wilson wrote: > Hello, > > I solved my previous problem (the driver was "Oracle" not "oracle"), > but I hit another snag (see attached). How do these parameters: > > { > 'port' => '1521', > 'schema_sql' => ['../biosql-schema/sql/biosqldb-mysql.sql'], > 'dbname' => 'biolori', > 'host' => 'Shanie', > 'database' => 'biosql', > 'password' => 'password', > 'user' => 'biolori at pennant', > 'driver' => 'Oracle', > } > > relate to the following excerpt from my TNSNames.ora file? > > PENNANT = > (DESCRIPTION = > (ADDRESS = (PROTOCOL = TCP)(HOST = Shanie)(PORT = 1521)) > (CONNECT_DATA = > (SERVER = DEDICATED) > (SERVICE_NAME = pennant.Shanie) > ) > ) > > Thanks again, > > Lori > > > Lori G. Wilson wrote: > >> I believe I have run all the prerequistes and am now attempting: >> >> build test >> >> I have attached a screen shot of the errors I'm getting. The only >> error seems to be: >> >> Can't locate object method "new" via package >> "Bio::DB::DBI::Oracle" (perhaps you forgot to load >> "Bio::DB::DBI::oracle"?) at ...\blib\lib/Bio/DB/SimpleDBContext.pm >> line 368. >> My SimpleDBContext.pm is attached. Line 368 is: >> >> $self->{'dbi'} = $dbimod->new(-dbcontext => $self); >> >> What do you suggest? >> >> Thank you, >> >> Lori >> 510-685-6571 > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at illinois.edu Thu Dec 11 09:55:36 2008 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 11 Dec 2008 08:55:36 -0600 Subject: [Bioperl-l] Fwd: [Bioperl-guts-l] [15134] bioperl-live/trunk/Bio/Microarray/Tools: use superclasses initialization and argument processing/ attribute setting as suggested in styleguide In-Reply-To: <4940F5AA020000C50007741D@gwsmtp2.uni-regensburg.de> References: <200812101410.mBAEALFw011802@dev.open-bio.org> <1952AD80-A0E9-4183-AFF0-4D0064F57584@illinois.edu> <4940F5AA020000C50007741D@gwsmtp2.uni-regensburg.de> Message-ID: <2F046501-87F0-41D1-A561-0DD8BCE25B92@illinois.edu> Just need a decently-supported perl-R package to help along those lines. RSPerl might work, but I find it too problematic to work with on my Mac OS and it isn't well-supported (doesn't find my local perl installation so mixes libraries and, well, crashes during compilation). The best bridging would generically bring R into perl (and BioC into BioPerl). Statistics::R is a pure perl method but it appears pretty messy. I may toy around with an XS-based solution myself after 1.6 is out. chris On Dec 11, 2008, at 4:12 AM, Marian thieme wrote: > I also had the impression that "it" was discouraged to use bioperl > for microarray processing. > As I know from my colleagues and also I did to good extemt) people > use R (especially Bioconductor) for most of the issues concerning > microarrays. (there are so many supoorted microarray designs, > preprocessing and normalization tools, and complete packages to > perform differential expression analysis). At least for the > expression chips but also for genotyping/SNP chips I think R/BioC is > method of choice. Probably for the resequencing chips they are not > that well supported, because its only a minority that uses this kind > of chips. Therefore I think ReseqChip has its right to exist, even > though it would reach more people if it would a R/BioC package. > (Moreover I believe that this kind of chips wont have broader > interest, because second generation sequencing methods will probably > be more appropriate in the next few years) > So to cut a long story short, I find Chris' idea of bridging bioperl > to BioC (or vice versa) very good: Dont compete against R/BioC, but > make it easier to use both together. > > marian > > > Marian Thieme > Institute of Functional Genomics > University Regensburg > Josef Engert Str. 9 > 93053 > Regensburg > Germany > P: 0049 (0)941 943 1584 > F: 0049 (0)941 943 5020 > E: marian.thieme at klinik.uni-regensburg.de > W: http://www-cgi.uni-regensburg.de/Klinik/FunktionelleGenomik > > >>>> Chris Fields 12/10/2008 7:59 PM >>> > Sounds like a good idea, with one caveat: Allen had pretty much given > up on bioperl-microarray last I heard (last significant commits were > ~6 yrs ago). It would be nice to revive with this theme in mind, > though maybe bioperl-expression would be better (could focus on other > expression-related issues along with microarray data). Marian, what > do you think? > > chris > > P.S. An aside: I'm planning on running lots of Illumina data myself > and have been thinking about making a BioC-BioPerl bridge, then seeing > how it fits into a bioperl-microarray. Just need a working perl-R > interface (NOT RSPerl). > > On Dec 10, 2008, at 12:42 PM, Jason Stajich wrote: > >> Since we've started discussing the idea of starting to move things >> out into smaller packages, does it make sense to move this >> Bio::Microarray into its own package before it gets bigger? What >> about the old bioperl-microarray stuff from Allen Day? >> >> I also know that as we haven't branched for 1.6 Chris we'll have to >> make some decisions about new code going in before then? >> >> Not trying to stifle any of the development with extra work but >> trying to see if we should start to make some logical slices of >> packages? >> >> -jason >> >> Begin forwarded message: >> >>> From: Marian Thieme >>> Date: December 10, 2008 6:10:21 AM PST >>> To: bioperl-guts-l at bioperl.org >>> Subject: [Bioperl-guts-l] [15134] bioperl-live/trunk/Bio/Microarray/ >>> Tools: use superclasses initialization and argument processing/ >>> attribute setting as suggested in styleguide >>> >>> Revision: 15134 >>> Author: thm09830 >>> Date: 2008-12-10 09:10:21 -0500 (Wed, 10 Dec 2008) >>> >>> Log Message: >>> ----------- >>> use superclasses initialization and argument processing/attribute >>> setting as suggested in styleguide >>> >>> Modified Paths: >>> -------------- >>> bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >>> bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm >>> >>> Modified: bioperl-live/trunk/Bio/Microarray/Tools/ >>> MitoChipV2Parser.pm >>> =================================================================== >>> --- bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >>> 2008-12-10 12:51:47 UTC (rev 15133) >>> +++ bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >>> 2008-12-10 14:10:21 UTC (rev 15134) >>> @@ -78,12 +78,13 @@ >>> >>> sub new { >>> >>> - my ($class, $file_name) = @_; >>> - my $self = $class->SUPER::new(); >>> + my ($class, @args) = @_; >>> + my $self = $class->SUPER::new(@args); >>> + my ($file_name)=$self->_rearrange([qw(AFFY_DESIGN_FILENAME)], >>> @args); >>> + >>> $self->{_frags_hash}=undef; >>> $self->{_oligos2calc_hash}=undef; >>> $self->throw("Must provide filename as first argument !") unless >>> $file_name; >>> - >>> >>> my %max_ins_hash=(); >>> $self->{_frags_hash}=$self- >>>> _parse_Affy_mtDNA_design_annotation_file($file_name); >>> >>> Modified: bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm >>> =================================================================== >>> --- bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm 2008-12-10 >>> 12:51:47 UTC (rev 15133) >>> +++ bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm 2008-12-10 >>> 14:10:21 UTC (rev 15134) >>> @@ -194,8 +194,11 @@ >>> >>> sub new { >>> >>> - my ($class, $design_file_name, $format, $refseq_max_ins_hash, >>> $refseq) = @_; >>> - my $self = $class->SUPER::new(); >>> + #my ($class, $design_file_name, $format, $refseq_max_ins_hash, >>> $refseq) = @_; >>> + my ($class, @args) = @_; >>> + my $self = $class->SUPER::new(@args); >>> + my ($design_file_name, $format, $refseq_max_ins_hash, $refseq)= >>> $self->_rearrange([qw(AFFY_DESIGN_FILENAME FORMAT_OF_DESIGN_FILE >>> MAX_INSERTION_HASH_REFERENCE REFERENCE_SEQUENCE)], @args); >>> + >>> $self->{_frags_hash}=undef; >>> $self->{_max_ins_hash}=undef; >>> $self->{_refseq}=undef; >>> >>> >>> _______________________________________________ >>> Bioperl-guts-l mailing list >>> Bioperl-guts-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l >> >> Jason Stajich >> jason at bioperl.org >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From hlapp at gmx.net Thu Dec 11 10:19:48 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 11 Dec 2008 10:19:48 -0500 Subject: [Bioperl-l] Fwd: [Bioperl-guts-l] [15134] bioperl-live/trunk/Bio/Microarray/Tools: use superclasses initialization and argument processing/ attribute setting as suggested in styleguide In-Reply-To: <2F046501-87F0-41D1-A561-0DD8BCE25B92@illinois.edu> References: <200812101410.mBAEALFw011802@dev.open-bio.org> <1952AD80-A0E9-4183-AFF0-4D0064F57584@illinois.edu> <4940F5AA020000C50007741D@gwsmtp2.uni-regensburg.de> <2F046501-87F0-41D1-A561-0DD8BCE25B92@illinois.edu> Message-ID: You guys do know about the BioLib project? http://biolib.open-bio.org/wiki/Main_Page Bridging R and BioC to the Bio* projects is one of the core goals if I remember correctly. -hilmar On Dec 11, 2008, at 9:55 AM, Chris Fields wrote: > Just need a decently-supported perl-R package to help along those > lines. RSPerl might work, but I find it too problematic to work > with on my Mac OS and it isn't well-supported (doesn't find my local > perl installation so mixes libraries and, well, crashes during > compilation). > > The best bridging would generically bring R into perl (and BioC into > BioPerl). Statistics::R is a pure perl method but it appears pretty > messy. I may toy around with an XS-based solution myself after 1.6 > is out. > > chris > > On Dec 11, 2008, at 4:12 AM, Marian thieme wrote: > >> I also had the impression that "it" was discouraged to use bioperl >> for microarray processing. >> As I know from my colleagues and also I did to good extemt) people >> use R (especially Bioconductor) for most of the issues concerning >> microarrays. (there are so many supoorted microarray designs, >> preprocessing and normalization tools, and complete packages to >> perform differential expression analysis). At least for the >> expression chips but also for genotyping/SNP chips I think R/BioC >> is method of choice. Probably for the resequencing chips they are >> not that well supported, because its only a minority that uses this >> kind of chips. Therefore I think ReseqChip has its right to exist, >> even though it would reach more people if it would a R/BioC >> package. (Moreover I believe that this kind of chips wont have >> broader interest, because second generation sequencing methods will >> probably be more appropriate in the next few years) >> So to cut a long story short, I find Chris' idea of bridging >> bioperl to BioC (or vice versa) very good: Dont compete against R/ >> BioC, but make it easier to use both together. >> >> marian >> >> >> Marian Thieme >> Institute of Functional Genomics >> University Regensburg >> Josef Engert Str. 9 >> 93053 >> Regensburg >> Germany >> P: 0049 (0)941 943 1584 >> F: 0049 (0)941 943 5020 >> E: marian.thieme at klinik.uni-regensburg.de >> W: http://www-cgi.uni-regensburg.de/Klinik/FunktionelleGenomik >> >> >>>>> Chris Fields 12/10/2008 7:59 PM >>> >> Sounds like a good idea, with one caveat: Allen had pretty much given >> up on bioperl-microarray last I heard (last significant commits were >> ~6 yrs ago). It would be nice to revive with this theme in mind, >> though maybe bioperl-expression would be better (could focus on other >> expression-related issues along with microarray data). Marian, what >> do you think? >> >> chris >> >> P.S. An aside: I'm planning on running lots of Illumina data myself >> and have been thinking about making a BioC-BioPerl bridge, then >> seeing >> how it fits into a bioperl-microarray. Just need a working perl-R >> interface (NOT RSPerl). >> >> On Dec 10, 2008, at 12:42 PM, Jason Stajich wrote: >> >>> Since we've started discussing the idea of starting to move things >>> out into smaller packages, does it make sense to move this >>> Bio::Microarray into its own package before it gets bigger? What >>> about the old bioperl-microarray stuff from Allen Day? >>> >>> I also know that as we haven't branched for 1.6 Chris we'll have to >>> make some decisions about new code going in before then? >>> >>> Not trying to stifle any of the development with extra work but >>> trying to see if we should start to make some logical slices of >>> packages? >>> >>> -jason >>> >>> Begin forwarded message: >>> >>>> From: Marian Thieme >>>> Date: December 10, 2008 6:10:21 AM PST >>>> To: bioperl-guts-l at bioperl.org >>>> Subject: [Bioperl-guts-l] [15134] bioperl-live/trunk/Bio/ >>>> Microarray/ >>>> Tools: use superclasses initialization and argument processing/ >>>> attribute setting as suggested in styleguide >>>> >>>> Revision: 15134 >>>> Author: thm09830 >>>> Date: 2008-12-10 09:10:21 -0500 (Wed, 10 Dec 2008) >>>> >>>> Log Message: >>>> ----------- >>>> use superclasses initialization and argument processing/attribute >>>> setting as suggested in styleguide >>>> >>>> Modified Paths: >>>> -------------- >>>> bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >>>> bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm >>>> >>>> Modified: bioperl-live/trunk/Bio/Microarray/Tools/ >>>> MitoChipV2Parser.pm >>>> =================================================================== >>>> --- bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >>>> 2008-12-10 12:51:47 UTC (rev 15133) >>>> +++ bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >>>> 2008-12-10 14:10:21 UTC (rev 15134) >>>> @@ -78,12 +78,13 @@ >>>> >>>> sub new { >>>> >>>> - my ($class, $file_name) = @_; >>>> - my $self = $class->SUPER::new(); >>>> + my ($class, @args) = @_; >>>> + my $self = $class->SUPER::new(@args); >>>> + my ($file_name)=$self->_rearrange([qw(AFFY_DESIGN_FILENAME)], >>>> @args); >>>> + >>>> $self->{_frags_hash}=undef; >>>> $self->{_oligos2calc_hash}=undef; >>>> $self->throw("Must provide filename as first argument !") unless >>>> $file_name; >>>> - >>>> >>>> my %max_ins_hash=(); >>>> $self->{_frags_hash}=$self- >>>>> _parse_Affy_mtDNA_design_annotation_file($file_name); >>>> >>>> Modified: bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm >>>> =================================================================== >>>> --- bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm 2008-12-10 >>>> 12:51:47 UTC (rev 15133) >>>> +++ bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm 2008-12-10 >>>> 14:10:21 UTC (rev 15134) >>>> @@ -194,8 +194,11 @@ >>>> >>>> sub new { >>>> >>>> - my ($class, $design_file_name, $format, $refseq_max_ins_hash, >>>> $refseq) = @_; >>>> - my $self = $class->SUPER::new(); >>>> + #my ($class, $design_file_name, $format, $refseq_max_ins_hash, >>>> $refseq) = @_; >>>> + my ($class, @args) = @_; >>>> + my $self = $class->SUPER::new(@args); >>>> + my ($design_file_name, $format, $refseq_max_ins_hash, $refseq)= >>>> $self->_rearrange([qw(AFFY_DESIGN_FILENAME FORMAT_OF_DESIGN_FILE >>>> MAX_INSERTION_HASH_REFERENCE REFERENCE_SEQUENCE)], @args); >>>> + >>>> $self->{_frags_hash}=undef; >>>> $self->{_max_ins_hash}=undef; >>>> $self->{_refseq}=undef; >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-guts-l mailing list >>>> Bioperl-guts-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l >>> >>> Jason Stajich >>> jason at bioperl.org >>> >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From ian.simpson at ed.ac.uk Thu Dec 11 10:19:20 2008 From: ian.simpson at ed.ac.uk (Dr. T. I. Simpson) Date: Thu, 11 Dec 2008 15:19:20 -0000 Subject: [Bioperl-l] Fwd: [Bioperl-guts-l] [15134] bioperl-live/trunk/Bio/Microarray/Tools: use superclasses initialization and argument processing/ attribute setting as suggested in styleguide In-Reply-To: <4940F5AA020000C50007741D@gwsmtp2.uni-regensburg.de> References: <200812101410.mBAEALFw011802@dev.open-bio.org> <1952AD80-A0E9-4183-AFF0-4D0064F57584@illinois.edu> <4940F5AA020000C50007741D@gwsmtp2.uni-regensburg.de> Message-ID: Hi guys, I am a newbie on here so hope this mail is appropriate. Just thought I would chip in here (sorry for the pun). I would like to echo Marian's comments. I work extensively with R/BioC and Perl taking experimental data from low-level array to lots of different downstream analyses. I made an effort to work with R through Perl about a year ago using RSPerl and it was mighty painful. As Marian suggests it wouldn't be a good idea to compete with R/BioC there are some absolutely gold standard packages like affy, affyPLM and limma to name just three that cope with serious statistics within the R environment. If it were possible to make a good bridge to execute R scripts and access/manipulate R variables (a run wrapper module for R ?) then that would be a very significant step forward for someone like me. I don't know how skillfully I could contribute to this, but happy to help wherever I can. Best wishes Ian. On Thu, 11 Dec 2008 10:12:42 -0000, Marian thieme wrote: > I also had the impression that "it" was discouraged to use bioperl for > microarray processing. > As I know from my colleagues and also I did to good extemt) people use R > (especially Bioconductor) for most of the issues concerning microarrays. > (there are so many supoorted microarray designs, preprocessing and > normalization tools, and complete packages to perform differential > expression analysis). At least for the expression chips but also for > genotyping/SNP chips I think R/BioC is method of choice. Probably for > the resequencing chips they are not that well supported, because its > only a minority that uses this kind of chips. Therefore I think > ReseqChip has its right to exist, even though it would reach more people > if it would a R/BioC package. (Moreover I believe that this kind of > chips wont have broader interest, because second generation sequencing > methods will probably be more appropriate in the next few years) > So to cut a long story short, I find Chris' idea of bridging bioperl to > BioC (or vice versa) very good: Dont compete against R/BioC, but make it > easier to use both together. > > marian > > Marian Thieme > Institute of Functional Genomics > University Regensburg > Josef Engert Str. 9 > 93053 > Regensburg > Germany > P: 0049 (0)941 943 1584 > F: 0049 (0)941 943 5020 > E: marian.thieme at klinik.uni-regensburg.de > W: http://www-cgi.uni-regensburg.de/Klinik/FunktionelleGenomik > > >>>> Chris Fields 12/10/2008 7:59 PM >>> > Sounds like a good idea, with one caveat: Allen had pretty much given > up on bioperl-microarray last I heard (last significant commits were > ~6 yrs ago). It would be nice to revive with this theme in mind, > though maybe bioperl-expression would be better (could focus on other > expression-related issues along with microarray data). Marian, what > do you think? > > chris > > P.S. An aside: I'm planning on running lots of Illumina data myself > and have been thinking about making a BioC-BioPerl bridge, then seeing > how it fits into a bioperl-microarray. Just need a working perl-R > interface (NOT RSPerl). > > On Dec 10, 2008, at 12:42 PM, Jason Stajich wrote: > >> Since we've started discussing the idea of starting to move things >> out into smaller packages, does it make sense to move this >> Bio::Microarray into its own package before it gets bigger? What >> about the old bioperl-microarray stuff from Allen Day? >> >> I also know that as we haven't branched for 1.6 Chris we'll have to >> make some decisions about new code going in before then? >> >> Not trying to stifle any of the development with extra work but >> trying to see if we should start to make some logical slices of >> packages? >> >> -jason >> >> Begin forwarded message: >> >>> From: Marian Thieme >>> Date: December 10, 2008 6:10:21 AM PST >>> To: bioperl-guts-l at bioperl.org >>> Subject: [Bioperl-guts-l] [15134] bioperl-live/trunk/Bio/Microarray/ >>> Tools: use superclasses initialization and argument processing/ >>> attribute setting as suggested in styleguide >>> >>> Revision: 15134 >>> Author: thm09830 >>> Date: 2008-12-10 09:10:21 -0500 (Wed, 10 Dec 2008) >>> >>> Log Message: >>> ----------- >>> use superclasses initialization and argument processing/attribute >>> setting as suggested in styleguide >>> >>> Modified Paths: >>> -------------- >>> bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >>> bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm >>> >>> Modified: bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >>> =================================================================== >>> --- bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >>> 2008-12-10 12:51:47 UTC (rev 15133) >>> +++ bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >>> 2008-12-10 14:10:21 UTC (rev 15134) >>> @@ -78,12 +78,13 @@ >>> >>> sub new { >>> >>> - my ($class, $file_name) = @_; >>> - my $self = $class->SUPER::new(); >>> + my ($class, @args) = @_; >>> + my $self = $class->SUPER::new(@args); >>> + my ($file_name)=$self->_rearrange([qw(AFFY_DESIGN_FILENAME)], >>> @args); >>> + >>> $self->{_frags_hash}=undef; >>> $self->{_oligos2calc_hash}=undef; >>> $self->throw("Must provide filename as first argument !") unless >>> $file_name; >>> - >>> >>> my %max_ins_hash=(); >>> $self->{_frags_hash}=$self- >>> >_parse_Affy_mtDNA_design_annotation_file($file_name); >>> >>> Modified: bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm >>> =================================================================== >>> --- bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm 2008-12-10 >>> 12:51:47 UTC (rev 15133) >>> +++ bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm 2008-12-10 >>> 14:10:21 UTC (rev 15134) >>> @@ -194,8 +194,11 @@ >>> >>> sub new { >>> >>> - my ($class, $design_file_name, $format, $refseq_max_ins_hash, >>> $refseq) = @_; >>> - my $self = $class->SUPER::new(); >>> + #my ($class, $design_file_name, $format, $refseq_max_ins_hash, >>> $refseq) = @_; >>> + my ($class, @args) = @_; >>> + my $self = $class->SUPER::new(@args); >>> + my ($design_file_name, $format, $refseq_max_ins_hash, $refseq)= >>> $self->_rearrange([qw(AFFY_DESIGN_FILENAME FORMAT_OF_DESIGN_FILE >>> MAX_INSERTION_HASH_REFERENCE REFERENCE_SEQUENCE)], @args); >>> + >>> $self->{_frags_hash}=undef; >>> $self->{_max_ins_hash}=undef; >>> $self->{_refseq}=undef; >>> >>> >>> _______________________________________________ >>> Bioperl-guts-l mailing list >>> Bioperl-guts-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l >> >> Jason Stajich >> jason at bioperl.org >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Dr T.I.Simpson School of Biomedical Sciences University of Edinburgh Hugh Robson Building George Square Edinburgh EH8 9XD ian.simpson at ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From cjfields at illinois.edu Thu Dec 11 11:32:40 2008 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 11 Dec 2008 10:32:40 -0600 Subject: [Bioperl-l] BioC and BioPerl Re: Fwd: [Bioperl-guts-l] [15134] yadayadayada In-Reply-To: References: <200812101410.mBAEALFw011802@dev.open-bio.org> <1952AD80-A0E9-4183-AFF0-4D0064F57584@illinois.edu> <4940F5AA020000C50007741D@gwsmtp2.uni-regensburg.de> <2F046501-87F0-41D1-A561-0DD8BCE25B92@illinois.edu> Message-ID: <47CD18F1-177B-489A-9BA5-C1AEDF838031@illinois.edu> Oops, my bad. This does involve R's affyio. Will have to investigate after 1.6. http://github.com/pjotrp/biolib/tree/master/src/clibs/affyio-1.8/README_BIOLIB chris On Dec 11, 2008, at 10:27 AM, Chris Fields wrote: > Yes. This is the way I intended to go (swig-based, so can apply to > other Bio*). The initial release already has some links to the > affymetrix library (http://biolib.open-bio.org/wiki/ > BioLib_Affymetrix), but that's independent of R. > > chris > > On Dec 11, 2008, at 9:19 AM, Hilmar Lapp wrote: > >> You guys do know about the BioLib project? >> >> http://biolib.open-bio.org/wiki/Main_Page >> >> Bridging R and BioC to the Bio* projects is one of the core goals >> if I remember correctly. >> >> -hilmar >> >> On Dec 11, 2008, at 9:55 AM, Chris Fields wrote: >> >>> Just need a decently-supported perl-R package to help along those >>> lines. RSPerl might work, but I find it too problematic to work >>> with on my Mac OS and it isn't well-supported (doesn't find my >>> local perl installation so mixes libraries and, well, crashes >>> during compilation). >>> >>> The best bridging would generically bring R into perl (and BioC >>> into BioPerl). Statistics::R is a pure perl method but it appears >>> pretty messy. I may toy around with an XS-based solution myself >>> after 1.6 is out. >>> >>> chris >>> >>> On Dec 11, 2008, at 4:12 AM, Marian thieme wrote: >>> >>>> I also had the impression that "it" was discouraged to use >>>> bioperl for microarray processing. >>>> As I know from my colleagues and also I did to good extemt) >>>> people use R (especially Bioconductor) for most of the issues >>>> concerning microarrays. (there are so many supoorted microarray >>>> designs, preprocessing and normalization tools, and complete >>>> packages to perform differential expression analysis). At least >>>> for the expression chips but also for genotyping/SNP chips I >>>> think R/BioC is method of choice. Probably for the resequencing >>>> chips they are not that well supported, because its only a >>>> minority that uses this kind of chips. Therefore I think >>>> ReseqChip has its right to exist, even though it would reach more >>>> people if it would a R/BioC package. (Moreover I believe that >>>> this kind of chips wont have broader interest, because second >>>> generation sequencing methods will probably be more appropriate >>>> in the next few years) >>>> So to cut a long story short, I find Chris' idea of bridging >>>> bioperl to BioC (or vice versa) very good: Dont compete against R/ >>>> BioC, but make it easier to use both together. >>>> >>>> marian >>>> >>>> >>>> Marian Thieme >>>> Institute of Functional Genomics >>>> University Regensburg >>>> Josef Engert Str. 9 >>>> 93053 >>>> Regensburg >>>> Germany >>>> P: 0049 (0)941 943 1584 >>>> F: 0049 (0)941 943 5020 >>>> E: marian.thieme at klinik.uni-regensburg.de >>>> W: http://www-cgi.uni-regensburg.de/Klinik/FunktionelleGenomik >>>> >>>> >>>>>>> Chris Fields 12/10/2008 7:59 PM >>> >>>> Sounds like a good idea, with one caveat: Allen had pretty much >>>> given >>>> up on bioperl-microarray last I heard (last significant commits >>>> were >>>> ~6 yrs ago). It would be nice to revive with this theme in mind, >>>> though maybe bioperl-expression would be better (could focus on >>>> other >>>> expression-related issues along with microarray data). Marian, >>>> what >>>> do you think? >>>> >>>> chris >>>> >>>> P.S. An aside: I'm planning on running lots of Illumina data myself >>>> and have been thinking about making a BioC-BioPerl bridge, then >>>> seeing >>>> how it fits into a bioperl-microarray. Just need a working perl-R >>>> interface (NOT RSPerl). >>>> >>>> On Dec 10, 2008, at 12:42 PM, Jason Stajich wrote: >>>> >>>>> Since we've started discussing the idea of starting to move things >>>>> out into smaller packages, does it make sense to move this >>>>> Bio::Microarray into its own package before it gets bigger? What >>>>> about the old bioperl-microarray stuff from Allen Day? >>>>> >>>>> I also know that as we haven't branched for 1.6 Chris we'll have >>>>> to >>>>> make some decisions about new code going in before then? >>>>> >>>>> Not trying to stifle any of the development with extra work but >>>>> trying to see if we should start to make some logical slices of >>>>> packages? >>>>> >>>>> -jason >>>>> >>>>> Begin forwarded message: >>>>> >>>>>> From: Marian Thieme >>>>>> Date: December 10, 2008 6:10:21 AM PST >>>>>> To: bioperl-guts-l at bioperl.org >>>>>> Subject: [Bioperl-guts-l] [15134] bioperl-live/trunk/Bio/ >>>>>> Microarray/ >>>>>> Tools: use superclasses initialization and argument processing/ >>>>>> attribute setting as suggested in styleguide >>>>>> >>>>>> Revision: 15134 >>>>>> Author: thm09830 >>>>>> Date: 2008-12-10 09:10:21 -0500 (Wed, 10 Dec 2008) >>>>>> >>>>>> Log Message: >>>>>> ----------- >>>>>> use superclasses initialization and argument processing/attribute >>>>>> setting as suggested in styleguide >>>>>> >>>>>> Modified Paths: >>>>>> -------------- >>>>>> bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >>>>>> bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm >>>>>> >>>>>> Modified: bioperl-live/trunk/Bio/Microarray/Tools/ >>>>>> MitoChipV2Parser.pm >>>>>> = >>>>>> = >>>>>> ================================================================= >>>>>> --- bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >>>>>> 2008-12-10 12:51:47 UTC (rev 15133) >>>>>> +++ bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >>>>>> 2008-12-10 14:10:21 UTC (rev 15134) >>>>>> @@ -78,12 +78,13 @@ >>>>>> >>>>>> sub new { >>>>>> >>>>>> - my ($class, $file_name) = @_; >>>>>> - my $self = $class->SUPER::new(); >>>>>> + my ($class, @args) = @_; >>>>>> + my $self = $class->SUPER::new(@args); >>>>>> + my ($file_name)=$self->_rearrange([qw(AFFY_DESIGN_FILENAME)], >>>>>> @args); >>>>>> + >>>>>> $self->{_frags_hash}=undef; >>>>>> $self->{_oligos2calc_hash}=undef; >>>>>> $self->throw("Must provide filename as first argument !") unless >>>>>> $file_name; >>>>>> - >>>>>> >>>>>> my %max_ins_hash=(); >>>>>> $self->{_frags_hash}=$self- >>>>>>> _parse_Affy_mtDNA_design_annotation_file($file_name); >>>>>> >>>>>> Modified: bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm >>>>>> = >>>>>> = >>>>>> ================================================================= >>>>>> --- bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm >>>>>> 2008-12-10 >>>>>> 12:51:47 UTC (rev 15133) >>>>>> +++ bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm >>>>>> 2008-12-10 >>>>>> 14:10:21 UTC (rev 15134) >>>>>> @@ -194,8 +194,11 @@ >>>>>> >>>>>> sub new { >>>>>> >>>>>> - my ($class, $design_file_name, $format, $refseq_max_ins_hash, >>>>>> $refseq) = @_; >>>>>> - my $self = $class->SUPER::new(); >>>>>> + #my ($class, $design_file_name, $format, $refseq_max_ins_hash, >>>>>> $refseq) = @_; >>>>>> + my ($class, @args) = @_; >>>>>> + my $self = $class->SUPER::new(@args); >>>>>> + my ($design_file_name, $format, $refseq_max_ins_hash, >>>>>> $refseq)= >>>>>> $self->_rearrange([qw(AFFY_DESIGN_FILENAME FORMAT_OF_DESIGN_FILE >>>>>> MAX_INSERTION_HASH_REFERENCE REFERENCE_SEQUENCE)], @args); >>>>>> + >>>>>> $self->{_frags_hash}=undef; >>>>>> $self->{_max_ins_hash}=undef; >>>>>> $self->{_refseq}=undef; >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-guts-l mailing list >>>>>> Bioperl-guts-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l >>>>> >>>>> Jason Stajich >>>>> jason at bioperl.org >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >> =========================================================== >> >> >> > From cjfields at illinois.edu Thu Dec 11 11:27:04 2008 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 11 Dec 2008 10:27:04 -0600 Subject: [Bioperl-l] BioC and BioPerl Re: Fwd: [Bioperl-guts-l] [15134] yadayadayada In-Reply-To: References: <200812101410.mBAEALFw011802@dev.open-bio.org> <1952AD80-A0E9-4183-AFF0-4D0064F57584@illinois.edu> <4940F5AA020000C50007741D@gwsmtp2.uni-regensburg.de> <2F046501-87F0-41D1-A561-0DD8BCE25B92@illinois.edu> Message-ID: Yes. This is the way I intended to go (swig-based, so can apply to other Bio*). The initial release already has some links to the affymetrix library (http://biolib.open-bio.org/wiki/ BioLib_Affymetrix), but that's independent of R. chris On Dec 11, 2008, at 9:19 AM, Hilmar Lapp wrote: > You guys do know about the BioLib project? > > http://biolib.open-bio.org/wiki/Main_Page > > Bridging R and BioC to the Bio* projects is one of the core goals if > I remember correctly. > > -hilmar > > On Dec 11, 2008, at 9:55 AM, Chris Fields wrote: > >> Just need a decently-supported perl-R package to help along those >> lines. RSPerl might work, but I find it too problematic to work >> with on my Mac OS and it isn't well-supported (doesn't find my >> local perl installation so mixes libraries and, well, crashes >> during compilation). >> >> The best bridging would generically bring R into perl (and BioC >> into BioPerl). Statistics::R is a pure perl method but it appears >> pretty messy. I may toy around with an XS-based solution myself >> after 1.6 is out. >> >> chris >> >> On Dec 11, 2008, at 4:12 AM, Marian thieme wrote: >> >>> I also had the impression that "it" was discouraged to use bioperl >>> for microarray processing. >>> As I know from my colleagues and also I did to good extemt) people >>> use R (especially Bioconductor) for most of the issues concerning >>> microarrays. (there are so many supoorted microarray designs, >>> preprocessing and normalization tools, and complete packages to >>> perform differential expression analysis). At least for the >>> expression chips but also for genotyping/SNP chips I think R/BioC >>> is method of choice. Probably for the resequencing chips they are >>> not that well supported, because its only a minority that uses >>> this kind of chips. Therefore I think ReseqChip has its right to >>> exist, even though it would reach more people if it would a R/BioC >>> package. (Moreover I believe that this kind of chips wont have >>> broader interest, because second generation sequencing methods >>> will probably be more appropriate in the next few years) >>> So to cut a long story short, I find Chris' idea of bridging >>> bioperl to BioC (or vice versa) very good: Dont compete against R/ >>> BioC, but make it easier to use both together. >>> >>> marian >>> >>> >>> Marian Thieme >>> Institute of Functional Genomics >>> University Regensburg >>> Josef Engert Str. 9 >>> 93053 >>> Regensburg >>> Germany >>> P: 0049 (0)941 943 1584 >>> F: 0049 (0)941 943 5020 >>> E: marian.thieme at klinik.uni-regensburg.de >>> W: http://www-cgi.uni-regensburg.de/Klinik/FunktionelleGenomik >>> >>> >>>>>> Chris Fields 12/10/2008 7:59 PM >>> >>> Sounds like a good idea, with one caveat: Allen had pretty much >>> given >>> up on bioperl-microarray last I heard (last significant commits were >>> ~6 yrs ago). It would be nice to revive with this theme in mind, >>> though maybe bioperl-expression would be better (could focus on >>> other >>> expression-related issues along with microarray data). Marian, what >>> do you think? >>> >>> chris >>> >>> P.S. An aside: I'm planning on running lots of Illumina data myself >>> and have been thinking about making a BioC-BioPerl bridge, then >>> seeing >>> how it fits into a bioperl-microarray. Just need a working perl-R >>> interface (NOT RSPerl). >>> >>> On Dec 10, 2008, at 12:42 PM, Jason Stajich wrote: >>> >>>> Since we've started discussing the idea of starting to move things >>>> out into smaller packages, does it make sense to move this >>>> Bio::Microarray into its own package before it gets bigger? What >>>> about the old bioperl-microarray stuff from Allen Day? >>>> >>>> I also know that as we haven't branched for 1.6 Chris we'll have to >>>> make some decisions about new code going in before then? >>>> >>>> Not trying to stifle any of the development with extra work but >>>> trying to see if we should start to make some logical slices of >>>> packages? >>>> >>>> -jason >>>> >>>> Begin forwarded message: >>>> >>>>> From: Marian Thieme >>>>> Date: December 10, 2008 6:10:21 AM PST >>>>> To: bioperl-guts-l at bioperl.org >>>>> Subject: [Bioperl-guts-l] [15134] bioperl-live/trunk/Bio/ >>>>> Microarray/ >>>>> Tools: use superclasses initialization and argument processing/ >>>>> attribute setting as suggested in styleguide >>>>> >>>>> Revision: 15134 >>>>> Author: thm09830 >>>>> Date: 2008-12-10 09:10:21 -0500 (Wed, 10 Dec 2008) >>>>> >>>>> Log Message: >>>>> ----------- >>>>> use superclasses initialization and argument processing/attribute >>>>> setting as suggested in styleguide >>>>> >>>>> Modified Paths: >>>>> -------------- >>>>> bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >>>>> bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm >>>>> >>>>> Modified: bioperl-live/trunk/Bio/Microarray/Tools/ >>>>> MitoChipV2Parser.pm >>>>> = >>>>> ================================================================== >>>>> --- bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >>>>> 2008-12-10 12:51:47 UTC (rev 15133) >>>>> +++ bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >>>>> 2008-12-10 14:10:21 UTC (rev 15134) >>>>> @@ -78,12 +78,13 @@ >>>>> >>>>> sub new { >>>>> >>>>> - my ($class, $file_name) = @_; >>>>> - my $self = $class->SUPER::new(); >>>>> + my ($class, @args) = @_; >>>>> + my $self = $class->SUPER::new(@args); >>>>> + my ($file_name)=$self->_rearrange([qw(AFFY_DESIGN_FILENAME)], >>>>> @args); >>>>> + >>>>> $self->{_frags_hash}=undef; >>>>> $self->{_oligos2calc_hash}=undef; >>>>> $self->throw("Must provide filename as first argument !") unless >>>>> $file_name; >>>>> - >>>>> >>>>> my %max_ins_hash=(); >>>>> $self->{_frags_hash}=$self- >>>>>> _parse_Affy_mtDNA_design_annotation_file($file_name); >>>>> >>>>> Modified: bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm >>>>> = >>>>> ================================================================== >>>>> --- bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm >>>>> 2008-12-10 >>>>> 12:51:47 UTC (rev 15133) >>>>> +++ bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm >>>>> 2008-12-10 >>>>> 14:10:21 UTC (rev 15134) >>>>> @@ -194,8 +194,11 @@ >>>>> >>>>> sub new { >>>>> >>>>> - my ($class, $design_file_name, $format, $refseq_max_ins_hash, >>>>> $refseq) = @_; >>>>> - my $self = $class->SUPER::new(); >>>>> + #my ($class, $design_file_name, $format, $refseq_max_ins_hash, >>>>> $refseq) = @_; >>>>> + my ($class, @args) = @_; >>>>> + my $self = $class->SUPER::new(@args); >>>>> + my ($design_file_name, $format, $refseq_max_ins_hash, $refseq)= >>>>> $self->_rearrange([qw(AFFY_DESIGN_FILENAME FORMAT_OF_DESIGN_FILE >>>>> MAX_INSERTION_HASH_REFERENCE REFERENCE_SEQUENCE)], @args); >>>>> + >>>>> $self->{_frags_hash}=undef; >>>>> $self->{_max_ins_hash}=undef; >>>>> $self->{_refseq}=undef; >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-guts-l mailing list >>>>> Bioperl-guts-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l >>>> >>>> Jason Stajich >>>> jason at bioperl.org >>>> >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > From jason at bioperl.org Thu Dec 11 13:12:51 2008 From: jason at bioperl.org (Jason Stajich) Date: Thu, 11 Dec 2008 10:12:51 -0800 Subject: [Bioperl-l] BioC and BioPerl Re: Fwd: [Bioperl-guts-l] [15134] yadayadayada In-Reply-To: References: <200812101410.mBAEALFw011802@dev.open-bio.org> <1952AD80-A0E9-4183-AFF0-4D0064F57584@illinois.edu> <4940F5AA020000C50007741D@gwsmtp2.uni-regensburg.de> Message-ID: Ian - I definitely agree - I think the only place the analysis needs to happen on the BioC/R side- great to hear your help volunteered Ian. I was mainly making comments about a) Whether or not these new commits should live in the "core" or a different main bioperl svn sub-repository b) if we can consider how we'll model this kind of data for manipulation in bioperl and also some generic representations that could capture Expression in general in terms of RNA-Seq type data c) semi-offhandly reminding myself and us that there is a dead svn repository called bioperl-microarray that we ought to probably formally described as deprecated I'd also be curious if this community wants to work towards some common tools for the sequence-based expression (short-read technology). This would certainly go in a separate repository to move in this spirit of de-monolithing bioperl. I like Chris's suggestion of bioperl-expression although it might be that we want some common solutions for chip-seq and genomic sequencing from ABI/Illumina/454 as well. I know there are a lot of tools out there already for aspects of these sequence-based analyses so I think it would be best focus on some specific goals here if we got into it rather than just writing parsers, etc. Certainly a lot of us have home-grown solutions but wonder whether there will be enough interest to architect some common tools. -jason On Dec 11, 2008, at 7:19 AM, Dr. T. I. Simpson wrote: > Hi guys, I am a newbie on here so hope this mail is appropriate. > > Just thought I would chip in here (sorry for the pun). I would like > to echo Marian's comments. I work extensively with R/BioC and Perl > taking experimental data from low-level array to lots of different > downstream analyses. I made an effort to work with R through Perl > about a year ago using RSPerl and it was mighty painful. As Marian > suggests it wouldn't be a good idea to compete with R/BioC there are > some absolutely gold standard packages like affy, affyPLM and limma > to name just three that cope with serious statistics within the R > environment. If it were possible to make a good bridge to execute R > scripts and access/manipulate R variables (a run wrapper module for > R ?) then that would be a very significant step forward for someone > like me. I don't know how skillfully I could contribute to this, but > happy to help wherever I can. > > Best wishes > > Ian. > > On Thu, 11 Dec 2008 10:12:42 -0000, Marian thieme > wrote: > >> I also had the impression that "it" was discouraged to use bioperl >> for microarray processing. >> As I know from my colleagues and also I did to good extemt) people >> use R (especially Bioconductor) for most of the issues concerning >> microarrays. (there are so many supoorted microarray designs, >> preprocessing and normalization tools, and complete packages to >> perform differential expression analysis). At least for the >> expression chips but also for genotyping/SNP chips I think R/BioC >> is method of choice. Probably for the resequencing chips they are >> not that well supported, because its only a minority that uses this >> kind of chips. Therefore I think ReseqChip has its right to exist, >> even though it would reach more people if it would a R/BioC >> package. (Moreover I believe that this kind of chips wont have >> broader interest, because second generation sequencing methods will >> probably be more appropriate in the next few years) >> So to cut a long story short, I find Chris' idea of bridging >> bioperl to BioC (or vice versa) very good: Dont compete against R/ >> BioC, but make it easier to use both together. >> >> marian >> >> Marian Thieme >> Institute of Functional Genomics >> University Regensburg >> Josef Engert Str. 9 >> 93053 >> Regensburg >> Germany >> P: 0049 (0)941 943 1584 >> F: 0049 (0)941 943 5020 >> E: marian.thieme at klinik.uni-regensburg.de >> W: http://www-cgi.uni-regensburg.de/Klinik/FunktionelleGenomik >> >> >>>>> Chris Fields 12/10/2008 7:59 PM >>> >> Sounds like a good idea, with one caveat: Allen had pretty much given >> up on bioperl-microarray last I heard (last significant commits were >> ~6 yrs ago). It would be nice to revive with this theme in mind, >> though maybe bioperl-expression would be better (could focus on other >> expression-related issues along with microarray data). Marian, what >> do you think? >> >> chris >> >> P.S. An aside: I'm planning on running lots of Illumina data myself >> and have been thinking about making a BioC-BioPerl bridge, then >> seeing >> how it fits into a bioperl-microarray. Just need a working perl-R >> interface (NOT RSPerl). >> >> On Dec 10, 2008, at 12:42 PM, Jason Stajich wrote: >> >>> Since we've started discussing the idea of starting to move things >>> out into smaller packages, does it make sense to move this >>> Bio::Microarray into its own package before it gets bigger? What >>> about the old bioperl-microarray stuff from Allen Day? >>> >>> I also know that as we haven't branched for 1.6 Chris we'll have to >>> make some decisions about new code going in before then? >>> >>> Not trying to stifle any of the development with extra work but >>> trying to see if we should start to make some logical slices of >>> packages? >>> >>> -jason >>> >>> Begin forwarded message: >>> >>>> From: Marian Thieme >>>> Date: December 10, 2008 6:10:21 AM PST >>>> To: bioperl-guts-l at bioperl.org >>>> Subject: [Bioperl-guts-l] [15134] bioperl-live/trunk/Bio/ >>>> Microarray/ >>>> Tools: use superclasses initialization and argument processing/ >>>> attribute setting as suggested in styleguide >>>> >>>> Revision: 15134 >>>> Author: thm09830 >>>> Date: 2008-12-10 09:10:21 -0500 (Wed, 10 Dec 2008) >>>> >>>> Log Message: >>>> ----------- >>>> use superclasses initialization and argument processing/attribute >>>> setting as suggested in styleguide >>>> >>>> Modified Paths: >>>> -------------- >>>> bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >>>> bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm >>>> >>>> Modified: bioperl-live/trunk/Bio/Microarray/Tools/ >>>> MitoChipV2Parser.pm >>>> =================================================================== >>>> --- bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >>>> 2008-12-10 12:51:47 UTC (rev 15133) >>>> +++ bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >>>> 2008-12-10 14:10:21 UTC (rev 15134) >>>> @@ -78,12 +78,13 @@ >>>> >>>> sub new { >>>> >>>> - my ($class, $file_name) = @_; >>>> - my $self = $class->SUPER::new(); >>>> + my ($class, @args) = @_; >>>> + my $self = $class->SUPER::new(@args); >>>> + my ($file_name)=$self->_rearrange([qw(AFFY_DESIGN_FILENAME)], >>>> @args); >>>> + >>>> $self->{_frags_hash}=undef; >>>> $self->{_oligos2calc_hash}=undef; >>>> $self->throw("Must provide filename as first argument !") unless >>>> $file_name; >>>> - >>>> >>>> my %max_ins_hash=(); >>>> $self->{_frags_hash}=$self- >>>> >_parse_Affy_mtDNA_design_annotation_file($file_name); >>>> >>>> Modified: bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm >>>> =================================================================== >>>> --- bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm 2008-12-10 >>>> 12:51:47 UTC (rev 15133) >>>> +++ bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm 2008-12-10 >>>> 14:10:21 UTC (rev 15134) >>>> @@ -194,8 +194,11 @@ >>>> >>>> sub new { >>>> >>>> - my ($class, $design_file_name, $format, $refseq_max_ins_hash, >>>> $refseq) = @_; >>>> - my $self = $class->SUPER::new(); >>>> + #my ($class, $design_file_name, $format, $refseq_max_ins_hash, >>>> $refseq) = @_; >>>> + my ($class, @args) = @_; >>>> + my $self = $class->SUPER::new(@args); >>>> + my ($design_file_name, $format, $refseq_max_ins_hash, $refseq)= >>>> $self->_rearrange([qw(AFFY_DESIGN_FILENAME FORMAT_OF_DESIGN_FILE >>>> MAX_INSERTION_HASH_REFERENCE REFERENCE_SEQUENCE)], @args); >>>> + >>>> $self->{_frags_hash}=undef; >>>> $self->{_max_ins_hash}=undef; >>>> $self->{_refseq}=undef; >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-guts-l mailing list >>>> Bioperl-guts-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l >>> >>> Jason Stajich >>> jason at bioperl.org >>> >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > Dr T.I.Simpson > School of Biomedical Sciences > University of Edinburgh > Hugh Robson Building > George Square > Edinburgh > EH8 9XD > > ian.simpson at ed.ac.uk > > > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. Jason Stajich jason at bioperl.org From cjfields at illinois.edu Thu Dec 11 14:13:28 2008 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 11 Dec 2008 13:13:28 -0600 Subject: [Bioperl-l] BioC and BioPerl Re: Fwd: [Bioperl-guts-l] [15134] yadayadayada In-Reply-To: References: <200812101410.mBAEALFw011802@dev.open-bio.org> <1952AD80-A0E9-4183-AFF0-4D0064F57584@illinois.edu> <4940F5AA020000C50007741D@gwsmtp2.uni-regensburg.de> Message-ID: <8E2D6939-9999-4BCB-AE13-62812BDAEA7A@illinois.edu> On Dec 11, 2008, at 12:12 PM, Jason Stajich wrote: > Ian - > I definitely agree - I think the only place the analysis needs to > happen on the BioC/R side- great to hear your help volunteered Ian. > > I was mainly making comments about > > a) Whether or not these new commits should live in the "core" or a > different main bioperl svn sub-repository > b) if we can consider how we'll model this kind of data for > manipulation in bioperl and also some generic representations that > could capture Expression in general in terms of RNA-Seq type data > c) semi-offhandly reminding myself and us that there is a dead svn > repository called bioperl-microarray that we ought to probably > formally described as deprecated a) +1 on separate repository. Shouldn't be necessary for core. b) +1 on design before implementation. c) +1 in general, with bioperl-ext eventually movin in the same direction as biolib takes over. > I'd also be curious if this community wants to work towards some > common tools for the sequence-based expression (short-read > technology). This would certainly go in a separate repository to > move in this spirit of de-monolithing bioperl. I like Chris's > suggestion of bioperl-expression although it might be that we want > some common solutions for chip-seq and genomic sequencing from ABI/ > Illumina/454 as well. > I know there are a lot of tools out there already for aspects of > these sequence-based analyses so I think it would be best focus on > some specific goals here if we got into it rather than just writing > parsers, etc. Certainly a lot of us have home-grown solutions but > wonder whether there will be enough interest to architect some > common tools. > > -jason I think there is interest here (at UIUC). We could possibly expand the scope from expression to include other bits (chip-chip, solexa, etc). I do think if we go down the solexa/454 route we may want to get our Bio::Assembly 'house' in order at some point. -c > On Dec 11, 2008, at 7:19 AM, Dr. T. I. Simpson wrote: > >> Hi guys, I am a newbie on here so hope this mail is appropriate. >> >> Just thought I would chip in here (sorry for the pun). I would like >> to echo Marian's comments. I work extensively with R/BioC and Perl >> taking experimental data from low-level array to lots of different >> downstream analyses. I made an effort to work with R through Perl >> about a year ago using RSPerl and it was mighty painful. As Marian >> suggests it wouldn't be a good idea to compete with R/BioC there >> are some absolutely gold standard packages like affy, affyPLM and >> limma to name just three that cope with serious statistics within >> the R environment. If it were possible to make a good bridge to >> execute R scripts and access/manipulate R variables (a run wrapper >> module for R ?) then that would be a very significant step forward >> for someone like me. I don't know how skillfully I could contribute >> to this, but happy to help wherever I can. >> >> Best wishes >> >> Ian. >> >> On Thu, 11 Dec 2008 10:12:42 -0000, Marian thieme > > wrote: >> >>> I also had the impression that "it" was discouraged to use bioperl >>> for microarray processing. >>> As I know from my colleagues and also I did to good extemt) people >>> use R (especially Bioconductor) for most of the issues concerning >>> microarrays. (there are so many supoorted microarray designs, >>> preprocessing and normalization tools, and complete packages to >>> perform differential expression analysis). At least for the >>> expression chips but also for genotyping/SNP chips I think R/BioC >>> is method of choice. Probably for the resequencing chips they are >>> not that well supported, because its only a minority that uses >>> this kind of chips. Therefore I think ReseqChip has its right to >>> exist, even though it would reach more people if it would a R/BioC >>> package. (Moreover I believe that this kind of chips wont have >>> broader interest, because second generation sequencing methods >>> will probably be more appropriate in the next few years) >>> So to cut a long story short, I find Chris' idea of bridging >>> bioperl to BioC (or vice versa) very good: Dont compete against R/ >>> BioC, but make it easier to use both together. >>> >>> marian >>> >>> Marian Thieme >>> Institute of Functional Genomics >>> University Regensburg >>> Josef Engert Str. 9 >>> 93053 >>> Regensburg >>> Germany >>> P: 0049 (0)941 943 1584 >>> F: 0049 (0)941 943 5020 >>> E: marian.thieme at klinik.uni-regensburg.de >>> W: http://www-cgi.uni-regensburg.de/Klinik/FunktionelleGenomik >>> >>> >>>>>> Chris Fields 12/10/2008 7:59 PM >>> >>> Sounds like a good idea, with one caveat: Allen had pretty much >>> given >>> up on bioperl-microarray last I heard (last significant commits were >>> ~6 yrs ago). It would be nice to revive with this theme in mind, >>> though maybe bioperl-expression would be better (could focus on >>> other >>> expression-related issues along with microarray data). Marian, what >>> do you think? >>> >>> chris >>> >>> P.S. An aside: I'm planning on running lots of Illumina data myself >>> and have been thinking about making a BioC-BioPerl bridge, then >>> seeing >>> how it fits into a bioperl-microarray. Just need a working perl-R >>> interface (NOT RSPerl). >>> >>> On Dec 10, 2008, at 12:42 PM, Jason Stajich wrote: >>> >>>> Since we've started discussing the idea of starting to move things >>>> out into smaller packages, does it make sense to move this >>>> Bio::Microarray into its own package before it gets bigger? What >>>> about the old bioperl-microarray stuff from Allen Day? >>>> >>>> I also know that as we haven't branched for 1.6 Chris we'll have to >>>> make some decisions about new code going in before then? >>>> >>>> Not trying to stifle any of the development with extra work but >>>> trying to see if we should start to make some logical slices of >>>> packages? >>>> >>>> -jason >>>> >>>> Begin forwarded message: >>>> >>>>> From: Marian Thieme >>>>> Date: December 10, 2008 6:10:21 AM PST >>>>> To: bioperl-guts-l at bioperl.org >>>>> Subject: [Bioperl-guts-l] [15134] bioperl-live/trunk/Bio/ >>>>> Microarray/ >>>>> Tools: use superclasses initialization and argument processing/ >>>>> attribute setting as suggested in styleguide >>>>> >>>>> Revision: 15134 >>>>> Author: thm09830 >>>>> Date: 2008-12-10 09:10:21 -0500 (Wed, 10 Dec 2008) >>>>> >>>>> Log Message: >>>>> ----------- >>>>> use superclasses initialization and argument processing/attribute >>>>> setting as suggested in styleguide >>>>> >>>>> Modified Paths: >>>>> -------------- >>>>> bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >>>>> bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm >>>>> >>>>> Modified: bioperl-live/trunk/Bio/Microarray/Tools/ >>>>> MitoChipV2Parser.pm >>>>> = >>>>> ================================================================== >>>>> --- bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >>>>> 2008-12-10 12:51:47 UTC (rev 15133) >>>>> +++ bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm >>>>> 2008-12-10 14:10:21 UTC (rev 15134) >>>>> @@ -78,12 +78,13 @@ >>>>> >>>>> sub new { >>>>> >>>>> - my ($class, $file_name) = @_; >>>>> - my $self = $class->SUPER::new(); >>>>> + my ($class, @args) = @_; >>>>> + my $self = $class->SUPER::new(@args); >>>>> + my ($file_name)=$self->_rearrange([qw(AFFY_DESIGN_FILENAME)], >>>>> @args); >>>>> + >>>>> $self->{_frags_hash}=undef; >>>>> $self->{_oligos2calc_hash}=undef; >>>>> $self->throw("Must provide filename as first argument !") unless >>>>> $file_name; >>>>> - >>>>> >>>>> my %max_ins_hash=(); >>>>> $self->{_frags_hash}=$self- >>>>> >_parse_Affy_mtDNA_design_annotation_file($file_name); >>>>> >>>>> Modified: bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm >>>>> = >>>>> ================================================================== >>>>> --- bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm >>>>> 2008-12-10 >>>>> 12:51:47 UTC (rev 15133) >>>>> +++ bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm >>>>> 2008-12-10 >>>>> 14:10:21 UTC (rev 15134) >>>>> @@ -194,8 +194,11 @@ >>>>> >>>>> sub new { >>>>> >>>>> - my ($class, $design_file_name, $format, $refseq_max_ins_hash, >>>>> $refseq) = @_; >>>>> - my $self = $class->SUPER::new(); >>>>> + #my ($class, $design_file_name, $format, $refseq_max_ins_hash, >>>>> $refseq) = @_; >>>>> + my ($class, @args) = @_; >>>>> + my $self = $class->SUPER::new(@args); >>>>> + my ($design_file_name, $format, $refseq_max_ins_hash, $refseq)= >>>>> $self->_rearrange([qw(AFFY_DESIGN_FILENAME FORMAT_OF_DESIGN_FILE >>>>> MAX_INSERTION_HASH_REFERENCE REFERENCE_SEQUENCE)], @args); >>>>> + >>>>> $self->{_frags_hash}=undef; >>>>> $self->{_max_ins_hash}=undef; >>>>> $self->{_refseq}=undef; >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-guts-l mailing list >>>>> Bioperl-guts-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l >>>> >>>> Jason Stajich >>>> jason at bioperl.org >>>> >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> >> >> -- >> Dr T.I.Simpson >> School of Biomedical Sciences >> University of Edinburgh >> Hugh Robson Building >> George Square >> Edinburgh >> EH8 9XD >> >> ian.simpson at ed.ac.uk >> >> >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. > > Jason Stajich > jason at bioperl.org > > > From hlapp at gmx.net Fri Dec 12 00:49:42 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 12 Dec 2008 00:49:42 -0500 Subject: [Bioperl-l] Trying to install bioPerl-db on Windows XP In-Reply-To: <49415080.2090508@earthlink.net> References: <494011B7.3020306@earthlink.net> <4940212F.4070305@earthlink.net> <915B3B21-3E9F-4FCA-9B1A-E5FE374D0D28@gmx.net> <49415080.2090508@earthlink.net> Message-ID: <6E32F343-E83D-4675-949F-FBB2A115D7A2@gmx.net> (please keep responses on the list - there are many more people who can help) Hi Lori, On Dec 11, 2008, at 12:40 PM, Lori G. Wilson wrote: > Hi, Hilmar, > > Thank you. I had the wrong ORACLE_SID. I do have a remote database > on another server in my network, but I don't know where TWO_TASK > gets set. it's part of the same initialization scripts that set ORACLE_SID. You can always set it by hand too. > [...] > > This problem is solved, but I'm still failing a lot of tests. I > have attached the latest screen shot of my errors. I can't do much from a screenshot. You'll have to capture the error output into a file and send me that file, or copy and paste the entire log. Based on the limited number of lines the screenshot shows, my suspicion would be that you running an old version of BioPerl. You will need to have v1.5.2 at least. > > I checked all the packages in my bioSQL installation and everything > seems to have compiled. BioSQL doesn't have any compiled code, only scripts, and likewise Bioperl-db, so compiler problems can't be responsible for this (unless your DBD::Oracle driver fails to even load). -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From philsf79 at gmail.com Sun Dec 14 14:45:31 2008 From: philsf79 at gmail.com (Felipe Figueiredo) Date: Sun, 14 Dec 2008 17:45:31 -0200 Subject: [Bioperl-l] phylip: dnadist x protdist Message-ID: <1229283931.16908.5.camel@localhost> Hello, Maybe I'm missing something, but if I'm not, now (pre 1.6) would be a good time to move dnadist into the Phylip namespace, where it should (?) be. Bio::Tools::Run::PiseApplication::dnadist Bio::Tools::Run::Phylo::Phylip::ProtDist On a second thought, maybe the proper dnadist module (equivalent to the ProtDist) is actually missing. Is this the case? regards FF From cjfields at illinois.edu Sun Dec 14 15:42:10 2008 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 14 Dec 2008 14:42:10 -0600 Subject: [Bioperl-l] phylip: dnadist x protdist In-Reply-To: <1229283931.16908.5.camel@localhost> References: <1229283931.16908.5.camel@localhost> Message-ID: PiseApplication::dnadist is part of the Pise application suite. As you surmised, Bio::Tools::Run::Phylo::Phylip::DNADist hasn't been implemented. You are more than welcome to work on adding that in, though it probably won't be for bioperl-run 1.6 unless it comes out fairly soon (within the next month). I'm planning on branching core 1.6 sometime later this week with an RC very soon after. chris On Dec 14, 2008, at 1:45 PM, Felipe Figueiredo wrote: > Hello, > > Maybe I'm missing something, but if I'm not, now (pre 1.6) would be a > good time to move dnadist into the Phylip namespace, where it should > (?) > be. > > Bio::Tools::Run::PiseApplication::dnadist > Bio::Tools::Run::Phylo::Phylip::ProtDist > > On a second thought, maybe the proper dnadist module (equivalent to > the > ProtDist) is actually missing. Is this the case? > > regards > FF > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From oso.oro at gmail.com Sun Dec 14 20:33:45 2008 From: oso.oro at gmail.com (oso) Date: Sun, 14 Dec 2008 17:33:45 -0800 (PST) Subject: [Bioperl-l] Using BLAT in BioPerl Message-ID: <21007049.post@talk.nabble.com> All, I am using the BioPerl module Bio::Tools::Run::Alignment::Blat to run standalone BLATs. The search I am doing works fine if I do it from a normal command line interface. The same sequences and genome are not working in the BioPerl interface. I think my problem might be how I defined the database, as it it isn't showing up in the resulting BLAT call. Does anyone see my problem? Find scripting below. ******** my $seqio_object = Bio::SeqIO -> new (-file => 'reads1.fa', -format => 'fasta'); my $database = 'chr2.fa'; my $db = Bio::DB::Fasta->new($database); my $factory = Bio::Tools::Run::Alignment::Blat->new(); #sets up a do-while loop as long as I still have sequences to blast while (my $blat_object = $seqio_object -> next_seq) { my $results = $factory -> run($blat_object,$db); } -- View this message in context: http://www.nabble.com/Using-BLAT-in-BioPerl-tp21007049p21007049.