From cjfields at illinois.edu Thu Oct 1 12:40:59 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 1 Oct 2009 11:40:59 -0500 Subject: [Bioperl-l] FIrst alphas of BioPerl-Run, BioPerl-DB, BioPerl-Network Message-ID: <212FF112-E54D-4FFA-8C7C-AFBED4745988@illinois.edu> Just a quick note that the first alphas for BioPerl-Run, BioPerl-DB, and BioPerl-Network have been uploaded to CPAN: http://search.cpan.org/~cjfields/BioPerl-Run-1.6.1_001/ http://search.cpan.org/~cjfields/BioPerl-DB-1.6.0_001/ http://search.cpan.org/~cjfields/BioPerl-Network-1.6.0_001/ And is available from the main BioPerl website: http://bioperl.org/DIST/RC/BioPerl-Run-1.6.1_001.tar.gz http://bioperl.org/DIST/RC/BioPerl-DB-1.6.0_001.tar.gz http://bioperl.org/DIST/RC/BioPerl-Network-1.6.0_001.tar.gz This is the first run where we've switched to a regular Module::Build installation, so expect some initial bumps! There are a few initial problems that I plan on addressing soon, the main one being none of the modules are assigned version numbers (this may be a consequence of not pulling the version from a specific module). The other, more serious one, is that the Build.PL script checks for DBI but isn't checking for any compatible DBD::* adaptors for BioPerl-DB (so it fails tests if DBI is installed). We have code in core to check for DBI drivers, so I may adapt that for BioPerl-DB. chris From e.osimo at gmail.com Thu Oct 1 12:42:16 2009 From: e.osimo at gmail.com (Emanuele Osimo) Date: Thu, 1 Oct 2009 18:42:16 +0200 Subject: [Bioperl-l] computing gc content of a list of sequences Message-ID: <2ac05d0f0910010942m3c63db74g4b669f1fec571227@mail.gmail.com> Dear all, I have a multifasta file with a list of sequences. How can I compute the gc % content of each of them? Is there a Bioperl tool? Thanks Emanuele From Russell.Smithies at agresearch.co.nz Thu Oct 1 17:05:13 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Fri, 2 Oct 2009 10:05:13 +1300 Subject: [Bioperl-l] computing gc content of a list of sequences In-Reply-To: <2ac05d0f0910010942m3c63db74g4b669f1fec571227@mail.gmail.com> References: <2ac05d0f0910010942m3c63db74g4b669f1fec571227@mail.gmail.com> Message-ID: <18DF7D20DFEC044098A1062202F5FFF32B62BE77EC@exchsth.agresearch.co.nz> Try bp_gccalc.pl [smithiesr at impala ~]$ bp_gccalc.pl temp/sequences.fasta Seq: 1 Len:149 GC content is 0.8255 Number of bases of type A= 22 Number of bases of type C= 49 Number of bases of type G= 74 Number of bases of type T= 4 -- Seq: 2 Len:5022 GC content is 0.5014 Number of bases of type A= 1282 Number of bases of type C= 1212 Number of bases of type G= 1306 Number of bases of type T= 1222 -- Seq: 3 Len:4923 GC content is 0.5452 Number of bases of type A= 1143 Number of bases of type C= 1307 Number of bases of type G= 1377 Number of bases of type T= 1096 --Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Emanuele Osimo > Sent: Friday, 2 October 2009 5:42 a.m. > To: perl bioperl ml > Subject: [Bioperl-l] computing gc content of a list of sequences > > Dear all, > I have a multifasta file with a list of sequences. > How can I compute the gc % content of each of them? Is there a Bioperl tool? > Thanks > Emanuele > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From armin.schmitt at agrar.hu-berlin.de Fri Oct 2 05:47:33 2009 From: armin.schmitt at agrar.hu-berlin.de (Armin Schmitt) Date: Fri, 02 Oct 2009 11:47:33 +0200 Subject: [Bioperl-l] Mutation analysis without liveseq objects Message-ID: <4AC5CC35.70002@agrar.hu-berlin.de> I would like to study the effect of DNA mutations. Of special interest would be to find out if a mutation causes an amino acid exchange or not. Bio::LiveSeq::Mutator does a perfect job, but the problem is that for many genes no LiveSeq objects can be generated. Does anybody know of a way how to perform such an analysis with normal sequence objects? Thank you very much. Armin Schmitt -- Dr. Armin Schmitt Humboldt-Universit?t zu Berlin Department for Crop and Animal Sciences Invalidenstra?e 42 10115 Berlin Tel.: +49-30-2093-9074 Fax: +49-30-2093-6397 E-mail: armin.schmitt at agrar.hu-berlin.de From ben.busby at gmail.com Fri Oct 2 12:29:40 2009 From: ben.busby at gmail.com (Ben Busby) Date: Fri, 2 Oct 2009 12:29:40 -0400 Subject: [Bioperl-l] Easily parsable command line BLAST output Message-ID: <4a831ca50910020929v5a4b532fma32e48dcdfe2a6c6@mail.gmail.com> Pardon the simple question, as I am new-ish to Perl, Bioperl, and Computational Biology.. I am doing a whole bunch of large BLAST searches and am wondering what the best command line BLAST commands are to put the output in a format best parsable by Bio::SearchIO. Thanks! Ben -- Economically, nothing is ever "extended by popular demand". From jason at bioperl.org Fri Oct 2 12:41:42 2009 From: jason at bioperl.org (Jason Stajich) Date: Fri, 2 Oct 2009 09:41:42 -0700 Subject: [Bioperl-l] Easily parsable command line BLAST output In-Reply-To: <4a831ca50910020929v5a4b532fma32e48dcdfe2a6c6@mail.gmail.com> References: <4a831ca50910020929v5a4b532fma32e48dcdfe2a6c6@mail.gmail.com> Message-ID: <546E0317-0D00-4528-82DA-4F10B652D7BB@bioperl.org> Depends on what information you want to parse out.... do you need the actual alignment? If no -> use -m 8 or -m 9 and you will have a tabular output that is easy to parse even without bioperl. On Oct 2, 2009, at 9:29 AM, Ben Busby wrote: > Pardon the simple question, as I am new-ish to Perl, Bioperl, and > Computational Biology.. > I am doing a whole bunch of large BLAST searches and am wondering > what the > best command line BLAST commands are to put the output in a format > best > parsable by Bio::SearchIO. > > Thanks! > > Ben > > > > -- > Economically, nothing is ever "extended by popular demand". > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich jason.stajich at gmail.com jason at bioperl.org From cjfields at illinois.edu Fri Oct 2 12:43:50 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 2 Oct 2009 11:43:50 -0500 Subject: [Bioperl-l] Easily parsable command line BLAST output In-Reply-To: <4a831ca50910020929v5a4b532fma32e48dcdfe2a6c6@mail.gmail.com> References: <4a831ca50910020929v5a4b532fma32e48dcdfe2a6c6@mail.gmail.com> Message-ID: <3ADF6629-1C90-47EE-A787-7C35BF036D72@illinois.edu> Ben, The following has that information: http://www.bioperl.org/wiki/Module:Bio::SearchIO http://www.bioperl.org/wiki/HOWTO:SearchIO#Design In short: -m type SearchIO -format 0 text blast 7 XML blastxml 8 tabular blasttable 9 tabular blasttable You should read the HOWTO and specific documentation for the Bio::SearchIO module just in case, and let us know if there are any spots that need improvement. There are varied reports some of the alignment-based output is parsable via AlignIO somehow, but I haven't attempted it. chris On Oct 2, 2009, at 11:29 AM, Ben Busby wrote: > Pardon the simple question, as I am new-ish to Perl, Bioperl, and > Computational Biology.. > I am doing a whole bunch of large BLAST searches and am wondering > what the > best command line BLAST commands are to put the output in a format > best > parsable by Bio::SearchIO. > > Thanks! > > Ben > > > > -- > Economically, nothing is ever "extended by popular demand". > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From shalabh.sharma7 at gmail.com Fri Oct 2 14:32:22 2009 From: shalabh.sharma7 at gmail.com (shalabh sharma) Date: Fri, 2 Oct 2009 14:32:22 -0400 Subject: [Bioperl-l] Refseq/COG to EC Message-ID: <9fcc48c70910021132i794812e1x99f0b66770e26f62@mail.gmail.com> Hi All, Is there any way i can convert or link Refseq id/COG to EC number? Is there any database or flat file which i can use for this purpose? I would really appreciate if anyone can help me out. Thanks Shalabh From cjfields at illinois.edu Mon Oct 5 14:23:34 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 5 Oct 2009 13:23:34 -0500 Subject: [Bioperl-l] Fwd: [Wg-phyloinformatics] NeXML schema update - RDFa-compliant metadata References: <3EE4E91F-F502-421B-A561-CD3EB281CC3D@nescent.org> Message-ID: <2D6494C0-D39C-464A-B12D-693BDEB01CE1@illinois.edu> Forwarding to bioperl-l just in case this wasn't noticed... chris Begin forwarded message: > From: Jim Balhoff > Date: October 5, 2009 1:11:50 PM CDT > To: nexml-discuss at lists.sourceforge.net, DB Interop Hackathon >, Wg-phyloinformatics at nescent.org > Subject: [Wg-phyloinformatics] NeXML schema update - RDFa-compliant > metadata > > Hi all (sorry for cross-posting), > > I have updated the NeXML schema to match the metadata requirements we > came up with at the NESCent database interoperability hackathon last > spring. The changes have been committed to an SVN branch which can be > browsed here: > > http://nexml.svn.sourceforge.net/viewvc/nexml/branches/rdfa-metadata/ > > NeXML changes > * All "id" attributes are now of type xs:ID instead of xs:NCName, and > must be unique within a document. > * All attributes used by one element to reference another (such as a > "char" referring to its "states") are now of type xs:IDREF or > xs:IDREFS (if multiple), and must refer to some valid ID in the > document. > * Removed from the Base > type, because of conflicts with the xs:ID attribute declaration on > IDTagged - will this cause a problem for anyone? (see > annotations.xsd). > * Removed all uses of the Dict type. > * Introduced Meta abstract type and two concrete subclasses, > ResourceMeta and LiteralMeta. > * Modified the Annotated type to contain optional "meta" elements of > type Meta. > * Imported the XHTML datatypes namespace to get types used with RDFa > attributes (CURIEs, etc.). > > Questions/things I need help with: > * Should "molecular" cells (observations) use IDREF for "state" > attribute? I want to make sure I handled these correctly. > * What should the NeXML version information be changed to? > * Do the meta elements satisfy the requirements we came up with at the > hackathon? > ** Please try putting metadata of your choice into a test document, > and validate. > ** Please test RDFa extraction of your metadata if you want to use it > that way. > * Need better documentation of meta elements and RDFa. > * Can someone figure out how to include xml:specialAttrs in a way that > works with the definition of IDTagged? This was giving me problems > when validating in Oxygen. > * All of the samples and code in the nexml project should be updated > as needed. > > Thanks, > Jim > > > ____________________________________________ > James P. Balhoff, Ph.D. > National Evolutionary Synthesis Center > 2024 West Main St., Suite A200 > Durham, NC 27705 > USA > > _______________________________________________ > Wg-phyloinformatics mailing list > Wg-phyloinformatics at nescent.org > https://lists.nescent.org/mailman/listinfo/wg-phyloinformatics From denzel.dz.li at gmail.com Mon Oct 5 14:35:20 2009 From: denzel.dz.li at gmail.com (Denzel Li) Date: Mon, 5 Oct 2009 14:35:20 -0400 Subject: [Bioperl-l] handling nexus files Message-ID: Hello all: Does bioperl support functions for handling nexus files? More specifically, I need two functions, 1) combine multiple nexus files into one, 2) split a nexus files into multiple nexus files. For example, given the following two files (file1.nex, file2.nex), is there function to combine them into one file as shown in "combinedFile.nex", or to split "combinedFile.nex" into two files (file1.nex, file2.nex). ------------------------------ # file1.nex begin data; dimensions ntax=2 nchar=3 b1 GGG b2 GGT ;end; --------------------------------- # file2.nex begin data; dimensions ntax=2 nchar=3 b1 AAA b2 AAT ;end; ------------------------------- # combinedFile.nex begin data; dimensions ntax=2 nchar=6 [alignment from file1.nex] b1 GGG b2 GGT [alignment from file2.nex] b1 AAA b2 AAT ;end; begin sets; charset a1=1-3; charset a2=4-6; end; -------------------------------- Any suggestion is highly appreciated. Thank you. Best, Denzel From shalabh.sharma7 at gmail.com Mon Oct 5 16:38:13 2009 From: shalabh.sharma7 at gmail.com (shalabh sharma) Date: Mon, 5 Oct 2009 16:38:13 -0400 Subject: [Bioperl-l] Blast problem Message-ID: <9fcc48c70910051338x546673dej5027add2a71ca7fa@mail.gmail.com> Hi All, This not exactly a bioperl query but i thought may be its a good place to ask. I am using blastall to blast sequences against my in house database. one of the query sequence is :- >JCVI_PEP_1105095073661 /read_id=JCVI_READ_391469 /begin=1 /end=1075 /orientation=-1 /5_prime_stop=TAA /3_prime_stop=0 /orf_id=JCVI_ORF_1105095073660 /ttable=11 /length=358 /ergatis_id=7720 /sample_id=JCVI_SMPL_1103283000001 /sample_name=GS000a /number_of_sites=2 /site_id_1=JCVI_SITE_GS000_S11 /location_1="Sargasso Station 11" /region_1="Sargasso Sea" /country_1=Bermuda /site_depth_1="5 m" LLNQESFRATPYTSRIEKQGVTAYTVYNHMLLPAAFGSLEESYHHLKKNVQIWDVAGERQVEISGKDSSKLVQLMTCRDL SKSKDGRCYYCPILDDEAGIINDPIVLRINENKWWISIADSDVILFAKGLAIGNKFEVKILEPNVDIMAVQGPKSFGLME KVFGKKITELKFFDFDYFDFEGAKHLIAKSGWSKQGGYEIYVENIESGLKLYDRLFEIGKEFYIRPGCPNLIERIESGLL SYGNDMDNGDNPFECGFDKFINLDADINFLGKEKLKKIKAEGIKKKLVGVKFDIKEISLSKSIDLKDESSNIIGELRSAC YSPHFGKVIGIAMIKKPYCEVSQIVKAEIIIFNVKKKK and exactly the same sequence is there in my database: >JCVI_PEP_1105095073661 LLNQESFRATPYTSRIEKQGVTAYTVYNHMLLPAAFGSLEESYHHLKKNVQIWDVAGERQVEISGKDSSKLVQLMTCRDLSKSKDGRCYYCPILDDEAGIINDPIVLRINENKWWISIADSDVILFAKGLAIGNKFEVKILEPNVDIMAVQGPKSFGLMEKVFGKKITELKFFDFDYFDFEGAKHLIAKSGWSKQGGYEIYVENIESGLKLYDRLFEIGKEFYIRPGCPNLIERIESGLLSYGNDMDNGDNPFECGFDKFINLDADINFLGKEKLKKIKAEGIKKKLVGVKFDIKEISLSKSIDLKDESSNIIGELRSACYSPHFGKVIGIAMIKKPYCEVSQIVKAEIIIFNVKKKK But the blast report that i am getting does not give me 100% identity, there is some region thats not aligned (though) its exactly the same. portion of a blast report: Score = 665 bits (1716), Expect = 0.0, Method: Compositional matrix adjust. Identities = 341/358 (95%), Positives = 341/358 (95%) Query: 1 LLNQESFRATPYTSRIEKQGVTAYTVYNHMLLPAAFGSLEESYHHLKKNVQIWDVAGERQ 60 LLNQESFRATPYTSRIEKQGVTAYTVYNHMLLPAAFGSLEESYHHLKKNVQIWDVAGERQ Sbjct: 1 LLNQESFRATPYTSRIEKQGVTAYTVYNHMLLPAAFGSLEESYHHLKKNVQIWDVAGERQ 60 --------------------------- -------------------------- Query: 241 SYGNDMDNGDNPFECGFDKFINLDADINFXXXXXXXXXXXXXXXXXLVGVKFDIKEISLS 300 SYGNDMDNGDNPFECGFDKFINLDADINF LVGVKFDIKEISLS Sbjct: 241 SYGNDMDNGDNPFECGFDKFINLDADINFLGKEKLKKIKAEGIKKKLVGVKFDIKEISLS 300 Query: 301 KSIDLKDESSNIIGELRSACYSPHFGKVIGIAMIKKPYCEVSQIVKAEIIIFNVKKKK 358 KSIDLKDESSNIIGELRSACYSPHFGKVIGIAMIKKPYCEVSQIVKAEIIIFNVKKKK Sbjct: 301 KSIDLKDESSNIIGELRSACYSPHFGKVIGIAMIKKPYCEVSQIVKAEIIIFNVKKKK 358 I would really appreciate if anyone can help me out. Thanks Shalabh From David.Messina at sbc.su.se Mon Oct 5 17:09:05 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Mon, 5 Oct 2009 23:09:05 +0200 Subject: [Bioperl-l] Blast problem In-Reply-To: <9fcc48c70910051338x546673dej5027add2a71ca7fa@mail.gmail.com> References: <9fcc48c70910051338x546673dej5027add2a71ca7fa@mail.gmail.com> Message-ID: <628aabb70910051409k169dd87dl635ce3569bae1c6a@mail.gmail.com> Hi Shalabh, It's a low-complexity region that's being ignored (X'd out) due to the compositional matrix adjustment that's on by default. Dave From jason at bioperl.org Mon Oct 5 18:16:50 2009 From: jason at bioperl.org (Jason Stajich) Date: Mon, 5 Oct 2009 15:16:50 -0700 Subject: [Bioperl-l] handling nexus files In-Reply-To: References: Message-ID: you can manipulate the alignments to do this - so see what you can do with Bio::Align objects like Bio::SimpleAlign which is what you get when parsing with Bio::AlignIO. The concatenation problem basically requires concatenating the data in the sequence objects. Here is really basic solution - you'd want to add some error checking in there for consistency of data, all IDs present in all files, etc. http://gist.github.com/202528 use Bio::AlignIO; use Bio::SimpleAlign; use strict; my %seqs; for my $file ( @ARGV ) { my $in = Bio::AlignIO->new(-format=> 'nexus', -file => $file); if ( my $aln = $in->next_aln ) { for my $seq ( $aln->each_seq ) { $seqs{$seq->display_id} .= $seq->seq; } } } my $newaln = Bio::SimpleAlign->new; for my $id ( keys %seqs ) { $newaln->add_seq(Bio::LocatableSeq->new(-id=> $id,-seq=>$seqs{$id})); } my $out = Bio::AlignIO->new(-format => 'nexus'); $out->write_aln($newaln); -jason On Oct 5, 2009, at 11:35 AM, Denzel Li wrote: > Hello all: > Does bioperl support functions for handling nexus files? More > specifically, > I need two functions, 1) combine multiple nexus files into one, 2) > split a > nexus files into multiple nexus files. For example, > given the following two files (file1.nex, file2.nex), is there > function to > combine them into one file as shown in "combinedFile.nex", or to split > "combinedFile.nex" into two files (file1.nex, file2.nex). > > ------------------------------ > # file1.nex > begin data; > dimensions ntax=2 nchar=3 > b1 GGG > b2 GGT > ;end; > --------------------------------- > # file2.nex > begin data; > dimensions ntax=2 nchar=3 > b1 AAA > b2 AAT > ;end; > ------------------------------- > > # combinedFile.nex > begin data; > dimensions ntax=2 nchar=6 > [alignment from file1.nex] > b1 GGG > b2 GGT > [alignment from file2.nex] > b1 AAA > b2 AAT > ;end; > > begin sets; > charset a1=1-3; > charset a2=4-6; > end; > -------------------------------- > Any suggestion is highly appreciated. Thank you. > > Best, > Denzel > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich jason.stajich at gmail.com jason at bioperl.org From premkrishnanbv at gmail.com Mon Oct 5 04:13:36 2009 From: premkrishnanbv at gmail.com (Prem) Date: Mon, 5 Oct 2009 13:43:36 +0530 Subject: [Bioperl-l] BioPerl Installation Problem...Please help me... Message-ID: <9ad2e0730910050113o5cd417a5x9561d21cb3abb6fb@mail.gmail.com> Hello sir, I am Prem Krishnan, doing MSc. in Computational Biology. I am interested in Perl language and now I am started studying Bioperl. But I met with some problems during the installation. Details are given below, Using operating system :- *Windows XP 2 version* Perl Version :- *Active Perl 5.8.8.819* I started installation using GUI method. I followed the guidelines from the site http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows. The steps in that link includes the following, Installation using the Perl Package Manager GUI Installation 1) Start the Perl Package Manager GUI from the Start menu. 2) Go to Edit >> Preferences and click the Repositories tab. Add a new repository for each of the following (note the difference based on the perl version): Repositories to add *Name * *perl 5.8 * *perl 5.10 * BioPerl-Regular Releases http://bioperl.org/DIST http://bioperl.org/DIST BioPerl-Release Candidates http://bioperl.org/DIST/RC http://bioperl.org/DIST/RC Kobes http://theoryx5.uwinnipeg.ca/ppms http://cpan.uwinnipeg.ca/PPMPackages/10xx/ Bribes http://www.Bribes.org/perl/ppm http://www.Bribes.org/perl/ppm tcool http://ppm.tcool.org/archives/ NA 3) Select View >> All Packages. 4) In the search box type bioperl. 5) Right click the latest version of Bioperl available and choose install. (Note for users of previous Bioperl releases: you should not have to use the Bundle-BioPerl package anymore.) 5a) From bioperl 1.5.2 onward, all 'optional' pre-requisites will be marked for installation. If you see that some of them complain about needing a command-line installation (eg. XML::SAX::ExpatXS), and you want those particular pre-requisites, stop now (skip step 6) and see the 'Command-line Installation' section. 6) Click the green arrow (Run marked actions) to complete the installation. *I had completed the first ?Three? steps*. But when I tried to execute the*fourth step * I couldn?t find any *bioperl packages*. What I can I do to make my installation successful? Please help me. I think the information explained above is enough for you to understand my problem. Thanks in advance? Prem krishnan There can be miracles if you believe in you... http://www.google.com/profiles/premkrishnanbv From cswmao at yahoo.com Sun Oct 4 11:43:13 2009 From: cswmao at yahoo.com (Dr. W Mao) Date: Sun, 4 Oct 2009 08:43:13 -0700 (PDT) Subject: [Bioperl-l] Questions on installing Bioperl Message-ID: <45535.57274.qm@web57410.mail.re1.yahoo.com> Hello, ?? I tried to use the >perl Build.PL to install it and I got the fllowing message. I can't run >./Build test. Could you please tell me waht's going on here? Thanks. ? ? Checking whether your kit is complete... Looks good Checking prerequisites... ?- ERROR: IO::String is not installed CPAN: File::HomeDir loaded ok (v0.86) (I think you ran Build.PL directly, so will use CPAN to install prerequisites on demand) CPAN: Storable loaded ok (v2.15) Going to read '/root/.cpan/Metadata' ? Database was generated on Sun, 04 Oct 2009 11:27:07 GMT Running install for module 'IO::String' Running make for G/GA/GAAS/IO-String-1.08.tar.gz CPAN: LWP::UserAgent loaded ok (v2.033) CPAN: Time::HiRes loaded ok (v1.9715) Warning: no success downloading '/root/.cpan/sources/authors/id/G/GA/GAAS/IO-String-1.08.tar.gz.tmp28623'. Giving up on it. at /usr/lib/perl5/5.8.8/CPAN/FTP.pm line 837 ??????? CPAN::FTP::hostdlhard('CPAN::FTP', 'ARRAY(0x76f0030)', 'authors/id/G/GA/GAAS/IO-String-1.08.tar.gz', '/root/.cpan/sources/authors/id/G/GA/GAAS/IO-String-1.08.tar.g...', 'HASH(0xdaa5a10)') called at /usr/lib/perl5/5.8.8/CPAN/FTP.pm line 515 ??????? CPAN::FTP::hostdlxxx('CPAN::FTP', 'dlhard', 'undef', 'ARRAY(0x76f0030)', 'authors/id/G/GA/GAAS/IO-String-1.08.tar.gz', '/root/.cpan/sources/authors/id/G/GA/GAAS/IO-String-1.08.tar.g...', 'HASH(0xdaa5a10)') called at /usr/lib/perl5/5.8.8/CPAN/FTP.pm line 442 ??????? CPAN::FTP::localize('CPAN::FTP', 'authors/id/G/GA/GAAS/IO-String-1.08.tar.gz', '/root/.cpan/sources/authors/id/G/GA/GAAS/IO-String-1.08.tar.gz') called at /usr/lib/perl5/5.8.8/CPAN/Distribution.pm line 379 ??????? CPAN::Distribution::get_file_onto_local_disk('CPAN::Distribution=HASH(0xd65ddb0)') called at /usr/lib/perl5/5.8.8/CPAN/Distribution.pm line 343 ??????? CPAN::Distribution::get('CPAN::Distribution=HASH(0xd65ddb0)') called at /usr/lib/perl5/5.8.8/CPAN/Distribution.pm line 1677 ??????? CPAN::Distribution::make('CPAN::Distribution=HASH(0xd65ddb0)') called at /usr/lib/perl5/5.8.8/CPAN/Distribution.pm line 2876 ??????? CPAN::Distribution::test('CPAN::Distribution=HASH(0xd65ddb0)') called at /usr/lib/perl5/5.8.8/CPAN/Distribution.pm line 3266 ??????? CPAN::Distribution::install('CPAN::Distribution=HASH(0xd65ddb0)') called at /usr/lib/perl5/5.8.8/CPAN/Module.pm line 474 ??????? eval {...} called at /usr/lib/perl5/5.8.8/CPAN/Module.pm line 473 ??????? CPAN::Module::rematein('CPAN::Module=HASH(0xb5e0af0)', 'install') called at /usr/lib/perl5/5.8.8/CPAN/Module.pm line 576 ??????? CPAN::Module::install('CPAN::Module=HASH(0xb5e0af0)') called at /usr/lib/perl5/5.8.8/CPAN/Shell.pm line 1755 ??????? CPAN::Shell::rematein('CPAN::Shell', 'install', 'IO::String') called at /usr/lib/perl5/5.8.8/CPAN/Shell.pm line 1935 ??????? CPAN::Shell::__ANON__('CPAN::Shell', 'IO::String') called at Bio/Root/Build.pm line 449 ??????? Bio::Root::Build::install_prereq('Bio::Root::Build=HASH(0x7104900)', 'IO::String', 0) called at Bio/Root/Build.pm line 473 ??????? Bio::Root::Build::install_required('Bio::Root::Build=HASH(0x7104900)', 'IO::String', 0, 'IO::String is not installed') called at Bio/Root/Build.pm line 414 ??????? Bio::Root::Build::prereq_failures('Bio::Root::Build=HASH(0x7104900)', 'HASH(0x6e02b40)') called at /usr/lib/perl5/site_perl/5.8.8/Module/Build/Base.pm line 1270 ??????? Module::Build::Base::check_prereq('Bio::Root::Build=HASH(0x7104900)') called at /usr/lib/perl5/site_perl/5.8.8/Module/Build/Base.pm line 39 ??????? Module::Build::Base::new('Bio::Root::Build', 'module_name', 'Bio', 'dist_name', 'BioPerl', 'dist_version_from', 'Bio/Root/Version.pm', 'dist_author', 'BioPerl Team ', ...) called at Build.PL line 21 You have not configured a urllist and do not allow connections to the internet to get a list of mirrors.? If you wish to get a list of CPAN mirrors to pick from, use this command ??? o conf init connect_to_internet_ok urllist If you do not wish to get a list of mirrors and would prefer to set your urllist manually, use just this command instead ??? o conf init urllist From cjfields at illinois.edu Wed Oct 7 08:57:07 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Oct 2009 07:57:07 -0500 Subject: [Bioperl-l] BioPerl Installation Problem...Please help me... In-Reply-To: <9ad2e0730910050113o5cd417a5x9561d21cb3abb6fb@mail.gmail.com> References: <9ad2e0730910050113o5cd417a5x9561d21cb3abb6fb@mail.gmail.com> Message-ID: The PPM hasn't been updated for Windows as of yet. I would assume if you use the specified version of ActivePerl it should work still, but only for 1.5.2. I am working on getting a PPM working for 1.6.1 (it was supposed to be posted last week) but have been flooded with other work, though it isn't off my agenda, just pushed back on the priority list a wee bit, until I can get a few other things going. chris On Oct 5, 2009, at 3:13 AM, Prem wrote: > Hello sir, > > > > I am Prem Krishnan, doing MSc. in Computational Biology. > > I am interested in Perl language and now I am started studying > Bioperl. > > But I met with some problems during the installation. > > > > Details are given below, > > > > Using operating system :- *Windows XP 2 version* > > Perl Version :- *Active Perl 5.8.8.819* > > > > I started installation using GUI method. > > I followed the guidelines from the site > http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows. > > > The steps in that link includes the following, > Installation using the Perl Package Manager GUI Installation > > 1) Start the Perl Package Manager GUI from the Start menu. > > 2) Go to Edit >> Preferences and click the Repositories tab. Add a new > repository for each of the following (note the difference based on > the perl > version): > > Repositories to add > > *Name * > > *perl 5.8 * > > *perl 5.10 * > > BioPerl-Regular Releases > > http://bioperl.org/DIST > > http://bioperl.org/DIST > > BioPerl-Release Candidates > > http://bioperl.org/DIST/RC > > http://bioperl.org/DIST/RC > > Kobes > > http://theoryx5.uwinnipeg.ca/ppms > > http://cpan.uwinnipeg.ca/PPMPackages/10xx/ > > Bribes > > http://www.Bribes.org/perl/ppm > > http://www.Bribes.org/perl/ppm > > tcool > > http://ppm.tcool.org/archives/ > > NA > > 3) Select View >> All Packages. > > 4) In the search box type bioperl. > > 5) Right click the latest version of Bioperl available and choose > install. > (Note for users of previous Bioperl releases: you should not have to > use the > Bundle-BioPerl package anymore.) > > 5a) From bioperl 1.5.2 onward, all 'optional' pre-requisites will be > marked > for installation. If you see that some of them complain about > needing a > command-line installation (eg. XML::SAX::ExpatXS), and you want those > particular pre-requisites, stop now (skip step 6) and see the > 'Command-line > Installation' section. > > 6) Click the green arrow (Run marked actions) to complete the > installation. > > > > *I had completed the first ?Three? steps*. But when I tried to execute > the*fourth step > * I couldn?t find any *bioperl packages*. > > > > What I can I do to make my installation successful? Please help me. > > I think the information explained above is enough for you to > understand my > problem. > > Thanks in advance? > > > Prem krishnan > There can be miracles if you believe in you... > http://www.google.com/profiles/premkrishnanbv > > _______________________________________________ > 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 Oct 7 09:00:12 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Oct 2009 08:00:12 -0500 Subject: [Bioperl-l] Questions on installing Bioperl In-Reply-To: <45535.57274.qm@web57410.mail.re1.yahoo.com> References: <45535.57274.qm@web57410.mail.re1.yahoo.com> Message-ID: The last two paragraphs from the CPAN error indicate the problem, namely you need to configure the urllist parameter (it's not a bioperl problem). The instructions there are pretty explicit: > You have not configured a urllist and do not allow connections to the > internet to get a list of mirrors. If you wish to get a list of CPAN > mirrors to pick from, use this command > o conf init connect_to_internet_ok urllist > If you do not wish to get a list of mirrors and would prefer to set > your urllist manually, use just this command instead > o conf init urllist chris On Oct 4, 2009, at 10:43 AM, Dr. W Mao wrote: > Hello, > I tried to use the >perl Build.PL to install it and I got the > fllowing message. I can't run >./Build test. Could you please tell > me waht's going on here? Thanks. > > > > > Checking whether your kit is complete... > Looks good > Checking prerequisites... > - ERROR: IO::String is not installed > CPAN: File::HomeDir loaded ok (v0.86) > (I think you ran Build.PL directly, so will use CPAN to install > prerequisites on demand) > CPAN: Storable loaded ok (v2.15) > Going to read '/root/.cpan/Metadata' > Database was generated on Sun, 04 Oct 2009 11:27:07 GMT > Running install for module 'IO::String' > Running make for G/GA/GAAS/IO-String-1.08.tar.gz > CPAN: LWP::UserAgent loaded ok (v2.033) > CPAN: Time::HiRes loaded ok (v1.9715) > Warning: no success downloading '/root/.cpan/sources/authors/id/G/GA/ > GAAS/IO-String-1.08.tar.gz.tmp28623'. Giving up on it. at /usr/lib/ > perl5/5.8.8/CPAN/FTP.pm line 837 > CPAN::FTP::hostdlhard('CPAN::FTP', 'ARRAY(0x76f0030)', > 'authors/id/G/GA/GAAS/IO-String-1.08.tar.gz', '/root/.cpan/sources/ > authors/id/G/GA/GAAS/IO-String-1.08.tar.g...', 'HASH(0xdaa5a10)') > called at /usr/lib/perl5/5.8.8/CPAN/FTP.pm line 515 > CPAN::FTP::hostdlxxx('CPAN::FTP', 'dlhard', 'undef', 'ARRAY > (0x76f0030)', 'authors/id/G/GA/GAAS/IO-String-1.08.tar.gz', '/ > root/.cpan/sources/authors/id/G/GA/GAAS/IO-String-1.08.tar.g...', > 'HASH(0xdaa5a10)') called at /usr/lib/perl5/5.8.8/CPAN/FTP.pm line 442 > CPAN::FTP::localize('CPAN::FTP', 'authors/id/G/GA/GAAS/IO- > String-1.08.tar.gz', '/root/.cpan/sources/authors/id/G/GA/GAAS/IO- > String-1.08.tar.gz') called at /usr/lib/perl5/5.8.8/CPAN/ > Distribution.pm line 379 > CPAN::Distribution::get_file_onto_local_disk > ('CPAN::Distribution=HASH(0xd65ddb0)') called at /usr/lib/ > perl5/5.8.8/CPAN/Distribution.pm line 343 > CPAN::Distribution::get('CPAN::Distribution=HASH > (0xd65ddb0)') called at /usr/lib/perl5/5.8.8/CPAN/Distribution.pm > line 1677 > CPAN::Distribution::make('CPAN::Distribution=HASH > (0xd65ddb0)') called at /usr/lib/perl5/5.8.8/CPAN/Distribution.pm > line 2876 > CPAN::Distribution::test('CPAN::Distribution=HASH > (0xd65ddb0)') called at /usr/lib/perl5/5.8.8/CPAN/Distribution.pm > line 3266 > CPAN::Distribution::install('CPAN::Distribution=HASH > (0xd65ddb0)') called at /usr/lib/perl5/5.8.8/CPAN/Module.pm line 474 > eval {...} called at /usr/lib/perl5/5.8.8/CPAN/Module.pm > line 473 > CPAN::Module::rematein('CPAN::Module=HASH(0xb5e0af0)', > 'install') called at /usr/lib/perl5/5.8.8/CPAN/Module.pm line 576 > CPAN::Module::install('CPAN::Module=HASH(0xb5e0af0)') called > at /usr/lib/perl5/5.8.8/CPAN/Shell.pm line 1755 > CPAN::Shell::rematein('CPAN::Shell', 'install', > 'IO::String') called at /usr/lib/perl5/5.8.8/CPAN/Shell.pm line 1935 > CPAN::Shell::__ANON__('CPAN::Shell', 'IO::String') called at > Bio/Root/Build.pm line 449 > Bio::Root::Build::install_prereq('Bio::Root::Build=HASH > (0x7104900)', 'IO::String', 0) called at Bio/Root/Build.pm line 473 > Bio::Root::Build::install_required('Bio::Root::Build=HASH > (0x7104900)', 'IO::String', 0, 'IO::String is not installed') called > at Bio/Root/Build.pm line 414 > Bio::Root::Build::prereq_failures('Bio::Root::Build=HASH > (0x7104900)', 'HASH(0x6e02b40)') called at /usr/lib/perl5/site_perl/ > 5.8.8/Module/Build/Base.pm line 1270 > Module::Build::Base::check_prereq('Bio::Root::Build=HASH > (0x7104900)') called at /usr/lib/perl5/site_perl/5.8.8/Module/Build/ > Base.pm line 39 > Module::Build::Base::new('Bio::Root::Build', 'module_name', > 'Bio', 'dist_name', 'BioPerl', 'dist_version_from', 'Bio/Root/ > Version.pm', 'dist_author', 'BioPerl Team l at bioperl.org>', ...) called at Build.PL line 21 > > You have not configured a urllist and do not allow connections to the > internet to get a list of mirrors. If you wish to get a list of CPAN > mirrors to pick from, use this command > o conf init connect_to_internet_ok urllist > If you do not wish to get a list of mirrors and would prefer to set > your urllist manually, use just this command instead > o conf init urllist > > > > _______________________________________________ > 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 Oct 7 09:21:40 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Oct 2009 08:21:40 -0500 Subject: [Bioperl-l] BioPerl Installation Problem...Please help me... In-Reply-To: References: <9ad2e0730910050113o5cd417a5x9561d21cb3abb6fb@mail.gmail.com> Message-ID: <2A754550-BF61-4D65-9E50-E0FE3604FC68@illinois.edu> That was a bit of a run-on. Shows I need my coffee... chris On Oct 7, 2009, at 7:57 AM, Chris Fields wrote: > The PPM hasn't been updated for Windows as of yet. I would assume > if you use the specified version of ActivePerl it should work still, > but only for 1.5.2. > > I am working on getting a PPM working for 1.6.1 (it was supposed to > be posted last week) but have been flooded with other work, though > it isn't off my agenda, just pushed back on the priority list a wee > bit, until I can get a few other things going. > > chris > > On Oct 5, 2009, at 3:13 AM, Prem wrote: > >> Hello sir, >> >> >> >> I am Prem Krishnan, doing MSc. in Computational Biology. >> >> I am interested in Perl language and now I am started studying >> Bioperl. >> >> But I met with some problems during the installation. >> >> >> >> Details are given below, >> >> >> >> Using operating system :- *Windows XP 2 version* >> >> Perl Version :- *Active Perl 5.8.8.819* >> >> >> >> I started installation using GUI method. >> >> I followed the guidelines from the site >> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows. >> >> >> The steps in that link includes the following, >> Installation using the Perl Package Manager GUI Installation >> >> 1) Start the Perl Package Manager GUI from the Start menu. >> >> 2) Go to Edit >> Preferences and click the Repositories tab. Add a >> new >> repository for each of the following (note the difference based on >> the perl >> version): >> >> Repositories to add >> >> *Name * >> >> *perl 5.8 * >> >> *perl 5.10 * >> >> BioPerl-Regular Releases >> >> http://bioperl.org/DIST >> >> http://bioperl.org/DIST >> >> BioPerl-Release Candidates >> >> http://bioperl.org/DIST/RC >> >> http://bioperl.org/DIST/RC >> >> Kobes >> >> http://theoryx5.uwinnipeg.ca/ppms >> >> http://cpan.uwinnipeg.ca/PPMPackages/10xx/ >> >> Bribes >> >> http://www.Bribes.org/perl/ppm >> >> http://www.Bribes.org/perl/ppm >> >> tcool >> >> http://ppm.tcool.org/archives/ >> >> NA >> >> 3) Select View >> All Packages. >> >> 4) In the search box type bioperl. >> >> 5) Right click the latest version of Bioperl available and choose >> install. >> (Note for users of previous Bioperl releases: you should not have >> to use the >> Bundle-BioPerl package anymore.) >> >> 5a) From bioperl 1.5.2 onward, all 'optional' pre-requisites will >> be marked >> for installation. If you see that some of them complain about >> needing a >> command-line installation (eg. XML::SAX::ExpatXS), and you want those >> particular pre-requisites, stop now (skip step 6) and see the >> 'Command-line >> Installation' section. >> >> 6) Click the green arrow (Run marked actions) to complete the >> installation. >> >> >> >> *I had completed the first ?Three? steps*. But when I tried to >> execute >> the*fourth step >> * I couldn?t find any *bioperl packages*. >> >> >> >> What I can I do to make my installation successful? Please help me. >> >> I think the information explained above is enough for you to >> understand my >> problem. >> >> Thanks in advance? >> >> >> Prem krishnan >> There can be miracles if you believe in you... >> http://www.google.com/profiles/premkrishnanbv >> >> _______________________________________________ >> 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 Oct 7 10:09:11 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Oct 2009 09:09:11 -0500 Subject: [Bioperl-l] Long /labels are wrapped, but can't be read In-Reply-To: <87vdj0g3rn.fsf@topper.koldfront.dk> References: <87hbunv764.fsf@topper.koldfront.dk> <86373CE8-4C61-4124-BCF3-35975523CC9C@illinois.edu> <87vdj0g3rn.fsf@topper.koldfront.dk> Message-ID: On Sep 30, 2009, at 4:50 AM, Adam Sj?gren wrote: > On Tue, 29 Sep 2009 22:54:04 -0500, Chris wrote: > >> Not sure, but this could be a case of 'both'. Labels that are quoted >> and aren't are currently distinguished via a global hash lookup >> (%FTQUAL_NO_QUOTE) due to the way the parser works; there is some >> logic behind this, just can't quite recall at the moment why it is >> this way. > > Yes, I saw that there is a number of qualifiers that aren't quoted > automatically. > > The very easy "fix" for me would be to simply remove "label" from > %FTQUAL_NO_QUOTE, but I'm not really sure what the reason for not > quoting all values is, so I was hesitant to just propose that. It's basically for more control over format IIRC. It appears to only play a role in output (via write_seq). >> You could set a hash key for the label in cases where it isn't >> quoted, >> that should work. You can also test out the Bio::SeqIO::embldriver >> version (-format => 'embldriver'). > > Ah, embldriver reads the wrapped qualifier when it isn't quoted > without > problem. Nice! I