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From David.Messina at sbc.su.se Mon Dec 15 03:23:12 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Mon, 15 Dec 2008 09:23:12 +0100 Subject: [Bioperl-l] Using BLAT in BioPerl In-Reply-To: <21007049.post@talk.nabble.com> References: <21007049.post@talk.nabble.com> Message-ID: <628aabb70812150023k628700dbv7b92748641e4ceb1@mail.gmail.com> Hi, Could you show us the error message you're seeing? Also, what version of BioPerl are you running? Dave From avilella at gmail.com Mon Dec 15 06:31:58 2008 From: avilella at gmail.com (Albert Vilella) Date: Mon, 15 Dec 2008 11:31:58 +0000 Subject: [Bioperl-l] Bio::Search::GenericHSP from cigar_line to pairwise alignment Message-ID: <358f4d650812150331s7e666ffck2628b530b473dbd5@mail.gmail.com> Hi, Does anybody have a working tested way to go from a cigar_line back to the pairwise alignment coming from a GenericHSP (like blastp, etc)? I can see that GenericHSP has the code for calculating the cigar_line from the alignment, but we (Ensembl) only store the cigar_lines, and would like people to be able to go back to the alignment in Bioperl. Just asking if anyone has done this before I get my hands dirty on it... Cheers, Albert. From oso.oro at gmail.com Mon Dec 15 11:56:28 2008 From: oso.oro at gmail.com (oso) Date: Mon, 15 Dec 2008 08:56:28 -0800 (PST) Subject: [Bioperl-l] Using BLAT in BioPerl In-Reply-To: <628aabb70812150023k628700dbv7b92748641e4ceb1@mail.gmail.com> References: <21007049.post@talk.nabble.com> <628aabb70812150023k628700dbv7b92748641e4ceb1@mail.gmail.com> Message-ID: <21017474.post@talk.nabble.com> Error Message: MSG: Blat call (blat /var/folders/zK/zKXnWXt8G8epLqENEIdNkE+++TI/-Tmp-/wcjQruYe8A /var/folders/zK/zKXnWXt8G8epLqENEIdNkE+++TI/-Tmp-/nePTpfPSKu -out=psl ) crashed: 65280 STACK Bio::Tools::Run::Alignment::Blat::_run /Library/Perl/5.8.8/Bio/Tools/Run/Alignment/Blat.pm:250 STACK Bio::Tools::Run::Alignment::Blat::run /Library/Perl/5.8.8/Bio/Tools/Run/Alignment/Blat.pm:167 STACK main::get_orfs /Users/blatSearch.pl:50 STACK toplevel /Users/blatSearch.pl:29 ******* I am running BioPerl version 1.5.2. Thanks for our help! Dave Messina-3 wrote: > > Hi, > > Could you show us the error message you're seeing? > > Also, what version of BioPerl are you running? > > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- View this message in context: http://www.nabble.com/Using-BLAT-in-BioPerl-tp21007049p21017474.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From jason at bioperl.org Mon Dec 15 12:15:13 2008 From: jason at bioperl.org (Jason Stajich) Date: Mon, 15 Dec 2008 09:15:13 -0800 Subject: [Bioperl-l] FastA and Bioperl In-Reply-To: References: Message-ID: <1FF889A1-6A7A-4623-BE8C-AEF0A2B779C1@bioperl.org> Please direct your questions to the mailing list. Sure it parses FastA - I assume you are talking about using Bio::SearchIO - you will want to make sure you are using at least version 1.5.2 that is available in CPAN or the website. If you need followup help please use the mailing list. -jason On Dec 15, 2008, at 4:16 AM, Heleen de Weerd wrote: > > Dear sir Stajich, > > I am using the latest version of fasta (fastx35_t). Now I want to > use the output that comes from this program and parse it with bioperl. > The problem I am facing at the moment is that bioperl doesn't > recognise this FastA output type. > Is there any chance that this will be able in the next version of > bioperl? > > Sincerely, > Heleen de Weerd > University College Cork > > _________________________________________________________________ > You live life online. So we put Windows on the web. > http://clk.atdmt.com/MRT/go/127032869/direct/01/ Jason Stajich jason at bioperl.org From mauricio at open-bio.org Mon Dec 15 16:53:57 2008 From: mauricio at open-bio.org (Mauricio Herrera Cuadra) Date: Mon, 15 Dec 2008 16:53:57 -0500 Subject: [Bioperl-l] OT - mac users: caution on 10.5.6 update Message-ID: <4946D1F5.1030606@open-bio.org> Just a heads up for those Mac users: http://discussions.apple.com/thread.jspa?threadID=1826694&start=0&tstart=0 Cheers, Mauricio. From jason at bioperl.org Tue Dec 16 12:19:59 2008 From: jason at bioperl.org (Jason Stajich) Date: Tue, 16 Dec 2008 09:19:59 -0800 Subject: [Bioperl-l] Fwd: [Bioperl-guts-l] [15178] bioperl-live/trunk: new test method test_output_dir(), a wrapper around Temp::File::tempdir References: <200812161248.mBGCmMLL026571@dev.open-bio.org> Message-ID: Bio::Root::IO already had a tempdir function which did some workarounds if File::Temp wasn't installed. I guess we assume File::Temp is installed as an essential module now then to install (in order to run tests)? Does it make sense to consolidate and depend on File::Temp aspects? -jason Begin forwarded message: > From: Senduran Balasubramaniam > Date: December 16, 2008 4:48:22 AM PST > To: bioperl-guts-l at bioperl.org > Subject: [Bioperl-guts-l] [15178] bioperl-live/trunk: new test > method test_output_dir(), a wrapper around Temp::File::tempdir > > Revision: 15178 > Author: sendu > Date: 2008-12-16 07:48:21 -0500 (Tue, 16 Dec 2008) > > Log Message: > ----------- > new test method test_output_dir(), a wrapper around > Temp::File::tempdir > > Modified Paths: > -------------- > bioperl-live/trunk/Bio/Root/Test.pm > bioperl-live/trunk/t/LocalDB/DBFasta.t > bioperl-live/trunk/t/LocalDB/DBQual.t > bioperl-live/trunk/t/LocalDB/Flat.t > bioperl-live/trunk/t/RemoteDB/Taxonomy.t > > Modified: bioperl-live/trunk/Bio/Root/Test.pm > =================================================================== > --- bioperl-live/trunk/Bio/Root/Test.pm 2008-12-16 07:49:26 UTC (rev > 15177) > +++ bioperl-live/trunk/Bio/Root/Test.pm 2008-12-16 12:48:21 UTC (rev > 15178) > @@ -51,6 +51,10 @@ > # deleted when the test script finishes > my $output_file = test_output_file(); > > + # we want the name of a directory we can store files in, that > will be > + # automatically deleted when the test script finishes > + my $output_dir = test_output_dir(); > + > =head1 DESCRIPTION > > This provides a common base for all Bioperl test scripts. It safely > handles the > @@ -104,7 +108,7 @@ > use strict; > use warnings; > > -use File::Temp (); > +use File::Temp qw(tempdir); > use File::Spec; > use Exporter qw(import); > > @@ -159,6 +163,7 @@ > test_begin > test_skip > test_output_file > + test_output_dir > test_input_file > test_network > test_debug); > @@ -292,6 +297,25 @@ > return $tmp->filename; > } > > +=head2 test_output_dir > + > + Title : test_output_dir > + Usage : my $output_dir = test_output_dir(); > + Function: Get the full path of a directory suitable for storing > temporary files > + in. > + When your test script ends, the directory and its > contents will be > + automatically deleted. > + Returns : string (path) > + Args : none > + > +=cut > + > +sub test_output_dir { > + die "test_output_dir takes no args\n" if @_; > + > + return tempdir(CLEANUP => 1); > +} > + From bix at sendu.me.uk Tue Dec 16 12:27:46 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 16 Dec 2008 17:27:46 +0000 Subject: [Bioperl-l] Fwd: [Bioperl-guts-l] [15178] bioperl-live/trunk: new test method test_output_dir(), a wrapper around Temp::File::tempdir In-Reply-To: References: <200812161248.mBGCmMLL026571@dev.open-bio.org> Message-ID: <4947E512.40503@sendu.me.uk> Jason Stajich wrote: > Bio::Root::IO already had a tempdir function which did some workarounds > if File::Temp wasn't installed. > I guess we assume File::Temp is installed as an essential module now > then to install (in order to run tests)? > > Does it make sense to consolidate and depend on File::Temp aspects? File::Temp is included in perl 5.6.1, which is required. So yes, it is safe to assume the existence of File::Temp and to get rid of workaround code. I only wrapped tempdir in Bio::Root::Test just for the sake of method name consistency (there is already a test_output_file() method) and ease-of-use. >> *From: *Senduran Balasubramaniam > > >> *Date: *December 16, 2008 4:48:22 AM PST >> *To: *bioperl-guts-l at bioperl.org >> *Subject: **[Bioperl-guts-l] [15178] bioperl-live/trunk: new test >> method test_output_dir(), a wrapper around Temp::File::tempdir* >> >> Revision: 15178 >> Author: sendu >> Date: 2008-12-16 07:48:21 -0500 (Tue, 16 Dec 2008) >> >> Log Message: >> ----------- >> new test method test_output_dir(), a wrapper around Temp::File::tempdir From cjfields at illinois.edu Tue Dec 16 12:59:18 2008 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 16 Dec 2008 11:59:18 -0600 Subject: [Bioperl-l] Fwd: [Bioperl-guts-l] [15178] bioperl-live/trunk: new test method test_output_dir(), a wrapper around Temp::File::tempdir In-Reply-To: References: <200812161248.mBGCmMLL026571@dev.open-bio.org> Message-ID: We probably could add it in unversioned just in case as a 'requires' but it shouldn't pop up. We require perl 5.6.1 and above, and File::Temp is listed as part of the perl core for those versions. I agree, I think it makes sense to consolidate any bioperl temp file creation in Root::IO on File::Temp. In fact, I would expand that to say just about any IO in BioPerl beyond DB connectivity should be going through Bio::Root::IO for consistency. chris On Dec 16, 2008, at 11:19 AM, Jason Stajich wrote: > Bio::Root::IO already had a tempdir function which did some > workarounds if File::Temp wasn't installed. > I guess we assume File::Temp is installed as an essential module now > then to install (in order to run tests)? > > Does it make sense to consolidate and depend on File::Temp aspects? > > -jason > Begin forwarded message: > >> From: Senduran Balasubramaniam >> Date: December 16, 2008 4:48:22 AM PST >> To: bioperl-guts-l at bioperl.org >> Subject: [Bioperl-guts-l] [15178] bioperl-live/trunk: new test >> method test_output_dir(), a wrapper around Temp::File::tempdir >> >> Revision: 15178 >> Author: sendu >> Date: 2008-12-16 07:48:21 -0500 (Tue, 16 Dec 2008) >> >> Log Message: >> ----------- >> new test method test_output_dir(), a wrapper around >> Temp::File::tempdir >> >> Modified Paths: >> -------------- >> bioperl-live/trunk/Bio/Root/Test.pm >> bioperl-live/trunk/t/LocalDB/DBFasta.t >> bioperl-live/trunk/t/LocalDB/DBQual.t >> bioperl-live/trunk/t/LocalDB/Flat.t >> bioperl-live/trunk/t/RemoteDB/Taxonomy.t >> >> Modified: bioperl-live/trunk/Bio/Root/Test.pm >> =================================================================== >> --- bioperl-live/trunk/Bio/Root/Test.pm 2008-12-16 07:49:26 UTC >> (rev 15177) >> +++ bioperl-live/trunk/Bio/Root/Test.pm 2008-12-16 12:48:21 UTC >> (rev 15178) >> @@ -51,6 +51,10 @@ >> # deleted when the test script finishes >> my $output_file = test_output_file(); >> >> + # we want the name of a directory we can store files in, that >> will be >> + # automatically deleted when the test script finishes >> + my $output_dir = test_output_dir(); >> + >> =head1 DESCRIPTION >> >> This provides a common base for all Bioperl test scripts. It safely >> handles the >> @@ -104,7 +108,7 @@ >> use strict; >> use warnings; >> >> -use File::Temp (); >> +use File::Temp qw(tempdir); >> use File::Spec; >> use Exporter qw(import); >> >> @@ -159,6 +163,7 @@ >> test_begin >> test_skip >> test_output_file >> + test_output_dir >> test_input_file >> test_network >> test_debug); >> @@ -292,6 +297,25 @@ >> return $tmp->filename; >> } >> >> +=head2 test_output_dir >> + >> + Title : test_output_dir >> + Usage : my $output_dir = test_output_dir(); >> + Function: Get the full path of a directory suitable for storing >> temporary files >> + in. >> + When your test script ends, the directory and its >> contents will be >> + automatically deleted. >> + Returns : string (path) >> + Args : none >> + >> +=cut >> + >> +sub test_output_dir { >> + die "test_output_dir takes no args\n" if @_; >> + >> + return tempdir(CLEANUP => 1); >> +} >> + > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From David.Messina at sbc.su.se Tue Dec 16 13:20:59 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 16 Dec 2008 19:20:59 +0100 Subject: [Bioperl-l] Using BLAT in BioPerl In-Reply-To: <21017474.post@talk.nabble.com> References: <21007049.post@talk.nabble.com> <628aabb70812150023k628700dbv7b92748641e4ceb1@mail.gmail.com> <21017474.post@talk.nabble.com> Message-ID: <628aabb70812161020k1d2429bv7f5505d9e8333206@mail.gmail.com> Hmm, tough to say what the problem is. One thing I noticed that seems a little odd is your blatSearch.pl script appears to be running in your /Users/ directory, which is normally owned by root and not writable by regular users. Also, it looks like it's attempting to create the temporary files in /var/folders, which as far as I remember is also owned by root. Not sure why running as root would necessarily cause a problem, but it's an unusual scenario, so you might try running as a regular user in a directory where you know you have write permissions. Otherwise, you could create a minimal example of your problem, such as a single small query sequence, a single small database, and a test script. You could post these in a bug report to Bugzilla so that someone can try to reproduce your problem. Dave On Mon, Dec 15, 2008 at 17:56, oso wrote: > > Error Message: > MSG: Blat call (blat > /var/folders/zK/zKXnWXt8G8epLqENEIdNkE+++TI/-Tmp-/wcjQruYe8A > /var/folders/zK/zKXnWXt8G8epLqENEIdNkE+++TI/-Tmp-/nePTpfPSKu -out=psl ) > crashed: 65280 > > STACK Bio::Tools::Run::Alignment::Blat::_run > /Library/Perl/5.8.8/Bio/Tools/Run/Alignment/Blat.pm:250 > STACK Bio::Tools::Run::Alignment::Blat::run > /Library/Perl/5.8.8/Bio/Tools/Run/Alignment/Blat.pm:167 > STACK main::get_orfs /Users/blatSearch.pl:50 > STACK toplevel /Users/blatSearch.pl:29 > > ******* > I am running BioPerl version 1.5.2. > > Thanks for our help! > > From jason at bioperl.org Tue Dec 16 13:27:42 2008 From: jason at bioperl.org (Jason Stajich) Date: Tue, 16 Dec 2008 10:27:42 -0800 Subject: [Bioperl-l] Using BLAT in BioPerl In-Reply-To: <628aabb70812161020k1d2429bv7f5505d9e8333206@mail.gmail.com> References: <21007049.post@talk.nabble.com> <628aabb70812150023k628700dbv7b92748641e4ceb1@mail.gmail.com> <21017474.post@talk.nabble.com> <628aabb70812161020k1d2429bv7f5505d9e8333206@mail.gmail.com> Message-ID: <7DC1D963-6EBE-46B2-9104-79B27BE5F405@bioperl.org> if it is indeed tempfile creation problems you can set the environment variable $TEMPDIR to specify where tempfiles are created on mac it should be /tmp or /var/tmp I would guess. -jason On Dec 16, 2008, at 10:20 AM, Dave Messina wrote: > Hmm, tough to say what the problem is. > One thing I noticed that seems a little odd is your blatSearch.pl > script > appears to be running in your /Users/ directory, which is normally > owned by > root and not writable by regular users. > > Also, it looks like it's attempting to create the temporary files in > /var/folders, which as far as I remember is also owned by root. > > Not sure why running as root would necessarily cause a problem, but > it's an > unusual scenario, so you might try running as a regular user in a > directory > where you know you have write permissions. > > Otherwise, you could create a minimal example of your problem, such > as a > single small query sequence, a single small database, and a test > script. You > could post these in a bug report to Bugzilla so that someone can try > to > reproduce your problem. > > > Dave > > > > > On Mon, Dec 15, 2008 at 17:56, oso wrote: > >> >> Error Message: >> MSG: Blat call (blat >> /var/folders/zK/zKXnWXt8G8epLqENEIdNkE+++TI/-Tmp-/wcjQruYe8A >> /var/folders/zK/zKXnWXt8G8epLqENEIdNkE+++TI/-Tmp-/nePTpfPSKu - >> out=psl ) >> crashed: 65280 >> >> STACK Bio::Tools::Run::Alignment::Blat::_run >> /Library/Perl/5.8.8/Bio/Tools/Run/Alignment/Blat.pm:250 >> STACK Bio::Tools::Run::Alignment::Blat::run >> /Library/Perl/5.8.8/Bio/Tools/Run/Alignment/Blat.pm:167 >> STACK main::get_orfs /Users/blatSearch.pl:50 >> STACK toplevel /Users/blatSearch.pl:29 >> >> ******* >> I am running BioPerl version 1.5.2. >> >> Thanks for our help! >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Jason Stajich jason at bioperl.org From cjfields at illinois.edu Tue Dec 16 18:44:32 2008 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 16 Dec 2008 17:44:32 -0600 Subject: [Bioperl-l] branching for 1.6 Message-ID: <276D7D58-D18F-4FFF-A0F7-3AFEDC6A5E21@illinois.edu> All, I'll probably start a branch for the 1.6 release series late Thur- Friday, depending on some pending bug fixes. I'll be following the general pattern for a release branch; for those interested: http://svnbook.red-bean.com/en/1.5/svn.branchmerge.commonpatterns.html This is primarily so we can merge changes back and forth between trunk and the 1.6 branch as needed. Once we're ready for an actual release I'll tag any RC's and point releases from branch-1.6. If all goes well I'll tag the RC on Monday. In the meantime, I'll be updating the DEPENDENCIES, INSTALL, and other files and work on incorporating any last-minute bug fixes. As for the actual 1.6 release, it will probably be very early January depending on how the RC goes. I'll be off-grid from Dec. 26-31 somewhere in Texas (won't have computer access) but I'll check up on email. Cheers! chris From bix at sendu.me.uk Tue Dec 16 19:12:33 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 17 Dec 2008 00:12:33 +0000 Subject: [Bioperl-l] branching for 1.6 In-Reply-To: <276D7D58-D18F-4FFF-A0F7-3AFEDC6A5E21@illinois.edu> References: <276D7D58-D18F-4FFF-A0F7-3AFEDC6A5E21@illinois.edu> Message-ID: <494843F1.7090608@sendu.me.uk> Chris Fields wrote: > All, > > I'll probably start a branch for the 1.6 release series late > Thur-Friday, depending on some pending bug fixes. I'll be following the > general pattern for a release branch; for those interested: > > http://svnbook.red-bean.com/en/1.5/svn.branchmerge.commonpatterns.html > > This is primarily so we can merge changes back and forth between trunk > and the 1.6 branch as needed. Cool. It may be explained well enough there, but can you keep notes as you go along and update our own wiki on how to handle this in svn (which still has all the old cvs intructions)? Cheers, Sendu. From cjfields at illinois.edu Tue Dec 16 19:24:36 2008 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 16 Dec 2008 18:24:36 -0600 Subject: [Bioperl-l] branching for 1.6 In-Reply-To: <494843F1.7090608@sendu.me.uk> References: <276D7D58-D18F-4FFF-A0F7-3AFEDC6A5E21@illinois.edu> <494843F1.7090608@sendu.me.uk> Message-ID: <11717B3E-F9F2-4753-86AA-5520637E4DF1@illinois.edu> On Dec 16, 2008, at 6:12 PM, Sendu Bala wrote: > Chris Fields wrote: >> All, >> I'll probably start a branch for the 1.6 release series late Thur- >> Friday, depending on some pending bug fixes. I'll be following the >> general pattern for a release branch; for those interested: >> http://svnbook.red-bean.com/en/1.5/ >> svn.branchmerge.commonpatterns.html >> This is primarily so we can merge changes back and forth between >> trunk and the 1.6 branch as needed. > > Cool. It may be explained well enough there, but can you keep notes > as you go along and update our own wiki on how to handle this in svn > (which still has all the old cvs intructions)? > > > Cheers, > Sendu. Will do (particularly re: merges). chris From kellert at ohsu.edu Tue Dec 16 17:35:37 2008 From: kellert at ohsu.edu (Thomas Keller) Date: Tue, 16 Dec 2008 14:35:37 -0800 Subject: [Bioperl-l] perl5.10 Message-ID: <4E77C58B-A603-4976-B4E9-255095450E2A@ohsu.edu> Greetings, Does the latest bioperl work with perl 5.10? Any caveats or hints for installation? thanks, Tom Keller kellert at ohsu.edu 503-494-2442 From cjfields at illinois.edu Tue Dec 16 23:30:10 2008 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 16 Dec 2008 22:30:10 -0600 Subject: [Bioperl-l] perl5.10 In-Reply-To: <4E77C58B-A603-4976-B4E9-255095450E2A@ohsu.edu> References: <4E77C58B-A603-4976-B4E9-255095450E2A@ohsu.edu> Message-ID: Should work just fine. We had some initial problems but we worked on carrying everything over, see: http://www.bioperl.org/wiki/Bioperl_and_Perl_5.10 I'm using 5.10 exclusively, particularly now that 5.8 has been end-of- life'd. chris On Dec 16, 2008, at 4:35 PM, Thomas Keller wrote: > Greetings, > Does the latest bioperl work with perl 5.10? Any caveats or hints > for installation? > > thanks, > > Tom Keller > kellert at ohsu.edu > 503-494-2442 > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From maj at fortinbras.us Wed Dec 17 10:15:08 2008 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 17 Dec 2008 10:15:08 -0500 Subject: [Bioperl-l] "Powered by" logo? Message-ID: <8409184628F5492399772A4D451D5C55@NewLife> Is there an official "powered by Bioperl" logo, or is that just too cheesy? cheers MAJ From bix at sendu.me.uk Wed Dec 17 12:15:24 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 17 Dec 2008 17:15:24 +0000 Subject: [Bioperl-l] "Powered by" logo? In-Reply-To: <8409184628F5492399772A4D451D5C55@NewLife> References: <8409184628F5492399772A4D451D5C55@NewLife> Message-ID: <494933AC.5070101@sendu.me.uk> Mark A. Jensen wrote: > Is there an official "powered by Bioperl" logo, or is that just too cheesy? I think you just volunteered to make one? ;) From bix at sendu.me.uk Wed Dec 17 12:13:09 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 17 Dec 2008 17:13:09 +0000 Subject: [Bioperl-l] Bio::LocatableSeq warning Message-ID: <49493325.70300@sendu.me.uk> I've just committed a test alignment file to bioperl-run t/data, and Bio::LocatableSeq spurts up a warning about it: perl -MBio::AlignIO -e '$ai = Bio::AlignIO->new(-file => "t/data/pal2nal.aln"); $aln = $ai->next_aln;' --------------------- WARNING --------------------- MSG: In sequence pseudogene residue count gives end value 183. Overriding value [178] with value 183 for Bio::LocatableSeq::end(). ----LNCIVNDSQKMGIIRNGDLP*PQLKNKF2-FQRMTTPSSAEGKENLVFLIRKNWFSITEKNQPLKYIINLVVSRESKEPPQRPPFLD*SLGDALKRIEQLKLANKQDVFFTVGGSSVYKESMN*-DHFKLFVTWIMQDFQSDTFFS4EGDLEKYKLLPEYPQGVVSDVEEEKGIKYKFEVYEKND --------------------------------------------------- Is there simply something wrong with the alignment file (quite possible), and this warning means something? Or is this just normal behaviour now for valid alignment files? What is this warning supposed to mean to the user? What should I do about it? Why do I need to see it? From maj at fortinbras.us Wed Dec 17 12:19:56 2008 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 17 Dec 2008 12:19:56 -0500 Subject: [Bioperl-l] "Powered by" logo? In-Reply-To: <494933AC.5070101@sendu.me.uk> References: <8409184628F5492399772A4D451D5C55@NewLife> <494933AC.5070101@sendu.me.uk> Message-ID: Curses! (oKAY....) ----- Original Message ----- From: "Sendu Bala" To: "Mark A. Jensen" Cc: Sent: Wednesday, December 17, 2008 12:15 PM Subject: Re: [Bioperl-l] "Powered by" logo? > Mark A. Jensen wrote: >> Is there an official "powered by Bioperl" logo, or is that just too cheesy? > > I think you just volunteered to make one? ;) > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From bernd.web at gmail.com Wed Dec 17 12:51:07 2008 From: bernd.web at gmail.com (Bernd Web) Date: Wed, 17 Dec 2008 18:51:07 +0100 Subject: [Bioperl-l] Bio::LocatableSeq warning In-Reply-To: <49493325.70300@sendu.me.uk> References: <49493325.70300@sendu.me.uk> Message-ID: <716af09c0812170951n3b2fde26wa1551bfaf6ba818f@mail.gmail.com> Hi, Using bioperl (1.005002102), I have had problems with alignment slicing, which might be of similar nature. In my case it is caused by the difference in "gap" symbols in LocatableSeq and SimpleAlign. I had errors on non-existing sequences after slicing the alignment in SimpleAlign. This was caused by : $slice_seq =~ s/\W//g; (line 932) in the slice subroutine of SimpleAlign, in combination with the _ungapped_len subroutine of LocatableSeq: $string =~ s/[\.\-]+//g; * is not a gap-char here. I now "solved" this issue by redefining the _ungapped_length routine in my script after loading the modules as: sub Bio::LocatableSeq::_ungapped_len { my $self = shift; my $string = $self->seq || ''; $string =~ s/[%.-]+//g; #where % represent the new gap symbol $self->seq ? (return $self->start + CORE::length($string) - 1 ) : undef; } In addition, you might have to include such a symbol in: $Bio::PrimarySeq::MATCHPATTERN = 'A-Za-z\-\.\*\?=%:'; for the sequence to validate. Regards, Bernd On Wed, Dec 17, 2008 at 6:13 PM, Sendu Bala wrote: > I've just committed a test alignment file to bioperl-run t/data, and > Bio::LocatableSeq spurts up a warning about it: > > perl -MBio::AlignIO -e '$ai = Bio::AlignIO->new(-file => > "t/data/pal2nal.aln"); $aln = $ai->next_aln;' > > --------------------- WARNING --------------------- > MSG: In sequence pseudogene residue count gives end value 183. > Overriding value [178] with value 183 for Bio::LocatableSeq::end(). > ----LNCIVNDSQKMGIIRNGDLP*PQLKNKF2-FQRMTTPSSAEGKENLVFLIRKNWFSITEKNQPLKYIINLVVSRESKEPPQRPPFLD*SLGDALKRIEQLKLANKQDVFFTVGGSSVYKESMN*-DHFKLFVTWIMQDFQSDTFFS4EGDLEKYKLLPEYPQGVVSDVEEEKGIKYKFEVYEKND > --------------------------------------------------- > > > Is there simply something wrong with the alignment file (quite possible), > and this warning means something? > > Or is this just normal behaviour now for valid alignment files? What is this > warning supposed to mean to the user? What should I do about it? Why do I > need to see it? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From maj at fortinbras.us Wed Dec 17 13:03:00 2008 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 17 Dec 2008 13:03:00 -0500 Subject: [Bioperl-l] Bio::LocatableSeq warning In-Reply-To: <49493325.70300@sendu.me.uk> References: <49493325.70300@sendu.me.uk> Message-ID: <8A30892D120941AD8C5AB39E7D0E7D84@NewLife> 178 was the length of the sequence calculated by AlignIO and set with $seq->end(178). This number evidently ignores the 5 characters *, 2, *, *, and 4. Lseq ran interference, removing the gaps but not the special chars for the length calculation and came up with 183 = 178+5. It reset the end of the sequence to 183 and told you about it. AlignIO::clustalw collects the end value by parsing a range in the sequence name, not by counting chars, as far as I can tell. So perhaps the alignment file is hosed. I agree it's not too friendly. ----- Original Message ----- From: "Sendu Bala" To: "bioperl-l" Sent: Wednesday, December 17, 2008 12:13 PM Subject: [Bioperl-l] Bio::LocatableSeq warning > I've just committed a test alignment file to bioperl-run t/data, and > Bio::LocatableSeq spurts up a warning about it: > > perl -MBio::AlignIO -e '$ai = Bio::AlignIO->new(-file => > "t/data/pal2nal.aln"); $aln = $ai->next_aln;' > > --------------------- WARNING --------------------- > MSG: In sequence pseudogene residue count gives end value 183. > Overriding value [178] with value 183 for Bio::LocatableSeq::end(). > ----LNCIVNDSQKMGIIRNGDLP*PQLKNKF2-FQRMTTPSSAEGKENLVFLIRKNWFSITEKNQPLKYIINLVVSRESKEPPQRPPFLD*SLGDALKRIEQLKLANKQDVFFTVGGSSVYKESMN*-DHFKLFVTWIMQDFQSDTFFS4EGDLEKYKLLPEYPQGVVSDVEEEKGIKYKFEVYEKND > --------------------------------------------------- > > > Is there simply something wrong with the alignment file (quite possible), and > this warning means something? > > Or is this just normal behaviour now for valid alignment files? What is this > warning supposed to mean to the user? What should I do about it? Why do I need > to see it? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From roy.chaudhuri at gmail.com Wed Dec 17 13:05:15 2008 From: roy.chaudhuri at gmail.com (Roy Chaudhuri) Date: Wed, 17 Dec 2008 18:05:15 +0000 Subject: [Bioperl-l] Bio::LocatableSeq warning In-Reply-To: <49493325.70300@sendu.me.uk> References: <49493325.70300@sendu.me.uk> Message-ID: <49493F5B.9030207@gmail.com> Depends what you mean by valid. Your file contains asterisks and digits, representing stop codons and frameshifts (using Genewise notation according to the Pal2Nal paper). Bio::AlignIO::clustalw ignores those by doing an s/[^A-Za-z]//g before calculating the sequence length. Bio::LocatableSeq notices the discrepancy and corrects the length while issuing a warning. Bio::AlignIO::clustalw would need to be fixed if you want it to parse files with non-letter residues correctly. I think ClustalW itself removes non-letter residues from the input data so will never output such files. Roy. -- Dr. Roy Chaudhuri Department of Veterinary Medicine University of Cambridge, U.K. Sendu Bala wrote: > I've just committed a test alignment file to bioperl-run t/data, and > Bio::LocatableSeq spurts up a warning about it: > > perl -MBio::AlignIO -e '$ai = Bio::AlignIO->new(-file => > "t/data/pal2nal.aln"); $aln = $ai->next_aln;' > > --------------------- WARNING --------------------- > MSG: In sequence pseudogene residue count gives end value 183. > Overriding value [178] with value 183 for Bio::LocatableSeq::end(). > ----LNCIVNDSQKMGIIRNGDLP*PQLKNKF2-FQRMTTPSSAEGKENLVFLIRKNWFSITEKNQPLKYIINLVVSRESKEPPQRPPFLD*SLGDALKRIEQLKLANKQDVFFTVGGSSVYKESMN*-DHFKLFVTWIMQDFQSDTFFS4EGDLEKYKLLPEYPQGVVSDVEEEKGIKYKFEVYEKND > --------------------------------------------------- > > > Is there simply something wrong with the alignment file (quite > possible), and this warning means something? > > Or is this just normal behaviour now for valid alignment files? What is > this warning supposed to mean to the user? What should I do about it? > Why do I need to see it? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From maj at fortinbras.us Wed Dec 17 13:41:30 2008 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 17 Dec 2008 13:41:30 -0500 Subject: [Bioperl-l] Bio::LocatableSeq warning In-Reply-To: <49493F5B.9030207@gmail.com> References: <49493325.70300@sendu.me.uk> <49493F5B.9030207@gmail.com> Message-ID: <8B9B23BD4CC24235988CBE66905E5CCD@NewLife> Yes- my bad- if the sequence name contains a range, then clustalw does use this range for the length; if it does not, it counts as Roy says- I agree; This is prob an AlignIO bug by now, eh? ----- Original Message ----- From: "Roy Chaudhuri" To: "Sendu Bala" Cc: "bioperl-l" Sent: Wednesday, December 17, 2008 1:05 PM Subject: Re: [Bioperl-l] Bio::LocatableSeq warning > Depends what you mean by valid. Your file contains asterisks and digits, > representing stop codons and frameshifts (using Genewise notation according to > the Pal2Nal paper). Bio::AlignIO::clustalw ignores those by doing an > s/[^A-Za-z]//g before calculating the sequence length. Bio::LocatableSeq > notices the discrepancy and corrects the length while issuing a warning. > Bio::AlignIO::clustalw would need to be fixed if you want it to parse files > with non-letter residues correctly. I think ClustalW itself removes non-letter > residues from the input data so will never output such files. > > Roy. > -- > Dr. Roy Chaudhuri > Department of Veterinary Medicine > University of Cambridge, U.K. > > Sendu Bala wrote: >> I've just committed a test alignment file to bioperl-run t/data, and >> Bio::LocatableSeq spurts up a warning about it: >> >> perl -MBio::AlignIO -e '$ai = Bio::AlignIO->new(-file => >> "t/data/pal2nal.aln"); $aln = $ai->next_aln;' >> >> --------------------- WARNING --------------------- >> MSG: In sequence pseudogene residue count gives end value 183. >> Overriding value [178] with value 183 for Bio::LocatableSeq::end(). >> ----LNCIVNDSQKMGIIRNGDLP*PQLKNKF2-FQRMTTPSSAEGKENLVFLIRKNWFSITEKNQPLKYIINLVVSRESKEPPQRPPFLD*SLGDALKRIEQLKLANKQDVFFTVGGSSVYKESMN*-DHFKLFVTWIMQDFQSDTFFS4EGDLEKYKLLPEYPQGVVSDVEEEKGIKYKFEVYEKND >> --------------------------------------------------- >> >> >> Is there simply something wrong with the alignment file (quite possible), and >> this warning means something? >> >> Or is this just normal behaviour now for valid alignment files? What is this >> warning supposed to mean to the user? What should I do about it? Why do I >> need to see it? >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Wed Dec 17 17:59:41 2008 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 17 Dec 2008 16:59:41 -0600 Subject: [Bioperl-l] Bio::LocatableSeq warning In-Reply-To: <8B9B23BD4CC24235988CBE66905E5CCD@NewLife> References: <49493325.70300@sendu.me.uk> <49493F5B.9030207@gmail.com> <8B9B23BD4CC24235988CBE66905E5CCD@NewLife> Message-ID: <209DFAF0-15FF-4DB0-A268-A6610D8AA1F4@illinois.edu> It is a problem with clustalw parsing not accounting for frameshifts, mapping, and other odd bits coming from this format. That could be added in; LocatableSeq now allows this by specifying position => shift in frameshifts() as a hash ref. There are other significant problems with LocatableSeq, though. Gaps, frameshifts, and residues are set and checked via globals and aren't set per instance (which is definitely not optimal). I'll file a bug report on this to track it. chris On Dec 17, 2008, at 12:41 PM, Mark A. Jensen wrote: > Yes- my bad- if the sequence name contains a range, then clustalw > does use this range for the length; if it does not, it counts as Roy > says- > I agree; This is prob an AlignIO bug by now, eh? > ----- Original Message ----- From: "Roy Chaudhuri" > > To: "Sendu Bala" > Cc: "bioperl-l" > Sent: Wednesday, December 17, 2008 1:05 PM > Subject: Re: [Bioperl-l] Bio::LocatableSeq warning > > >> Depends what you mean by valid. Your file contains asterisks and >> digits, representing stop codons and frameshifts (using Genewise >> notation according to the Pal2Nal paper). Bio::AlignIO::clustalw >> ignores those by doing an s/[^A-Za-z]//g before calculating the >> sequence length. Bio::LocatableSeq notices the discrepancy and >> corrects the length while issuing a warning. Bio::AlignIO::clustalw >> would need to be fixed if you want it to parse files with non- >> letter residues correctly. I think ClustalW itself removes non- >> letter residues from the input data so will never output such files. >> >> Roy. >> -- >> Dr. Roy Chaudhuri >> Department of Veterinary Medicine >> University of Cambridge, U.K. >> >> Sendu Bala wrote: >>> I've just committed a test alignment file to bioperl-run t/data, >>> and Bio::LocatableSeq spurts up a warning about it: >>> >>> perl -MBio::AlignIO -e '$ai = Bio::AlignIO->new(-file => "t/data/ >>> pal2nal.aln"); $aln = $ai->next_aln;' >>> >>> --------------------- WARNING --------------------- >>> MSG: In sequence pseudogene residue count gives end value 183. >>> Overriding value [178] with value 183 for Bio::LocatableSeq::end(). >>> ----LNCIVNDSQKMGIIRNGDLP*PQLKNKF2- >>> FQRMTTPSSAEGKENLVFLIRKNWFSITEKNQPLKYIINLVVSRESKEPPQRPPFLD >>> *SLGDALKRIEQLKLANKQDVFFTVGGSSVYKESMN*- >>> DHFKLFVTWIMQDFQSDTFFS4EGDLEKYKLLPEYPQGVVSDVEEEKGIKYKFEVYEKND >>> --------------------------------------------------- >>> >>> >>> Is there simply something wrong with the alignment file (quite >>> possible), and this warning means something? >>> >>> Or is this just normal behaviour now for valid alignment files? >>> What is this warning supposed to mean to the user? What should I >>> do about it? Why do I need to see it? >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Wed Dec 17 18:18:15 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 17 Dec 2008 23:18:15 +0000 Subject: [Bioperl-l] Bio::LocatableSeq warning In-Reply-To: <209DFAF0-15FF-4DB0-A268-A6610D8AA1F4@illinois.edu> References: <49493325.70300@sendu.me.uk> <49493F5B.9030207@gmail.com> <8B9B23BD4CC24235988CBE66905E5CCD@NewLife> <209DFAF0-15FF-4DB0-A268-A6610D8AA1F4@illinois.edu> Message-ID: <494988B7.5080706@sendu.me.uk> Chris Fields wrote: > It is a problem with clustalw parsing not accounting for frameshifts, > mapping, and other odd bits coming from this format. That could be > added in; LocatableSeq now allows this by specifying position => shift > in frameshifts() as a hash ref. > > There are other significant problems with LocatableSeq, though. Gaps, > frameshifts, and residues are set and checked via globals and aren't set > per instance (which is definitely not optimal). I'll file a bug report > on this to track it. In this instance though, is there anything actually wrong with the alignment object I get? If not, perhaps it would be appropriate to revert to the old behaviour and have the message be a debug() and not a warn()? I don't know - I didn't consider the implications - just a suggestion. From maj at fortinbras.us Wed Dec 17 19:52:30 2008 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 17 Dec 2008 19:52:30 -0500 Subject: [Bioperl-l] Bio::LocatableSeq warning In-Reply-To: <494988B7.5080706@sendu.me.uk> References: <49493325.70300@sendu.me.uk> <49493F5B.9030207@gmail.com><8B9B23BD4CC24235988CBE66905E5CCD@NewLife><209DFAF0-15FF-4DB0-A268-A6610D8AA1F4@illinois.edu> <494988B7.5080706@sendu.me.uk> Message-ID: ----- Original Message ----- From: "Sendu Bala" To: "Chris Fields" Cc: "bioperl-l" ; "Mark A. Jensen" Sent: Wednesday, December 17, 2008 6:18 PM Subject: Re: [Bioperl-l] Bio::LocatableSeq warning > Chris Fields wrote: >> It is a problem with clustalw parsing not accounting for frameshifts, >> mapping, and other odd bits coming from this format. That could be added in; >> LocatableSeq now allows this by specifying position => shift in frameshifts() >> as a hash ref. >> >> There are other significant problems with LocatableSeq, though. Gaps, >> frameshifts, and residues are set and checked via globals and aren't set per >> instance (which is definitely not optimal). I'll file a bug report on this >> to track it. > > In this instance though, is there anything actually wrong with the alignment > object I get? > > If not, perhaps it would be appropriate to revert to the old behaviour and > have the message be a debug() and not a warn()? I don't know - I didn't > consider the implications - just a suggestion. > A softer warning would be convenient. I will frequently set end() just to get the side-effect of a correct recalculation of the end coord. (This is kludgy in itself, of course.) From analia at deb.uminho.pt Wed Dec 17 09:44:00 2008 From: analia at deb.uminho.pt (analia at deb.uminho.pt) Date: Wed, 17 Dec 2008 14:44:00 +0000 Subject: [Bioperl-l] Problem When searching PubMed Message-ID: <49491030.7020400@deb.uminho.pt> > Hi all, > > I am using your BioPerl eutils search modules. Probably it is my > fault, but when I try to run a query for which PubMed returns a large > number of documents, the get_count never meets the overall figures! > When retrieving the results, the program fails eventually. > > Any idea of what I am doing wrong? I am sending to examples... > > Cheers, > An?lia > > Here are two examples: > > > my $biblio = new Bio::Biblio (-access => 'eutils'); > print $biblio->find ("Escherichia coli")->get_count . "\n"; > > > Output : 100000 whereas PubMed says 258953! > > my %docs=(); > my $biblio = new Bio::Biblio (-access => 'eutils'); > my $collection = $biblio = $biblio->find("Escherichia coli"); > > while ( $collection->has_next) { > my $reader = Bio::Biblio::IO->new ('-data' => > $collection->get_next , > '-format' => 'medlinexml'); > if(my $citation = $reader->next_bibref()){ > $docs{$citation->{'_pmid'}}{title}=$citation->{'_title'}; > $docs{$citation->{'_pmid'}}{type}=$citation->{'_type'}; > $docs{$citation->{'_pmid'}}{date}=$citation->{'_date'}||"null"; > } > } > print scalar(keys %docs); > > Output: never get output, crashes the perl interpreter!!! From s_oheigeartaigh at yahoo.co.uk Thu Dec 18 08:00:11 2008 From: s_oheigeartaigh at yahoo.co.uk (Sean ohEigeartaigh) Date: Thu, 18 Dec 2008 13:00:11 +0000 (GMT) Subject: [Bioperl-l] Hit orientation using SearchIO Message-ID: <3891.54524.qm@web27408.mail.ukl.yahoo.com> Hi, I'm trying to find out the orientation of blast hits (relative to the query sequence) using SearchIO to process a StandAloneBlast report. I can get the start and end points of the query and the hits using $hsp->start/end('hit'), $hsp->start/end('query') but it always lists the coordinates from lowest to highest. How do I find out if, for example, the query runs 1-60 and the hit runs 240-180? The information is in the BLAST OUT file so it must be accessible. Thanks very much for your time, Se?n ? h?igeartaigh, bioinformatics phD student. From Kevin.M.Brown at asu.edu Thu Dec 18 10:09:50 2008 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Thu, 18 Dec 2008 08:09:50 -0700 Subject: [Bioperl-l] Hit orientation using SearchIO In-Reply-To: <3891.54524.qm@web27408.mail.ukl.yahoo.com> References: <3891.54524.qm@web27408.mail.ukl.yahoo.com> Message-ID: <1A4207F8295607498283FE9E93B775B4059ABFBB@EX02.asurite.ad.asu.edu> Check the Strand property to determine which orientation the match has. $hsp->strand('hit') $hsp->strand('query') > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Sean ohEigeartaigh > Sent: Thursday, December 18, 2008 6:00 AM > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] Hit orientation using SearchIO > > Hi, > > I'm trying to find out the orientation of blast hits > (relative to the query sequence) using SearchIO to process a > StandAloneBlast report. I can get the start and end points of > the query and the hits using $hsp->start/end('hit'), > $hsp->start/end('query') but it always lists the coordinates > from lowest to highest. How do I find out if, for example, > the query runs 1-60 and the hit runs 240-180? The information > is in the BLAST OUT file so it must be accessible. > > Thanks very much for your time, > Se?n ? h?igeartaigh, bioinformatics phD student. > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Thu Dec 18 12:46:24 2008 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 18 Dec 2008 11:46:24 -0600 Subject: [Bioperl-l] Problem When searching PubMed In-Reply-To: <49491030.7020400@deb.uminho.pt> References: <49491030.7020400@deb.uminho.pt> Message-ID: <114AE89B-1F16-437E-BE67-B1B1B0F25CEF@illinois.edu> On Dec 17, 2008, at 8:44 AM, analia at deb.uminho.pt wrote: >> Hi all, >> >> I am using your BioPerl eutils search modules. Probably it is my >> fault, but when I try to run a query for which PubMed returns a >> large number of documents, the get_count never meets the overall >> figures! When retrieving the results, the program fails eventually. >> >> Any idea of what I am doing wrong? I am sending to examples... >> >> Cheers, >> An?lia >> >> Here are two examples: >> >> >> my $biblio = new Bio::Biblio (-access => 'eutils'); >> print $biblio->find ("Escherichia coli")->get_count . "\n"; >> >> >> Output : 100000 whereas PubMed says 258953! >> >> my %docs=(); >> my $biblio = new Bio::Biblio (-access => 'eutils'); >> my $collection = $biblio = $biblio->find("Escherichia coli"); >> >> while ( $collection->has_next) { >> my $reader = Bio::Biblio::IO->new ('-data' => $collection- >> >get_next , >> '-format' => 'medlinexml'); >> if(my $citation = $reader->next_bibref()){ >> $docs{$citation->{'_pmid'}}{title}=$citation->{'_title'}; >> $docs{$citation->{'_pmid'}}{type}=$citation->{'_type'}; >> $docs{$citation->{'_pmid'}}{date}=$citation->{'_date'}||"null"; >> } >> } >> print scalar(keys %docs); >> >> Output: never get output, crashes the perl interpreter!!! The 100000 is likely from retmax being set somewhere in Bio::Biblio code. It appears that can be changed via $Bio::DB::Biblio::eutils:: $MAX_RECORDS. Most importantly I can confirm the seg fault. It doesn't surprise me too much if one thinks about what you are trying to do (attempting to retrieve ~100000 records in one go). Bio::DB::Biblio::eutils apparently isn't set up to lazily retrieve and parse XML (or to send back small bits of XML by piecemeal retrieval of IDs), so you will likely run into problems like this with very large XML files unless you attempt retrieving the XML in small chunks. Unfortunately, Bio::Biblio doesn't appear to have a workaround either so it's a bug (there needs to be a way to retrieve a list of IDs). Following is a workaround where you can use Bio::DB::EUtilities and pipe in returned XML to the parser (this iterates through the IDs stored on NCBI's server via 'usehistory'). Note that this calls the server over and over with a timeout in between; I would highly recommend NOT retrieving 100000 records at NCBI peak use times as you'll probably run into server issues (I have a fallback built in below JIC). chris # BEGIN CODE #!/usr/bin/perl -w use strict; use warnings; use Bio::Biblio::IO; use Bio::DB::EUtilities; my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch', -db => 'pubmed', -term => 'Escherichia coli', -usehistory => 'y', #-retmax => 100000 ); # uncommenting the above retmax changes the below count my $count = $eutil->get_count; print "Count: $count\n"; my $hist = $eutil->next_History || die 'No history data returned'; my ($start, $end); $eutil->set_parameters(-eutil => 'efetch', -history => $hist); # change retmax to vary chunk size returned my ($retmax, $retstart) = (500,0); my $tries = 0; RETRIEVE_XML: while ($retstart < $count) { $eutil->set_parameters(-retmax => $retmax, -retstart => $retstart); my $xml; eval{ $xml = $eutil->get_Response()->content; }; if ($@) { die "Server error: $@. Try again later" if $tries == 5; print STDERR "Server error, redo #$tries\n"; $tries++ && redo RETRIEVE_XML; } # then parse smaller XML chunk here # If you want to persist data and save some memory, # maybe tie below hash to a DB_File outside of this loop my %docs=(); my $reader = Bio::Biblio::IO->new ('-data' => $xml, '-format' => 'medlinexml'); while (my $citation = $reader->next_bibref()){ $docs{$citation->{'_pmid'}}{title}=$citation->{'_title'}; $docs{$citation->{'_pmid'}}{type}=$citation->{'_type'}; $docs{$citation->{'_pmid'}}{date}=$citation->{'_date'}||"null"; } print "Retrieved ".($retstart+1)." to ".($retstart+$retmax)."\n"; print scalar(keys %docs)."\n"; $retstart += $retmax; } From cjfields at illinois.edu Thu Dec 18 12:51:55 2008 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 18 Dec 2008 11:51:55 -0600 Subject: [Bioperl-l] Bio::LocatableSeq warning In-Reply-To: <494988B7.5080706@sendu.me.uk> References: <49493325.70300@sendu.me.uk> <49493F5B.9030207@gmail.com> <8B9B23BD4CC24235988CBE66905E5CCD@NewLife> <209DFAF0-15FF-4DB0-A268-A6610D8AA1F4@illinois.edu> <494988B7.5080706@sendu.me.uk> Message-ID: On Dec 17, 2008, at 5:18 PM, Sendu Bala wrote: > Chris Fields wrote: >> It is a problem with clustalw parsing not accounting for >> frameshifts, mapping, and other odd bits coming from this format. >> That could be added in; LocatableSeq now allows this by specifying >> position => shift in frameshifts() as a hash ref. >> There are other significant problems with LocatableSeq, though. >> Gaps, frameshifts, and residues are set and checked via globals and >> aren't set per instance (which is definitely not optimal). I'll >> file a bug report on this to track it. > > In this instance though, is there anything actually wrong with the > alignment object I get? The LocatableSeq has the ending reset; if it doesn't correspond to the actual end then something is wrong, but that would be with the parser (AlignIO::clustalw) not catching this and processing the data as needed. As Roy said, this is Genewise-like and indicates frameshifts, something that LocatableSeq can handle. > If not, perhaps it would be appropriate to revert to the old > behaviour and have the message be a debug() and not a warn()? I > don't know - I didn't consider the implications - just a suggestion. I'll file this as a bug as the set ending doesn't correspond to true end passed in by the parser. I'll take a look at the example file you have (if it's in svn) and see if we can add this in prior to the 1.6 branch. chris From jason at bioperl.org Thu Dec 18 13:49:22 2008 From: jason at bioperl.org (Jason Stajich) Date: Thu, 18 Dec 2008 13:49:22 -0500 Subject: [Bioperl-l] Hit orientation using SearchIO In-Reply-To: <1A4207F8295607498283FE9E93B775B4059ABFBB@EX02.asurite.ad.asu.edu> References: <3891.54524.qm@web27408.mail.ukl.yahoo.com> <1A4207F8295607498283FE9E93B775B4059ABFBB@EX02.asurite.ad.asu.edu> Message-ID: TMTOWTDI You can get the query and hit information as Bio::SeqFeatureI objects with $hsp->query or $hsp->hit SO $hsp->query->strand $hsp->hit->strand This should be demonstrated in the SearchIO HOWTO as well. -jason On Dec 18, 2008, at 10:09 AM, Kevin Brown wrote: > Check the Strand property to determine which orientation the match > has. > > $hsp->strand('hit') > $hsp->strand('query') > >> -----Original Message----- >> From: bioperl-l-bounces at lists.open-bio.org >> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of >> Sean ohEigeartaigh >> Sent: Thursday, December 18, 2008 6:00 AM >> To: bioperl-l at lists.open-bio.org >> Subject: [Bioperl-l] Hit orientation using SearchIO >> >> Hi, >> >> I'm trying to find out the orientation of blast hits >> (relative to the query sequence) using SearchIO to process a >> StandAloneBlast report. I can get the start and end points of >> the query and the hits using $hsp->start/end('hit'), >> $hsp->start/end('query') but it always lists the coordinates >> from lowest to highest. How do I find out if, for example, >> the query runs 1-60 and the hit runs 240-180? The information >> is in the BLAST OUT file so it must be accessible. >> >> Thanks very much for your time, >> Se?n ? h?igeartaigh, bioinformatics phD student. >> >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Jason Stajich jason at bioperl.org From cjfields at illinois.edu Thu Dec 18 13:50:51 2008 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 18 Dec 2008 12:50:51 -0600 Subject: [Bioperl-l] Bio::LocatableSeq warning In-Reply-To: References: <49493325.70300@sendu.me.uk> <49493F5B.9030207@gmail.com><8B9B23BD4CC24235988CBE66905E5CCD@NewLife><209DFAF0-15FF-4DB0-A268-A6610D8AA1F4@illinois.edu> <494988B7.5080706@sendu.me.uk> Message-ID: On Dec 17, 2008, at 6:52 PM, Mark A. Jensen wrote: > > ----- Original Message ----- From: "Sendu Bala" > To: "Chris Fields" > Cc: "bioperl-l" ; "Mark A. Jensen" > > Sent: Wednesday, December 17, 2008 6:18 PM > Subject: Re: [Bioperl-l] Bio::LocatableSeq warning > > >> Chris Fields wrote: >>> It is a problem with clustalw parsing not accounting for >>> frameshifts, mapping, and other odd bits coming from this format. >>> That could be added in; LocatableSeq now allows this by specifying >>> position => shift in frameshifts() as a hash ref. >>> >>> There are other significant problems with LocatableSeq, though. >>> Gaps, frameshifts, and residues are set and checked via globals >>> and aren't set per instance (which is definitely not optimal). >>> I'll file a bug report on this to track it. >> >> In this instance though, is there anything actually wrong with the >> alignment object I get? >> >> If not, perhaps it would be appropriate to revert to the old >> behaviour and have the message be a debug() and not a warn()? I >> don't know - I didn't consider the implications - just a suggestion. >> > > A softer warning would be convenient. I will frequently set end() just > to get the side-effect of a correct recalculation of the end coord. > (This is kludgy > in itself, of course.) It's never a good idea to rely on this behavior, particularly when considering the issues with global variables I point out here: http://bugzilla.open-bio.org/show_bug.cgi?id=2715 We can certainly change the warning to not reset passed end() values, but it should definitely remain a warning to indicate a problem that needs to be addressed. chris From hlapp at gmx.net Thu Dec 18 15:24:35 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 18 Dec 2008 15:24:35 -0500 Subject: [Bioperl-l] Problem When searching PubMed In-Reply-To: <114AE89B-1F16-437E-BE67-B1B1B0F25CEF@illinois.edu> References: <49491030.7020400@deb.uminho.pt> <114AE89B-1F16-437E-BE67-B1B1B0F25CEF@illinois.edu> Message-ID: <7AA64291-8AF6-4831-BA48-7741B834336B@gmx.net> On Dec 18, 2008, at 12:46 PM, Chris Fields wrote: > Note that this calls the server over and over with a timeout in > between; I would highly recommend NOT retrieving 100000 records at > NCBI peak use times NCBI may (and in the past has) also block your IP if you do that. Be nice to them, they're providing a great service. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at illinois.edu Thu Dec 18 16:12:20 2008 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 18 Dec 2008 15:12:20 -0600 Subject: [Bioperl-l] Problem When searching PubMed In-Reply-To: <7AA64291-8AF6-4831-BA48-7741B834336B@gmx.net> References: <49491030.7020400@deb.uminho.pt> <114AE89B-1F16-437E-BE67-B1B1B0F25CEF@illinois.edu> <7AA64291-8AF6-4831-BA48-7741B834336B@gmx.net> Message-ID: <5D6F097E-3938-47B2-B8E6-EABE9DD48BF3@illinois.edu> On Dec 18, 2008, at 2:24 PM, Hilmar Lapp wrote: > > On Dec 18, 2008, at 12:46 PM, Chris Fields wrote: > >> Note that this calls the server over and over with a timeout in >> between; I would highly recommend NOT retrieving 100000 records at >> NCBI peak use times > > > NCBI may (and in the past has) also block your IP if you do that. Be > nice to them, they're providing a great service. > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== They are usually forgiving when we go with the 3s timeout. I have thought about implementing something for EUtilities that uses localtime to determine when the request is sent and scale the timeout longer if it is at peak times (for this very reason, i.e. don't abuse the server). chris From MAB at stowers-institute.org Fri Dec 19 18:25:27 2008 From: MAB at stowers-institute.org (Blanchette, Marco) Date: Fri, 19 Dec 2008 17:25:27 -0600 Subject: [Bioperl-l] K-mer generating script Message-ID: Dear all, Does anyone have a little function that I could use to generate all possible k-mer DNA sequences? For instance all possible 3-mer (AAA, AAT, AAC, AAG, etc...). I need something that I could input the value of k and get all possible sequences... I know that it's a problem that need to use recursive programming but I can't get my brain around the problem. Many thanks Marco -- Marco Blanchette, Ph.D. Assistant Investigator Stowers Institute for Medical Research 1000 East 50th St. Kansas City, MO 64110 Tel: 816-926-4071 Cell: 816-726-8419 Fax: 816-926-2018 From MAB at stowers-institute.org Fri Dec 19 19:26:51 2008 From: MAB at stowers-institute.org (Blanchette, Marco) Date: Fri, 19 Dec 2008 18:26:51 -0600 Subject: [Bioperl-l] K-mer generating script In-Reply-To: <02D52A31-CB91-4B64-B67F-FF0FB61FE29F@lbl.gov> Message-ID: Thanks Mike! Exactly what I needed. I think I was searching too deeply! Have a good night Marco On 12/19/08 6:18 PM, "Michael Eisen" wrote: #!/usr/bin/perl # $k = shift; @bases = ('A','C','G','T'); @words = @bases; for ($i=1;$i<$k;$i++) { undef @newwords; foreach $w (@words) { foreach $b (@bases) { push (@newwords,$w.$b); } } undef @words; @words = @newwords; } foreach $w (@words) { print "$w\n"; } -- Marco Blanchette, Ph.D. Assistant Investigator Stowers Institute for Medical Research 1000 East 50th St. Kansas City, MO 64110 Tel: 816-926-4071 Cell: 816-726-8419 Fax: 816-926-2018 From mbeisen at lbl.gov Fri Dec 19 19:18:33 2008 From: mbeisen at lbl.gov (Michael Eisen) Date: Fri, 19 Dec 2008 16:18:33 -0800 Subject: [Bioperl-l] K-mer generating script In-Reply-To: References: Message-ID: <02D52A31-CB91-4B64-B67F-FF0FB61FE29F@lbl.gov> here's a quick one: #!/usr/bin/perl # $k = shift; @bases = ('A','C','G','T'); @words = @bases; for ($i=1;$i<$k;$i++) { undef @newwords; foreach $w (@words) { foreach $b (@bases) { push (@newwords,$w.$b); } } undef @words; @words = @newwords; } foreach $w (@words) { print "$w\n"; } On Dec 19, 2008, at 3:25 PM, Blanchette, Marco wrote: > Dear all, > > Does anyone have a little function that I could use to generate all > possible k-mer DNA sequences? For instance all possible 3-mer (AAA, > AAT, AAC, AAG, etc...). I need something that I could input the > value of k and get all possible sequences... > > I know that it's a problem that need to use recursive programming > but I can't get my brain around the problem. > > Many thanks > > Marco > -- > Marco Blanchette, Ph.D. > Assistant Investigator > Stowers Institute for Medical Research > 1000 East 50th St. > > Kansas City, MO 64110 > > Tel: 816-926-4071 > Cell: 816-726-8419 > Fax: 816-926-2018 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From jestill at plantbio.uga.edu Fri Dec 19 19:07:11 2008 From: jestill at plantbio.uga.edu (James Estill) Date: Fri, 19 Dec 2008 19:07:11 -0500 Subject: [Bioperl-l] K-mer generating script In-Reply-To: C5718987.BDED%MAB@Stowers-Institute.org Message-ID: <20081220000711.51c7f3e2@dogwood.plantbio.uga.edu> SeqIO works great for this. I've used something like the following. This is part of a larger program, so some of this not relevant to what you need ... ======================== ?