hadn't noticed embldriver. > > I wonder which one is correct in this case? > > And should I switch to using embldriver to read, or does it make sense > to try and concoct a patch that changes embl? Bio::SeqIO::embldriver is an attempt to coalesce the parsers into a generic driver/parser-handler framework; the various parsers (the drivers) would parse data into simple chunks, basically hash refs of data. These would be passed on to the handler object, which has methods designed to handle the chunks passed in. Basically it's like a souped-up XML parser, but the data is grouped together in a related, meaningful way (like an entire seqfeature, for instance). The main job of the driver is simply to parse the incoming data stream into chunks of naturally related data (think XML, but larger chunks of data, like an entire seqfeature) and pass it on to the handler object. For the moment they're still experimental, but I put them out with the release so they can be tested. The current problem with them at the moment is there is no specification on how a data chunk is defined and labeled, but I am thinking of using something like JSON for that. > Thanks for the feedback! > > Adam > > -- > Adam Sj?gren > adsj at novozymes.com np. chris From rmb32 at cornell.edu Wed Oct 7 14:03:19 2009 From: rmb32 at cornell.edu (Robert Buels) Date: Wed, 07 Oct 2009 11:03:19 -0700 Subject: [Bioperl-l] BioPerl Installation Problem...Please help me... In-Reply-To: <2A754550-BF61-4D65-9E50-E0FE3604FC68@illinois.edu> References: <9ad2e0730910050113o5cd417a5x9561d21cb3abb6fb@mail.gmail.com> <2A754550-BF61-4D65-9E50-E0FE3604FC68@illinois.edu> Message-ID: <4ACCD7E7.4000304@cornell.edu> Chris Fields wrote: > That was a bit of a run-on. Shows I need my coffee... > > chris I think that would probably just make it worse. From cjfields at illinois.edu Wed Oct 7 15:07:29 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Oct 2009 14:07:29 -0500 Subject: [Bioperl-l] BioPerl Installation Problem...Please help me... In-Reply-To: <4ACCD7E7.4000304@cornell.edu> References: <9ad2e0730910050113o5cd417a5x9561d21cb3abb6fb@mail.gmail.com> <2A754550-BF61-4D65-9E50-E0FE3604FC68@illinois.edu> <4ACCD7E7.4000304@cornell.edu> Message-ID: Nope, that fixed it up. Now just too jittery to code... chris On Oct 7, 2009, at 1:03 PM, Robert Buels wrote: > Chris Fields wrote: >> That was a bit of a run-on. Shows I need my coffee... >> chris > > I think that would probably just make it worse. > > From jonathanmflowers at gmail.com Wed Oct 7 18:13:46 2009 From: jonathanmflowers at gmail.com (Jonathan Flowers) Date: Wed, 7 Oct 2009 18:13:46 -0400 Subject: [Bioperl-l] Bio::SeqFeature::Generic unexpected behavior Message-ID: Hi, I am building Bio::SeqFeature::Gene::Transcript objects to facilitate easy parsing of cds and intron sequences. I ran across an unexpected problem when creating two or more Transcript objects and attaching independent Bio::Seq objects to them. In the following code, 2 transcript objects are constructed independently (not cloned). However, extracting the cds for one transcript gives an errant (and unexpected result). Curiously, extracting the introns from the same transcript objects gives the correct result. I have highlighted the unexpected outcome below. Finally, I noticed that reversing the order of the attach_seq commands determines which cds is printed. The following example illustrates the problem. Can someone explain this? Jonathan #! usr/bin/env perl use strict; use warnings; use Bio::FeatureIO::gff; use Bio::SeqFeature::Annotated; use Bio::SeqFeature::Gene::Transcript; use Bio::SeqFeature::Gene::Exon; #use Bio::SeqFeature::Gene::UTR; #use Bio::SeqFeature::Gene::Intron; #Build the objects... my $seq1 = Bio::Seq->new(-seq => 'AAAAA'); my $seq2 = Bio::Seq->new(-seq => 'TTTTT'); my $tscript1 = Bio::SeqFeature::Gene::Transcript->new(-start => 1, -end => 5, -strand => +1); my $tscript2 = Bio::SeqFeature::Gene::Transcript->new(-start => 1, -end => 5, -strand => +1); my $exon1 = Bio::SeqFeature::Gene::Exon->new(-start => 1 , -end => 2, -strand => +1); my $exon2 = Bio::SeqFeature::Gene::Exon->new(-start => 4 , -end => 5, -strand => +1); $tscript1->add_exon($exon1); $tscript1->add_exon($exon2); $tscript2->add_exon($exon1); $tscript2->add_exon($exon2); $tscript1->attach_seq($seq1); $tscript2->attach_seq($seq2); #now extract the desired features and print print $tscript1->cds->seq,"\n"; #prints 'TTTT' <- unexpected !!! print $tscript2->cds->seq,"\n"; #prints 'TTTT' <- as expected foreach($tscript1->introns){ print $_->seq->seq,"\n"; #prints 'A' <- as expected } foreach($tscript2->introns){ print $_->seq->seq,"\n"; #prints 'T' <- as expected } From cjfields at illinois.edu Wed Oct 7 23:52:12 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Oct 2009 22:52:12 -0500 Subject: [Bioperl-l] Bio::SeqFeature::Generic unexpected behavior In-Reply-To: References: Message-ID: On Oct 7, 2009, at 5:13 PM, Jonathan Flowers wrote: > Hi, > > I am building Bio::SeqFeature::Gene::Transcript objects to > facilitate easy > parsing of cds and intron sequences. I ran across an unexpected > problem > when creating two or more Transcript objects and attaching independent > Bio::Seq objects to them. In the following code, 2 transcript > objects are > constructed independently (not cloned). However, extracting the cds > for one > transcript gives an errant (and unexpected result). Curiously, > extracting > the introns from the same transcript objects gives the correct > result. I > have highlighted the unexpected outcome below. Finally, I noticed > that > reversing the order of the attach_seq commands determines which cds is > printed. So, is this a problem with Bio::SeqFeature::Generic, or Bio::SeqFeature::Gene? Just a bit confused by the subject line. > The following example illustrates the problem. > > Can someone explain this? > > Jonathan > > #! usr/bin/env perl > use strict; > use warnings; > use Bio::FeatureIO::gff; > use Bio::SeqFeature::Annotated; > use Bio::SeqFeature::Gene::Transcript; > use Bio::SeqFeature::Gene::Exon; > #use Bio::SeqFeature::Gene::UTR; > #use Bio::SeqFeature::Gene::Intron; > > #Build the objects... > my $seq1 = Bio::Seq->new(-seq => 'AAAAA'); > my $seq2 = Bio::Seq->new(-seq => 'TTTTT'); > > my $tscript1 = Bio::SeqFeature::Gene::Transcript->new(-start => 1, - > end => > 5, -strand => +1); > my $tscript2 = Bio::SeqFeature::Gene::Transcript->new(-start => 1, - > end => > 5, -strand => +1); > > my $exon1 = Bio::SeqFeature::Gene::Exon->new(-start => 1 , -end => 2, > -strand => +1); > my $exon2 = Bio::SeqFeature::Gene::Exon->new(-start => 4 , -end => 5, > -strand => +1); > > $tscript1->add_exon($exon1); > $tscript1->add_exon($exon2); > > $tscript2->add_exon($exon1); > $tscript2->add_exon($exon2); > > $tscript1->attach_seq($seq1); > $tscript2->attach_seq($seq2); So, my guess is Bio::SF::Gene::Transcript is attaching the sequences to the contained exons (you are using the same two exon instances for both transcripts). I don't think this is a bug; you should create a different set of exons for the second transcript, not use the same exon instances for both. This behavior, to me, makes sense using the following logic: if two (or more) transcripts share the same exons (such as in alternatively spliced transcripts), underlying sequence changes should affect both transcripts and their shared exons. Otherwise they shouldn't share exons (i.e. require different instances). If you change the above to the following: my $exon3 = Bio::SeqFeature::Gene::Exon->new(-start => 1 , -end => 2, -strand => +1); my $exon4 = Bio::SeqFeature::Gene::Exon->new(-start => 4 , -end => 5, -strand => +1); $tscript2->add_exon($exon3); $tscript2->add_exon($exon4); it works; the first statement prints 'AAAA' and the second 'TTTT'. There is a subtle bug pointed with your example, though. The the two transcripts have two different sequences but the exons for both now point to the same sequence (your first transcript prints 'A', but everything else has T's). I don't think there is an easy workaround for that, unless there is a way to call the parent transcript feature from the exon features. > #now extract the desired features and print > print $tscript1->cds->seq,"\n"; #prints 'TTTT' <- unexpected !!! > print $tscript2->cds->seq,"\n"; #prints 'TTTT' <- as expected > > foreach($tscript1->introns){ > print $_->seq->seq,"\n"; #prints 'A' <- as expected > } > > foreach($tscript2->introns){ > print $_->seq->seq,"\n"; #prints 'T' <- as expected > } Hope that explanation helps! chris From ss2489 at cornell.edu Thu Oct 8 10:21:20 2009 From: ss2489 at cornell.edu (Surya Saha) Date: Thu, 8 Oct 2009 10:21:20 -0400 Subject: [Bioperl-l] Parsing PhyloGibbs output Message-ID: Hi Everybody, I could not find a class to parse output produced by PhyloGibbs v1.2 ( http://www.phylogibbs.unibas.ch/cgi-bin/phylogibbs.pl) in BioPerl. Am I missing something that is out there? Is anybody working on a parser for Phylogibbs? If not, I am writing a quick one for myself right now and might be interested to contribute it to bioperl at a later date. Thanks Cheers, Surya From deequan at gmail.com Thu Oct 8 17:31:19 2009 From: deequan at gmail.com (deequan) Date: Thu, 8 Oct 2009 14:31:19 -0700 (PDT) Subject: [Bioperl-l] handling multiple rid's in remoteblast Message-ID: <25811987.post@talk.nabble.com> Hello there, I am wondering is there is a function i missed that allows the used to combine the results from multiple rid's into one output file. I could be wrong, but it does not appear that the save_output method operates in a way that accomodates this. Thanks a lot! David Quan -- View this message in context: http://www.nabble.com/handling-multiple-rid%27s-in-remoteblast-tp25811987p25811987.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From cjfields at illinois.edu Thu Oct 8 18:50:55 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 8 Oct 2009 17:50:55 -0500 Subject: [Bioperl-l] handling multiple rid's in remoteblast In-Reply-To: <25811987.post@talk.nabble.com> References: <25811987.post@talk.nabble.com> Message-ID: <5C15FDF6-00CB-4537-A57A-ECE98CAF09C9@illinois.edu> David, The code looks like it just opens the file for write-only (no append). You could try passing in something like ">myfile.blast", which might work. chris On Oct 8, 2009, at 4:31 PM, deequan wrote: > > Hello there, > > I am wondering is there is a function i missed that allows the > used > to combine the results from multiple rid's into one output file. I > could be > wrong, but it does not appear that the save_output method operates > in a way > that accomodates this. Thanks a lot! > > David Quan > -- > View this message in context: http://www.nabble.com/handling-multiple-rid%27s-in-remoteblast-tp25811987p25811987.html > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From dan.kortschak at adelaide.edu.au Fri Oct 9 02:54:08 2009 From: dan.kortschak at adelaide.edu.au (Dan Kortschak) Date: Fri, 09 Oct 2009 17:24:08 +1030 Subject: [Bioperl-l] Bio::DB::EntrezGene or Bio::DB::Query::GenBank to obtain sequence metadata without sequence Message-ID: <1255071248.27558.9.camel@zoidberg.mbs.adelaide.edu.au> Hi, I am looking to query NCBI for sequence metadata (LOCUS/length, DEFINITION/name etc) without obtaining the sequence associated with the entry (pulling sequence data for chromosome when only the metadata is needed is a waste). I'm wondering what would be the most appropriate bioperl module to use - Bio::DB::EntrezGene or Bio::DB::Query::GenBank seem like the best bet and from the description the latter seems best, but I'm wondering if this is best and what database would both provide this data and be parsable. thanks for any help. Dan From djibrilo at yahoo.fr Fri Oct 9 09:19:49 2009 From: djibrilo at yahoo.fr (djibrilo) Date: Fri, 9 Oct 2009 13:19:49 +0000 (GMT) Subject: [Bioperl-l] Bug - Bio::Tools::Run::Alignment::Clustalw - patch Message-ID: <546592.43713.qm@web23004.mail.ird.yahoo.com> Dear, I have detected some problems on this module (Bio::Tools::Run::Alignment::Clustalw) when I use it from Windows. The executable crashed when there are some spaces on my path files because the system command crash on DOS. To resolv this problem, you have to add double quote in the module around -outfile and -infile values. That is a patch to resolv it. I have tested and it is work well on WinXP, Win2000, Vista with Perl 5.8. --- C:/Perl/site/lib/Bio/Tools/Run/Alignment/Clustalw.pm Fri Oct 9 15:02:04 2009 +++ C:/Perl/site/lib/Bio/Tools/Run/Alignment/Clustalw_new.pm Fri Oct 9 15:05:41 2009 @@ -592,7 +592,7 @@ $instring = "$infile1"; $command = ''; } else { - $instring = " -infile=$infile1"; + $instring = " -infile=". '"' . $infile1 . '"'; } $param_string .= " $infile2"; @@ -775,7 +775,8 @@ next unless (defined $value); my $attr_key = lc $attr; #put params in format expected by clustalw $attr_key = ' -'.$attr_key; - $param_string .= $attr_key.'='.$value; + $param_string .= $attr_key . '=' . '"' . $value . '"'; + #$param_string .= $attr_key.'='.$value; } for $attr ( @CLUSTALW_SWITCHES) { From maj at fortinbras.us Fri Oct 9 19:28:35 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Fri, 9 Oct 2009 19:28:35 -0400 Subject: [Bioperl-l] SQLite for BioPerl indexing Message-ID: Hi All, My AnyDBM_File hack to allow ActiveState a workaround for DB_File (see http://lists.open-bio.org/pipermail/bioperl-l/2009-September/031309.html) turned into a "BioPerl Autumn of Code" project. Bio::DB::SQLite_File is a nearly complete emulation of DB_File, down to the access functions (get(), put(), del(), seq()) and user-provided comparision functions. If you're interested, please see http://www.bioperl.org/wiki/HOWTO:SQLite_for_BioPerl_indexing for exhausting discussion and download. I would REALLY appreciate a core dev/power user or two checking out the anydbm-branch branch and performing a straight build sequence, and letting me know how it goes. See the wiki for those paths. Thanks-- MAJ From cjfields at illinois.edu Fri Oct 9 22:13:35 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 9 Oct 2009 21:13:35 -0500 Subject: [Bioperl-l] SQLite for BioPerl indexing In-Reply-To: References: Message-ID: I'll check it out, but it prob. won't be until Monday. chris On Oct 9, 2009, at 6:28 PM, Mark A. Jensen wrote: > Hi All, > > My AnyDBM_File hack to allow ActiveState a workaround > for DB_File (see http://lists.open-bio.org/pipermail/bioperl-l/2009-September/031309.html > ) > turned into a "BioPerl Autumn of Code" project. > Bio::DB::SQLite_File is a nearly complete emulation of DB_File, > down to the access functions (get(), put(), del(), seq()) and > user-provided comparision functions. > > If you're interested, please see > http://www.bioperl.org/wiki/HOWTO:SQLite_for_BioPerl_indexing > for exhausting discussion and download. I would REALLY > appreciate a core dev/power user or two checking out the > anydbm-branch branch and performing a straight build sequence, > and letting me know how it goes. See the wiki for those paths. > > Thanks-- > MAJ > > _______________________________________________ > 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 Oct 10 01:24:37 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 10 Oct 2009 00:24:37 -0500 Subject: [Bioperl-l] BioPerl Core 1.6.1 PPM now available Message-ID: The first cut at the ActivePerl PPM distribution for BioPerl core 1.6.1 is now available. Instructions for installing on Windows are here: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows I have made this installation architecture-independent, but it has only been testing on WinXP using ActivePerl 5.10.1.1006. A couple of modules may give warnings (specifically SOAP::Lite and XML::SAX::Writer), but the installation should proceed. We would appreciate feedback on trying to install this with other versions of ActivePerl or on more recent versions of Windows (Vista, Win7). Enjoy! chris From maj at fortinbras.us Sat Oct 10 17:15:08 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 10 Oct 2009 17:15:08 -0400 Subject: [Bioperl-l] BioPerl Core 1.6.1 PPM now available In-Reply-To: References: Message-ID: Hey Chris- I'm trying this out from the ppm-shell. I see that bioperl-1.4 is considered a dependency and is loaded and installed. Not sure yet what happens to it, seems strange. I'm using repos activestate, trouchelle58, and uwinnipeg58. More as this develops. MAJ ----- Original Message ----- From: "Chris Fields" To: "BioPerl List" Sent: Saturday, October 10, 2009 1:24 AM Subject: [Bioperl-l] BioPerl Core 1.6.1 PPM now available > The first cut at the ActivePerl PPM distribution for BioPerl core 1.6.1 is > now available. Instructions for installing on Windows are here: > > http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows > > I have made this installation architecture-independent, but it has only been > testing on WinXP using ActivePerl 5.10.1.1006. A couple of modules may give > warnings (specifically SOAP::Lite and XML::SAX::Writer), but the installation > should proceed. We would appreciate feedback on trying to install this with > other versions of ActivePerl or on more recent versions of Windows (Vista, > Win7). > > Enjoy! > > chris > _______________________________________________ > 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 Oct 10 17:16:39 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 10 Oct 2009 17:16:39 -0400 Subject: [Bioperl-l] BioPerl Core 1.6.1 PPM now available In-Reply-To: References: Message-ID: <71132A02730F4CF88E5857EB53BDB9A7@NewLife> (P.S. - my current worry is that Bio::ASN1::EntrezGene is enforcing bioperl-1.4 dependency) ----- Original Message ----- From: "Chris Fields" To: "BioPerl List" Sent: Saturday, October 10, 2009 1:24 AM Subject: [Bioperl-l] BioPerl Core 1.6.1 PPM now available > The first cut at the ActivePerl PPM distribution for BioPerl core 1.6.1 is > now available. Instructions for installing on Windows are here: > > http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows > > I have made this installation architecture-independent, but it has only been > testing on WinXP using ActivePerl 5.10.1.1006. A couple of modules may give > warnings (specifically SOAP::Lite and XML::SAX::Writer), but the installation > should proceed. We would appreciate feedback on trying to install this with > other versions of ActivePerl or on more recent versions of Windows (Vista, > Win7). > > Enjoy! > > chris > _______________________________________________ > 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 Oct 10 17:53:12 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 10 Oct 2009 17:53:12 -0400 Subject: [Bioperl-l] BioPerl Core 1.6.1 PPM now available In-Reply-To: References: Message-ID: More detail: The setup: To install BioPerl via ppm, we require