$fasta_in = "your_file.fasta"; $k = 3; my $in_seq_num = 0; my $inseq = Bio::SeqIO->new( -file => "<$fasta_in", -format => 'fasta'); while (my $seq = $inseq->next_seq) { $in_seq_num++; if ($in_seq_num == 2) { print "\a"; die "Input file should be a single sequence record\n"; } # Calculate base cooridate data my $seq_len = $seq->length(); my $max_start = $seq->length() - $k; # Print some summary data print STDERR "\n==============================\n" if $verbose; print STDERR "SEQ LEN: $seq_len\n" if $verbose; print STDERR "MAX START: $max_start\n" if $verbose; print STDERR "==============================\n" if $verbose; # CREATE FASTA FILE OF ALL K LENGTH OLIGOS # IN THE INPUT SEQUENCE print STDERR "Creating oligo fasta file\n" if $verbose; open (FASTAOUT, ">$temp_fasta") || die "Can not open temp fasta file:\n $temp_fasta\n"; for ($i=0; $i<=$max_start; $i++) { $start_pos = $i + 1; $end_pos = $start_pos + $k - 1; my $oligo = $seq->subseq($start_pos, $end_pos); # Set counts array to zero $counts[$i] = 0; print FASTAOUT ">$start_pos\n"; print FASTAOUT "$oligo\n"; } close (FASTAOUT); } -- Jamie Estill -- jestill at uga.edu -- http://jestill.myweb.uga.edu -- http://www.epernicus.com/people/jestill _____ From: Blanchette, Marco [mailto:MAB at stowers-institute.org] To: bioperl-l at lists.open-bio.org [mailto:bioperl-l at lists.open-bio.org] Sent: Fri, 19 Dec 2008 18:25:27 -0500 Subject: [Bioperl-l] K-mer generating script Dear all, Does anyone have a little function that I could use to generate all possible k-mer DNA sequences? For instance all possible 3-mer (AAA, AAT, AAC, AAG, etc...). I need something that I could input the value of k and get all possible sequences... I know that it's a problem that need to use recursive programming but I can't get my brain around the problem. Many thanks Marco -- Marco Blanchette, Ph.D. Assistant Investigator Stowers Institute for Medical Research 1000 East 50th St. Kansas City, MO 64110 Tel: 816-926-4071 Cell: 816-726-8419 Fax: 816-926-2018 _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From David.Messina at sbc.su.se Fri Dec 19 20:11:00 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Sat, 20 Dec 2008 02:11:00 +0100 Subject: [Bioperl-l] K-mer generating script In-Reply-To: References: Message-ID: <628aabb70812191711t7d2701cat240c17eb4cb18e7a@mail.gmail.com> Hi Marco, Here's some code to generate and print all possible nmers. I'm really just using the module Math::Combinatorics to do all the dirty work here, so probably won't be as fast as if you wrote a custom recursive function as you suggest. But gets the job done anyway. See also Bio::Tools::SeqWords and Bio::Tools::SeqStats for related goodies. Dave -------------- example code -------------- #!/usr/local/bin/perl use strict; use warnings; use Math::Combinatorics; # do all codons (3-mers) as an example generate_possible_kmers(3); =head2 generate_possible_kmers Title : generate_possible_kamers Usage : my $possible_perms = generate_possible_kmers() Function: create and print the list of possible DNA kmers Returns : none Args : n - the length of the desired 'mer' =cut sub generate_possible_kmers { my ($n) = @_; my $alphabet = [ qw( A C G T ) ]; my $words_per_row = 10; my $i=0; my $o = Math::Combinatorics->new( count=>$n, data=>$alphabet, frequency=>[$n,$n,$n,$n] ); while ( my @x = $o->next_multiset ) { my $p = Math::Combinatorics->new( data=>\@x , frequency=>[map{1} @x] ); while ( my @y = $p->next_string ) { print join('', @y), ' '; $i++; if (($i % $words_per_row) == 0) { print "\n"; } } } } ----------------- end code ----------------- From maj at fortinbras.us Fri Dec 19 19:45:00 2008 From: maj at fortinbras.us (Mark A. Jensen) Date: Fri, 19 Dec 2008 19:45:00 -0500 Subject: [Bioperl-l] K-mer generating script In-Reply-To: References: Message-ID: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> A little sloppy, but it recurses and is general--- # ex... @combs = doit(3, [ qw( A T G C ) ]); 1; # code sub doit { my ($n, $sym) = @_; my $a = []; doit_guts($n, $sym, $a, ''); return map {$_ || ()} @$a; } sub doit_guts { my ($n, $sym, $store, $str) = @_; if (!$n) { return $str; } else { foreach my $s (@$sym) { push @$store, doit_guts($n-1, $sym, $store, $str.$s); } } } ----- Original Message ----- From: "Blanchette, Marco" To: Sent: Friday, December 19, 2008 6:25 PM Subject: [Bioperl-l] K-mer generating script > Dear all, > > Does anyone have a little function that I could use to generate all possible > k-mer DNA sequences? For instance all possible 3-mer (AAA, AAT, AAC, AAG, > etc...). I need something that I could input the value of k and get all > possible sequences... > > I know that it's a problem that need to use recursive programming but I can't > get my brain around the problem. > > Many thanks > > Marco > -- > Marco Blanchette, Ph.D. > Assistant Investigator > Stowers Institute for Medical Research > 1000 East 50th St. > > Kansas City, MO 64110 > > Tel: 816-926-4071 > Cell: 816-726-8419 > Fax: 816-926-2018 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From jason at bioperl.org Sat Dec 20 00:02:56 2008 From: jason at bioperl.org (Jason Stajich) Date: Sat, 20 Dec 2008 00:02:56 -0500 Subject: [Bioperl-l] K-mer generating script In-Reply-To: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> Message-ID: <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> Does someone want to put this on the wiki too? Maybe we could start a little bit of perl snippets for examples like these. -j On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: > A little sloppy, but it recurses and is general--- > > # ex... > @combs = doit(3, [ qw( A T G C ) ]); > 1; > # code > > sub doit { > my ($n, $sym) = @_; > my $a = []; > doit_guts($n, $sym, $a, ''); > return map {$_ || ()} @$a; > } > > sub doit_guts { > my ($n, $sym, $store, $str) = @_; > if (!$n) { > return $str; > } > else { > foreach my $s (@$sym) { > push @$store, doit_guts($n-1, $sym, $store, $str.$s); > } > } > } > > > ----- Original Message ----- From: "Blanchette, Marco" > > To: > Sent: Friday, December 19, 2008 6:25 PM > Subject: [Bioperl-l] K-mer generating script > > >> Dear all, >> >> Does anyone have a little function that I could use to generate all >> possible k-mer DNA sequences? For instance all possible 3-mer (AAA, >> AAT, AAC, AAG, etc...). I need something that I could input the >> value of k and get all possible sequences... >> >> I know that it's a problem that need to use recursive programming >> but I can't get my brain around the problem. >> >> Many thanks >> >> Marco >> -- >> Marco Blanchette, Ph.D. >> Assistant Investigator >> Stowers Institute for Medical Research >> 1000 East 50th St. >> >> Kansas City, MO 64110 >> >> Tel: 816-926-4071 >> Cell: 816-726-8419 >> Fax: 816-926-2018 >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Jason Stajich jason at bioperl.org From cjfields at illinois.edu Sat Dec 20 00:53:59 2008 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 19 Dec 2008 23:53:59 -0600 Subject: [Bioperl-l] K-mer generating script In-Reply-To: <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> Message-ID: <0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> To add to the pile: Mark-Jason Dominus tackles this problem in Higher-Order Perl using iterators, which also allows other nifty bits like 'give variants of A(CTG)T(TGA)', where anything in parentheses are wild-cards. The nice advantage of the iterator approach is you don't tank memory for long strings. Furthermore, as a bonus, you can now download the book for free: http://hop.perl.plover.com/book/ The relevant chapter is here (p. 135): http://hop.perl.plover.com/book/pdf/04Iterators.pdf chris On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote: > Does someone want to put this on the wiki too? > > Maybe we could start a little bit of perl snippets for examples like > these. > > -j > On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: > >> A little sloppy, but it recurses and is general--- >> >> # ex... >> @combs = doit(3, [ qw( A T G C ) ]); >> 1; >> # code >> >> sub doit { >> my ($n, $sym) = @_; >> my $a = []; >> doit_guts($n, $sym, $a, ''); >> return map {$_ || ()} @$a; >> } >> >> sub doit_guts { >> my ($n, $sym, $store, $str) = @_; >> if (!$n) { >> return $str; >> } >> else { >> foreach my $s (@$sym) { >> push @$store, doit_guts($n-1, $sym, $store, $str.$s); >> } >> } >> } >> >> >> ----- Original Message ----- From: "Blanchette, Marco" > > >> To: >> Sent: Friday, December 19, 2008 6:25 PM >> Subject: [Bioperl-l] K-mer generating script >> >> >>> Dear all, >>> >>> Does anyone have a little function that I could use to generate >>> all possible k-mer DNA sequences? For instance all possible 3-mer >>> (AAA, AAT, AAC, AAG, etc...). I need something that I could input >>> the value of k and get all possible sequences... >>> >>> I know that it's a problem that need to use recursive programming >>> but I can't get my brain around the problem. >>> >>> Many thanks >>> >>> Marco >>> -- >>> Marco Blanchette, Ph.D. >>> Assistant Investigator >>> Stowers Institute for Medical Research >>> 1000 East 50th St. >>> >>> Kansas City, MO 64110 >>> >>> Tel: 816-926-4071 >>> Cell: 816-726-8419 >>> Fax: 816-926-2018 >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Jason Stajich > jason at bioperl.org > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Sat Dec 20 01:25:56 2008 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 20 Dec 2008 00:25:56 -0600 Subject: [Bioperl-l] branch-1-6 now in svn Message-ID: All, The 1.6 branch is now in subversion (wanted to get this out earlier but we had this icestorm thingy here in the midwest...). I'll be working on both the branch and main trunk, merging bits over to the 1.6 branch as needed over the next couple of days (updated docs, etc). The only branch-specific tasks will be dealing with modules which won't be in the final release. If there are any commits that should be included feel free to commit them to trunk and I'll merge them over to the branch as needed (this includes any documentation, etc.). Core devs should feel free to make changes as needed. My goal is to tag an RC for Monday so we can start a few preliminary rounds of tests (it may be early Tuesday due to other commitments I have this weekend). I will be gone between Dec. 26-31, but should be back in time to address any testing issues not covered. chris From maj at fortinbras.us Sat Dec 20 01:34:01 2008 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 20 Dec 2008 01:34:01 -0500 Subject: [Bioperl-l] K-mer generating script In-Reply-To: <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> Message-ID: Jason - Have a look at http://www.bioperl.org/wiki/Category:Scrapbook could be cool- MAJ ----- Original Message ----- From: "Jason Stajich" To: "Mark A. Jensen" ; "Blanchette, Marco" Cc: "bioperl list" Sent: Saturday, December 20, 2008 12:02 AM Subject: Re: [Bioperl-l] K-mer generating script > Does someone want to put this on the wiki too? > > Maybe we could start a little bit of perl snippets for examples like these. > > -j > On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: > >> A little sloppy, but it recurses and is general--- >> >> # ex... >> @combs = doit(3, [ qw( A T G C ) ]); >> 1; >> # code >> >> sub doit { >> my ($n, $sym) = @_; >> my $a = []; >> doit_guts($n, $sym, $a, ''); >> return map {$_ || ()} @$a; >> } >> >> sub doit_guts { >> my ($n, $sym, $store, $str) = @_; >> if (!$n) { >> return $str; >> } >> else { >> foreach my $s (@$sym) { >> push @$store, doit_guts($n-1, $sym, $store, $str.$s); >> } >> } >> } >> >> >> ----- Original Message ----- From: "Blanchette, Marco" >> > > >> To: >> Sent: Friday, December 19, 2008 6:25 PM >> Subject: [Bioperl-l] K-mer generating script >> >> >>> Dear all, >>> >>> Does anyone have a little function that I could use to generate all >>> possible k-mer DNA sequences? For instance all possible 3-mer (AAA, AAT, >>> AAC, AAG, etc...). I need something that I could input the value of k and >>> get all possible sequences... >>> >>> I know that it's a problem that need to use recursive programming but I >>> can't get my brain around the problem. >>> >>> Many thanks >>> >>> Marco >>> -- >>> Marco Blanchette, Ph.D. >>> Assistant Investigator >>> Stowers Institute for Medical Research >>> 1000 East 50th St. >>> >>> Kansas City, MO 64110 >>> >>> Tel: 816-926-4071 >>> Cell: 816-726-8419 >>> Fax: 816-926-2018 >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Jason Stajich > jason at bioperl.org > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From diriano at uni-potsdam.de Sat Dec 20 08:30:32 2008 From: diriano at uni-potsdam.de (diriano at uni-potsdam.de) Date: Sat, 20 Dec 2008 14:30:32 +0100 Subject: [Bioperl-l] K-mer generating script In-Reply-To: References: Message-ID: <20081220143032.58e4mlrio8ssgww0@webmail.uni-potsdam.de> Dear Marco, just another option, why not just counting? Any DNA sequence is a number in base four (4),isn't it? So you yous have to count from zero to the number (in base 4) that you want. I have a script that does this, among other things, you can have a look at: http://diriano.googlepages.com/matrix_realizations.txt the relevant section is "Transcode base 4 numbers into DNA words", it uses Math::BigInt and Math::BaseArith. Hope this helps as the otehrs. Best, Diego Quoting "Blanchette, Marco" : > Dear all, > > Does anyone have a little function that I could use to generate all > possible k-mer DNA sequences? For instance all possible 3-mer (AAA, > AAT, AAC, AAG, etc...). I need something that I could input the > value of k and get all possible sequences... > > I know that it's a problem that need to use recursive programming > but I can't get my brain around the problem. > > Many thanks > > Marco > -- > Marco Blanchette, Ph.D. > Assistant Investigator > Stowers Institute for Medical Research > 1000 East 50th St. > > Kansas City, MO 64110 > > Tel: 816-926-4071 > Cell: 816-726-8419 > Fax: 816-926-2018 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Diego Mauricio Riano Pachon Biologist Institute of Biology and Biochemistry University of Potsdam Karl-Liebknecht-Str. 24-25 Haus 20 14476 Golm Germany Tel:0331/977-2809 http://www.geocities.com/dmrp.geo/ From MAB at stowers-institute.org Sat Dec 20 09:21:41 2008 From: MAB at stowers-institute.org (Blanchette, Marco) Date: Sat, 20 Dec 2008 08:21:41 -0600 Subject: [Bioperl-l] K-mer generating script In-Reply-To: Message-ID: This is a very good idea! I never realized this was on the BioPerl website. Is there a clear link on the home page? Thanks to all, I have several very nice options. Cheers, Marco On 12/20/08 12:34 AM, "Mark A. Jensen" wrote: Jason - Have a look at http://www.bioperl.org/wiki/Category:Scrapbook could be cool- MAJ ----- Original Message ----- From: "Jason Stajich" To: "Mark A. Jensen" ; "Blanchette, Marco" Cc: "bioperl list" Sent: Saturday, December 20, 2008 12:02 AM Subject: Re: [Bioperl-l] K-mer generating script > Does someone want to put this on the wiki too? > > Maybe we could start a little bit of perl snippets for examples like these. > > -j > On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: > >> A little sloppy, but it recurses and is general--- >> >> # ex... >> @combs = doit(3, [ qw( A T G C ) ]); >> 1; >> # code >> >> sub doit { >> my ($n, $sym) = @_; >> my $a = []; >> doit_guts($n, $sym, $a, ''); >> return map {$_ || ()} @$a; >> } >> >> sub doit_guts { >> my ($n, $sym, $store, $str) = @_; >> if (!$n) { >> return $str; >> } >> else { >> foreach my $s (@$sym) { >> push @$store, doit_guts($n-1, $sym, $store, $str.$s); >> } >> } >> } >> >> >> ----- Original Message ----- From: "Blanchette, Marco" >> > > >> To: >> Sent: Friday, December 19, 2008 6:25 PM >> Subject: [Bioperl-l] K-mer generating script >> >> >>> Dear all, >>> >>> Does anyone have a little function that I could use to generate all >>> possible k-mer DNA sequences? For instance all possible 3-mer (AAA, AAT, >>> AAC, AAG, etc...). I need something that I could input the value of k and >>> get all possible sequences... >>> >>> I know that it's a problem that need to use recursive programming but I >>> can't get my brain around the problem. >>> >>> Many thanks >>> >>> Marco >>> -- >>> Marco Blanchette, Ph.D. >>> Assistant Investigator >>> Stowers Institute for Medical Research >>> 1000 East 50th St. >>> >>> Kansas City, MO 64110 >>> >>> Tel: 816-926-4071 >>> Cell: 816-726-8419 >>> Fax: 816-926-2018 >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Jason Stajich > jason at bioperl.org > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Marco Blanchette, Ph.D. Assistant Investigator Stowers Institute for Medical Research 1000 East 50th St. Kansas City, MO 64110 Tel: 816-926-4071 Cell: 816-726-8419 Fax: 816-926-2018 From cjfields at illinois.edu Sat Dec 20 10:19:10 2008 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 20 Dec 2008 09:19:10 -0600 Subject: [Bioperl-l] K-mer generating script In-Reply-To: References: Message-ID: <7EB8DAEB-697E-41B9-A5FD-AB86CC75A973@illinois.edu> Added links to the main page and to the sidebar now. Great idea Mark! chris On Dec 20, 2008, at 8:21 AM, Blanchette, Marco wrote: > This is a very good idea! I never realized this was on the BioPerl > website. Is there a clear link on the home page? > > Thanks to all, I have several very nice options. > > Cheers, > > Marco > > > On 12/20/08 12:34 AM, "Mark A. Jensen" wrote: > > Jason - > Have a look at > http://www.bioperl.org/wiki/Category:Scrapbook > could be cool- > MAJ > ----- Original Message ----- > From: "Jason Stajich" > To: "Mark A. Jensen" ; "Blanchette, Marco" > > Cc: "bioperl list" > Sent: Saturday, December 20, 2008 12:02 AM > Subject: Re: [Bioperl-l] K-mer generating script > > >> Does someone want to put this on the wiki too? >> >> Maybe we could start a little bit of perl snippets for examples >> like these. >> >> -j >> On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: >> >>> A little sloppy, but it recurses and is general--- >>> >>> # ex... >>> @combs = doit(3, [ qw( A T G C ) ]); >>> 1; >>> # code >>> >>> sub doit { >>> my ($n, $sym) = @_; >>> my $a = []; >>> doit_guts($n, $sym, $a, ''); >>> return map {$_ || ()} @$a; >>> } >>> >>> sub doit_guts { >>> my ($n, $sym, $store, $str) = @_; >>> if (!$n) { >>> return $str; >>> } >>> else { >>> foreach my $s (@$sym) { >>> push @$store, doit_guts($n-1, $sym, $store, $str.$s); >>> } >>> } >>> } >>> >>> >>> ----- Original Message ----- From: "Blanchette, Marco" >>> >>> >>> To: >>> Sent: Friday, December 19, 2008 6:25 PM >>> Subject: [Bioperl-l] K-mer generating script >>> >>> >>>> Dear all, >>>> >>>> Does anyone have a little function that I could use to generate all >>>> possible k-mer DNA sequences? For instance all possible 3-mer >>>> (AAA, AAT, >>>> AAC, AAG, etc...). I need something that I could input the value >>>> of k and >>>> get all possible sequences... >>>> >>>> I know that it's a problem that need to use recursive >>>> programming but I >>>> can't get my brain around the problem. >>>> >>>> Many thanks >>>> >>>> Marco >>>> -- >>>> Marco Blanchette, Ph.D. >>>> Assistant Investigator >>>> Stowers Institute for Medical Research >>>> 1000 East 50th St. >>>> >>>> Kansas City, MO 64110 >>>> >>>> Tel: 816-926-4071 >>>> Cell: 816-726-8419 >>>> Fax: 816-926-2018 >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> Jason Stajich >> jason at bioperl.org >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > -- > Marco Blanchette, Ph.D. > Assistant Investigator > Stowers Institute for Medical Research > 1000 East 50th St. > > Kansas City, MO 64110 > > Tel: 816-926-4071 > Cell: 816-726-8419 > Fax: 816-926-2018 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From maj at fortinbras.us Sat Dec 20 10:57:09 2008 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 20 Dec 2008 10:57:09 -0500 Subject: [Bioperl-l] K-mer generating script In-Reply-To: <7EB8DAEB-697E-41B9-A5FD-AB86CC75A973@illinois.edu> References: <7EB8DAEB-697E-41B9-A5FD-AB86CC75A973@illinois.edu> Message-ID: Prime mover was Jason- cheers all ----- Original Message ----- From: "Chris Fields" To: "Blanchette, Marco" Cc: "bioperl list" ; "Mark A. Jensen" Sent: Saturday, December 20, 2008 10:19 AM Subject: Re: [Bioperl-l] K-mer generating script > Added links to the main page and to the sidebar now. Great idea Mark! > > chris > > On Dec 20, 2008, at 8:21 AM, Blanchette, Marco wrote: > >> This is a very good idea! I never realized this was on the BioPerl website. >> Is there a clear link on the home page? >> >> Thanks to all, I have several very nice options. >> >> Cheers, >> >> Marco >> >> >> On 12/20/08 12:34 AM, "Mark A. Jensen" wrote: >> >> Jason - >> Have a look at >> http://www.bioperl.org/wiki/Category:Scrapbook >> could be cool- >> MAJ >> ----- Original Message ----- >> From: "Jason Stajich" >> To: "Mark A. Jensen" ; "Blanchette, Marco" >> >> Cc: "bioperl list" >> Sent: Saturday, December 20, 2008 12:02 AM >> Subject: Re: [Bioperl-l] K-mer generating script >> >> >>> Does someone want to put this on the wiki too? >>> >>> Maybe we could start a little bit of perl snippets for examples like >>> these. >>> >>> -j >>> On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: >>> >>>> A little sloppy, but it recurses and is general--- >>>> >>>> # ex... >>>> @combs = doit(3, [ qw( A T G C ) ]); >>>> 1; >>>> # code >>>> >>>> sub doit { >>>> my ($n, $sym) = @_; >>>> my $a = []; >>>> doit_guts($n, $sym, $a, ''); >>>> return map {$_ || ()} @$a; >>>> } >>>> >>>> sub doit_guts { >>>> my ($n, $sym, $store, $str) = @_; >>>> if (!$n) { >>>> return $str; >>>> } >>>> else { >>>> foreach my $s (@$sym) { >>>> push @$store, doit_guts($n-1, $sym, $store, $str.$s); >>>> } >>>> } >>>> } >>>> >>>> >>>> ----- Original Message ----- From: "Blanchette, Marco" >>>> >>>> >>>> To: >>>> Sent: Friday, December 19, 2008 6:25 PM >>>> Subject: [Bioperl-l] K-mer generating script >>>> >>>> >>>>> Dear all, >>>>> >>>>> Does anyone have a little function that I could use to generate all >>>>> possible k-mer DNA sequences? For instance all possible 3-mer (AAA, AAT, >>>>> AAC, AAG, etc...). I need something that I could input the value of k >>>>> and >>>>> get all possible sequences... >>>>> >>>>> I know that it's a problem that need to use recursive programming but I >>>>> can't get my brain around the problem. >>>>> >>>>> Many thanks >>>>> >>>>> Marco >>>>> -- >>>>> Marco Blanchette, Ph.D. >>>>> Assistant Investigator >>>>> Stowers Institute for Medical Research >>>>> 1000 East 50th St. >>>>> >>>>> Kansas City, MO 64110 >>>>> >>>>> Tel: 816-926-4071 >>>>> Cell: 816-726-8419 >>>>> Fax: 816-926-2018 >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> Jason Stajich >>> jason at bioperl.org >>> >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> -- >> Marco Blanchette, Ph.D. >> Assistant Investigator >> Stowers Institute for Medical Research >> 1000 East 50th St. >> >> Kansas City, MO 64110 >> >> Tel: 816-926-4071 >> Cell: 816-726-8419 >> Fax: 816-926-2018 >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From bosborne11 at verizon.net Sat Dec 20 16:28:09 2008 From: bosborne11 at verizon.net (Brian Osborne) Date: Sat, 20 Dec 2008 16:28:09 -0500 Subject: [Bioperl-l] K-mer generating script In-Reply-To: References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> Message-ID: Good idea. I have a bunch of regular expressions for sequence searching, I think I'll put them into this Scrapbook category. Brian O. On Dec 20, 2008, at 1:34 AM, Mark A. Jensen wrote: > Jason - > Have a look at > http://www.bioperl.org/wiki/Category:Scrapbook > could be cool- > MAJ > ----- Original Message ----- From: "Jason Stajich" > To: "Mark A. Jensen" ; "Blanchette, Marco" > > Cc: "bioperl list" > Sent: Saturday, December 20, 2008 12:02 AM > Subject: Re: [Bioperl-l] K-mer generating script > > >> Does someone want to put this on the wiki too? >> >> Maybe we could start a little bit of perl snippets for examples >> like these. >> >> -j >> On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: >> >>> A little sloppy, but it recurses and is general--- >>> >>> # ex... >>> @combs = doit(3, [ qw( A T G C ) ]); >>> 1; >>> # code >>> >>> sub doit { >>> my ($n, $sym) = @_; >>> my $a = []; >>> doit_guts($n, $sym, $a, ''); >>> return map {$_ || ()} @$a; >>> } >>> >>> sub doit_guts { >>> my ($n, $sym, $store, $str) = @_; >>> if (!$n) { >>> return $str; >>> } >>> else { >>> foreach my $s (@$sym) { >>> push @$store, doit_guts($n-1, $sym, $store, $str.$s); >>> } >>> } >>> } >>> >>> >>> ----- Original Message ----- From: "Blanchette, Marco" >> > >>> To: >>> Sent: Friday, December 19, 2008 6:25 PM >>> Subject: [Bioperl-l] K-mer generating script >>> >>> >>>> Dear all, >>>> >>>> Does anyone have a little function that I could use to generate >>>> all possible k-mer DNA sequences? For instance all possible 3-mer >>>> (AAA, AAT, AAC, AAG, etc...). I need something that I could >>>> input the value of k and get all possible sequences... >>>> >>>> I know that it's a problem that need to use recursive >>>> programming but I can't get my brain around the problem. >>>> >>>> Many thanks >>>> >>>> Marco >>>> -- >>>> Marco Blanchette, Ph.D. >>>> Assistant Investigator >>>> Stowers Institute for Medical Research >>>> 1000 East 50th St. >>>> >>>> Kansas City, MO 64110 >>>> >>>> Tel: 816-926-4071 >>>> Cell: 816-726-8419 >>>> Fax: 816-926-2018 >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> Jason Stajich >> jason at bioperl.org >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From MAB at stowers-institute.org Sat Dec 20 18:10:08 2008 From: MAB at stowers-institute.org (Blanchette, Marco) Date: Sat, 20 Dec 2008 17:10:08 -0600 Subject: [Bioperl-l] Help with threads and shared variable Message-ID: Dear all, I am not sure this is the best place to post that questions but I don't really know where else to go... So, let's give it a shot. I am using the Perl threads utility to successfully multi threads several of my computing jobs on my workstation. My current problem is that I need to perform multiple processes using the same humongous array (more than 2x10e6 items). My problem is that the computing time for each iteration is not very long but I have a lot of iterations to do and every time a thread is created I am passing the huge array to the function and a fresh copy of the array is created. Thus, there is a huge amount of wasted resources (time and memory) use to create these data structures that are used by each threads but not modified. The logical alternative is to use shared memory where all thread would have access to the same copy of the huge array. In principal Perl provide such a mechanism through the module threads::shared but I am unable to understand how to use the shared variables. Anyone has experience to share on threads::shared? Here is a couple of unsuccessful attempts to use that module: ### first example my $var :shared; #create a shared scalar $var = make_uge_array; #return a pointer to a huge array and trying to assign it the the shared pointer my $thr = threads->create(\&doTheJob,$var); #spawn a thread $thr->join; #Wait for the thread to return ### Generate the following error ### Invalid value for shared scalar at ... ### second example my $var = make_uge_array; #return a pointer to a huge array print scalar(@{$var}), "\n"; #print 2,000,000 share($var); print scalar(@{$var}), "\n"; #print 0 my $thr = threads->create(\&doTheJob,$var); #spawn a thread $thr->join; #Wait for the thread to return ### third example my @array :shared; #create a share array make_uge_array(\@array) #pass a ref fo the array to a function populate it with 2,000,000 items print scalar(@array), "\n"; #print 2,000,000 my $thr = threads->create(\&doTheJob,$var); #spawn a thread $thr->join; #Wait for the thread to return sub doTheJob{ scalar(@_), "\n"} ## print O Finally I tried to pass to the thread creation utility a ref of the huge shared array but the main process never stop at the join() utility, it bailed out with the thread still running. Any suggestion will be appreciated. Also, feel free to suggest me a better place to post this request. Many thanks, Marco -- Marco Blanchette, Ph.D. Assistant Investigator Stowers Institute for Medical Research 1000 East 50th St. Kansas City, MO 64110 Tel: 816-926-4071 Cell: 816-726-8419 Fax: 816-926-2018 From heikki.lehvaslaiho at gmail.com Sun Dec 21 02:33:49 2008 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Sun, 21 Dec 2008 09:33:49 +0200 Subject: [Bioperl-l] K-mer generating script In-Reply-To: References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> Message-ID: Thank you for everyone for these entertaining entries. In my books, Michel Eisen's version wins with sheer clarity. Recursion is always recommendable, too. Below are cleaned versions of these two. Feel free to improve them further. -Heikki -------------------------------------------------------------------- #!