the following in order to get a working DB_File for 5.8: (possibly required: C:> ppm install PPM-Repositories then... ) C:> ppm repo add http://bioperl.org/DIST C:> ppm repo add trouchelle58 We try C:> ppm install BioPerl (case is important -- not 'bioperl' eg), but this borks. When BioPerl is installed, Bundle-BioPerl-Core is subinstalled, bioperl-1.4 is installed. Pops back up to BioPerl 1.6.1 installation. HTML is generated, then "Updating files in site area." Here ppm borks when it tries to make a ppm backup for the first BioPerl module it finds, since the file it wants to make already exists. * theory: Bio::ASN1::EntrezGene (one of the deps installed by Bundle-BioPerl-Core) requires Bio::Index::EntrezGene, so obtains a provider that submits bioperl-1.4 The following procedure succeeds: Install Bundle-BioPerl-Core explicitly first: C:> ppm install Bundle-BioPerl-Core This succeeds, but now C:> perl -MBio::Perl -e "print $Bio::Perl::VERSION" 1.4 Now install BioPerl C:> ppm install BioPerl and we end up with C:> perl -MBio::Perl -e "print $Bio::Perl::VERSION" 1.006001 MAJ ----- Original Message ----- From: "Chris Fields" To: "BioPerl List" Sent: Saturday, October 10, 2009 1:24 AM Subject: [Bioperl-l] BioPerl Core 1.6.1 PPM now available > The first cut at the ActivePerl PPM distribution for BioPerl core > 1.6.1 is now available. Instructions for installing on Windows are > here: > > http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows > > I have made this installation architecture-independent, but it has > only been testing on WinXP using ActivePerl 5.10.1.1006. A couple of > modules may give warnings (specifically SOAP::Lite and > XML::SAX::Writer), but the installation should proceed. We would > appreciate feedback on trying to install this with other versions of > ActivePerl or on more recent versions of Windows (Vista, Win7). > > Enjoy! > > 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 Oct 10 18:45:16 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 10 Oct 2009 17:45:16 -0500 Subject: [Bioperl-l] BioPerl Core 1.6.1 PPM now available In-Reply-To: References: Message-ID: Mark, Definitely suboptimal. Are you using ActivePerl 5.8? (I used 5.10.1) I'm wondering if there are a few Bio::ASN1::EntrezGene out there floating around in other repos. The one in the bioperl PPM repo doesn't have that requirement. The only way I can think of to direct installation of the BioPerl PPM for Bio::ASN1::EntrezGene is to indicate the bioperl repo needs to be first in the repo list. chris On Oct 10, 2009, at 4:53 PM, Mark A. Jensen wrote: > More detail: > > The setup: > > To install BioPerl via ppm, we require the following in order to get > a working DB_File for 5.8: > > (possibly required: > C:> ppm install PPM-Repositories > then... > ) > > C:> ppm repo add http://bioperl.org/DIST > C:> ppm repo add trouchelle58 > > We try > > C:> ppm install BioPerl > > (case is important -- not 'bioperl' eg), but this borks. > > When BioPerl is installed, Bundle-BioPerl-Core is subinstalled, > bioperl-1.4 is installed. Pops back up to BioPerl 1.6.1 > installation. HTML is generated, then "Updating files in site area." > Here > ppm borks when it tries to make a ppm backup for the first BioPerl > module it finds, since the file it wants to make already exists. > > * theory: Bio::ASN1::EntrezGene (one of the deps installed by > Bundle-BioPerl-Core) requires Bio::Index::EntrezGene, so obtains a > provider that submits bioperl-1.4 > > The following procedure succeeds: > > Install Bundle-BioPerl-Core explicitly first: > > C:> ppm install Bundle-BioPerl-Core > > This succeeds, but now > > C:> perl -MBio::Perl -e "print $Bio::Perl::VERSION" > 1.4 > > Now install BioPerl > > C:> ppm install BioPerl > > and we end up with > > C:> perl -MBio::Perl -e "print $Bio::Perl::VERSION" > 1.006001 > > MAJ > ----- Original Message ----- From: "Chris Fields" > > To: "BioPerl List" > Sent: Saturday, October 10, 2009 1:24 AM > Subject: [Bioperl-l] BioPerl Core 1.6.1 PPM now available > > >> The first cut at the ActivePerl PPM distribution for BioPerl core >> 1.6.1 is now available. Instructions for installing on Windows >> are here: >> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows >> I have made this installation architecture-independent, but it has >> only been testing on WinXP using ActivePerl 5.10.1.1006. A couple >> of modules may give warnings (specifically SOAP::Lite and >> XML::SAX::Writer), but the installation should proceed. We would >> appreciate feedback on trying to install this with other versions >> of ActivePerl or on more recent versions of Windows (Vista, Win7). >> Enjoy! >> 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 maj at fortinbras.us Sat Oct 10 19:58:59 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 10 Oct 2009 19:58:59 -0400 Subject: [Bioperl-l] BioPerl Core 1.6.1 PPM now available In-Reply-To: References: Message-ID: <04EF23C5C4A44F4EB487794E6FC35EAD@NewLife> Yeah-- It is 5.8-- I'll try with 5.10. The Bio::ASN1::EntrezGene package contains the Bio::ASN1::EntrezGene::Indexer module, which has the bioperl dependency-- What I'm going for (for a class I'm teaching) is a ppm installation that will transparently include B::A::E, since we'll be doing some DB and EUtils stuff that I believe needs NCBIHelper. (Agggh...). I'm trying to make the install as painless as possible for the participants.... cheers ----- Original Message ----- From: "Chris Fields" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Saturday, October 10, 2009 6:45 PM Subject: Re: [Bioperl-l] BioPerl Core 1.6.1 PPM now available > Mark, > > Definitely suboptimal. Are you using ActivePerl 5.8? (I used 5.10.1) > > I'm wondering if there are a few Bio::ASN1::EntrezGene out there floating > around in other repos. The one in the bioperl PPM repo doesn't have that > requirement. The only way I can think of to direct installation of the > BioPerl PPM for Bio::ASN1::EntrezGene is to indicate the bioperl repo needs > to be first in the repo list. > > chris > > On Oct 10, 2009, at 4:53 PM, Mark A. Jensen wrote: > >> More detail: >> >> The setup: >> >> To install BioPerl via ppm, we require the following in order to get a >> working DB_File for 5.8: >> >> (possibly required: >> C:> ppm install PPM-Repositories >> then... >> ) >> >> C:> ppm repo add http://bioperl.org/DIST >> C:> ppm repo add trouchelle58 >> >> We try >> >> C:> ppm install BioPerl >> >> (case is important -- not 'bioperl' eg), but this borks. >> >> When BioPerl is installed, Bundle-BioPerl-Core is subinstalled, >> bioperl-1.4 is installed. Pops back up to BioPerl 1.6.1 installation. HTML >> is generated, then "Updating files in site area." Here >> ppm borks when it tries to make a ppm backup for the first BioPerl >> module it finds, since the file it wants to make already exists. >> >> * theory: Bio::ASN1::EntrezGene (one of the deps installed by >> Bundle-BioPerl-Core) requires Bio::Index::EntrezGene, so obtains a >> provider that submits bioperl-1.4 >> >> The following procedure succeeds: >> >> Install Bundle-BioPerl-Core explicitly first: >> >> C:> ppm install Bundle-BioPerl-Core >> >> This succeeds, but now >> >> C:> perl -MBio::Perl -e "print $Bio::Perl::VERSION" >> 1.4 >> >> Now install BioPerl >> >> C:> ppm install BioPerl >> >> and we end up with >> >> C:> perl -MBio::Perl -e "print $Bio::Perl::VERSION" >> 1.006001 >> >> MAJ >> ----- Original Message ----- From: "Chris Fields" > > >> To: "BioPerl List" >> Sent: Saturday, October 10, 2009 1:24 AM >> Subject: [Bioperl-l] BioPerl Core 1.6.1 PPM now available >> >> >>> The first cut at the ActivePerl PPM distribution for BioPerl core 1.6.1 is >>> now available. Instructions for installing on Windows are here: >>> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows >>> I have made this installation architecture-independent, but it has only >>> been testing on WinXP using ActivePerl 5.10.1.1006. A couple of modules >>> may give warnings (specifically SOAP::Lite and XML::SAX::Writer), but the >>> installation should proceed. We would appreciate feedback on trying to >>> install this with other versions of ActivePerl or on more recent versions >>> of Windows (Vista, Win7). >>> Enjoy! >>> 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 Russell.Smithies at agresearch.co.nz Sun Oct 11 15:46:59 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Mon, 12 Oct 2009 08:46:59 +1300 Subject: [Bioperl-l] Bio::DB::EntrezGene or Bio::DB::Query::GenBank to obtain sequence metadata without sequence In-Reply-To: <1255071248.27558.9.camel@zoidberg.mbs.adelaide.edu.au> References: <1255071248.27558.9.camel@zoidberg.mbs.adelaide.edu.au> Message-ID: <18DF7D20DFEC044098A1062202F5FFF32B62C8D40B@exchsth.agresearch.co.nz> I guess it depends on what you've got to start with, how many queries, and which species. For example, if you want metadata on all human genes, I'd probably do it "manually" from NCBI's website by searching the gene database for "human[orgn]", switching to "gene table" view, then save to file. It gives you an easily parsed text file with contents as below: ------------------------------------------ 1: TGFB1 transforming growth factor, beta 1 [ Homo sapiens ] GeneID: 7040 updated 07-Oct-2009 RefSeq status: REVIEWED total gene size: 23166 bp mRNA bp exons Protein aa exons NM_000660.3 2346 7 NP_000651.3 390 7 Exon information: NM_000660.3 length: 2346 bp, number of exons: 7 NP_000651.3 length: 390 aa, number of exons: 7 EXON Coding EXON INTRON coords length coords length coords length 1 - 1222 1222 bp 868 - 1222 355 bp 1223 - 5456 4234 bp 5457 - 5617 161 bp 5457 - 5617 161 bp 5618 - 9047 3430 bp 9048 - 9165 118 bp 9048 - 9165 118 bp 9166 - 11664 2499 bp 11665 - 11742 78 bp 11665 - 11742 78 bp 11743 - 11881 139 bp 11882 - 12029 148 bp 11882 - 12029 148 bp 12030 - 21630 9601 bp 21631 - 21784 154 bp 21631 - 21784 154 bp 21785 - 22701 917 bp 22702 - 23166 465 bp 22702 - 22860 159 bp ------------------------------------------ Or you could try using Bio::DB::Eutilities, specifying 'gene' as the database and 'table' as the retype. I'm not sure what retypes are allowed under B:D:E but it should be in the docs. Take a look at http://www.bioperl.org/wiki/Getting_Genomic_Sequences or http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook Hope this helps, Russell Smithies Bioinformatics Applications Developer T +64 3 489 9085 E? russell.smithies at agresearch.co.nz Invermay? Research Centre Puddle Alley, Mosgiel, New Zealand T? +64 3 489 3809?? F? +64 3 489 9174? www.agresearch.co.nz > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Dan Kortschak > Sent: Friday, 9 October 2009 7:54 p.m. > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] Bio::DB::EntrezGene or Bio::DB::Query::GenBank to obtain > sequence metadata without sequence > > Hi, > > I am looking to query NCBI for sequence metadata (LOCUS/length, > DEFINITION/name etc) without obtaining the sequence associated with the > entry (pulling sequence data for chromosome when only the metadata is > needed is a waste). > > I'm wondering what would be the most appropriate bioperl module to use - > Bio::DB::EntrezGene or Bio::DB::Query::GenBank seem like the best bet > and from the description the latter seems best, but I'm wondering if > this is best and what database would both provide this data and be > parsable. > > thanks for any help. > Dan > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. 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If you have received this message in error, please notify the sender immediately. ======================================================================= From dan.kortschak at adelaide.edu.au Sun Oct 11 18:03:52 2009 From: dan.kortschak at adelaide.edu.au (Dan Kortschak) Date: Mon, 12 Oct 2009 08:33:52 +1030 Subject: [Bioperl-l] Bio::DB::EntrezGene or Bio::DB::Query::GenBank to obtain sequence metadata without sequence In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF32B62C8D40B@exchsth.agresearch.co.nz> References: <1255071248.27558.9.camel@zoidberg.mbs.adelaide.edu.au> <18DF7D20DFEC044098A1062202F5FFF32B62C8D40B@exchsth.agresearch.co.nz> Message-ID: <1255298632.31853.11.camel@zoidberg.mbs.adelaide.edu.au> Hi Russell, I ended up using a hodgepodge of Bio::DB::GenBank and Bio::DB::EUtililties #!/usr/bin/perl use Bio::DB::EUtilities; use Bio::DB::GenBank; my @uids = qw(89161185 89161199 89161205 89161207 51511721 89161210 89161213 51511724 89161216 89161187 51511727 89161190 51511729 51511730 51511731 51511732 51511734 51511735 42406306 51511747 51511750 89161203 17981852 89161218 89161220); my $gb = Bio::DB::GenBank->new(-complexity => 1,-seq_stop=>1); my $seqio = $gb->get_Stream_by_gi(\@uids); my $summary = Bio::DB::EUtilities->new(-eutil => 'esummary', -db => 'nucleotide', -id => \@uids); print "chromosome,refSeq,name,length\n"; my $index=0; while (my $seq = $seqio->next_seq() and my $ds = $summary->next_DocSum) { warn "Database queries don't reconcile",$seq->primary_id,"-",$ds->get_id,"\n" if $seq->primary_id != $ds->get_id; print $index++,",",$seq->id(),".",$seq->version,","; ($feat)=$seq->get_SeqFeatures; if( defined $seq->species && $feat->annotation->get_Annotations('chromosome')) { print $seq->species->binomial; print " chromosome ",$feat->annotation->get_Annotations('chromosome'),","; } elsif (defined $seq->species && $feat->annotation->get_Annotations('organelle')) { print $seq->species->binomial; print " ",$feat->annotation->get_Annotations('organelle'),","; } else { $_=$seq->desc; /^([[:alnum:] ]+)[[:graph:]]/; print "$1,"; } print $ds->get_contents_by_name('Length') if $ds->get_contents_by_name('Length'); print "\n"; } If Bio::DB:EUtilities gives rich seq or equivalent I might change over from Bio::DB::GenBank, but it pretty much works at the moment (the fail-overs give me grief and I don't like the kludge of asking for a single base, but they work to get some of the details that the DocSum doesn't - sensible title for example). cheers Dan On Mon, 2009-10-12 at 08:46 +1300, Smithies, Russell wrote: > Or you could try using Bio::DB::Eutilities, specifying 'gene' as the database and 'table' as the retype. > I'm not sure what retypes are allowed under B:D:E but it should be in the docs. From cjfields at illinois.edu Sun Oct 11 18:53:18 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Oct 2009 17:53:18 -0500 Subject: [Bioperl-l] Bio::DB::EntrezGene or Bio::DB::Query::GenBank to obtain sequence metadata without sequence In-Reply-To: <1255298632.31853.11.camel@zoidberg.mbs.adelaide.edu.au> References: <1255071248.27558.9.camel@zoidberg.mbs.adelaide.edu.au> <18DF7D20DFEC044098A1062202F5FFF32B62C8D40B@exchsth.agresearch.co.nz> <1255298632.31853.11.camel@zoidberg.mbs.adelaide.edu.au> Message-ID: <16B58928-B58D-41AF-9524-A528E4066BFE@illinois.edu> On Oct 11, 2009, at 5:03 PM, Dan Kortschak wrote: > Hi Russell, > > I ended up using a hodgepodge of Bio::DB::GenBank and > Bio::DB::EUtililties > > #!/usr/bin/perl > > use Bio::DB::EUtilities; > use Bio::DB::GenBank; > > my @uids = qw(89161185 89161199 89161205 89161207 51511721 89161210 > 89161213 51511724 89161216 89161187 51511727 89161190 51511729 > 51511730 51511731 51511732 51511734 51511735 42406306 51511747 > 51511750 89161203 17981852 89161218 89161220); > > my $gb = Bio::DB::GenBank->new(-complexity => 1,-seq_stop=>1); > my $seqio = $gb->get_Stream_by_gi(\@uids); > my $summary = Bio::DB::EUtilities->new(-eutil => 'esummary', > -db => 'nucleotide', > -id => \@uids); > > print "chromosome,refSeq,name,length\n"; > > my $index=0; > > while (my $seq = $seqio->next_seq() and my $ds = $summary- > >next_DocSum) { > warn "Database queries don't reconcile",$seq->primary_id,"-",$ds- > >get_id,"\n" if $seq->primary_id != $ds->get_id; > print $index++,",",$seq->id(),".",$seq->version,","; > ($feat)=$seq->get_SeqFeatures; > if( defined $seq->species && $feat->annotation->get_Annotations > ('chromosome')) { > print $seq->species->binomial; > print " chromosome ",$feat->annotation->get_Annotations > ('chromosome'),","; > } elsif (defined $seq->species && $feat->annotation->get_Annotations > ('organelle')) { > print $seq->species->binomial; > print " ",$feat->annotation->get_Annotations('organelle'),","; > } else { > $_=$seq->desc; > /^([[:alnum:] ]+)[[:graph:]]/; > print "$1,"; > } > print $ds->get_contents_by_name('Length') if $ds- > >get_contents_by_name('Length'); > print "\n"; > } > > > If Bio::DB:EUtilities gives rich seq or equivalent I might change over > from Bio::DB::GenBank, but it pretty much works at the moment (the > fail-overs give me grief and I don't like the kludge of asking for a > single base, but they work to get some of the details that the DocSum > doesn't - sensible title for example). > > cheers > Dan Bio::DB::EUtilities is a generic front-end to NCBI's eutils, so you can retrieve the gene info in whatever format via efetch and pass it on to the appropriate parser (Bio::SeqIO::entrezgene, which requires ASN1 at this time). It's probably best to save the ASN1 data to a temp file prior to that (getting the raw content as a file handle isn't set up yet). chris From maj at fortinbras.us Tue Oct 13 07:35:03 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Tue, 13 Oct 2009 07:35:03 -0400 Subject: [Bioperl-l] a Main Page proposal In-Reply-To: References: <094CC6C2C9DE448F9A8097AEEFE86B03@NewLife><7C51BBB552AB4EBEA5ED60B49BDB9171@NewLife><628aabb70909211003w221b4c9fn5c11f7ff08fc952d@mail.gmail.com><42FBB964C0EA44FABCB50364C567A009@NewLife> Message-ID: I liked the idea of moving the search box up the page, but couldn't make it happen from the wiki; it appears to be added internally after the sidebar is rendered...Can this be done? cheers MAJ ----- Original Message ----- From: Brian Osborne To: Mark A. Jensen Cc: BioPerl List Sent: Friday, September 25, 2009 10:42 PM Subject: Re: [Bioperl-l] a Main Page proposal Mark, I don't love the italics in the version that Chris made but that's just personal preference. He's right in thinking that putting more in the top of the page is good: less scrolling. One could color the backgrounds of his tables, that might look nice. Either way, or a combination of both, is preferable to what we have. There really is no need to wait since the current page is abysmal. I can say that freely since I'm probably one of its authors! One thought though: move the "search" up to a center-left location, below "main links". The Wiki search is pretty good at finding pages so if someone doesn't find what they're looking for in the main section they might be drawn to search for it. Brian O. On Sep 25, 2009, at 10:22 PM, Mark A. Jensen wrote: Cheers, Brian-- I am becoming swayed now by Chris' whack at it, on his talk page. My thought is that we'll hammer out the final