/usr/bin/env perl use warnings; use strict; sub kmers ($;$) { my $k = shift; my $alphabet = shift || [ qw( A T G C ) ]; my @bases = @$alphabet; my @words = @bases; for ( 1 .. --$k ) { my @newwords; foreach my $w (@words) { foreach my $b (@bases) { push (@newwords, $w.$b); } } @words = @newwords; } return @words; } my $k = shift; die "positive integer needed as the argument!" unless $k > 0 and $k =~ /^\d$/; map {print "$_\n"} kmers($k); -------------------------------------------------------------------- -------------------------------------------------------------------- #!/usr/bin/env perl use warnings; use strict; sub kmers ($;$) { my $n = shift; my $sym = shift || [ qw( A T G C ) ]; sub kmers_guts { my ($n, $sym, $store, $str) = @_; if ($n) { foreach my $s (@$sym) { push @$store, kmers_guts($n-1, $sym, $store, $str.$s); } } else { return $str; } } my $a = []; kmers_guts($n, $sym, $a, ''); return map {$_ || ()} @$a; } my $k = shift; die "positive integer needed as the argument!" unless $k =~ /^\d$/; map {print "$_\n"} kmers($k); -------------------------------------------------------------------- From jason at bioperl.org Sun Dec 21 13:07:18 2008 From: jason at bioperl.org (Jason Stajich) Date: Sun, 21 Dec 2008 13:07:18 -0500 Subject: [Bioperl-l] Fwd: Need urgent help regarding your perl script References: Message-ID: You need to ask your questions on the mailing list. You can also find examples of what you want to do on the website - http://bioperl.org - I would suggest you look there and post to the list if you have specific problems. This sounds much too much like homework. -jason Begin forwarded message: > From: Anuraj > Date: December 21, 2008 12:29:41 AM EST > Subject: Need urgent help regarding your perl script > > Hi, > > this is Anuraj a bioinformatics students who is interesting to learn > perl. I > have seen your perl script in Genbank documentation. I think you can > help me > plss > > my accession num is:NM_007297 > sequence should be in FASTA format. > > pls provide me the full per programm for retrieval of this sequence > from > Genbank. > > pls provide me the program starting to end > > #!/usr/bin/perl -w > > including above syntax > > because i am getting lot of errors plss help me out > > -- > Thanks and Regards > Anuraj Jason Stajich jason at bioperl.org From jason at bioperl.org Sun Dec 21 13:15:44 2008 From: jason at bioperl.org (Anuraj) Date: Sun, 21 Dec 2008 06:15:44 -1200 Subject: [Bioperl-l] Need urgent help regarding your perl script In-Reply-To: References: Message-ID: Hi thanks for the reply i already gone throught that very long back. i used the following syntax format use Bio::DB::GenBank; $gb = Bio::DB::GenBank->new(); $seq = $gb->get_Seq_by_acc('--------------'); # use your Accession Number ther $seq = $gb->get_Seq_by_version('-----------'); # use your Accession.version num ther $seq = $gb->get_Seq_by_gi('--------------'); # use your particular GI Number ther # to get a stream via a query string by boolean operators as you are searching from NCBI my $query = Bio::DB::Query::GenBank->new (-query =>'Oryza sativa[Organism] AND EST', -reldate => '30', -db => 'nucleotide'); # or gene database you may give my $seqio = $gb->get_Stream_by_query($query); while( my $seq = $seqio->next_seq ) { print "seq length is ", $seq->length,"\n"; } # or ... best when downloading very large files, prevents # keeping all of the file in memory # also if you don't want features, just sequence so let's save bandwith # and get the sequence in Fasta format $gb = Bio::DB::GenBank->new(-retrievaltype => 'tempfile' , -format => 'Fasta'); my $seqio = $gb->get_Stream_by_acc(['.........', '............'] ); # Accession number you give instead of dash. while( my $clone = $seqio->next_seq ) { print "cloneid is ", $clone->display_id, " ", $clone->accession_number, "\n"; } # note that get_Stream_by_version is not implemented # don't want the entire sequence or more options my $gb = Bio::DB::GenBank->new(-format => 'Fasta', -seq_start => 100, -seq_stop => 200, -strand => 1, -complexity => 4)); my $seqi = $gb->get_Stream_by_query($query); ------------------------------------------------------------- But i have totally confused with many steps here. plss help me out. js show me an example. i will be really happy if you could show me the full code of a perl script which we can retieve a gnen sequence from genbank. - Thanks in Advance Anuraj On 12/21/08, Jason Stajich wrote: > > You need to ask your questions on the mailing list. > > You can also find examples of what you want to do on the website - > http://bioperl.org - I would suggest you look there and post to the > list > if you have specific problems. This sounds much too much like > homework. > > -jason > > Begin forwarded message: > > *From: *Anuraj > *Date: *December 21, 2008 12:29:41 AM EST > *Subject: **Need urgent help regarding your perl script* > > > Hi, > > this is Anuraj a bioinformatics students who is interesting to learn > perl. > I > have seen your perl script in Genbank documentation. I think you can > help > me > plss > > my accession num is:NM_007297 > sequence should be in FASTA format. > > pls provide me the full per programm for retrieval of this sequence > from > Genbank. > > pls provide me the program starting to end > > #!/usr/bin/perl -w > > including above syntax > > because i am getting lot of errors plss help me out > > -- > Thanks and Regards > Anuraj > > > > Jason Stajich > jason at bioperl.org > > > > > > -- Thanks and Regards Anuraj From David.Messina at sbc.su.se Sun Dec 21 14:41:35 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Sun, 21 Dec 2008 20:41:35 +0100 Subject: [Bioperl-l] Need urgent help regarding your perl script In-Reply-To: References: Message-ID: <628aabb70812211141y3a288988k6c9c81ec2209130e@mail.gmail.com> Anuraj, Two things: 1) You can't just throw various bits of example code together and expect it to just work. You have to test code step by step, whether it's something you wrote or not. 2) You can't just demand that others do your work for you. There is a ton of example code on the website. Try the HOWTOs section. Look in the scripts directory that comes with BioPerl. People on this list are generally quite willing to help, but you have to have made an effort to learn on your own first, using the abundant resources that are available to you. You haven't done that. I know it's frustrating when you're struggling to understand something new. When I hit the wall like that, I step away from the computer and do something else for a while, then come back to it later when I'm ready to give it another go. Dave From maj at fortinbras.us Sun Dec 21 21:54:06 2008 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 21 Dec 2008 21:54:06 -0500 Subject: [Bioperl-l] Code scrapbook gaining steam Message-ID: Just want to draw people's attention to the Code Scrapbook (http://www.bioperl.org/wiki/Category:Scrapbook), which is emerging now with some nice contributions. I hope experienced folks will add their short solutions to frequently encountered programming problems, esp. with a bioperl slant, and newbies will browse it for helpful hints and solid examples of Bioperl style. Contributors: unless you're either extremely humble (in which case, reread the three canonical traits) or extremely famous (such that by your code alone you are recognized), please put your name or handle prominently on your post, so that you may receive your due glory (or, of course, blame). Thanks to Marco Blanchette for a question that stimulated this, and Jason for the suggestion to wikify. cheers MAJ From maj at fortinbras.us Sun Dec 21 22:31:47 2008 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 21 Dec 2008 22:31:47 -0500 Subject: [Bioperl-l] Code scrapbook gaining steam (with new "Linebreak Action"! In-Reply-To: References: Message-ID: Just want to draw people's attention to the Code Scrapbook (http://www.bioperl.org/wiki/Category:Scrapbook), which is emerging now with some nice contributions. I hope experienced folks will add their short solutions to frequently encountered programming problems, esp. with a bioperl slant, and newbies will browse it for helpful hints and solid examples of Bioperl style. Contributors: unless you're either extremely humble (in which case, reread the three canonical traits) or extremely famous (such that by your code alone you are recognized), please put your name or handle prominently on your post, so that you may receive your due glory (or, of course, blame). Thanks to Marco Blanchette for a question that stimulated this, and Jason for the suggestion to wikify. cheers MAJ From lengjingmao at gmail.com Tue Dec 23 14:02:42 2008 From: lengjingmao at gmail.com (shaohua.fan) Date: Tue, 23 Dec 2008 20:02:42 +0100 Subject: [Bioperl-l] EST annotation module in bioperl? In-Reply-To: References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife><3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> Message-ID: <000001c96531$09bd17c0$1ab2a8c0@6B2F7FFC298C46F> Hi, everyone, Is there an EST annotation module in Bioperl? I have thousands of 454 sequencing ESTs need to be annotated. Thanks. Cheers, Shaohua Fan From sdavis2 at mail.nih.gov Tue Dec 23 14:45:39 2008 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Tue, 23 Dec 2008 14:45:39 -0500 Subject: [Bioperl-l] EST annotation module in bioperl? In-Reply-To: <000001c96531$09bd17c0$1ab2a8c0@6B2F7FFC298C46F> References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> <000001c96531$09bd17c0$1ab2a8c0@6B2F7FFC298C46F> Message-ID: <264855a00812231145u3df693d0h7192d80722f7dd72@mail.gmail.com> On Tue, Dec 23, 2008 at 2:02 PM, shaohua.fan wrote: > Hi, everyone, > Is there an EST annotation module in Bioperl? I have thousands of 454 > sequencing ESTs need to be annotated. > What do you mean by "annotated"? And what do you mean by "thousands of 454 sequencing ESTs"? Sean From cjfields at illinois.edu Tue Dec 23 14:58:27 2008 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 23 Dec 2008 13:58:27 -0600 Subject: [Bioperl-l] EST annotation module in bioperl? In-Reply-To: <264855a00812231145u3df693d0h7192d80722f7dd72@mail.gmail.com> References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> <000001c96531$09bd17c0$1ab2a8c0@6B2F7FFC298C46F> <264855a00812231145u3df693d0h7192d80722f7dd72@mail.gmail.com> Message-ID: On Dec 23, 2008, at 1:45 PM, Sean Davis wrote: > On Tue, Dec 23, 2008 at 2:02 PM, shaohua.fan > wrote: > >> Hi, everyone, >> Is there an EST annotation module in Bioperl? I have thousands of 454 >> sequencing ESTs need to be annotated. >> > > What do you mean by "annotated"? And what do you mean by "thousands > of 454 > sequencing ESTs"? > > Sean You know those ESTs don't just annotate themselves ;> chris From sdavis2 at mail.nih.gov Tue Dec 23 15:03:42 2008 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Tue, 23 Dec 2008 15:03:42 -0500 Subject: [Bioperl-l] =?utf-8?b?562U5aSNOiAgRVNUIGFubm90YXRpb24gbW9kdWxl?= =?utf-8?q?_in_bioperl=3F?= In-Reply-To: <000601c96538$64d870d0$1ab2a8c0@6B2F7FFC298C46F> References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> <000001c96531$09bd17c0$1ab2a8c0@6B2F7FFC298C46F> <264855a00812231145u3df693d0h7192d80722f7dd72@mail.gmail.com> <000601c96538$64d870d0$1ab2a8c0@6B2F7FFC298C46F> Message-ID: <264855a00812231203j5582302ar714b1155d009b3ad@mail.gmail.com> 2008/12/23 shaohua.fan > Hi, sean, > > > > I have thousands of ESTs generated by 454 sequencing, and I want to know > the functions of the ESTs. > I would start with something like BLAST and there are tools in Bioperl to help with that. Sean > Shaohua > ------------------------------ > > *???:* seandavi at gmail.com [mailto:seandavi at gmail.com] *?? *Sean Davis > *????:* 23 December 2008 20:46 > *???:* shaohua.fan > *??:* bioperl list > *??:* Re: [Bioperl-l] EST annotation module in bioperl? > > > > > > On Tue, Dec 23, 2008 at 2:02 PM, shaohua.fan > wrote: > > Hi, everyone, > Is there an EST annotation module in Bioperl? I have thousands of 454 > sequencing ESTs need to be annotated. > > > What do you mean by "annotated"? And what do you mean by "thousands of 454 > sequencing ESTs"? > > Sean > > > From David.Messina at sbc.su.se Tue Dec 23 15:16:08 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 23 Dec 2008 21:16:08 +0100 Subject: [Bioperl-l] EST annotation module in bioperl? In-Reply-To: <000001c96531$09bd17c0$1ab2a8c0@6B2F7FFC298C46F> References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> <000001c96531$09bd17c0$1ab2a8c0@6B2F7FFC298C46F> Message-ID: <628aabb70812231216w481fd96ah73ffc39f9c416dfb@mail.gmail.com> > > Is there an EST annotation module in Bioperl? I have thousands of 454 > sequencing ESTs need to be annotated. > Seriously? That's like asking: "Is there a book-writing module in BioPerl? I have thousands of blank pieces of paper that need to be written on." Dave From philsf79 at gmail.com Tue Dec 23 15:57:25 2008 From: philsf79 at gmail.com (Felipe Figueiredo) Date: Tue, 23 Dec 2008 18:57:25 -0200 Subject: [Bioperl-l] EST annotation module in bioperl? In-Reply-To: <000001c96531$09bd17c0$1ab2a8c0@6B2F7FFC298C46F> References: <000001c96531$09bd17c0$1ab2a8c0@6B2F7FFC298C46F> Message-ID: <200812231857.25639.philsf79@gmail.com> On Tuesday 23 December 2008 17:02:42 shaohua.fan wrote: > Hi, everyone, > Is there an EST annotation module in Bioperl? I have thousands of 454 > sequencing ESTs need to be annotated. > STINGRAY[1] is your friend. It uses bioperl internally. Disclaimer: I am a PhD student in the same institution that made it ( Fiocruz[2] ). 1. http://stingray.biowebdb.org/ 2. http://www.ioc.fiocruz.br/ regards FF From jonathancrabtree at gmail.com Wed Dec 24 13:03:25 2008 From: jonathancrabtree at gmail.com (Jonathan Crabtree) Date: Wed, 24 Dec 2008 13:03:25 -0500 Subject: [Bioperl-l] Help with threads and shared variable In-Reply-To: References: Message-ID: <8e5b8bf80812241003t20a2f15er8f6b9f85394d7678@mail.gmail.com> Hi Marco, I can't be exactly sure what's going wrong in your examples, since you haven't posted the crucial "make_uge_array" function, or told us which version of Perl you are using. However, I'd guess that perhaps you're creating a multi-dimensional array without sharing anything except the top-level array. Here is a short test program, which runs correctly on perl 5.8.8 and may help to illustrate how the Perl threads::shared module expects you to create and share nested data structures. You have to manually share any nested references and I think that the order in which the sharing calls are made may also be significant: #!/usr/bin/perl use strict; use warnings; use threads; use threads::shared; # threads::shared test/demo program # creates a shared 2-dimensional array and checks that it can be seen in a thread # tested in perl v5.8.8 built for i486-linux-gnu-thread-multi ## ---------------------------------------- ## globals ## ---------------------------------------- # set the width and height of the 2d array to this value: my $ARRAY_SIZE = 10; ## ---------------------------------------- ## main program ## ---------------------------------------- # calls to &share take place in here, so a shared value is returned my $array = &make_shared_array(); # print array contents before running thread print "shared array before running thread:\n"; &check_and_print_array($array); # run thread my $thr = threads->create(\&do_the_job, $array); my $retval = $thr->join(); print "join() returned: $retval\n"; # print array contents after running thread print "shared array after running thread:\n"; &check_and_print_array($array); exit(0); ## ---------------------------------------- ## subroutines ## ---------------------------------------- sub make_shared_array { # outermost array object must be made shared first my $a = &share([]); for (my $i = 0;$i < $ARRAY_SIZE;++$i) { # each of the rows must be explicitly shared my $row = &share([]); # and then added to the containing array $a->[$i] = $row; # assign each cell a unique integer for verification purposes my $base = $i * $ARRAY_SIZE; for (my $j = 0;$j < $ARRAY_SIZE;++$j) { $row->[$j] = $base + $j; } } return $a; } # print out the array, checking that its dimensions match what we expect sub check_and_print_array { my $arr = shift; die "not an array" if ((ref $arr) ne 'ARRAY'); my $nr = scalar(@$arr); die "wrong number of rows in array" if ($nr != $ARRAY_SIZE); for (my $i = 0;$i < $nr;++$i) { my $row = $arr->[$i]; die "row $i not an array" if ((ref $row) ne 'ARRAY'); my $nc = scalar(@$row); die "wrong number of columns in row $i" if ($nc != $ARRAY_SIZE); for (my $j = 0;$j < $nc;++$j) { my $val = $row->[$j]; printf("%10s", $val); } print "\n"; } } # work to execute in the thread sub do_the_job { my $var = shift; # print the array once more in the thread print "shared array in thread:\n"; &check_and_print_array($var); return "do_the_job returned ok"; } When I run it (on Ubuntu) the output looks like this: shared array before running thread: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 shared array in thread: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 join() returned: do_the_job returned ok shared array after running thread: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 I haven't verified that doing this actually yields the memory savings you're looking for, but I don't see why it shouldn't. Hope this helps, Jonathan On Sat, Dec 20, 2008 at 6:10 PM, Blanchette, Marco wrote: > Dear all, > > I am not sure this is the best place to post that questions but I don't really know where else to go... So, let's give it a shot. > > I am using the Perl threads utility to successfully multi threads several of my computing jobs on my workstation. My current problem is that I need to perform multiple processes using the same humongous array (more than 2x10e6 items). My problem is that the computing time for each iteration is not very long but I have a lot of iterations to do and every time a thread is created I am passing the huge array to the function and a fresh copy of the array is created. Thus, there is a huge amount of wasted resources (time and memory) use to create these data structures that are used by each threads but not modified. > > The logical alternative is to use shared memory where all thread would have access to the same copy of the huge array. In principal Perl provide such a mechanism through the module threads::shared but I am unable to understand how to use the shared variables. > > Anyone has experience to share on threads::shared? Here is a couple of unsuccessful attempts to use that module: > > > ### first example > my $var :shared; #create a shared scalar > $var = make_uge_array; #return a pointer to a huge array and trying to assign it the the shared pointer > my $thr = threads->create(\&doTheJob,$var); #spawn a thread > $thr->join; #Wait for the thread to return > ### Generate the following error > ### Invalid value for shared scalar at ... > > ### second example > my $var = make_uge_array; #return a pointer to a huge array > print scalar(@{$var}), "\n"; #print 2,000,000 > > share($var); > print scalar(@{$var}), "\n"; #print 0 > > my $thr = threads->create(\&doTheJob,$var); #spawn a thread > $thr->join; #Wait for the thread to return > > ### third example > my @array :shared; #create a share array > make_uge_array(\@array) #pass a ref fo the array to a function populate it with 2,000,000 items > print scalar(@array), "\n"; #print 2,000,000 > > my $thr = threads->create(\&doTheJob,$var); #spawn a thread > $thr->join; #Wait for the thread to return > > sub doTheJob{ scalar(@_), "\n"} ## print O > > Finally I tried to pass to the thread creation utility a ref of the huge shared array but the main process never stop at the join() utility, it bailed out with the thread still running. > > Any suggestion will be appreciated. > > Also, feel free to suggest me a better place to post this request. > > Many thanks, > > Marco > > -- > Marco Blanchette, Ph.D. > Assistant Investigator > Stowers Institute for Medical Research > 1000 East 50th St. > > Kansas City, MO 64110 > > Tel: 816-926-4071 > Cell: 816-726-8419 > Fax: 816-926-2018 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Wed Dec 24 16:27:33 2008 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 24 Dec 2008 15:27:33 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 Message-ID: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> All, I am proud to announce that the first release candidate for BioPerl 1.6 is available for testing. A quick note on versioning: due to issues with alpha numbered versions on CPAN possibly overwriting a stable release, this release candidate has a VERSION of 1.005009_001 (or 1.005009001). This will be switched to 1.006000 (no alpha) once the release is final. The RC is currently being uploaded to CPAN and should be available in the next 24-48 hours under authorname CJFIELDS. In the meantime, the release candidates can be directly downloaded here: http://bioperl.org/DIST/BioPerl-1.5.9_1.tar.bz2 http://bioperl.org/DIST/BioPerl-1.5.9_1.tar.gz http://bioperl.org/DIST/BioPerl-1.5.9_1.zip Signature file: http://bioperl.org/DIST/SIGNATURES.md5 A preliminary ActiveState PPM is also available and is located in the BioPerl Release Candidate repository; the directions for installation are here: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows Please feel free to report issues with testing, installation, etc. on the mail list and on this page: http://www.bioperl.org/wiki/Release_1.6_Testing I will be gone from Dec. 26-31 but will attempt to keep tabs on test results and anticipate addressing any issues once I return. The final release should be ready in the first couple weeks of January 2009, of course depending on issues that arise with this RC. We will be releasing bioperl-run, bioperl-db, bioperl-network, and others separately once the final 1.6 release is complete. Enjoy, and Happy Holidays! chris From wesleyarthur at optusnet.com.au Thu Dec 25 21:28:31 2008 From: wesleyarthur at optusnet.com.au (Wesley Arthur) Date: Fri, 26 Dec 2008 11:28:31 +0900 Subject: [Bioperl-l] BioPerl Candidate Release 1.6 Message-ID: JESUS IS LORD! To Chris Fields and the other Bioperl Developers, Thank you for the new candidate 1.6 release of Bioperl. I attempted to install this last night using ppm. The status Tab seemed to indicate a success with the following errors; STATUS TAB Synchronizing Database ... Downloading ActiveState Package Repository packlist ... done Updating ActiveState Package Repository database ... done Downloading BioPerl-Regular Releases packlist ... not modified Downloading Kobes packlist ... done Updating Kobes database ... done Downloading Bribes packlist ... done Updating Bribes database ... done Downloading tcool packlist ... done Updating tcool database ... done Downloading tcool packlist ... done Synchronizing Database done Downloading ActiveState Package Repository packlist ... not modified Downloading BioPerl-Regular Releases packlist ... not modified Downloading BioPerl-Release Candidates packlist ... done Updating BioPerl-Release Candidates database ... done Synchronizing Database ... Downloading ActiveState Package Repository packlist ... not modified Synchronizing Database done BioPerl marked for install BioPerl depends on Bundle-BioPerl-Core BioPerl depends on Math-Random BioPerl depends on SVG-Graph BioPerl depends on Bio-ASN1-EntrezGene BioPerl depends on Data-Stag BioPerl depends on Algorithm-Munkres BioPerl depends on GraphViz BioPerl depends on XML-Writer BioPerl depends on Graph BioPerl depends on XML-DOM-XPath BioPerl depends on PostScript BioPerl depends on Spreadsheet-ParseExcel BioPerl depends on XML-SAX BioPerl depends on AcePerl BioPerl depends on Array-Compare BioPerl depends on Convert-Binary-C BioPerl depends on XML-Twig BioPerl depends on Set-Scalar BioPerl depends on libxml-perl BioPerl depends on XML-SAX-Writer BioPerl depends on Clone BioPerl depends on DB_File BioPerl depends on SVG BioPerl depends on Math-Derivative BioPerl depends on Math-Spline BioPerl depends on Statistics-Descriptive BioPerl depends on Tree-DAG_Node BioPerl depends on IPC-Run BioPerl depends on XML-DOM BioPerl depends on XML-XPathEngine BioPerl depends on IO-stringy BioPerl depends on OLE-Storage_Lite BioPerl depends on Ocsinventory-Agent BioPerl depends on Cache-Cache BioPerl depends on Text-Iconv BioPerl depends on XML-Filter-BufferText BioPerl depends on XML-NamespaceSupport BioPerl depends on XML-RegExp BioPerl depends on Error Synchronizing Database ... Downloading ActiveState Package Repository packlist ... not modified Synchronizing Database done BioPerl marked for install BioPerl depends on Bundle-BioPerl-Core BioPerl depends on Math-Random BioPerl depends on SVG-Graph BioPerl depends on Bio-ASN1-EntrezGene BioPerl depends on Data-Stag BioPerl depends on Algorithm-Munkres BioPerl depends on GraphViz BioPerl depends on XML-Writer BioPerl depends on Graph BioPerl depends on XML-DOM-XPath BioPerl depends on PostScript BioPerl depends on Spreadsheet-ParseExcel BioPerl depends on XML-SAX BioPerl depends on AcePerl BioPerl depends on Array-Compare BioPerl depends on Convert-Binary-C BioPerl depends on XML-Twig BioPerl depends on Set-Scalar BioPerl depends on libxml-perl BioPerl depends on XML-SAX-Writer BioPerl depends on Clone BioPerl depends on DB_File BioPerl depends on SVG BioPerl depends on Math-Derivative BioPerl depends on Math-Spline BioPerl depends on Statistics-Descriptive BioPerl depends on Tree-DAG_Node BioPerl depends on IPC-Run BioPerl depends on XML-DOM BioPerl depends on XML-XPathEngine BioPerl depends on IO-stringy BioPerl depends on OLE-Storage_Lite BioPerl depends on Ocsinventory-Agent BioPerl depends on Cache-Cache BioPerl depends on Text-Iconv BioPerl depends on XML-Filter-BufferText BioPerl depends on XML-NamespaceSupport BioPerl depends on XML-RegExp BioPerl depends on Error Installing 40 packages ... Downloading BioPerl-1.5.9_1 ... done Downloading Bundle-BioPerl-Core-1.5.9_1 ... not found Installing 40 packages failed ERROR: 404 Not Found I thought I would report this to you. I assume that this means candidate 16 has installed successfully and that it has upgraded the previous 1.5.2 to 1.6. I am very new to bioperl and have been studying you HOW-TO section. I don't know much about this but would like to help if you have something for me to do. However I am not a programmer. If it is too much of a distraction for you, do not respond. I do not mind hearing what you think about the error messages, but it is not urgent. Have a Happy new year all of you. Wesley Arthur. From wesleyarthur at optusnet.com.au Fri Dec 26 06:19:19 2008 From: wesleyarthur at optusnet.com.au (Wesley Arthur) Date: Fri, 26 Dec 2008 20:19:19 +0900 Subject: [Bioperl-l] Bioperl candidate 1.6 release Message-ID: <0C2CFC8E532C496ABC41096D28698062@OwnerPC> JESUS is LORD! To Chris Fields and the Bioperl team, I wish to correct my last email to this list. I went to check my ppm after trying to install Bioperl 1.5.9_1 and when I clicked the view installed packages tab the Bioperl 1.5.9_1 Bioinformatics toolkit disappeared. So The new bioperl candidate has not been installed correctly and was aborted. The following messages appeared in the STATUS tab after I tried to reinstall it; Synchronizing Database ... Downloading ActiveState Package Repository packlist ... done Updating ActiveState Package Repository database ... done Downloading BioPerl-Regular Releases packlist ... not modified Downloading Kobes packlist ... done Updating Kobes database ... done Downloading Bribes packlist ... not modified Downloading tcool packlist ... not modified Downloading tcool packlist ... done Downloading BioPerl-Release Candidates packlist ... not modified Synchronizing Database done Synchronizing Database ... Downloading ActiveState Package Repository packlist ... not modified Synchronizing Database done BioPerl marked for install BioPerl depends on Bundle-BioPerl-Core BioPerl depends on Math-Random BioPerl depends on SVG-Graph BioPerl depends on Bio-ASN1-EntrezGene BioPerl depends on Data-Stag BioPerl depends on Algorithm-Munkres BioPerl depends on GraphViz BioPerl depends on XML-Writer BioPerl depends on Graph BioPerl depends on XML-DOM-XPath BioPerl depends on PostScript BioPerl depends on Spreadsheet-ParseExcel BioPerl depends on XML-SAX BioPerl depends on AcePerl BioPerl depends on Array-Compare BioPerl depends on Convert-Binary-C BioPerl depends on XML-Twig BioPerl depends on Set-Scalar BioPerl depends on libxml-perl BioPerl depends on XML-SAX-Writer BioPerl depends on Clone BioPerl depends on DB_File BioPerl depends on SVG BioPerl depends on Math-Derivative BioPerl depends on Math-Spline BioPerl depends on Statistics-Descriptive BioPerl depends on Tree-DAG_Node BioPerl depends on IPC-Run BioPerl depends on XML-DOM BioPerl depends on XML-XPathEngine BioPerl depends on IO-stringy BioPerl depends on OLE-Storage_Lite BioPerl depends on Ocsinventory-Agent BioPerl depends on Cache-Cache BioPerl depends on Text-Iconv BioPerl depends on XML-Filter-BufferText BioPerl depends on XML-NamespaceSupport BioPerl depends on XML-RegExp BioPerl depends on Error