version after the release, then pull the trigger-- Your thoughts? MAJ ----- Original Message ----- From: "Brian Osborne" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Friday, September 25, 2009 10:13 PM Subject: Re: [Bioperl-l] a Main Page proposal Mark, Really nice, and a significant improvement over the existing. You've gotten good feedback, you've considered these thoughts and incorporated them - is it time to move the beta to Main? Yes. In my opinion your 'beta' is far superior - just do it. Brian O. On Sep 21, 2009, at 1:45 PM, Mark A. Jensen wrote: A nearly completely minimal solution is at Main Page Beta ----- Original Message ----- From: "Dave Messina" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Monday, September 21, 2009 1:03 PM Subject: Re: [Bioperl-l] a Main Page proposal Hi Mark, Thanks for taking on this (much needed) refresh. I think your current version is substantially better than what we have now. Still, I'd argue that something much more concise like the Biopython page would make a bigger impact on visitors' ability to find what they're looking for. It's not that the details you have under each section shouldn't be available, but rather that they could be clicked through to instead of being on the front page. The About section is a good example. I would bet most visitors to the BioPerl website skip over the About section because they already know what BioPerl is, and that section has the most valuable real estate on the page. Those who don't know and are curious will probably be able to find it (the word About on the front page of a website has become an idiom for "click her to read the details about this"). Dave _______________________________________________ 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 _______________________________________________ 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 Tue Oct 13 10:53:12 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Tue, 13 Oct 2009 10:53:12 -0400 Subject: [Bioperl-l] BioPerl Core 1.6.1 PPM now available In-Reply-To: References: Message-ID: <490173E6AE6B40D8BD81E4214A6344F5@NewLife> I find with the 5.10 install that the ActiveState repo borks on an install of SOAP::Lite 0.71 ("no provider of Apache:: found for package SOAP::Lite"). The message makes me think the .ppd is wrong on their end. The trouchelle and uwinnipeg repo versions (both 0.69) install find; maybe a workaround is to specify version 0.69 in the Bundle-BioPerl-Core spec. cheers MAJ ----- Original Message ----- From: "Chris Fields" To: "BioPerl List" Sent: Saturday, October 10, 2009 1:24 AM Subject: [Bioperl-l] BioPerl Core 1.6.1 PPM now available > The first cut at the ActivePerl PPM distribution for BioPerl core > 1.6.1 is now available. Instructions for installing on Windows are > here: > > http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows > > I have made this installation architecture-independent, but it has > only been testing on WinXP using ActivePerl 5.10.1.1006. A couple of > modules may give warnings (specifically SOAP::Lite and > XML::SAX::Writer), but the installation should proceed. We would > appreciate feedback on trying to install this with other versions of > ActivePerl or on more recent versions of Windows (Vista, Win7). > > Enjoy! > > 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 Tue Oct 13 14:42:56 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Oct 2009 13:42:56 -0500 Subject: [Bioperl-l] BioPerl Core 1.6.1 PPM now available In-Reply-To: <490173E6AE6B40D8BD81E4214A6344F5@NewLife> References: <490173E6AE6B40D8BD81E4214A6344F5@NewLife> Message-ID: <71D8E056-AD94-4A57-8755-2BB3AD517538@illinois.edu> Mark, That might work, though I think that indicates the minimal version, not requiring a specific version. Makes me think we should have a local PPM for SOAP::Lite as well that doesn't ask for this. One would think the automated process ActiveState has for building PPMs would have pointed this out! chris On Oct 13, 2009, at 9:53 AM, Mark A. Jensen wrote: > I find with the 5.10 install that the ActiveState repo borks on an > install of SOAP::Lite 0.71 ("no provider of Apache:: found for > package SOAP::Lite"). > The message makes me think the .ppd is wrong on their end. The > trouchelle and uwinnipeg repo versions (both 0.69) install find; > maybe a workaround is to specify version 0.69 in the Bundle-BioPerl- > Core > spec. cheers MAJ > ----- Original Message ----- From: "Chris Fields" > > To: "BioPerl List" > Sent: Saturday, October 10, 2009 1:24 AM > Subject: [Bioperl-l] BioPerl Core 1.6.1 PPM now available > > >> The first cut at the ActivePerl PPM distribution for BioPerl core >> 1.6.1 is now available. Instructions for installing on Windows >> are here: >> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows >> I have made this installation architecture-independent, but it has >> only been testing on WinXP using ActivePerl 5.10.1.1006. A couple >> of modules may give warnings (specifically SOAP::Lite and >> XML::SAX::Writer), but the installation should proceed. We would >> appreciate feedback on trying to install this with other versions >> of ActivePerl or on more recent versions of Windows (Vista, Win7). >> Enjoy! >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> From clements at nescent.org Wed Oct 14 14:38:02 2009 From: clements at nescent.org (Dave Clements) Date: Wed, 14 Oct 2009 11:38:02 -0700 Subject: [Bioperl-l] a Main Page proposal In-Reply-To: References: <094CC6C2C9DE448F9A8097AEEFE86B03@NewLife> <7C51BBB552AB4EBEA5ED60B49BDB9171@NewLife> <628aabb70909211003w221b4c9fn5c11f7ff08fc952d@mail.gmail.com> <42FBB964C0EA44FABCB50364C567A009@NewLife> Message-ID: Hi Mark, Yes. See http://www.mediawiki.org/wiki/Manual:Interface/Sidebar#Order_of_elements Dave C. On Tue, Oct 13, 2009 at 4:35 AM, Mark A. Jensen wrote: > I liked the idea of moving the search box up the page, but couldn't make it > happen from the wiki; it appears to be added internally after the sidebar is > rendered...Can this be done? cheers MAJ > ----- Original Message ----- > From: Brian Osborne > To: Mark A. Jensen > Cc: BioPerl List > Sent: Friday, September 25, 2009 10:42 PM > Subject: Re: [Bioperl-l] a Main Page proposal > > > Mark, > > > I don't love the italics in the version that Chris made but that's just > personal preference. He's right in thinking that putting more in the top of > the page is good: less scrolling. > > > One could color the backgrounds of his tables, that might look nice. > > > Either way, or a combination of both, is preferable to what we have. There > really is no need to wait since the current page is abysmal. I can say that > freely since I'm probably one of its authors! > > > One thought though: move the "search" up to a center-left location, below > "main links". The Wiki search is pretty good at finding pages so if someone > doesn't find what they're looking for in the main section they might be > drawn to search for it. > > > Brian O. > > > > > On Sep 25, 2009, at 10:22 PM, Mark A. Jensen wrote: > > > Cheers, Brian-- I am becoming swayed now by Chris' whack at it, on his > talk page. My thought is that we'll hammer out the final version after the > release, then pull the trigger-- Your thoughts? > MAJ > ----- Original Message ----- From: "Brian Osborne" < > bosborne11 at verizon.net> > To: "Mark A. Jensen" > Cc: "BioPerl List" > Sent: Friday, September 25, 2009 10:13 PM > Subject: Re: [Bioperl-l] a Main Page proposal > > > > Mark, > > Really nice, and a significant improvement over the existing. > > You've gotten good feedback, you've considered these thoughts and > incorporated them - is it time to move the beta to Main? Yes. In my > opinion your 'beta' is far superior - just do it. > > Brian O. > > On Sep 21, 2009, at 1:45 PM, Mark A. Jensen wrote: > > A nearly completely minimal solution is at Main Page Beta > > ----- Original Message ----- From: "Dave Messina" < > David.Messina at sbc.su.se > > > To: "Mark A. Jensen" > > Cc: "BioPerl List" > > Sent: Monday, September 21, 2009 1:03 PM > > Subject: Re: [Bioperl-l] a Main Page proposal > > > > > > Hi Mark, > > Thanks for taking on this (much needed) refresh. > > I think your current version is substantially better than what we > have now. > > Still, I'd argue that something much more concise like the > Biopython page > > would make a bigger impact on visitors' ability to find what > they're looking > > for. > > It's not that the details you have under each section shouldn't be > > available, but rather that they could be clicked through to > instead of being > > on the front page. > > The About section is a good example. I would bet most visitors to > the > > BioPerl website skip over the About section because they already > know what > > BioPerl is, and that section has the most valuable real estate on > the page. > > Those who don't know and are curious will probably be able to find > it (the > > word About on the front page of a website has become an idiom for > "click her > > to read the details about this"). > > Dave > > _______________________________________________ > > 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 > > > > _______________________________________________ > 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 > -- GMOD News: http://gmod.org/wiki/GMOD_News From maj at fortinbras.us Wed Oct 14 14:43:54 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 14 Oct 2009 14:43:54 -0400 Subject: [Bioperl-l] a Main Page proposal In-Reply-To: References: <094CC6C2C9DE448F9A8097AEEFE86B03@NewLife> <7C51BBB552AB4EBEA5ED60B49BDB9171@NewLife> <628aabb70909211003w221b4c9fn5c11f7ff08fc952d@mail.gmail.com> <42FBB964C0EA44FABCB50364C567A009@NewLife> Message-ID: <60BCE3A9C3E34CB7A378790C0F20649C@NewLife> excellent-- thanks a lot Dave- MAJ ----- Original Message ----- From: Dave Clements To: Mark A. Jensen Cc: Chris Fields ; BioPerl List ; Brian Osborne Sent: Wednesday, October 14, 2009 2:38 PM Subject: Re: [Bioperl-l] a Main Page proposal Hi Mark, Yes. See http://www.mediawiki.org/wiki/Manual:Interface/Sidebar#Order_of_elements Dave C. On Tue, Oct 13, 2009 at 4:35 AM, Mark A. Jensen wrote: I liked the idea of moving the search box up the page, but couldn't make it happen from the wiki; it appears to be added internally after the sidebar is rendered...Can this be done? cheers MAJ ----- Original Message ----- From: Brian Osborne To: Mark A. Jensen Cc: BioPerl List Sent: Friday, September 25, 2009 10:42 PM Subject: Re: [Bioperl-l] a Main Page proposal Mark, I don't love the italics in the version that Chris made but that's just personal preference. He's right in thinking that putting more in the top of the page is good: less scrolling. One could color the backgrounds of his tables, that might look nice. Either way, or a combination of both, is preferable to what we have. There really is no need to wait since the current page is abysmal. I can say that freely since I'm probably one of its authors! One thought though: move the "search" up to a center-left location, below "main links". The Wiki search is pretty good at finding pages so if someone doesn't find what they're looking for in the main section they might be drawn to search for it. Brian O. On Sep 25, 2009, at 10:22 PM, Mark A. Jensen wrote: Cheers, Brian-- I am becoming swayed now by Chris' whack at it, on his talk page. My thought is that we'll hammer out the final version after the release, then pull the trigger-- Your thoughts? MAJ ----- Original Message ----- From: "Brian Osborne" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Friday, September 25, 2009 10:13 PM Subject: Re: [Bioperl-l] a Main Page proposal Mark, Really nice, and a significant improvement over the existing. You've gotten good feedback, you've considered these thoughts and incorporated them - is it time to move the beta to Main? Yes. In my opinion your 'beta' is far superior - just do it. Brian O. On Sep 21, 2009, at 1:45 PM, Mark A. Jensen wrote: A nearly completely minimal solution is at Main Page Beta ----- Original Message ----- From: "Dave Messina" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Monday, September 21, 2009 1:03 PM Subject: Re: [Bioperl-l] a Main Page proposal Hi Mark, Thanks for taking on this (much needed) refresh. I think your current version is substantially better than what we have now. Still, I'd argue that something much more concise like the Biopython page would make a bigger impact on visitors' ability to find what they're looking for. It's not that the details you have under each section shouldn't be available, but rather that they could be clicked through to instead of being on the front page. The About section is a good example. I would bet most visitors to the BioPerl website skip over the About section because they already know what BioPerl is, and that section has the most valuable real estate on the page. Those who don't know and are curious will probably be able to find it (the word About on the front page of a website has become an idiom for "click her to read the details about this"). Dave _______________________________________________ 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 _______________________________________________ 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 -- GMOD News: http://gmod.org/wiki/GMOD_News From maj at fortinbras.us Thu Oct 15 07:39:14 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Thu, 15 Oct 2009 07:39:14 -0400 Subject: [Bioperl-l] Fw: Announcing AB-BLAST 3.0 Availability Message-ID: The Return of the King? MAJ ----- Original Message ----- From: Warren Gish To: undisclosed-recipients Sent: Thursday, October 15, 2009 12:59 AM Subject: Announcing AB-BLAST 3.0 Availability Dear Colleague, This message has been sent to you because of a previous inquiry you made about the discontinued WU-BLAST software or its successor AB-BLAST (Advanced Biocomputing BLAST). AB-BLAST is now generally available for academic/nonprofit and commercial licensing. In addition, a new licensing option is available: AB-BLAST may be readily licensed on-line at no cost to individuals for their personal use on personally owned computer hardware. (Some restrictions and limitations of support apply). AB-BLAST represents the future direction of WU-BLAST. For more information about the software, please see http://blast.advbiocomp.com/doc/README.html For further information about licensing of AB-BLAST, please visit http://blast.advbiocomp.com/licensing. To go directly to the personal use licensing page, see http://blast.advbiocomp.com/licensing/personal.html Inquiries about academic/nonprofit or commercial licensing should be addressed to licensing at advbiocomp.com and will be responded to as soon as possible. Please note that academic/nonprofit licensing of AB-BLAST is now necessarily fee based, in order to defray the costs of development, maintenance and support. Thank you for your past support of WU-BLAST and your future support of AB-BLAST! Sincerely, --Warren Warren Gish, Ph.D. President Advanced Biocomputing, LLC P.O. Box 410085 St. Louis, MO 63141-0085 Web: http://www.advbiocomp.com E-mail: gish at advbiocomp.com From jorismeys at gmail.com Fri Oct 16 15:35:02 2009 From: jorismeys at gmail.com (joris meys) Date: Fri, 16 Oct 2009 21:35:02 +0200 Subject: [Bioperl-l] Bootstrapping positions in alignment Message-ID: Dear all, I'm using the packages AlignIO and AlignI to construct a bootstrapping procedure on my alignments. There is a function slice() in AlignI I can use, but I actually need just a number of positions, not a slice. Is there any other way of accessing the object so I can just specify one position? Thx in advance Joris From maj at fortinbras.us Fri Oct 16 21:27:34 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Fri, 16 Oct 2009 21:27:34 -0400 Subject: [Bioperl-l] Bootstrapping positions in alignment In-Reply-To: References: Message-ID: <8E1E3E59BF8E46D2AF08DA5BC7DE9808@NewLife> Hi Joris - You may find what you're looking for in this post: http://lists.open-bio.org/pipermail/bioperl-l/2009-September/031292.html cheers MAJ ----- Original Message ----- From: "joris meys" To: Sent: Friday, October 16, 2009 3:35 PM Subject: [Bioperl-l] Bootstrapping positions in alignment > Dear all, > > I'm using the packages AlignIO and AlignI to construct a bootstrapping > procedure on my alignments. There is a function slice() in AlignI I > can use, but I actually need just a number of positions, not a slice. > Is there any other way of accessing the object so I can just specify > one position? > > Thx in advance > Joris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From jorismeys at gmail.com Fri Oct 16 22:51:47 2009 From: jorismeys at gmail.com (joris meys) Date: Sat, 17 Oct 2009 04:51:47 +0200 Subject: [Bioperl-l] Bootstrapping positions in alignment - Utilities package Message-ID: Thanks, but it's not really what I'm looking for. My alignments are flushed, so basically a matrix from which I need to select columns. These column indices come from an array with random numbers. It works with slice() from AlignI, I was just wondering if you could use an index of some sort like for an array. Something like $newaln = $oldaln [ @indices ] Thing is, I use this loop for it, but it doesn't want to work. $aln is a simpleAlign object use Bio::Align::Utilities qw(:all); my $out = Bio::SimpleAlign -> new; foreach (@indices){ my $temp = $aln -> slice($_ ,$_); eval{$out = &cat($out,$temp)} or print $@ and $out = $temp; } I use the eval construction to get passed a first error, but it doesn't work. I get as output : Undefined subroutine &main::cat called at... and then the result of the last round in the loop. I must be doing something wrong with the cat function from Align::Utilities. But I have no clue what. The other function from the Utilities package, bootstrap_replicates, works just fine. Any tips are welcome Kind regards Joris On Sat, Oct 17, 2009 at 3:27 AM, Mark A. Jensen wrote: > Hi Joris > You may find what you're looking for in this post: > http://lists.open-bio.org/pipermail/bioperl-l/2009-September/031292.html > cheers MAJ > ----- Original Message ----- From: "joris meys" > To: > Sent: Friday, October 16, 2009 3:35 PM > Subject: [Bioperl-l] Bootstrapping positions in alignment > > >> Dear all, >> >> I'm using the packages AlignIO and AlignI to construct a bootstrapping >> procedure on my alignments. There is a function slice() in AlignI I >> can use, but I actually need just a number of positions, not a slice. >> Is there any other way of accessing the object so I can just specify >> one position? >> >> Thx in advance >> Joris >> _______________________________________________ >> 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 Fri Oct 16 23:42:40 