Installing 40 packages ... Downloading BioPerl-1.5.9_1 ... done Installing 40 packages failed ERROR: Aborted download (3777719 bytes expected, got 1419656). Thank You. Wesley Arthur. From cjfields at illinois.edu Fri Dec 26 08:03:30 2008 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 26 Dec 2008 07:03:30 -0600 Subject: [Bioperl-l] Bioperl candidate 1.6 release In-Reply-To: <0C2CFC8E532C496ABC41096D28698062@OwnerPC> References: <0C2CFC8E532C496ABC41096D28698062@OwnerPC> Message-ID: I have reuploaded the PPM just in case the original upload was interrupted. You can try again. Note that I don't have access to an ActiveState installation yet and won't be able to test this until I get back on Jan 2. chris On Dec 26, 2008, at 5:19 AM, Wesley Arthur wrote: > JESUS is LORD! > > To Chris Fields and the Bioperl team, > I wish to > correct my last email to this list. I went to check my ppm after > trying to install Bioperl 1.5.9_1 and when I clicked the view > installed packages tab the Bioperl 1.5.9_1 Bioinformatics toolkit > disappeared. So The new bioperl candidate has not been installed > correctly and was aborted. The following messages appeared in the > STATUS tab after I tried to reinstall it; > > Synchronizing Database ... > Downloading ActiveState Package Repository packlist ... done > Updating ActiveState Package Repository database ... done > Downloading BioPerl-Regular Releases packlist ... not modified > Downloading Kobes packlist ... done > Updating Kobes database ... done > Downloading Bribes packlist ... not modified > Downloading tcool packlist ... not modified > Downloading tcool packlist ... done > Downloading BioPerl-Release Candidates packlist ... not modified > Synchronizing Database done > Synchronizing Database ... > Downloading ActiveState Package Repository packlist ... not modified > Synchronizing Database done > BioPerl marked for install > BioPerl depends on Bundle-BioPerl-Core > BioPerl depends on Math-Random > BioPerl depends on SVG-Graph > BioPerl depends on Bio-ASN1-EntrezGene > BioPerl depends on Data-Stag > BioPerl depends on Algorithm-Munkres > BioPerl depends on GraphViz > BioPerl depends on XML-Writer > BioPerl depends on Graph > BioPerl depends on XML-DOM-XPath > BioPerl depends on PostScript > BioPerl depends on Spreadsheet-ParseExcel > BioPerl depends on XML-SAX > BioPerl depends on AcePerl > BioPerl depends on Array-Compare > BioPerl depends on Convert-Binary-C > BioPerl depends on XML-Twig > BioPerl depends on Set-Scalar > BioPerl depends on libxml-perl > BioPerl depends on XML-SAX-Writer > BioPerl depends on Clone > BioPerl depends on DB_File > BioPerl depends on SVG > BioPerl depends on Math-Derivative > BioPerl depends on Math-Spline > BioPerl depends on Statistics-Descriptive > BioPerl depends on Tree-DAG_Node > BioPerl depends on IPC-Run > BioPerl depends on XML-DOM > BioPerl depends on XML-XPathEngine > BioPerl depends on IO-stringy > BioPerl depends on OLE-Storage_Lite > BioPerl depends on Ocsinventory-Agent > BioPerl depends on Cache-Cache > BioPerl depends on Text-Iconv > BioPerl depends on XML-Filter-BufferText > BioPerl depends on XML-NamespaceSupport > BioPerl depends on XML-RegExp > BioPerl depends on Error > Installing 40 packages ... > Downloading BioPerl-1.5.9_1 ... done > Installing 40 packages failed > > ERROR: Aborted download (3777719 bytes expected, got 1419656). > > > Thank You. > Wesley Arthur. > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From alexl at users.sourceforge.net Fri Dec 26 16:16:25 2008 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Fri, 26 Dec 2008 14:16:25 -0700 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> (Chris Fields's message of "Wed\, 24 Dec 2008 15\:27\:33 -0600") References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> Message-ID: >>>>> "CF" == Chris Fields writes: CF> All, I am proud to announce that the first release candidate for CF> BioPerl 1.6 is available for testing. CF> A quick note on versioning: due to issues with alpha numbered CF> versions on CPAN possibly overwriting a stable release, this CF> release candidate has a VERSION of 1.005009_001 (or 1.005009001). CF> This will be switched to 1.006000 (no alpha) once the release is CF> final. CF> The RC is currently being uploaded to CPAN and should be available CF> in the next 24-48 hours under authorname CJFIELDS. In the CF> meantime, the release candidates can be directly downloaded here: CF> http://bioperl.org/DIST/BioPerl-1.5.9_1.tar.bz2 CF> http://bioperl.org/DIST/BioPerl-1.5.9_1.tar.gz CF> http://bioperl.org/DIST/BioPerl-1.5.9_1.zip CF> Signature file: http://bioperl.org/DIST/SIGNATURES.md5 CF> A preliminary ActiveState PPM is also available and is located in CF> the BioPerl Release Candidate repository; the directions for CF> installation are here: CF> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows Hi there, I'm the Fedora packager for bioperl. I note on the release notes page that Bio::Graphics has been split off into it's own CPAN module. Since in most Linux distributions a single tarball = a single RPM = a single package. How many .tar.gz files (and therefore packages) are now required to install bioperl? If Bio::Graphics is now not included inside the bioperl tarball and is required for bioperl, it will mean that a new package (perl-Bio-Graphics) of the CPAN module will need to be reviewed and packaged before the new version bioperl can be shipped. Also is the version number 1.5.9 or 1.5.9.1 and will the next RC candidate be 1.5.9.2? Can you tell me the exact sequence of version numbers you expect before going to 1.6.0? From a Linux distribution POV the exact version numbers are very important because they are used to determine whether one release is more recent than another and therefore whether to update a package or not. Having release candidate tarball with the version 1.5.9._1 (i.e. with the underscore) is very non-standard and can confuse package managers. Thanks, Alex From alexl at users.sourceforge.net Fri Dec 26 16:39:00 2008 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Fri, 26 Dec 2008 14:39:00 -0700 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: (Alex Lancaster's message of "Fri\, 26 Dec 2008 14\:16\:25 -0700") References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> Message-ID: >>>>> "AL" == Alex Lancaster writes: [...] AL> Also is the version number 1.5.9 or 1.5.9.1 and will the next RC AL> candidate be 1.5.9.2? Can you tell me the exact sequence of AL> version numbers you expect before going to 1.6.0? From a Linux AL> distribution POV the exact version numbers are very important AL> because they are used to determine whether one release is more AL> recent than another and therefore whether to update a package or AL> not. Having release candidate tarball with the version 1.5.9._1 AL> (i.e. with the underscore) is very non-standard and can confuse AL> package managers. Some other oddness: when the Build.PL script checks for the dependencies, it notes a few optional CPAN packages which aren't yet packaged for Fedora such as 'Algorithm::Munkres' and 'Math::Random', are missing. Since they are optional and missing dependencies, I would have expected that the relevant bioperl modules such Bio::PhyloNetwork should also not be installed, but it appears that the .pm files are installed, see lines like: Copying Bio/PhyloNetwork/Factory.pm -> blib/lib/Bio/PhyloNetwork/Factory.pm from the full build.log: https://koji.fedoraproject.org/koji/getfile?taskID=1022511&name=build.log This causes problems because RPM then generates Requires such as: Requires: perl(Algorithm::Munkres) (see bottom of the build.log referred to above) which can't (yet) be fullfilled by any other package in the Fedora package set, leading to broken dependencies. Is this the expected behaviour upon missing optional dependencies? Alex From bix at sendu.me.uk Fri Dec 26 17:07:46 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 26 Dec 2008 22:07:46 +0000 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> Message-ID: <495555B2.6050103@sendu.me.uk> Alex Lancaster wrote: > Some other oddness: when the Build.PL script checks for the > dependencies, it notes a few optional CPAN packages which aren't yet > packaged for Fedora such as 'Algorithm::Munkres' and 'Math::Random', > are missing. Since they are optional and missing dependencies, I > would have expected that the relevant bioperl modules such > Bio::PhyloNetwork should also not be installed, but it appears that > the .pm files are installed, see lines like: > > Copying Bio/PhyloNetwork/Factory.pm -> blib/lib/Bio/PhyloNetwork/Factory.pm > > from the full build.log: > > https://koji.fedoraproject.org/koji/getfile?taskID=1022511&name=build.log > > This causes problems because RPM then generates Requires such as: > > Requires: perl(Algorithm::Munkres) > > (see bottom of the build.log referred to above) which can't (yet) be > fullfilled by any other package in the Fedora package set, leading to > broken dependencies. > > Is this the expected behaviour upon missing optional dependencies? Yes, though I can see how it's broken from your point of view. It is set up to install everything, but simply not everything will work without the optionals. I hadn't considered not installing the modules that won't work. Something to think about, but it's probably not going to happen for 1.6? From bix at sendu.me.uk Fri Dec 26 17:15:07 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 26 Dec 2008 22:15:07 +0000 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> Message-ID: <4955576B.9010907@sendu.me.uk> Alex Lancaster wrote: > I'm the Fedora packager for bioperl. I note on the release notes page > that Bio::Graphics has been split off into it's own CPAN module. > Since in most Linux distributions a single tarball = a single RPM = a > single package. How many .tar.gz files (and therefore packages) are > now required to install bioperl? BioPerl has started to move toward a number of smaller packages that will let people install only what they actually need. There will be a 'core' package of essential modules, and a bunch of these new smaller packages that rely on core. From a certain point of view it could be that 'to install bioperl' == 'to install bioperl core', in which case the answer to your question is '1' .tar.gz to install. As a convenience to the user who wants to install all BioPerl packages, there will be a CPAN Bundle (at the least). Fedora package-wise, I guess you'd do whatever you currently do to emulate CPAN bundles. > If Bio::Graphics is now not included inside the bioperl tarball and is > required for bioperl It isn't. Bio::Graphics depends on BioPerl, but BioPerl does not depend on Bio::Graphics. From hlapp at gmx.net Fri Dec 26 19:15:22 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 26 Dec 2008 19:15:22 -0500 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> Message-ID: On Dec 26, 2008, at 4:39 PM, Alex Lancaster wrote: > it notes a few optional CPAN packages which aren't yet > packaged for Fedora such as 'Algorithm::Munkres' and 'Math::Random', > are missing. Since they are optional and missing dependencies, I > would have expected that the relevant bioperl modules such > Bio::PhyloNetwork should also not be installed I may have failed to chime in here earlier at the appropriate opportunity, but I would be very hesitant about putting Bio::PhyloNetwork into the stable release. These modules have never been announced or discussed on the mailing list with other developers AFAIAA, and so have never received any scrutiny. I'm also not sure who else other than the authors are using them, so I don't think there's a user base yet that could substitute for developer scrutiny. One simple suggestion for example would be to move them into Bio::Phylo::Network, so as not to unnecessarily proliferate the first level package directory. So at the very least it should be obvious to anyone that the API including the module names are subject to change. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From wesleyarthur at optusnet.com.au Fri Dec 26 20:53:11 2008 From: wesleyarthur at optusnet.com.au (Wesley Arthur) Date: Sat, 27 Dec 2008 10:53:11 +0900 Subject: [Bioperl-l] Bioperl 1.6 RC1 Message-ID: <6A11C4EEAC5B4F3B83B33215331F13A1@OwnerPC> Dear Chris Fields and colleagues, Thank you for your response and for reuploading the PPM version of Bioperl 1.6. I retried to install last night. The Perl package manager went a little further, but failed to install again. For your reference I am using Windows Vista and Active Perl 5.8.8.824. The results of the status tab are indicated below and the second attempt is highlighted in blue. STATUS TAB Synchronizing Database ... Downloading Active State Package Repository packlist ... done Updating ActiveState Package Repository database ... done Downloading BioPerl-Regular Releases packlist ... not modified Downloading Kobes packlist ... done Updating Kobes database ... done Downloading Bribes packlist ... not modified Downloading tcool packlist ... not modified Downloading tcool packlist ... done Downloading BioPerl-Release Candidates packlist ... not modified Synchronizing Database done Synchronizing Database ... Downloading ActiveState Package Repository packlist ... not modified Synchronizing Database done BioPerl marked for install BioPerl depends on Bundle-BioPerl-Core BioPerl depends on Math-Random BioPerl depends on SVG-Graph BioPerl depends on Bio-ASN1-EntrezGene BioPerl depends on Data-Stag BioPerl depends on Algorithm-Munkres BioPerl depends on GraphViz BioPerl depends on XML-Writer BioPerl depends on Graph BioPerl depends on XML-DOM-XPath BioPerl depends on PostScript BioPerl depends on Spreadsheet-ParseExcel BioPerl depends on XML-SAX BioPerl depends on AcePerl BioPerl depends on Array-Compare BioPerl depends on Convert-Binary-C BioPerl depends on XML-Twig BioPerl depends on Set-Scalar BioPerl depends on libxml-perl BioPerl depends on XML-SAX-Writer BioPerl depends on Clone BioPerl depends on DB_File BioPerl depends on SVG BioPerl depends on Math-Derivative BioPerl depends on Math-Spline BioPerl depends on Statistics-Descriptive BioPerl depends on Tree-DAG_Node BioPerl depends on IPC-Run BioPerl depends on XML-DOM BioPerl depends on XML-XPathEngine BioPerl depends on IO-stringy BioPerl depends on OLE-Storage_Lite BioPerl depends on Ocsinventory-Agent BioPerl depends on Cache-Cache BioPerl depends on Text-Iconv BioPerl depends on XML-Filter-BufferText BioPerl depends on XML-NamespaceSupport BioPerl depends on XML-RegExp BioPerl depends on Error Installing 40 packages ... Downloading BioPerl-1.5.9_1 ... done Installing 40 packages failed ERROR: Aborted download (3777719 bytes expected, got 1419656). Installing 40 packages ... Downloading BioPerl-1.5.9_1 ... done Downloading Bundle-BioPerl-Core-1.5.9_1 ... not found Installing 40 packages failed ERROR: 404 Not Found Just letting you know, do respond if you want to other wise I will wait for you to return and have access to the ActiveState Installation. This is not urgent Good Luck. Wesley Arthur. From alexl at users.sourceforge.net Sat Dec 27 22:03:01 2008 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Sat, 27 Dec 2008 20:03:01 -0700 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <495555B2.6050103@sendu.me.uk> (Sendu Bala's message of "Fri\, 26 Dec 2008 22\:07\:46 +0000") References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <495555B2.6050103@sendu.me.uk> Message-ID: >>>>> "SB" == Sendu Bala writes: SB> Alex Lancaster wrote: [...] >> Is this the expected behaviour upon missing optional dependencies? SB> Yes, though I can see how it's broken from your point of view. It SB> is set up to install everything, but simply not everything will SB> work without the optionals. I hadn't considered not installing the SB> modules that won't work. Yes, not installing modules for which optional deps are missing would be the most sensible and would conform with the principle of least surprise. C programs built using autoconf/automake with the usual "./configure", "make", "make install" series steps, if an optional dep (say a shared library) is missing, the configure script notices that and program is compiled without that feature and any relevant files aren't installed. Even though Perl programs don't link at compile-time, conceptually it should be no different to the way a C program handles missing shared libraries or other deps. SB> Something to think about, but it's probably not going to happen SB> for 1.6? Sure, so for the moment (while I'm packaging the deps) I can simply remove the relevant .pm files from before final packaging of the RPM so that the automatic Perl dependency generator won't find them, but in the long term it would be better to not install the files for which deps are missing. Would it be best to open up a bug for this? (don't have a bugzilla account myself just now). On a related note, it would also be good if command-line options could be passed to the Build.PL script to provide answers to the questions that the Build.PL asks. Running interactive prompts during the build means that the Fedora .spec file has to simulate the interactive answering of questions (as shown at the top of the build.log, below) and makes the process of generating the RPM very fragile: http://koji.fedoraproject.org/koji/getfile?taskID=1022511&name=build.log Thanks, Alex From alexl at users.sourceforge.net Sat Dec 27 22:19:24 2008 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Sat, 27 Dec 2008 20:19:24 -0700 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <4955576B.9010907@sendu.me.uk> (Sendu Bala's message of "Fri\, 26 Dec 2008 22\:15\:07 +0000") References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> Message-ID: >>>>> "SB" == Sendu Bala writes: SB> Alex Lancaster wrote: >> I'm the Fedora packager for bioperl. I note on the release notes >> page that Bio::Graphics has been split off into it's own CPAN >> module. Since in most Linux distributions a single tarball = a >> single RPM = a single package. How many .tar.gz files (and >> therefore packages) are now required to install bioperl? SB> BioPerl has started to move toward a number of smaller packages SB> that will let people install only what they actually need. There SB> will be a core' package of essential modules, and a bunch of these SB> new smaller packages that rely on core. OK, so this will happen sometime post-1.6? It seems that currently for 1.5.9 there is still just one tarball/CPAN module. How many separate modules are we talking about? If it's core + 4-5 separate CPAN modules that doesn't seem too bad, but atomising it into 40-50+ modules doesn't seem like a good idea. I raised this point in an earlier thread on bioperl-l (and it seemed that others agreed): http://lists.open-bio.org/pipermail/bioperl-l/2008-March/027392.html The situation I want to avoid is having to push a huge number of CPAN modules through Fedora package review, then having to individually update them regularly just to get the same functionality as we have right now with the single perl-bioperl package. (Packaging Bioconductor for R is a nightmare for this very reason). SB> From a certain point of view it could be that 'to install bioperl' SB> == to install bioperl core', in which case the answer to your SB> question is 1' .tar.gz to install. SB> As a convenience to the user who wants to install all BioPerl SB> packages, there will be a CPAN Bundle (at the least). Fedora SB> package-wise, I guess you'd do whatever you currently do to SB> emulate CPAN bundles. Would these CPAN bundles be updated to include the latest CPAN modules as they are individually updated? What is possible in RPM is to take a single tarball and make subpackages from the single tarball, which would allow the user the benefit of a more fine-grained installation of particular bioperl modules without having the overhead of maintaining each package separately, e.g.: perl-bioperl (core package) perl-bioperl-foobar (optional subpackage) perl-bioperl-baz (" " ) >> If Bio::Graphics is now not included inside the bioperl tarball and >> is required for bioperl SB> It isn't. Bio::Graphics depends on BioPerl, but BioPerl does not SB> depend on Bio::Graphics. OK, thanks for the clarification, although I'm still puzzled as to why the package still generates: "Requires: perl(Bio::Graphics)" see bottom of: http://koji.fedoraproject.org/koji/getfile?taskID=1022559&name=build.log Is this a circular dependency like Bio::ASN1::EntrezGene ? Alex From bix at sendu.me.uk Sun Dec 28 08:37:04 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Sun, 28 Dec 2008 13:37:04 +0000 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> Message-ID: <49578100.1040402@sendu.me.uk> Alex Lancaster wrote: >>>>>> "SB" == Sendu Bala writes: > > SB> Alex Lancaster wrote: >>> I'm the Fedora packager for bioperl. I note on the release notes >>> page that Bio::Graphics has been split off into it's own CPAN >>> module. Since in most Linux distributions a single tarball = a >>> single RPM = a single package. How many .tar.gz files (and >>> therefore packages) are now required to install bioperl? > > SB> BioPerl has started to move toward a number of smaller packages > SB> that will let people install only what they actually need. There > SB> will be a core' package of essential modules, and a bunch of these > SB> new smaller packages that rely on core. > > OK, so this will happen sometime post-1.6? It seems that currently > for 1.5.9 there is still just one tarball/CPAN module. > > How many separate modules are we talking about? If it's core + 4-5 > separate CPAN modules that doesn't seem too bad It'll be a small number. Note that currently it is a large core + Bio::Graphics + Bio::ASN1::EntrezGene + BioPerl-run + BioPerl-db + BioPerl-network + BioPerl-ext. So already it's at least 7 different tarballs if you wanted 'everything' BioPerl related. > SB> From a certain point of view it could be that 'to install bioperl' > SB> == to install bioperl core', in which case the answer to your > SB> question is 1' .tar.gz to install. > > SB> As a convenience to the user who wants to install all BioPerl > SB> packages, there will be a CPAN Bundle (at the least). Fedora > SB> package-wise, I guess you'd do whatever you currently do to > SB> emulate CPAN bundles. > > Would these CPAN bundles be updated to include the latest CPAN modules > as they are individually updated? There would most likely be a single CPAN bundle specifying all the different BioPerl packages but without any version number specifications. When a user installs the bundle it would install the latest version of each package. Each individual sub-package, on the other hand, would specify the version of any other sub-packages or core that it depends on. >>> If Bio::Graphics is now not included inside the bioperl tarball and >>> is required for bioperl > > SB> It isn't. Bio::Graphics depends on BioPerl, but BioPerl does not > SB> depend on Bio::Graphics. > > OK, thanks for the clarification, although I'm still puzzled as to why > the package still generates: > > "Requires: perl(Bio::Graphics)" > > see bottom of: > > http://koji.fedoraproject.org/koji/getfile?taskID=1022559&name=build.log I don't understand that output. Can you state what caused that particular require? Nothing should: it's a bug that must be fixed. Cheers, Sendu. From maj at fortinbras.us Sun Dec 28 15:00:51 2008 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 28 Dec 2008 15:00:51 -0500 Subject: [Bioperl-l] Being nice to GenBank Message-ID: <3B55AE1FD03341BC87229717584FAAA8@NewLife> Suppose I have a bunch of GB accessions. Can someone point me quickly to the nicest way to request the sequences (i.e., not one hit/accno ), via Bio::DB::GenBank, or another way? I appreciate it- MAJ From akozik at atgc.org Sun Dec 28 15:06:10 2008 From: akozik at atgc.org (Alexander Kozik) Date: Sun, 28 Dec 2008 12:06:10 -0800 Subject: [Bioperl-l] Being nice to GenBank In-Reply-To: <3B55AE1FD03341BC87229717584FAAA8@NewLife> References: <3B55AE1FD03341BC87229717584FAAA8@NewLife> Message-ID: <4957DC32.5030004@atgc.org> Use Batch Entrez to upload a file of GIs or accession numbers from the Nucleotide or Protein databases: http://www.ncbi.nlm.nih.gov/sites/batchentrez -Alex -- Alexander Kozik Bioinformatics Specialist Genome and Biomedical Sciences Facility 451 Health Sciences Drive Genome Center, 4-th floor, room 4302 University of California Davis, CA 95616-8816 Phone: (530) 754-9127 email#1: akozik at atgc.org email#2: akozik at gmail.com web: http://www.atgc.org/ Mark A. Jensen wrote: > Suppose I have a bunch of GB accessions. Can someone point me quickly to the nicest way to request the sequences (i.e., not one hit/accno ), via Bio::DB::GenBank, or another way? > I appreciate it- MAJ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From David.Messina at sbc.su.se Sun Dec 28 16:39:45 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Sun, 28 Dec 2008 22:39:45 +0100 Subject: [Bioperl-l] Being nice to GenBank In-Reply-To: <3B55AE1FD03341BC87229717584FAAA8@NewLife> References: <3B55AE1FD03341BC87229717584FAAA8@NewLife> Message-ID: <628aabb70812281339r37321b6er15d0fcae077a2812@mail.gmail.com> Hey Mark, For the Bio::DB::Genbank route, I think get_stream_by_query() will take a list of accessions and automatically make a batch query. You might also try looking at the EUtilities Cookbook HOWTO to see if that fits your bill. Apologies for not being more specific: I rarely need to do this in an automated fashion myself, so I usually just do boring ol' Batch Entrez retrieval on the website. Hope that helps, Dave From maj at fortinbras.us Sun Dec 28 16:55:49 2008 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 28 Dec 2008 16:55:49 -0500 Subject: [Bioperl-l] Being nice to GenBank In-Reply-To: <3B55AE1FD03341BC87229717584FAAA8@NewLife> References: <3B55AE1FD03341BC87229717584FAAA8@NewLife> Message-ID: <6B357D609C77414AAB7B60A9F8DD7323@NewLife> thanks guys! ----- Original Message ----- From: "Mark A. Jensen" To: "bioperl list" Sent: Sunday, December 28, 2008 3:00 PM Subject: [Bioperl-l] Being nice to GenBank > Suppose I have a bunch of GB accessions. Can someone point me quickly to the > nicest way to request the sequences (i.e., not one hit/accno ), via > Bio::DB::GenBank, or another way? > I appreciate it- MAJ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From alexl at users.sourceforge.net Sun Dec 28 18:20:20 2008 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Sun, 28 Dec 2008 16:20:20 -0700 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <49578100.1040402@sendu.me.uk> (Sendu Bala's message of "Sun\, 28 Dec 2008 13\:37\:04 +0000") References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> Message-ID: >>>>>>> "SB" == Sendu Bala writes: [...] > SB> BioPerl has started to move toward a number of smaller packages > SB> that will let people install only what they actually need. There > SB> will be a core' package of essential modules, and a bunch of these > SB> new smaller packages that rely on core. > Alex Lancaster wrote: > OK, so this will happen sometime post-1.6? It seems that currently > for 1.5.9 there is still just one tarball/CPAN module. > How many separate modules are we talking about? If it's core + 4-5 > separate CPAN modules that doesn't seem too bad SB> It'll be a small number. Note that currently it is a large core + SB> Bio::Graphics + Bio::ASN1::EntrezGene + BioPerl-run + BioPerl-db + SB> BioPerl-network + BioPerl-ext. So already it's at least 7 SB> different tarballs if you wanted 'everything' BioPerl related. Right, and Fedora currently only packages two of them: bioperl (core) and bioperl-run. At the time I generated the original packages, bioperl-{db,network,ext} seemed in flux with respect to the 1.5.2 release that I wasn't sure if it was appropriate to package them as yet and core + -run seemed like it was the part of bioperl used by 90% of users, so it was a good place to start. Also can you clarify the expected name of the tarball, is it bioperl, or BioPerl? The 1.5.2 release used bioperl-1.5.2_102.tar.bz2 whereas 1.5.9._1 uses BioPerl-1.5.9._1.tar.bz2 and it would be good if there was consistency as it really helps from maintaining the packages and generating links etc. > SB> From a certain point of view it could be that 'to install bioperl' > SB> == to install bioperl core', in which case the answer to your > SB> question is 1' .tar.gz to install. > SB> As a convenience to the user who wants to install all BioPerl > SB> packages, there will be a CPAN Bundle (at the least). Fedora > SB> package-wise, I guess you'd do whatever you currently do to > SB> emulate CPAN bundles. > Would these CPAN bundles be updated to include the latest CPAN modules > as they are individually updated? SB> There would most likely be a single CPAN bundle specifying all the SB> different BioPerl packages but without any version number SB> specifications. When a user installs the bundle it would install SB> the latest version of each package. SB> Each individual sub-package, on the other hand, would specify the SB> version of any other sub-packages or core that it depends on. OK, right. So if any of the sub-packages were incremented independently, would a new bundle be generated, or would