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Fri, 16 Oct 2009 23:42:40 -0400 Subject: [Bioperl-l] Bootstrapping positions in alignment - Utilities package In-Reply-To: References: Message-ID: <6C0917C7DDCE48A084924EE8052EA62C@NewLife> leave out the ampersand. ----- Original Message ----- From: "joris meys" To: "Mark A. Jensen" Cc: Sent: Friday, October 16, 2009 10:51 PM Subject: Re: [Bioperl-l] Bootstrapping positions in alignment - Utilities package > Thanks, but it's not really what I'm looking for. My alignments are > flushed, so basically a matrix from which I need to select columns. > These column indices come from an array with random numbers. It works > with slice() from AlignI, I was just wondering if you could use an > index of some sort like for an array. Something like > > $newaln = $oldaln [ @indices ] > > Thing is, I use this loop for it, but it doesn't want to work. $aln is > a simpleAlign object > > use Bio::Align::Utilities qw(:all); > > my $out = Bio::SimpleAlign -> new; > foreach (@indices){ > my $temp = $aln -> slice($_ ,$_); > eval{$out = &cat($out,$temp)} or print $@ and $out = $temp; > } > I use the eval construction to get passed a first error, but it > doesn't work. I get as output : > > Undefined subroutine &main::cat called at... > and then the result of the last round in the loop. I must be doing > something wrong with the cat function from Align::Utilities. But I > have no clue what. > > The other function from the Utilities package, bootstrap_replicates, > works just fine. > > Any tips are welcome > Kind regards > Joris > > On Sat, Oct 17, 2009 at 3:27 AM, Mark A. Jensen wrote: >> Hi Joris >> You may find what you're looking for in this post: >> http://lists.open-bio.org/pipermail/bioperl-l/2009-September/031292.html >> cheers MAJ >> ----- Original Message ----- From: "joris meys" >> To: >> Sent: Friday, October 16, 2009 3:35 PM >> Subject: [Bioperl-l] Bootstrapping positions in alignment >> >> >>> Dear all, >>> >>> I'm using the packages AlignIO and AlignI to construct a bootstrapping >>> procedure on my alignments. There is a function slice() in AlignI I >>> can use, but I actually need just a number of positions, not a slice. >>> Is there any other way of accessing the object so I can just specify >>> one position? >>> >>> Thx in advance >>> Joris >>> _______________________________________________ >>> 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 Fri Oct 16 23:38:05 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 16 Oct 2009 22:38:05 -0500 Subject: [Bioperl-l] Bootstrapping positions in alignment - Utilities package In-Reply-To: References: Message-ID: Did you try bootstrap_replicates() from Bio::Align::Utilities? chris On Oct 16, 2009, at 9:51 PM, joris meys wrote: > Thanks, but it's not really what I'm looking for. My alignments are > flushed, so basically a matrix from which I need to select columns. > These column indices come from an array with random numbers. It works > with slice() from AlignI, I was just wondering if you could use an > index of some sort like for an array. Something like > > $newaln = $oldaln [ @indices ] > > Thing is, I use this loop for it, but it doesn't want to work. $aln is > a simpleAlign object > > use Bio::Align::Utilities qw(:all); > > my $out = Bio::SimpleAlign -> new; > foreach (@indices){ > my $temp = $aln -> slice($_ ,$_); > eval{$out = &cat($out,$temp)} or print $@ and $out = $temp; > } > I use the eval construction to get passed a first error, but it > doesn't work. I get as output : > > Undefined subroutine &main::cat called at... > and then the result of the last round in the loop. I must be doing > something wrong with the cat function from Align::Utilities. But I > have no clue what. > > The other function from the Utilities package, bootstrap_replicates, > works just fine. > > Any tips are welcome > Kind regards > Joris > > On Sat, Oct 17, 2009 at 3:27 AM, Mark A. Jensen > wrote: >> Hi Joris >> You may find what you're looking for in this post: >> http://lists.open-bio.org/pipermail/bioperl-l/2009-September/031292.html >> cheers MAJ >> ----- Original Message ----- From: "joris meys" >> To: >> Sent: Friday, October 16, 2009 3:35 PM >> Subject: [Bioperl-l] Bootstrapping positions in alignment >> >> >>> Dear all, >>> >>> I'm using the packages AlignIO and AlignI to construct a >>> bootstrapping >>> procedure on my alignments. There is a function slice() in AlignI I >>> can use, but I actually need just a number of positions, not a >>> slice. >>> Is there any other way of accessing the object so I can just specify >>> one position? >>> >>> Thx in advance >>> Joris >>> _______________________________________________ >>> 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 vincenza.maselli at gmail.com Sat Oct 17 03:45:17 2009 From: vincenza.maselli at gmail.com (Vincenza Maselli) Date: Sat, 17 Oct 2009 00:45:17 -0700 (PDT) Subject: [Bioperl-l] Invitation to connect on LinkedIn Message-ID: <45839563.143299.1255765517625.JavaMail.app@ech3-cdn11.prod> LinkedIn ------------ I'd like to add you to my professional network on LinkedIn. - Vincenza Confirm that you know Vincenza Maselli https://www.linkedin.com/e/isd/802660236/4jNj4lUf/ Every day, millions of professionals like Vincenza Maselli use LinkedIn to connect with colleagues, find experts, and explore opportunities. ------ (c) 2009, LinkedIn Corporation From jorismeys at gmail.com Sat Oct 17 08:48:03 2009 From: jorismeys at gmail.com (joris meys) Date: Sat, 17 Oct 2009 14:48:03 +0200 Subject: [Bioperl-l] Bootstrapping positions in alignment - Utilities package In-Reply-To: References: Message-ID: I did, and that one works. But I can't specify here that I want only 100 positions from an alignment of 300 long for example. That's why I have to do it myself. I did lose the ampersand in the statement, but that didn't help one bit. Next to that, my program is now complaining about unblessed references when I put an alignment as an argument for a subroutine, and I have no clue why. Guess I'm not so OOP minded. I'll struggle on, thanks for the hints. Cheers Joris On Sat, Oct 17, 2009 at 5:38 AM, Chris Fields wrote: > Did you try bootstrap_replicates() from Bio::Align::Utilities? > > chris > > On Oct 16, 2009, at 9:51 PM, joris meys wrote: > >> Thanks, but it's not really what I'm looking for. My alignments are >> flushed, so basically a matrix from which I need to select columns. >> These column indices come from an array with random numbers. It works >> with slice() from AlignI, I was just wondering if you could use an >> index of some sort like for an array. Something like >> >> $newaln = $oldaln [ @indices ] >> >> Thing is, I use this loop for it, but it doesn't want to work. $aln is >> a simpleAlign object >> >> use Bio::Align::Utilities qw(:all); >> >> my $out = Bio::SimpleAlign -> new; >> foreach (@indices){ >> ? ? ? my $temp = $aln -> slice($_ ,$_); >> ? ? ? eval{$out = &cat($out,$temp)} or print $@ and $out = $temp; >> ? } >> I use the eval construction to get passed a first error, but it >> doesn't work. I get as output : >> >> Undefined subroutine &main::cat called at... >> and then the result of the last round in the loop. I must be doing >> something wrong with the cat function from Align::Utilities. ?But I >> have no clue what. >> >> The other function from the Utilities package, bootstrap_replicates, >> works just fine. >> >> Any tips are welcome >> Kind regards >> Joris >> >> On Sat, Oct 17, 2009 at 3:27 AM, Mark A. Jensen wrote: >>> >>> Hi Joris >>> You may find what you're looking for in this post: >>> http://lists.open-bio.org/pipermail/bioperl-l/2009-September/031292.html >>> cheers MAJ >>> ----- Original Message ----- From: "joris meys" >>> To: >>> Sent: Friday, October 16, 2009 3:35 PM >>> Subject: [Bioperl-l] Bootstrapping positions in alignment >>> >>> >>>> Dear all, >>>> >>>> I'm using the packages AlignIO and AlignI to construct a bootstrapping >>>> procedure on my alignments. There is a function slice() in AlignI I >>>> can use, but I actually need just a number of positions, not a slice. >>>> Is there any other way of accessing the object so I can just specify >>>> one position? >>>> >>>> Thx in advance >>>> Joris >>>> _______________________________________________ >>>> 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 jorismeys at gmail.com Sat Oct 17 09:14:26 2009 From: jorismeys at gmail.com (joris meys) Date: Sat, 17 Oct 2009 15:14:26 +0200 Subject: [Bioperl-l] Bootstrapping positions in alignment - Utilities package In-Reply-To: References: Message-ID: Found the unblessed reference problem, but with or without ampersand, I get the same error out of the eval. It doesn't find the function somehow, and I'm baffled about why. Cheers Joris On Sat, Oct 17, 2009 at 2:48 PM, joris meys wrote: > I did, and that one works. But I can't specify here that I want only > 100 positions from an alignment of 300 long for example. That's why I > have to do it myself. > > I did lose the ampersand in the statement, but that didn't help one > bit. Next to that, my program is now complaining about unblessed > references when I put an alignment as an argument for a subroutine, > and I have no clue why. > > Guess I'm not so OOP minded. I'll struggle on, thanks for the hints. > Cheers > Joris > > On Sat, Oct 17, 2009 at 5:38 AM, Chris Fields wrote: >> Did you try bootstrap_replicates() from Bio::Align::Utilities? >> >> chris >> >> On Oct 16, 2009, at 9:51 PM, joris meys wrote: >> >>> Thanks, but it's not really what I'm looking for. My alignments are >>> flushed, so basically a matrix from which I need to select columns. >>> These column indices come from an array with random numbers. It works >>> with slice() from AlignI, I was just wondering if you could use an >>> index of some sort like for an array. Something like >>> >>> $newaln = $oldaln [ @indices ] >>> >>> Thing is, I use this loop for it, but it doesn't want to work. $aln is >>> a simpleAlign object >>> >>> use Bio::Align::Utilities qw(:all); >>> >>> my $out = Bio::SimpleAlign -> new; >>> foreach (@indices){ >>> ? ? ? my $temp = $aln -> slice($_ ,$_); >>> ? ? ? eval{$out = &cat($out,$temp)} or print $@ and $out = $temp; >>> ? } >>> I use the eval construction to get passed a first error, but it >>> doesn't work. I get as output : >>> >>> Undefined subroutine &main::cat called at... >>> and then the result of the last round in the loop. I must be doing >>> something wrong with the cat function from Align::Utilities. ?But I >>> have no clue what. >>> >>> The other function from the Utilities package, bootstrap_replicates, >>> works just fine. >>> >>> Any tips are welcome >>> Kind regards >>> Joris >>> >>> On Sat, Oct 17, 2009 at 3:27 AM, Mark A. Jensen wrote: >>>> >>>> Hi Joris >>>> You may find what you're looking for in this post: >>>> http://lists.open-bio.org/pipermail/bioperl-l/2009-September/031292.html >>>> cheers MAJ >>>> ----- Original Message ----- From: "joris meys" >>>> To: >>>> Sent: Friday, October 16, 2009 3:35 PM >>>> Subject: [Bioperl-l] Bootstrapping positions in alignment >>>> >>>> >>>>> Dear all, >>>>> >>>>> I'm using the packages AlignIO and AlignI to construct a bootstrapping >>>>> procedure on my alignments. There is a function slice() in AlignI I >>>>> can use, but I actually need just a number of positions, not a slice. >>>>> Is there any other way of accessing the object so I can just specify >>>>> one position? >>>>> >>>>> Thx in advance >>>>> Joris >>>>> _______________________________________________ >>>>> 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 jorismeys at gmail.com Sat Oct 17 09:24:01 2009 From: jorismeys at gmail.com (joris meys) Date: Sat, 17 Oct 2009 15:24:01 +0200 Subject: [Bioperl-l] Bootstrapping positions in alignment - Utilities package In-Reply-To: References: Message-ID: Ah-HA! Problem is -off course- the obvious : I checked the Utilities.pm file, but that one doesn't contain the cat function. Somebody should update his packages before complaining... Thx for the help! Cheers Joris On Sat, Oct 17, 2009 at 3:14 PM, joris meys wrote: > Found the unblessed reference problem, but with or without ampersand, > I get the same error out of the eval. It doesn't find the function > somehow, and I'm baffled about why. > > Cheers > Joris > > On Sat, Oct 17, 2009 at 2:48 PM, joris meys wrote: >> I did, and that one works. But I can't specify here that I want only >> 100 positions from an alignment of 300 long for example. That's why I >> have to do it myself. >> >> I did lose the ampersand in the statement, but that didn't help one >> bit. Next to that, my program is now complaining about unblessed >> references when I put an alignment as an argument for a subroutine, >> and I have no clue why. >> >> Guess I'm not so OOP minded. I'll struggle on, thanks for the hints. >> Cheers >> Joris >> >> On Sat, Oct 17, 2009 at 5:38 AM, Chris Fields wrote: >>> Did you try bootstrap_replicates() from Bio::Align::Utilities? >>> >>> chris >>> >>> On Oct 16, 2009, at 9:51 PM, joris meys wrote: >>> >>>> Thanks, but it's not really what I'm looking for. My alignments are >>>> flushed, so basically a matrix from which I need to select columns. >>>> These column indices come from an array with random numbers. It works >>>> with slice() from AlignI, I was just wondering if you could use an >>>> index of some sort like for an array. Something like >>>> >>>> $newaln = $oldaln [ @indices ] >>>> >>>> Thing is, I use this loop for it, but it doesn't want to work. $aln is >>>> a simpleAlign object >>>> >>>> use Bio::Align::Utilities qw(:all); >>>> >>>> my $out = Bio::SimpleAlign -> new; >>>> foreach (@indices){ >>>> ? ? ? my $temp = $aln -> slice($_ ,$_); >>>> ? ? ? eval{$out = &cat($out,$temp)} or print $@ and $out = $temp; >>>> ? } >>>> I use the eval construction to get passed a first error, but it >>>> doesn't work. I get as output : >>>> >>>> Undefined subroutine &main::cat called at... >>>> and then the result of the last round in the loop. I must be doing >>>> something wrong with the cat function from Align::Utilities. ?But I >>>> have no clue what. >>>> >>>> The other function from the Utilities package, bootstrap_replicates, >>>> works just fine. >>>> >>>> Any tips are welcome >>>> Kind regards >>>> Joris >>>> >>>> On Sat, Oct 17, 2009 at 3:27 AM, Mark A. Jensen wrote: >>>>> >>>>> Hi Joris >>>>> You may find what you're looking for in this post: >>>>> http://lists.open-bio.org/pipermail/bioperl-l/2009-September/031292.html >>>>> cheers MAJ >>>>> ----- Original Message ----- From: "joris meys" >>>>> To: >>>>> Sent: Friday, October 16, 2009 3:35 PM >>>>> Subject: [Bioperl-l] Bootstrapping positions in alignment >>>>> >>>>> >>>>>> Dear all, >>>>>> >>>>>> I'm using the packages AlignIO and AlignI to construct a bootstrapping >>>>>> procedure on my alignments. There is a function slice() in AlignI I >>>>>> can use, but I actually need just a number of positions, not a slice. >>>>>> Is there any other way of accessing the object so I can just specify >>>>>> one position? >>>>>> >>>>>> Thx in advance >>>>>> Joris >>>>>> _______________________________________________ >>>>>> 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 jorismeys at gmail.com Sat Oct 17 09:47:18 2009 From: jorismeys at gmail.com (joris meys) Date: Sat, 17 Oct 2009 15:47:18 +0200 Subject: [Bioperl-l] Bioperl not available from bioperl.org/DIST through package manager??? Message-ID: Dear all, I have to update my version of bioperl, but my package manager doesn't seem to find it. I have following repositories in my list : ActiveState Package Repository : http://ppm4.activestate.com/MSWin32-x86/5.10/1004/package.xml (11.456 packages) BioPerl-Release Candidates : http://bioperl.org/DIST/RC (3 packages) BioPerl-Regular Releases : http://bioperl.org/DIST (0 packages) --> how so, 0 packages??? CHecked the site, and the ppd file for BioPerl is there. Yet, somehow the package manager says it's not. Anybody a clue as to what is wrong here? Working with ActiveState Perl 5.10.0 Cheers Joris From maj at fortinbras.us Sat Oct 17 10:54:01 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 17 Oct 2009 10:54:01 -0400 Subject: [Bioperl-l] Bioperl not available from bioperl.org/DIST throughpackage manager??? In-Reply-To: References: Message-ID: <009DB529E5264DC69080E8076977BBEA@NewLife> Joris-- I've had this happen occasionally- might try removing and adding the repo again, or try an install BioPerl anyway, to get the cache to kick over- cheers ----- Original Message ----- From: "joris meys" To: Sent: Saturday, October 17, 2009 9:47 AM Subject: [Bioperl-l] Bioperl not available from bioperl.org/DIST throughpackage manager??? > Dear all, > > I have to update my version of bioperl, but my package manager doesn't > seem to find it. I have following repositories in my list : > > ActiveState Package Repository : > http://ppm4.activestate.com/MSWin32-x86/5.10/1004/package.xml (11.456 > packages) > BioPerl-Release Candidates : http://bioperl.org/DIST/RC (3 packages) > BioPerl-Regular Releases : http://bioperl.org/DIST (0 packages) --> > how so, 0 packages??? > > CHecked the site, and the ppd file for BioPerl is there. Yet, somehow > the package manager says it's not. Anybody a clue as to what is wrong > here? > > Working with ActiveState Perl 5.10.0 > > Cheers > Joris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From jorismeys at gmail.com Sat Oct 17 11:35:03 2009 From: jorismeys at gmail.com (joris meys) Date: Sat, 17 Oct 2009 17:35:03 +0200 Subject: [Bioperl-l] Bioperl not available from bioperl.org/DIST through package manager??? In-Reply-To: References: Message-ID: I found the problem. Refreshing, removing and readding the repository, and even a complete reboot of the computer doesn't help. Yet, It works when specifying : BioPerl-Regular Releases : http://bioperl.org/DIST/package.xml as a repository. I think this should be adjusted on the installation page in the WIKI. http://bioperl.open-bio.org/wiki/Installing_Bioperl_on_Windows Cheers Joris On Sat, Oct 17, 2009 at 3:47 PM, joris meys wrote: > Dear all, > > I have to update my version of bioperl, but my package manager doesn't > seem to find it. I have following repositories in my list : > > ActiveState Package Repository : > http://ppm4.activestate.com/MSWin32-x86/5.10/1004/package.xml (11.456 > packages) > BioPerl-Release Candidates : http://bioperl.org/DIST/RC (3 packages) > BioPerl-Regular Releases : http://bioperl.org/DIST (0 packages) ?--> > how so, 0 packages??? > > CHecked the site, and the ppd file for BioPerl is there. Yet, somehow > the package manager says it's not. Anybody a clue as to what is wrong > here? > > Working with ActiveState Perl 5.10.0 > > Cheers > Joris > From cjfields at illinois.edu Sat Oct 17 12:15:36 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Oct 2009 11:15:36 -0500 Subject: [Bioperl-l] Bioperl not available from bioperl.org/DIST through package manager??? In-Reply-To: References: Message-ID: <5C2D0E36-ECAF-442E-B7E0-B6D7A927D644@illinois.edu> The package.xml should be found automatically (i.e. the repo path shouldn't be explicit). Just curious, but are you running ActivePerl 5.10.0 or 5.10.1? On windows? chris On Oct 17, 2009, at 10:35 AM, joris meys wrote: > I found the problem. Refreshing, removing and readding the > repository, and even a complete reboot of the computer doesn't help. > Yet, It works when specifying : > > BioPerl-Regular Releases : http://bioperl.org/DIST/package.xml > as a repository. > > I think this should be adjusted on the installation page in the WIKI. > http://bioperl.open-bio.org/wiki/Installing_Bioperl_on_Windows > > Cheers > Joris > > On Sat, Oct 17, 2009 at 3:47 PM, joris meys > wrote: >> Dear all, >> >> I have to update my version of bioperl, but my package manager >> doesn't >> seem to find it. I have following repositories in my list : >> >> ActiveState Package Repository : >> http://ppm4.activestate.com/MSWin32-x86/5.10/1004/package.xml (11.456 >> packages) >> BioPerl-Release Candidates : http://bioperl.org/DIST/RC (3 packages) >> BioPerl-Regular Releases : http://bioperl.org/DIST (0 packages) --> >> how so, 0 packages??? >> >> CHecked the site, and the ppd file for BioPerl is there. Yet, somehow >> the package manager says it's not. Anybody a clue as to what is wrong >> here? >> >> Working with ActiveState Perl 5.10.0 >> >> Cheers >> Joris >> > > _______________________________________________ > 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 Oct 17 12:10:15 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 17 Oct 2009 12:10:15 -0400 Subject: [Bioperl-l] Bioperl not available from bioperl.org/DIST throughpackage manager??? In-Reply-To: References: Message-ID: Ach, it should just work. I'm not a ppm build guru--- Chris? ----- Original Message ----- From: "joris meys" To: Cc: "Mark A. Jensen" Sent: Saturday, October 17, 2009 11:35 AM Subject: Re: [Bioperl-l] Bioperl not available from bioperl.org/DIST throughpackage manager??? I found the problem. Refreshing, removing and readding the repository, and even a complete reboot of the computer doesn't help. Yet, It works when specifying : BioPerl-Regular Releases : http://bioperl.org/DIST/package.xml as a repository. I think this should be adjusted on the installation page in the WIKI. http://bioperl.open-bio.org/wiki/Installing_Bioperl_on_Windows Cheers Joris On Sat, Oct 17, 2009 at 3:47 PM, joris meys wrote: > Dear all, > > I have to update my version of bioperl, but my package manager doesn't > seem to find it. I have following repositories in my list : > > ActiveState Package Repository : > http://ppm4.activestate.com/MSWin32-x86/5.10/1004/package.xml (11.456 > packages) > BioPerl-Release Candidates : http://bioperl.org/DIST/RC (3 packages) > BioPerl-Regular Releases : http://bioperl.org/DIST (0 packages) --> > how so, 0 packages??? > > CHecked the site, and the ppd file for BioPerl is there. Yet, somehow > the package manager says it's not. Anybody a clue as to what is wrong > here? > > Working with ActiveState Perl 5.10.0 > > Cheers > Joris > _______________________________________________ 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 Mon Oct 19 21:56:36 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 19 Oct 2009 21:56:36 -0400 Subject: [Bioperl-l] BioPerl irony Message-ID: Bio::SimpleAlign inherits from 4 classes, and possess 79 methods. From sidd.basu at gmail.com Tue Oct 20 12:11:12 2009 From: sidd.basu at gmail.com (Siddhartha Basu) Date: Tue, 20 Oct 2009 11:11:12 -0500 Subject: [Bioperl-l] bp_search2gff.pl and strand information Message-ID: <4adde124.0637560a.29c8.062b@mx.google.com> Hi, The bp_search2gff.pl seems to be not giving out strand information for hit entries when i am trying a tblastn format conversion. Here is the test case tried on sample 'tblastn' data file from the latest bioperl. bp_search2gff.pl -i tblastn.out -o tblastn.gff3 -f blast -t hit \ -s tblastn_test --method match_part --addid --target --version 3 The output .... gi|10040111|emb|AL390796.6|AL390796 tblastn_test match_part 7603 7671 34 . 0 ID=HAHU;Target=Sequence:HAHU 56 78;score=34 gi|10040111|emb|AL390796.6|AL390796 tblastn_test match_part 7069 7152 33 . 0 ID=HAHU;Target=Sequence:HAHU 31 58;score=33 test6 tblastn_test match_part 3822 3848 30 . 2 ID=HAHU;Target=Sequence:HAHU 72 80;score=30 test6 tblastn_test match_part 1794 1814 29 . 1 ID=HAHU;Target=Sequence:HAHU 93 99;score=29 I am not sure about the expected behaviour, but assume it will give out the strand information for hit as given in the HSP module documentation and described in the GMOD wiki(http://gmod.org/wiki/Load_BLAST_Into_Chado#Convert_BLAST_analysis_to_GFF3) One thing that i noticed is in line 237 of the script(bp_search2gff.pl), $feature->strand ( $proxyfor->strand * $otherf->strand); will definitely produce the 0(unknown) for tblastn as the query strand is 0 for tblastn report. So, is this behaviour is a feature or bug. What am i missing here. thanks, -siddhartha From robrunyowa at gmail.com Tue Oct 20 13:20:39 2009 From: robrunyowa at gmail.com (Robin Runyowa) Date: Tue, 20 Oct 2009 10:20:39 -0700 Subject: [Bioperl-l] Bio::PopGen::PopStats Message-ID: <1677ba770910201020i4039360emdc7962854dd7be3f@mail.gmail.com> Hi, I am a newbie in bioperl and I am trying to use to Bio::PopGen::PopStats. Unfortunately, I am not sure how to create arrays of objects so I keep getting an error message. My input files are below: testpop3.cvs: SAMPLE,rs0001 Person1,A T Person2,T T Person3,A A Person4,T A Person5,A A testpop4.cvs SAMPLE,rs0001 Per1,A T Per2,T T Per3,A A Per4,T A Per5,A A My script: use Bio::PopGen::PopStats; use Bio::PopGen::Individual; use Bio::PopGen::Genotype; use Bio::PopGen::Population; use Bio::PopGen::IO; my $handle = new Bio::PopGen::IO (-format => 'csv', -file => 'testpop3.cvs'); my $handle2 = new Bio::PopGen::IO (-format => 'csv', -file => 'testpop4.cvs'); my $YRI = $handle ->next_population; my $CEU = $handle2 ->next_population; my @pop = (); push @pop, $YRI; push @pop, $CEU; @markers = $YRI->get_marker_names; my $fst = $stats->Fst(\@pop,\@marker); Thanks, Rob From stubben at lanl.gov Wed Oct 21 11:29:03 2009 From: stubben at lanl.gov (Chris Stubben) Date: Wed, 21 Oct 2009 08:29:03 -0700 (PDT) Subject: [Bioperl-l] How to parse DBLINK Project linetype in Genbank file Message-ID: <25994776.post@talk.nabble.com> I have some Genbank files (from genome sequences) with a DBLINK line type listing the Entrez genome project id. Is there a way to parse this line? I can't seem to find it among the Annotation objects using bioperl 1.6.0 (printing all annotations or just dblinks below) my @annotations = $so->annotation->get_Annotations('dblink'); # nothing --- LOCUS NC_001664 159322 bp DNA linear VRL 16-OCT-2009 DEFINITION Human herpesvirus 6A, complete genome. ACCESSION NC_001664 VERSION NC_001664.2 GI:224020395 DBLINK Project:14462 KEYWORDS . SOURCE Human herpesvirus 6 (HHV-6A) Thanks, Chris Stubben -- View this message in context: http://www.nabble.com/How-to-parse-DBLINK-Project-linetype-in-Genbank-file-tp25994776p25994776.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From maj at fortinbras.us Wed Oct 21 12:06:04 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 21 Oct 2009 12:06:04 -0400 Subject: [Bioperl-l] How to parse DBLINK Project linetype in Genbank file In-Reply-To: <25994776.post@talk.nabble.com> References: <25994776.post@talk.nabble.com> Message-ID: <79833D83CE6D4FA294FCBBEE836E0EE6@NewLife> Chris-- This might be a bug; the HOWTO (at http://www.bioperl.org/wiki/HOWTO:Feature-Annotation#Getting_the_Annotations) states that the GenBank text is 'DBSOURCE'. Maybe we're not parsing the 'DBLINK' GenBank tag? A guru will surely chime in here. MAJ ----- Original Message ----- From: "Chris Stubben" To: Sent: Wednesday, October 21, 2009 11:29 AM Subject: [Bioperl-l] How to parse DBLINK Project linetype in Genbank file > > I have some Genbank files (from genome sequences) with a DBLINK line type > listing the Entrez genome project id. Is there a way to parse this line? > I can't seem to find it among the Annotation objects using bioperl 1.6.0 > (printing all annotations or just dblinks below) > > my @annotations = $so->annotation->get_Annotations('dblink'); # nothing > > --- > LOCUS NC_001664 159322 bp DNA linear VRL > 16-OCT-2009 > DEFINITION Human herpesvirus 6A, complete genome. > ACCESSION NC_001664 > VERSION NC_001664.2 GI:224020395 > DBLINK Project:14462 > KEYWORDS . > SOURCE Human herpesvirus 6 (HHV-6A) > > > Thanks, > > Chris Stubben > -- > View this message in context: > http://www.nabble.com/How-to-parse-DBLINK-Project-linetype-in-Genbank-file-tp25994776p25994776.html > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From SMarkel at accelrys.com Wed Oct 21 12:26:29 2009 From: SMarkel at accelrys.com (Scott Markel) Date: Wed, 21 Oct 2009 12:26:29 -0400 Subject: [Bioperl-l] How to parse DBLINK Project linetype in Genbank file In-Reply-To: <25994776.post@talk.nabble.com> References: <25994776.post@talk.nabble.com> Message-ID: <1F1240778FB0AF46B4E5A72C44D2C7473360A53D@exch1-hi.accelrys.net> Chris, Looking at the code for Bio::SeqIO::genbank dblink annotations are created for DBSOURCE lines, not for DBLINK lines. If you use your script on NP_042883, for example, you'll see a dblink annotation. A case-sensitive grep on DBLINK shows no matches in genbank.pm, so those lines don't currently lead to any annotations. Scott Scott Markel, Ph.D. Principal Bioinformatics Architect email: smarkel at accelrys.com Accelrys (SciTegic R&D) mobile: +1 858 205 3653 10188 Telesis Court, Suite 100 voice: +1 858 799 5603 San Diego, CA 92121 fax: +1 858 799 5222 USA web: http://www.accelrys.com http://www.linkedin.com/in/smarkel Vice President, Board of Directors: International Society for Computational Biology Chair: ISCB Publications Committee Associate Editor: PLoS Computational Biology Editorial Board: Briefings in Bioinformatics -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Stubben Sent: Wednesday, 21 October 2009 8:29 AM To: Bioperl-l at lists.open-bio.org Subject: [Bioperl-l] How to parse DBLINK Project linetype in Genbank file I have some Genbank files (from genome sequences) with a DBLINK line type listing the Entrez genome project id. Is there a way to parse this line? I can't seem to find it among the Annotation objects using bioperl 1.6.0 (printing all annotations or just dblinks below) my @annotations = $so->annotation->get_Annotations('dblink'); # nothing --- LOCUS NC_001664 159322 bp DNA linear VRL 16-OCT-2009 DEFINITION Human herpesvirus 6A, complete genome. ACCESSION NC_001664 VERSION NC_001664.2 GI:224020395 DBLINK Project:14462 KEYWORDS . SOURCE Human herpesvirus 6 (HHV-6A) Thanks, Chris Stubben -- View this message in context: http://www.nabble.com/How-to-parse-DBLINK-Project-linetype-in-Genbank-file-tp25994776p25994776.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. _______________________________________________ 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 Oct 21 12:38:40 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Oct 2009 11:38:40 -0500 Subject: [Bioperl-l] How to parse DBLINK Project linetype in Genbank file In-Reply-To: <79833D83CE6D4FA294FCBBEE836E0EE6@NewLife> References: <25994776.post@talk.nabble.com> <79833D83CE6D4FA294FCBBEE836E0EE6@NewLife> Message-ID: <50F5F8A8-1DE0-499B-A702-18C7756F0A4C@illinois.edu> This should be parsed and available as Bio::Annotation::DBlink. I'll give it a check JIC. chris On Oct 21, 2009, at 11:06 AM, Mark A. Jensen wrote: > Chris-- This might be a bug; the HOWTO > (at http://www.bioperl.org/wiki/HOWTO:Feature-Annotation#Getting_the_Annotations > ) > states that the GenBank text is 'DBSOURCE'. Maybe we're not parsing > the 'DBLINK' GenBank tag? > A guru will surely chime in here. > MAJ > ----- Original Message ----- From: "Chris Stubben" > To: > Sent: Wednesday, October 21, 2009 11:29 AM > Subject: [Bioperl-l] How to parse DBLINK Project linetype in Genbank > file > > >> >> I have some Genbank files (from genome sequences) with a DBLINK >> line type >> listing the Entrez genome project id. Is there a way to parse this >> line? >> I can't seem to find it among the Annotation objects using bioperl >> 1.6.0 >> (printing all annotations or just dblinks below) >> >> my @annotations = $so->annotation->get_Annotations('dblink'); # >> nothing >> >> --- >> LOCUS NC_001664 159322 bp DNA linear VRL >> 16-OCT-2009 >> DEFINITION Human herpesvirus 6A, complete genome. >> ACCESSION NC_001664 >> VERSION NC_001664.2 GI:224020395 >> DBLINK Project:14462 >> KEYWORDS . >> SOURCE Human herpesvirus 6 (HHV-6A) >> >> >> Thanks, >> >> Chris Stubben >> -- >> View this message in context: http://www.nabble.com/How-to-parse-DBLINK-Project-linetype-in-Genbank-file-tp25994776p25994776.html >> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. >> >> _______________________________________________ >> 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 Oct 21 16:05:31 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Oct 2009 15:05:31 -0500 Subject: [Bioperl-l] How to parse DBLINK Project linetype in Genbank file In-Reply-To: <50F5F8A8-1DE0-499B-A702-18C7756F0A4C@illinois.edu> References: <25994776.post@talk.nabble.com> <79833D83CE6D4FA294FCBBEE836E0EE6@NewLife> <50F5F8A8-1DE0-499B-A702-18C7756F0A4C@illinois.edu> Message-ID: Chris, Mark, Looks like it isn't parsed. I'll add a bug report to track, should be easy enough to add. Notably, gbdriver catches it but chokes b/c the type mapper is expecting a Bio::Annotation::DBlink (any non-specific information is by default pushed into a Bio::Annotation::SimpleValue, hence the painful death). chris On Oct 21, 2009, at 11:38 AM, Chris Fields wrote: > This should be parsed and available as Bio::Annotation::DBlink. > I'll give it a check JIC. > > chris > > On Oct 21, 2009, at 11:06 AM, Mark A. Jensen wrote: > >> Chris-- This might be a bug; the HOWTO >> (at http://www.bioperl.org/wiki/HOWTO:Feature-Annotation#Getting_the_Annotations >> ) >> states that the GenBank text is 'DBSOURCE'. Maybe we're not parsing >> the 'DBLINK' GenBank tag? >> A guru will surely chime in here. >> MAJ >> ----- Original Message ----- From: "Chris Stubben" >> To: >> Sent: Wednesday, October 21, 2009 11:29 AM >> Subject: [Bioperl-l] How to parse DBLINK Project linetype in >> Genbank file >> >> >>> >>> I have some Genbank files (from genome sequences) with a DBLINK >>> line type >>> listing the Entrez genome project id. Is there a way to parse >>> this line? >>> I can't seem to find it among the Annotation objects using bioperl >>> 1.6.0 >>> (printing all annotations or just dblinks below) >>> >>> my @annotations = $so->annotation->get_Annotations('dblink'); # >>> nothing >>> >>> --- >>> LOCUS NC_001664 159322 bp DNA linear VRL >>> 16-OCT-2009 >>> DEFINITION Human herpesvirus 6A, complete genome. >>> ACCESSION NC_001664 >>> VERSION NC_001664.2 GI:224020395 >>> DBLINK Project:14462 >>> KEYWORDS . >>> SOURCE Human herpesvirus 6 (HHV-6A) >>> >>> >>> Thanks, >>> >>> Chris Stubben >>> -- >>> View this message in context: http://www.nabble.com/How-to-parse-DBLINK-Project-linetype-in-Genbank-file-tp25994776p25994776.html >>> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. >>> >>> _______________________________________________ >>> 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 adam at ali.as Wed Oct 21 20:21:09 2009 From: adam at ali.as (Adam Kennedy) Date: Thu, 22 Oct 2009 11:21:09 +1100 Subject: [Bioperl-l] Testing Needed: Strawberry Perl October 2009 to provide support for BioPerl Message-ID: <255d58530910211721k59552dfeod14f3f4c58320196@mail.gmail.com> Dear BioPeople Since we added a "Live Support Chat" link to the frontpage of the Strawberry Perl website ( http://strawberryperl.com/ ) we've noticed that one of the main types of visitors that we see in the IRC channel ( #win32 on irc.perl.org ) is biologists trying to install various things. As a result, for the October 2009 release of Strawberry Perl, we've prioritised adding support for CPAN-installation of BioPerl. Changes include a major improvement to crypto support which provides OpenSSL and support for https:// URL, we now ship Postgres and MySQL DBI drivers in the default installation, and we have added Berkely DB support as well. I'm happy to report that we now believe we are in a position to officially support the installation of BioPerl. Running "install BioPerl" from the CPAN client should now work correctly, for the default set of options, and BioPerl-dependant packages on the CPAN should recursively install correctly. Prior to the official release next week, we would appreciate testing from the BioPerl community. Release candidate installers for the October release are available at the following URLs http://strawberryperl.com/download/strawberryperl-5.10.1.0.msi http://strawberryperl.com/download/strawberryperl-5.8.9.3.msi Once installed, run Start -> Program Files -> Strawberry Perl -> CPAN Client >From the CPAN client command line, run "install BioPerl" and select the default options. Once installed, you should be able to do anything you do normally with a BioPerl install. Assuming all goes well in this release, for the next release January 2010 we plan to also produce a "Strawberry Perl Professional" distribution that will bundle BioPerl as part of the default installation, as well as a Perl IDE and other useful packages. Success or failure of the release candidate can be reported either here or to #win32 on irc.perl.org. Adam K From cjfields at illinois.edu Thu Oct 22 00:02:56 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Oct 2009 23:02:56 -0500 Subject: [Bioperl-l] Testing Needed: Strawberry Perl October 2009 to provide support for BioPerl In-Reply-To: <255d58530910211721k59552dfeod14f3f4c58320196@mail.gmail.com> References: <255d58530910211721k59552dfeod14f3f4c58320196@mail.gmail.com> Message-ID: Adam, I can test this using Remote Desktop on a couple PC's here running XP (don't have access to Vista). The links didn't work for me, though. chris On Oct 21, 2009, at 7:21 PM, Adam Kennedy wrote: > Dear BioPeople > > Since we added a "Live Support Chat" link to the frontpage of the > Strawberry Perl website ( http://strawberryperl.com/ ) we've noticed > that one of the main types of visitors that we see in the IRC channel > ( #win32 on irc.perl.org ) is biologists trying to install various > things. > > As a result, for the October 2009 release of Strawberry Perl, we've > prioritised adding support for CPAN-installation