new bundles only be updated for major releases? Hmm, I'm not sure if subpackages with different version numbers from the main package can be generated from a single SRPM, so that might be a bit tricky. But if core is only a small number of CPAN pakcages, that might not be so bad, although it would mean having to go through review for each of the (new) CPAN modules and more maintainance, so it might be a while before it would be in Fedora. When is this scheduled to happen? (post-1.6, I hope!) [...] > OK, thanks for the clarification, although I'm still puzzled as to why > the package still generates: > "Requires: perl(Bio::Graphics)" > see bottom of: > http://koji.fedoraproject.org/koji/getfile?taskID=1022559&name=build.log SB> I don't understand that output. Can you state what caused that SB> particular require? Nothing should: it's a bug that must be fixed. RPM has a script with heuristics that search .pm and .pl files for 'use ' type constructs to automatically generate 'Requires", that sometimes guess wrong. To check, I grepped an exploded package for instances of 'Bio::Graphics' and what returned is below, at the end of the e-mail. I suspect that the 'use Bio::Graphics' in some of the installed scripts in bin/ such as bp_glyphs2-demo.pl are causing the issue. Shouldn't these scripts perhaps be moved to the Bio::Graphics CPAN module (along with the scripts in examples/)? If the Bio::Graphics is truly not needed, for the moment it is possible to also override and filter out the bogus Requires until such time as these scripts are moved to the appropriate place. Alex $ grep -r 'Bio::Graphics' * bin/bp_glyphs2-demo.pl:use Bio::Graphics::Panel; bin/bp_glyphs2-demo.pl:bp_glyphs2-demo.pl - Second demo of Bio::Graphics glyphs bin/bp_glyphs2-demo.pl:Generates a PNG image of some of the more esoteric Bio::Graphics glyphs. bin/bp_glyphs2-demo.pl:L, the BioGraphics HOWTO. bin/bp_glyphs2-demo.pl:my $ftr = 'Bio::Graphics::Feature'; bin/bp_glyphs2-demo.pl:my $panel = Bio::Graphics::Panel->new( bin/bp_embl2picture.pl:use Bio::Graphics; bin/bp_embl2picture.pl:L, the BioGraphics HOWTO. bin/bp_embl2picture.pl:my $panel = Bio::Graphics::Panel->new( bin/bp_glyphs1-demo.pl:use Bio::Graphics::Panel; bin/bp_glyphs1-demo.pl:bp_glyphs1-demo.pl - First demo of Bio::Graphics glyphs bin/bp_glyphs1-demo.pl:Generates a PNG image of some of the more esoteric Bio::Graphics glyphs. bin/bp_glyphs1-demo.pl:L, the BioGraphics HOWTO. bin/bp_glyphs1-demo.pl:my $ftr = 'Bio::Graphics::Feature'; bin/bp_glyphs1-demo.pl:my $panel = Bio::Graphics::Panel->new( lib/perl5/vendor_perl/5.10.0/Bio/Das/SegmentI.pm:the Bio::Graphics engine to render segments just like a feature in order lib/perl5/vendor_perl/5.10.0/Bio/Das/SegmentI.pm:that identifies it as being strandless. This allows the Bio::Graphics lib/perl5/vendor_perl/5.10.0/Bio/SeqFeature/Lite.pm:with Bio::Graphics::Panel. With it you can create lightweight feature lib/perl5/vendor_perl/5.10.0/Bio/SeqFeature/Lite.pm: -url a URL to link to when rendered with Bio::Graphics lib/perl5/vendor_perl/5.10.0/Bio/SeqFeature/Lite.pm:L lib/perl5/vendor_perl/5.10.0/Bio/DB/GFF.pm:SeqFeatureI interface, allowing their use by the Bio::Graphics and lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature.pm:Bio::Graphics::Feature-Enew(). The most important difference is the lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature.pm: -segments a list of subfeatures (see Bio::Graphics::Feature) lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature.pm: -url a URL to link to when rendered with Bio::Graphics lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature/NormalizedFeature.pm:Bio::Graphics::Feature-Enew(). The most important difference is the lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature/NormalizedFeature.pm: -segments a list of subfeatures (see Bio::Graphics::Feature) lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature/NormalizedFeature.pm: -url a URL to link to when rendered with Bio::Graphics lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature/NormalizedFeature.pm:convenience for Bio::Graphics, which looks for notes() when it lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm: URL A URL to link to (via the Bio::Graphics library). lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm: Note A note to attach to the feature for display by the Bio::Graphics library. lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm:Return the default SeqFeatureI class (Bio::Graphics::Feature). lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm: return 'Bio::Graphics::Feature'; lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature/Store.pm:Bio::Graphics::Feature-Enew(). The most important difference is the lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature/Store.pm: -segments a list of subfeatures (see Bio::Graphics::Feature) lib/perl5/vendor_perl/5.10.0/Bio/DB/SeqFeature/Store.pm: -url a URL to link to when rendered with Bio::Graphics lib/perl5/vendor_perl/5.10.0/Bio/DB/GFF/Aggregator/orf.pm:L, L share/doc/perl-bioperl-1.5.9/examples/biographics/all_glyphs.pl:use Bio::Graphics::Panel; share/doc/perl-bioperl-1.5.9/examples/biographics/all_glyphs.pl:use Bio::Graphics::Feature; share/doc/perl-bioperl-1.5.9/examples/biographics/all_glyphs.pl:my $ftr = 'Bio::Graphics::Feature'; share/doc/perl-bioperl-1.5.9/examples/biographics/all_glyphs.pl:my $panel = Bio::Graphics::Panel->new( share/doc/perl-bioperl-1.5.9/examples/biographics/lots_of_glyphs.pl:use Bio::Graphics::Panel; share/doc/perl-bioperl-1.5.9/examples/biographics/lots_of_glyphs.pl:use Bio::Graphics::Feature; share/doc/perl-bioperl-1.5.9/examples/biographics/lots_of_glyphs.pl:my $ftr = 'Bio::Graphics::Feature'; share/doc/perl-bioperl-1.5.9/examples/biographics/lots_of_glyphs.pl:my $pan* Shengqiang Shu - Bio::Graphics::Glyph share/doc/perl-bioperl-1.5.9/ChangeLog:* [r15129] remove Bio::Graphics (separate package now) share/doc/perl-bioperl-1.5.9/ChangeLog:* [r15127] Remove dependencies for Bio::Graphics and deprecated share/doc/perl-bioperl-1.5.9/ChangeLog:* [r15125] removed Bio::Graphics itself share/doc/perl-bioperl-1.5.9/ChangeLog:* [r15119] Bio::Graphics has become its own module; latest version share/doc/perl-bioperl-1.5.9/ChangeLog:* [r14794] added feature grouping to SVG output from Bio::Graphics share/doc/perl-bioperl-1.5.9/ChangeLog:* [r14734] Bio::Graphics::Glyph::minmax is the base class that share/doc/perl-bioperl-1.5.9/ChangeLog: rendering correctly on Bio::Graphics::Panels (label missing) share/doc/perl-bioperl-1.5.9/ChangeLog: Bio::Graphics::Panel to fail under some versions of perl share/doc/perl-bioperl-1.5.9/ChangeLog: # Bio::Graphics::FeatureBase->new (or to Bio::DB::SeqFeature, share/doc/perl-bioperl-1.5.9/ChangeLog: # Bio::Graphics::Feature). Such homogenous subfeatures created in share/doc/perl-bioperl-1.5.9/ChangeLog: Bio::Graphics::FeatureBase; (1) was dumping empty Alias share/doc/perl-bioperl-1.5.9/ChangeLog:* [r11164] made Bio::Graphics::FeatureBase more consistent with share/doc/perl-bioperl-1.5.9/ChangeLog: Bio::Graphics::FeatureBase->to_FTString() behaves a little more share/doc/perl-bioperl-1.5.9/Changes: o Bio::Graphics share/doc/perl-bioperl-1.5.9/Changes: o Bio::Graphics has many bug fixes and shiny new glyphs. share/doc/perl-bioperl-1.5.9/Changes: o Bio::Graphics will work with gd1 or gd2 share/doc/perl-bioperl-1.5.9/Changes: o Bio::Graphics share/doc/perl-bioperl-1.5.9/Changes: o Bio::Graphics share/doc/perl-bioperl-1.5.9/Changes: o Bio::Graphics glyph set improved and extended for GBrowse release share/doc/perl-bioperl-1.5.9/Changes: o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has From bix at sendu.me.uk Mon Dec 29 21:31:43 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 30 Dec 2008 02:31:43 +0000 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> Message-ID: <4959880F.4040205@sendu.me.uk> Alex Lancaster wrote: >>>>>>>> "SB" == Sendu Bala writes: > Also can you clarify the expected name of the tarball, is it bioperl, > or BioPerl? The 1.5.2 release used bioperl-1.5.2_102.tar.bz2 whereas > 1.5.9._1 uses BioPerl-1.5.9._1.tar.bz2 and it would be good if there > was consistency as it really helps from maintaining the packages and > generating links etc. Naming consistency is built into the system. ./Build dist generates a file named: bioperl-1.5.9_1.tar.bz2 I guess Chris decided to rename the file before uploading, and its up to him what future files are named, but I second your suggestion this should be consistent. Chris: I note that extraneous files like 'test.txt' and others made it into the RC1 .tar.gz you uploaded. What I always did was a clean export of the tag and built from there. BTW, the dist action also warns you about modules with their own version: Bio::DB::GFF::Aggregator::orf in this case. You might want to investigate that. > SB> There would most likely be a single CPAN bundle specifying all the > SB> different BioPerl packages but without any version number > SB> specifications. When a user installs the bundle it would install > SB> the latest version of each package. > > SB> Each individual sub-package, on the other hand, would specify the > SB> version of any other sub-packages or core that it depends on. > > OK, right. So if any of the sub-packages were incremented > independently, would a new bundle be generated, or would new bundles > only be updated for major releases? Hmm, I'm not sure if subpackages > with different version numbers from the main package can be generated > from a single SRPM, so that might be a bit tricky. But if core is > only a small number of CPAN pakcages, that might not be so bad, > although it would mean having to go through review for each of the > (new) CPAN modules and more maintainance, so it might be a while > before it would be in Fedora. When is this scheduled to happen? > (post-1.6, I hope!) 'core' will only ever be one CPAN package (one tarball). A new bundle would not be generated when a sub-package is incremented. The whole point of sub-packages is that they're independent and can be developed and released without affecting core or the other sub-packages. The only reason for a bundle update would be to add more new sub-packages to it. Again, how does Fedora currently emulate CPAN Bundles? Just so we're not getting our wires crossed, in this context 'core' would be BioPerl-1.5.9._1.tar.bz2 and 6 examples of sub-packages would be the .tar.bz2 distribution files for Bio::Graphics, Bio::ASN1::EntrezGene, BioPerl-run, BioPerl-db, BioPerl-network and BioPerl-ext. The kind of thing that could then happen in the future is that (to take some random imaginary examples) BioPerl-1.7.0.tar.bz2 is released as 'core' which is a bit smaller than BioPerl-1.5.9._1.tar.bz2 because Bio::Structure is missing from it, and there is a new independent sub-package released for Bio::Structure, just like what happened with Bio::Graphics. >> "Requires: perl(Bio::Graphics)" > > RPM has a script with heuristics that search .pm and .pl files for > 'use ' type constructs to automatically generate > 'Requires", that sometimes guess wrong. To check, I grepped an > exploded package for instances of 'Bio::Graphics' and what returned is > below, at the end of the e-mail. I suspect that the 'use > Bio::Graphics' in some of the installed scripts in bin/ such as > bp_glyphs2-demo.pl are causing the issue. Shouldn't these scripts > perhaps be moved to the Bio::Graphics CPAN module (along with the > scripts in examples/)? Thanks for pointing that out. I'll leave it to Chris to sort that out... > If the Bio::Graphics is truly not needed, for the moment it is > possible to also override and filter out the bogus Requires until such > time as these scripts are moved to the appropriate place. Great, go ahead and do that if you like. From alperyilmaz at gmail.com Tue Dec 30 10:02:34 2008 From: alperyilmaz at gmail.com (Alper Yilmaz) Date: Tue, 30 Dec 2008 10:02:34 -0500 Subject: [Bioperl-l] construct chromosome sequences from bac sequences Message-ID: Hi, I have FPC report and BAC sequences in hand. I was wondering what is the most practical way to build chromosomes from these available information. I HAVE: FPC file: accession chr chr_start chr_end contig contig_start contig_end aaaaaaaaaa 1 14700 215600 ctg1 14700 215600 bbbbbbbbbb 1 196000 362600 ctg1 196000 362600 cccccccccc 1 352800 524300 ctg1 352800 524300 . . BAC fasta file: >aaaaaaaaaa GATCGATCAGCATCGACTACGACT... >bbbbbbbbbb AGTAGCAGTAGCTAGCACTACGAC... >cccccccccc ACGATCAGCATCAGCATCGACTAC... . . . I WANT: >chr1 GACGACTAGCTACGACTAC... >chr2 AGCTGATCACGATCACGAC... In theory a sequence object called "Chr1" can be created and then according to start and end locations of each BAC in FPC file, subsequences of Chr1 can be retrieved. However, there are two facts which might prevent using standard sequence objects. 1) There will be gaps in chromosomes. Is there a function to convert unassigned locations to N? 2) There are overlaps between BAC sequences. If the overlapping sequences are exactly same, it won't be problem, but if there are discrepancies between them, a decision has to be made as to which sequence to use in final Chr1 sequence. thanks, Alper Yilmaz From cjfields at illinois.edu Tue Dec 30 11:16:16 2008 From: cjfields at illinois.edu (Christopher Fields) Date: Tue, 30 Dec 2008 10:16:16 -0600 (CST) Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <4959880F.4040205@sendu.me.uk> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> Message-ID: <20081230101616.BMU14207@expms6.cites.uiuc.edu> All, I can't respond adequately until I return from vacation; I'm responding from a dial-up line in Texas (?!?) so responding to each message in kind will take a year or two (I did mention that I would be away from Dec 26-31, but it looks like that will be until Jan 1). ---- Original message ---- >Date: Tue, 30 Dec 2008 02:31:43 +0000 >From: Sendu Bala >Subject: Re: [Bioperl-l] BioPerl 1.6 RC1 >To: Alex Lancaster >Cc: bioperl-l at lists.open-bio.org, Chris Fields > >Alex Lancaster wrote: >>>>>>>>> "SB" == Sendu Bala writes: >> Also can you clarify the expected name of the tarball, is it bioperl, >> or BioPerl? The 1.5.2 release used bioperl-1.5.2_102.tar.bz2 whereas >> 1.5.9._1 uses BioPerl-1.5.9._1.tar.bz2 and it would be good if there >> was consistency as it really helps from maintaining the packages and >> generating links etc. > >Naming consistency is built into the system. >./Build dist >generates a file named: >bioperl-1.5.9_1.tar.bz2 > >I guess Chris decided to rename the file before uploading, and its up to >him what future files are named, but I second your suggestion this >should be consistent. The package is named after the toolkit (BioPerl vs bioperl). We can revert back to simply 'bioperl', but since we keep referring to the package as 'BioPerl' on the wiki and elsewhere we should use that for the CPAN from this point on. >Chris: I note that extraneous files like 'test.txt' and others made it >into the RC1 .tar.gz you uploaded. What I always did was a clean export >of the tag and built from there. BTW, the dist action also warns you >about modules with their own version: Bio::DB::GFF::Aggregator::orf in >this case. You might want to investigate that. I noticed that it's packaging up everything in the local directory, yes (that was after the upload unfortunately). That'll be fixed for RC2; I'll look for a more amenable fix when I get back (a packlist of files would work around this, but I'm not sure how well that will work with a large distro like BioPerl). >> SB> There would most likely be a single CPAN bundle specifying all the >> SB> different BioPerl packages but without any version number >> SB> specifications. When a user installs the bundle it would install >> SB> the latest version of each package. >> >> SB> Each individual sub-package, on the other hand, would specify the >> SB> version of any other sub-packages or core that it depends on. >> >> OK, right. So if any of the sub-packages were incremented >> independently, would a new bundle be generated, or would new bundles >> only be updated for major releases? Hmm, I'm not sure if subpackages >> with different version numbers from the main package can be generated >> from a single SRPM, so that might be a bit tricky. But if core is >> only a small number of CPAN pakcages, that might not be so bad, >> although it would mean having to go through review for each of the >> (new) CPAN modules and more maintainance, so it might be a while >> before it would be in Fedora. When is this scheduled to happen? >> (post-1.6, I hope!) > >'core' will only ever be one CPAN package (one tarball). >A new bundle would not be generated when a sub-package is incremented. >The whole point of sub-packages is that they're independent and can be >developed and released without affecting core or the other sub-packages. > >The only reason for a bundle update would be to add more new >sub-packages to it. > >Again, how does Fedora currently emulate CPAN Bundles? > > >Just so we're not getting our wires crossed, in this context 'core' >would be BioPerl-1.5.9._1.tar.bz2 and 6 examples of sub-packages would >be the .tar.bz2 distribution files for Bio::Graphics, >Bio::ASN1::EntrezGene, BioPerl-run, BioPerl-db, BioPerl-network and >BioPerl-ext. > >The kind of thing that could then happen in the future is that (to take >some random imaginary examples) BioPerl-1.7.0.tar.bz2 is released as >'core' which is a bit smaller than BioPerl-1.5.9._1.tar.bz2 because >Bio::Structure is missing from it, and there is a new independent >sub-package released for Bio::Structure, just like what happened with >Bio::Graphics. > > >>> "Requires: perl(Bio::Graphics)" >> >> RPM has a script with heuristics that search .pm and .pl files for >> 'use ' type constructs to automatically generate >> 'Requires", that sometimes guess wrong. To check, I grepped an >> exploded package for instances of 'Bio::Graphics' and what returned is >> below, at the end of the e-mail. I suspect that the 'use >> Bio::Graphics' in some of the installed scripts in bin/ such as >> bp_glyphs2-demo.pl are causing the issue. Shouldn't these scripts >> perhaps be moved to the Bio::Graphics CPAN module (along with the >> scripts in examples/)? > >Thanks for pointing that out. I'll leave it to Chris to sort that out... Yes, those scripts should be moved over (already have indicated this to Lincoln). I can't check my local svn co (it's sitting about ~1000 miles away from me in a closet right now). >> If the Bio::Graphics is truly not needed, for the moment it is >> possible to also override and filter out the bogus Requires until such >> time as these scripts are moved to the appropriate place. > >Great, go ahead and do that if you like. I'm not quite sure why we are attempting to RPM package up a release candidate unless it's strictly for the purposes of testing things out. I anticipate the final 1.6 will be out in short period of time (within a few weeks). Maybe this has already been answered, just haven't had time to read back along the thread yet. Anyway, patience everyone. This is an RC not a final release, and I anticipated that a few things would probably be screwy. It appears only a few things need to be addressed and cleaned up prior to a final release, so overall RC1 did what I wanted (including uncovering an odd PAML bug according to CPAN Testers). -c (from the backwoods in Texas) From cain.cshl at gmail.com Tue Dec 30 13:48:55 2008 From: cain.cshl at gmail.com (Scott Cain) Date: Tue, 30 Dec 2008 13:48:55 -0500 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <20081230101616.BMU14207@expms6.cites.uiuc.edu> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> Message-ID: <536f21b00812301048m4d40a5eei3078a9d7603c14b6@mail.gmail.com> Hi, For the scripts currently in BioPerl core that use BioGraphics, do we think that they should no longer be distributed with BioPerl but should instead be moved to the BioGraphics distribution? I imagine someone trying to use bp_embl2picture.pl and being surprised that it doesn't work. Thoughts? Scott On Tue, Dec 30, 2008 at 11:16 AM, Christopher Fields wrote: > All, > > I can't respond adequately until I return from vacation; I'm responding from a dial-up line in Texas (?!?) so responding to each message in kind will take a year or two (I did mention that I would be away from Dec 26-31, but it looks like that will be until Jan 1). > > > ---- Original message ---- >>Date: Tue, 30 Dec 2008 02:31:43 +0000 >>From: Sendu Bala >>Subject: Re: [Bioperl-l] BioPerl 1.6 RC1 >>To: Alex Lancaster >>Cc: bioperl-l at lists.open-bio.org, Chris Fields >> >>Alex Lancaster wrote: >>>>>>>>>> "SB" == Sendu Bala writes: >>> Also can you clarify the expected name of the tarball, is it bioperl, >>> or BioPerl? The 1.5.2 release used bioperl-1.5.2_102.tar.bz2 whereas >>> 1.5.9._1 uses BioPerl-1.5.9._1.tar.bz2 and it would be good if there >>> was consistency as it really helps from maintaining the packages and >>> generating links etc. >> >>Naming consistency is built into the system. >>./Build dist >>generates a file named: >>bioperl-1.5.9_1.tar.bz2 >> >>I guess Chris decided to rename the file before uploading, and its up to >>him what future files are named, but I second your suggestion this >>should be consistent. > > The package is named after the toolkit (BioPerl vs bioperl). We can revert back to simply 'bioperl', but since we keep referring to the package as 'BioPerl' on the wiki and elsewhere we should use that for the CPAN from this point on. > >>Chris: I note that extraneous files like 'test.txt' and others made it >>into the RC1 .tar.gz you uploaded. What I always did was a clean export >>of the tag and built from there. BTW, the dist action also warns you >>about modules with their own version: Bio::DB::GFF::Aggregator::orf in >>this case. You might want to investigate that. > > I noticed that it's packaging up everything in the local directory, yes (that was after the upload unfortunately). That'll be fixed for RC2; I'll look for a more amenable fix when I get back (a packlist of files would work around this, but I'm not sure how well that will work with a large distro like BioPerl). > >>> SB> There would most likely be a single CPAN bundle specifying all the >>> SB> different BioPerl packages but without any version number >>> SB> specifications. When a user installs the bundle it would install >>> SB> the latest version of each package. >>> >>> SB> Each individual sub-package, on the other hand, would specify the >>> SB> version of any other sub-packages or core that it depends on. >>> >>> OK, right. So if any of the sub-packages were incremented >>> independently, would a new bundle be generated, or would new bundles >>> only be updated for major releases? Hmm, I'm not sure if subpackages >>> with different version numbers from the main package can be generated >>> from a single SRPM, so that might be a bit tricky. But if core is >>> only a small number of CPAN pakcages, that might not be so bad, >>> although it would mean having to go through review for each of the >>> (new) CPAN modules and more maintainance, so it might be a while >>> before it would be in Fedora. When is this scheduled to happen? >>> (post-1.6, I hope!) >> >>'core' will only ever be one CPAN package (one tarball). >>A new bundle would not be generated when a sub-package is incremented. >>The whole point of sub-packages is that they're independent and can be >>developed and released without affecting core or the other sub-packages. >> >>The only reason for a bundle update would be to add more new >>sub-packages to it. >> >>Again, how does Fedora currently emulate CPAN Bundles? >> >> >>Just so we're not getting our wires crossed, in this context 'core' >>would be BioPerl-1.5.9._1.tar.bz2 and 6 examples of sub-packages would >>be the .tar.bz2 distribution files for Bio::Graphics, >>Bio::ASN1::EntrezGene, BioPerl-run, BioPerl-db, BioPerl-network and >>BioPerl-ext. >> >>The kind of thing that could then happen in the future is that (to take >>some random imaginary examples) BioPerl-1.7.0.tar.bz2 is released as >>'core' which is a bit smaller than BioPerl-1.5.9._1.tar.bz2 because >>Bio::Structure is missing from it, and there is a new independent >>sub-package released for Bio::Structure, just like what happened with >>Bio::Graphics. >> >> >>>> "Requires: perl(Bio::Graphics)" >>> >>> RPM has a script with heuristics that search .pm and .pl files for >>> 'use ' type constructs to automatically generate >>> 'Requires", that sometimes guess wrong. To check, I grepped an >>> exploded package for instances of 'Bio::Graphics' and what returned is >>> below, at the end of the e-mail. I suspect that the 'use >>> Bio::Graphics' in some of the installed scripts in bin/ such as >>> bp_glyphs2-demo.pl are causing the issue. Shouldn't these scripts >>> perhaps be moved to the Bio::Graphics CPAN module (along with the >>> scripts in examples/)? >> >>Thanks for pointing that out. I'll leave it to Chris to sort that out... > > Yes, those scripts should be moved over (already have indicated this to Lincoln). I can't check my local svn co (it's sitting about ~1000 miles away from me in a closet right now). > >>> If the Bio::Graphics is truly not needed, for the moment it is >>> possible to also override and filter out the bogus Requires until such >>> time as these scripts are moved to the appropriate place. >> >>Great, go ahead and do that if you like. > > I'm not quite sure why we are attempting to RPM package up a release candidate unless it's strictly for the purposes of testing things out. I anticipate the final 1.6 will be out in short period of time (within a few weeks). Maybe this has already been answered, just haven't had time to read back along the thread yet. > > Anyway, patience everyone. This is an RC not a final release, and I anticipated that a few things would probably be screwy. It appears only a few things need to be addressed and cleaned up prior to a final release, so overall RC1 did what I wanted (including uncovering an odd PAML bug according to CPAN Testers). > > -c (from the backwoods in Texas) > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From bix at sendu.me.uk Tue Dec 30 20:59:29 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 31 Dec 2008 01:59:29 +0000 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <20081230101616.BMU14207@expms6.cites.uiuc.edu> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> Message-ID: <495AD201.4080500@sendu.me.uk> Christopher Fields wrote: >> Chris: I note that extraneous files like 'test.txt' and others made >> it into the RC1 .tar.gz you uploaded. What I always did was a clean >> export of the tag and built from there. BTW, the dist action also >> warns you about modules with their own version: >> Bio::DB::GFF::Aggregator::orf in this case. You might want to >> investigate that. > > I noticed that it's packaging up everything in the local directory, > yes (that was after the upload unfortunately). That'll be fixed for > RC2; I'll look for a more amenable fix when I get back (a packlist of > files would work around this, but I'm not sure how well that will > work with a large distro like BioPerl). No, no, it wouldn't work at all. The dist action is what /generates/ the 'packlist' (MANIFEST) - we don't want to have to manually specify anything because it would be too easy to forget to add new files and there would be no obvious indication anything was left out of a distribution. It's very important this remain automatic and fool proof. It should package up everything under version control. Only if there are things under version control that we don't want packaged should /exceptions/ manually be added (MANIFEST.SKIP, ne Build.PL). Again, all you have to and should do is build from a fresh export of the tag, not from your normal working directory. You should never do that in any case, because you might have been working on a module and have uncommitted changes. From bix at sendu.me.uk Wed Dec 31 07:18:29 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 31 Dec 2008 12:18:29 +0000 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <20081230101616.BMU14207@expms6.cites.uiuc.edu> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> Message-ID: <495B6315.3030901@sendu.me.uk> Christopher Fields wrote: >> Alex Lancaster wrote: >>>>>>>>>> "SB" == Sendu Bala writes: >>> Also can you clarify the expected name of the tarball, is it >>> bioperl, or BioPerl? The 1.5.2 release used >>> bioperl-1.5.2_102.tar.bz2 whereas 1.5.9._1 uses >>> BioPerl-1.5.9._1.tar.bz2 and it would be good if there was >>> consistency as it really helps from maintaining the packages and >>> generating links etc. >> Naming consistency is built into the system. ./Build dist generates >> a file named: bioperl-1.5.9_1.tar.bz2 >> >> I guess Chris decided to rename the file before uploading, and its >> up to him what future files are named, but I second your suggestion >> this should be consistent. > > The package is named after the toolkit (BioPerl vs bioperl). We can > revert back to simply 'bioperl', but since we keep referring to the > package as 'BioPerl' on the wiki and elsewhere we should use that for > the CPAN from this point on. Makes sense. ./Build dist now generates a file named BioPerl-x.x.x.tar.xxx