of BioPerl. > > Changes include a major improvement to crypto support which provides > OpenSSL and support for https:// URL, we now ship Postgres and MySQL > DBI drivers in the default installation, and we have added Berkely DB > support as well. > > I'm happy to report that we now believe we are in a position to > officially support the installation of BioPerl. > > Running "install BioPerl" from the CPAN client should now work > correctly, for the default set of options, and BioPerl-dependant > packages on the CPAN should recursively install correctly. > > Prior to the official release next week, we would appreciate testing > from the BioPerl community. > > Release candidate installers for the October release are available at > the following URLs > > http://strawberryperl.com/download/strawberryperl-5.10.1.0.msi > > http://strawberryperl.com/download/strawberryperl-5.8.9.3.msi > > Once installed, run Start -> Program Files -> Strawberry Perl -> > CPAN Client > >> From the CPAN client command line, run "install BioPerl" and select > the default options. > > Once installed, you should be able to do anything you do normally with > a BioPerl install. > > Assuming all goes well in this release, for the next release January > 2010 we plan to also produce a "Strawberry Perl Professional" > distribution that will bundle BioPerl as part of the default > installation, as well as a Perl IDE and other useful packages. > > Success or failure of the release candidate can be reported either > here or to #win32 on irc.perl.org. > > Adam K > _______________________________________________ > 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 Thu Oct 22 00:27:57 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Thu, 22 Oct 2009 00:27:57 -0400 Subject: [Bioperl-l] Testing Needed: Strawberry Perl October 2009 toprovide support for BioPerl In-Reply-To: References: <255d58530910211721k59552dfeod14f3f4c58320196@mail.gmail.com> Message-ID: <41457A424DB54AEC9FCAE100D3BD4FDB@NewLife> Hi Guys, I'll see if I can squish it through Vista. (Adam, this is excellent.) cheers MAJ ----- Original Message ----- From: "Chris Fields" To: "Adam Kennedy" Cc: Sent: Thursday, October 22, 2009 12:02 AM Subject: Re: [Bioperl-l] Testing Needed: Strawberry Perl October 2009 toprovide support for BioPerl > Adam, > > I can test this using Remote Desktop on a couple PC's here running XP (don't > have access to Vista). The links didn't work for me, though. > > chris > > On Oct 21, 2009, at 7:21 PM, Adam Kennedy wrote: > >> Dear BioPeople >> >> Since we added a "Live Support Chat" link to the frontpage of the >> Strawberry Perl website ( http://strawberryperl.com/ ) we've noticed >> that one of the main types of visitors that we see in the IRC channel >> ( #win32 on irc.perl.org ) is biologists trying to install various >> things. >> >> As a result, for the October 2009 release of Strawberry Perl, we've >> prioritised adding support for CPAN-installation of BioPerl. >> >> Changes include a major improvement to crypto support which provides >> OpenSSL and support for https:// URL, we now ship Postgres and MySQL >> DBI drivers in the default installation, and we have added Berkely DB >> support as well. >> >> I'm happy to report that we now believe we are in a position to >> officially support the installation of BioPerl. >> >> Running "install BioPerl" from the CPAN client should now work >> correctly, for the default set of options, and BioPerl-dependant >> packages on the CPAN should recursively install correctly. >> >> Prior to the official release next week, we would appreciate testing >> from the BioPerl community. >> >> Release candidate installers for the October release are available at >> the following URLs >> >> http://strawberryperl.com/download/strawberryperl-5.10.1.0.msi >> >> http://strawberryperl.com/download/strawberryperl-5.8.9.3.msi >> >> Once installed, run Start -> Program Files -> Strawberry Perl -> CPAN Client >> >>> From the CPAN client command line, run "install BioPerl" and select >> the default options. >> >> Once installed, you should be able to do anything you do normally with >> a BioPerl install. >> >> Assuming all goes well in this release, for the next release January >> 2010 we plan to also produce a "Strawberry Perl Professional" >> distribution that will bundle BioPerl as part of the default >> installation, as well as a Perl IDE and other useful packages. >> >> Success or failure of the release candidate can be reported either >> here or to #win32 on irc.perl.org. >> >> Adam K >> _______________________________________________ >> 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 adamkennedybackup at gmail.com Thu Oct 22 00:44:03 2009 From: adamkennedybackup at gmail.com (Adam Kennedy) Date: Thu, 22 Oct 2009 15:44:03 +1100 Subject: [Bioperl-l] Testing Needed: Strawberry Perl October 2009 to provide support for BioPerl In-Reply-To: References: <255d58530910211721k59552dfeod14f3f4c58320196@mail.gmail.com> Message-ID: My apologies, there's a hyphen missing in there. http://strawberryperl.com/download/strawberry-perl-5.10.1.0.msi http://strawberryperl.com/download/strawberry-perl-5.8.9.3.msi Adam K 2009/10/22 Chris Fields : > Adam, > > I can test this using Remote Desktop on a couple PC's here running XP (don't > have access to Vista). ?The links didn't work for me, though. > > chris > > On Oct 21, 2009, at 7:21 PM, Adam Kennedy wrote: > >> Dear BioPeople >> >> Since we added a "Live Support Chat" link to the frontpage of the >> Strawberry Perl website ( http://strawberryperl.com/ ) we've noticed >> that one of the main types of visitors that we see in the IRC channel >> ( #win32 on irc.perl.org ) is biologists trying to install various >> things. >> >> As a result, for the October 2009 release of Strawberry Perl, we've >> prioritised adding support for CPAN-installation of BioPerl. >> >> Changes include a major improvement to crypto support which provides >> OpenSSL and support for https:// URL, we now ship Postgres and MySQL >> DBI drivers in the default installation, and we have added Berkely DB >> support as well. >> >> I'm happy to report that we now believe we are in a position to >> officially support the installation of BioPerl. >> >> Running "install BioPerl" from the CPAN client should now work >> correctly, for the default set of options, and BioPerl-dependant >> packages on the CPAN should recursively install correctly. >> >> Prior to the official release next week, we would appreciate testing >> from the BioPerl community. >> >> Release candidate installers for the October release are available at >> the following URLs >> >> http://strawberryperl.com/download/strawberryperl-5.10.1.0.msi >> >> http://strawberryperl.com/download/strawberryperl-5.8.9.3.msi >> >> Once installed, run Start -> Program Files -> Strawberry Perl -> CPAN >> Client >> >>> From the CPAN client command line, run "install BioPerl" and select >> >> the default options. >> >> Once installed, you should be able to do anything you do normally with >> a BioPerl install. >> >> Assuming all goes well in this release, for the next release January >> 2010 we plan to also produce a "Strawberry Perl Professional" >> distribution that will bundle BioPerl as part of the default >> installation, as well as a Perl IDE and other useful packages. >> >> Success or failure of the release candidate can be reported either >> here or to #win32 on irc.perl.org. >> >> Adam K >> _______________________________________________ >> 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 adam at ali.as Thu Oct 22 00:44:43 2009 From: adam at ali.as (Adam Kennedy) Date: Thu, 22 Oct 2009 15:44:43 +1100 Subject: [Bioperl-l] Testing Needed: Strawberry Perl October 2009 to provide support for BioPerl In-Reply-To: References: <255d58530910211721k59552dfeod14f3f4c58320196@mail.gmail.com> Message-ID: <255d58530910212144j5a4b2f38td916bc048508b4a9@mail.gmail.com> Note: These are the corrected link. http://strawberryperl.com/download/strawberry-perl-5.10.1.0.msi http://strawberryperl.com/download/strawberry-perl-5.8.9.3.msi Adam K On Thu, Oct 22, 2009 at 3:02 PM, Chris Fields wrote: > Adam, > > I can test this using Remote Desktop on a couple PC's here running XP (don't > have access to Vista). ?The links didn't work for me, though. > > chris > > On Oct 21, 2009, at 7:21 PM, Adam Kennedy wrote: > >> Dear BioPeople >> >> Since we added a "Live Support Chat" link to the frontpage of the >> Strawberry Perl website ( http://strawberryperl.com/ ) we've noticed >> that one of the main types of visitors that we see in the IRC channel >> ( #win32 on irc.perl.org ) is biologists trying to install various >> things. >> >> As a result, for the October 2009 release of Strawberry Perl, we've >> prioritised adding support for CPAN-installation of BioPerl. >> >> Changes include a major improvement to crypto support which provides >> OpenSSL and support for https:// URL, we now ship Postgres and MySQL >> DBI drivers in the default installation, and we have added Berkely DB >> support as well. >> >> I'm happy to report that we now believe we are in a position to >> officially support the installation of BioPerl. >> >> Running "install BioPerl" from the CPAN client should now work >> correctly, for the default set of options, and BioPerl-dependant >> packages on the CPAN should recursively install correctly. >> >> Prior to the official release next week, we would appreciate testing >> from the BioPerl community. >> >> Release candidate installers for the October release are available at >> the following URLs >> >> http://strawberryperl.com/download/strawberryperl-5.10.1.0.msi >> >> http://strawberryperl.com/download/strawberryperl-5.8.9.3.msi >> >> Once installed, run Start -> Program Files -> Strawberry Perl -> CPAN >> Client >> >>> From the CPAN client command line, run "install BioPerl" and select >> >> the default options. >> >> Once installed, you should be able to do anything you do normally with >> a BioPerl install. >> >> Assuming all goes well in this release, for the next release January >> 2010 we plan to also produce a "Strawberry Perl Professional" >> distribution that will bundle BioPerl as part of the default >> installation, as well as a Perl IDE and other useful packages. >> >> Success or failure of the release candidate can be reported either >> here or to #win32 on irc.perl.org. >> >> Adam K >> _______________________________________________ >> 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 Oct 22 08:25:40 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Oct 2009 07:25:40 -0500 Subject: [Bioperl-l] Testing Needed: Strawberry Perl October 2009 to provide support for BioPerl In-Reply-To: <255d58530910212144j5a4b2f38td916bc048508b4a9@mail.gmail.com> References: <255d58530910211721k59552dfeod14f3f4c58320196@mail.gmail.com> <255d58530910212144j5a4b2f38td916bc048508b4a9@mail.gmail.com> Message-ID: <06116C4D-3ED6-4926-A1BC-347EC64E27FC@illinois.edu> Okay, will test and report back. chris On Oct 21, 2009, at 11:44 PM, Adam Kennedy wrote: > Note: These are the corrected link. > > http://strawberryperl.com/download/strawberry-perl-5.10.1.0.msi > > http://strawberryperl.com/download/strawberry-perl-5.8.9.3.msi > > Adam K > > On Thu, Oct 22, 2009 at 3:02 PM, Chris Fields > wrote: >> Adam, >> >> I can test this using Remote Desktop on a couple PC's here running >> XP (don't >> have access to Vista). The links didn't work for me, though. >> >> chris >> >> On Oct 21, 2009, at 7:21 PM, Adam Kennedy wrote: >> >>> Dear BioPeople >>> >>> Since we added a "Live Support Chat" link to the frontpage of the >>> Strawberry Perl website ( http://strawberryperl.com/ ) we've noticed >>> that one of the main types of visitors that we see in the IRC >>> channel >>> ( #win32 on irc.perl.org ) is biologists trying to install various >>> things. >>> >>> As a result, for the October 2009 release of Strawberry Perl, we've >>> prioritised adding support for CPAN-installation of BioPerl. >>> >>> Changes include a major improvement to crypto support which provides >>> OpenSSL and support for https:// URL, we now ship Postgres and MySQL >>> DBI drivers in the default installation, and we have added Berkely >>> DB >>> support as well. >>> >>> I'm happy to report that we now believe we are in a position to >>> officially support the installation of BioPerl. >>> >>> Running "install BioPerl" from the CPAN client should now work >>> correctly, for the default set of options, and BioPerl-dependant >>> packages on the CPAN should recursively install correctly. >>> >>> Prior to the official release next week, we would appreciate testing >>> from the BioPerl community. >>> >>> Release candidate installers for the October release are available >>> at >>> the following URLs >>> >>> http://strawberryperl.com/download/strawberryperl-5.10.1.0.msi >>> >>> http://strawberryperl.com/download/strawberryperl-5.8.9.3.msi >>> >>> Once installed, run Start -> Program Files -> Strawberry Perl -> >>> CPAN >>> Client >>> >>>> From the CPAN client command line, run "install BioPerl" and select >>> >>> the default options. >>> >>> Once installed, you should be able to do anything you do normally >>> with >>> a BioPerl install. >>> >>> Assuming all goes well in this release, for the next release January >>> 2010 we plan to also produce a "Strawberry Perl Professional" >>> distribution that will bundle BioPerl as part of the default >>> installation, as well as a Perl IDE and other useful packages. >>> >>> Success or failure of the release candidate can be reported either >>> here or to #win32 on irc.perl.org. >>> >>> Adam K >>> _______________________________________________ >>> 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 maj at fortinbras.us Thu Oct 22 10:26:41 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Thu, 22 Oct 2009 10:26:41 -0400 Subject: [Bioperl-l] Testing Needed: Strawberry Perl October 2009 toprovide support for BioPerl In-Reply-To: References: <255d58530910211721k59552dfeod14f3f4c58320196@mail.gmail.com> Message-ID: <62EFB1F17D8F441087229D3E3E0A683D@NewLife> At this moment, plain "install BioPerl" yields a 'don't know what it is error' for the 5.10 distribution on Vista. MAJ ----- Original Message ----- From: "Adam Kennedy" To: "Chris Fields" Cc: Sent: Thursday, October 22, 2009 12:44 AM Subject: Re: [Bioperl-l] Testing Needed: Strawberry Perl October 2009 toprovide support for BioPerl My apologies, there's a hyphen missing in there. http://strawberryperl.com/download/strawberry-perl-5.10.1.0.msi http://strawberryperl.com/download/strawberry-perl-5.8.9.3.msi Adam K 2009/10/22 Chris Fields : > Adam, > > I can test this using Remote Desktop on a couple PC's here running XP (don't > have access to Vista). The links didn't work for me, though. > > chris > > On Oct 21, 2009, at 7:21 PM, Adam Kennedy wrote: > >> Dear BioPeople >> >> Since we added a "Live Support Chat" link to the frontpage of the >> Strawberry Perl website ( http://strawberryperl.com/ ) we've noticed >> that one of the main types of visitors that we see in the IRC channel >> ( #win32 on irc.perl.org ) is biologists trying to install various >> things. >> >> As a result, for the October 2009 release of Strawberry Perl, we've >> prioritised adding support for CPAN-installation of BioPerl. >> >> Changes include a major improvement to crypto support which provides >> OpenSSL and support for https:// URL, we now ship Postgres and MySQL >> DBI drivers in the default installation, and we have added Berkely DB >> support as well. >> >> I'm happy to report that we now believe we are in a position to >> officially support the installation of BioPerl. >> >> Running "install BioPerl" from the CPAN client should now work >> correctly, for the default set of options, and BioPerl-dependant >> packages on the CPAN should recursively install correctly. >> >> Prior to the official release next week, we would appreciate testing >> from the BioPerl community. >> >> Release candidate installers for the October release are available at >> the following URLs >> >> http://strawberryperl.com/download/strawberryperl-5.10.1.0.msi >> >> http://strawberryperl.com/download/strawberryperl-5.8.9.3.msi >> >> Once installed, run Start -> Program Files -> Strawberry Perl -> CPAN >> Client >> >>> From the CPAN client command line, run "install BioPerl" and select >> >> the default options. >> >> Once installed, you should be able to do anything you do normally with >> a BioPerl install. >> >> Assuming all goes well in this release, for the next release January >> 2010 we plan to also produce a "Strawberry Perl Professional" >> distribution that will bundle BioPerl as part of the default >> installation, as well as a Perl IDE and other useful packages. >> >> Success or failure of the release candidate can be reported either >> here or to #win32 on irc.perl.org. >> >> Adam K >> _______________________________________________ >> 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 maj at fortinbras.us Thu Oct 22 10:45:30 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Thu, 22 Oct 2009 10:45:30 -0400 Subject: [Bioperl-l] Testing Needed: Strawberry Perl October 2009 toprovide support for BioPerl In-Reply-To: References: <255d58530910211721k59552dfeod14f3f4c58320196@mail.gmail.com> Message-ID: <5EE2D3A054F144B28A61F4C2337B34F2@NewLife> Also for the 5.8.9 dist, at this moment, plain "install BioPerl" yields a 'don't know what it is error' on Vista. MAJ ----- Original Message ----- From: "Adam Kennedy" To: "Chris Fields" Cc: Sent: Thursday, October 22, 2009 12:44 AM Subject: Re: [Bioperl-l] Testing Needed: Strawberry Perl October 2009 toprovide support for BioPerl My apologies, there's a hyphen missing in there. http://strawberryperl.com/download/strawberry-perl-5.10.1.0.msi http://strawberryperl.com/download/strawberry-perl-5.8.9.3.msi Adam K 2009/10/22 Chris Fields : > Adam, > > I can test this using Remote Desktop on a couple PC's here running XP (don't > have access to Vista). The links didn't work for me, though. > > chris > > On Oct 21, 2009, at 7:21 PM, Adam Kennedy wrote: > >> Dear BioPeople >> >> Since we added a "Live Support Chat" link to the frontpage of the >> Strawberry Perl website ( http://strawberryperl.com/ ) we've noticed >> that one of the main types of visitors that we see in the IRC channel >> ( #win32 on irc.perl.org ) is biologists trying to install various >> things. >> >> As a result, for the October 2009 release of Strawberry Perl, we've >> prioritised adding support for CPAN-installation of BioPerl. >> >> Changes include a major improvement to crypto support which provides >> OpenSSL and support for https:// URL, we now ship Postgres and MySQL >> DBI drivers in the default installation, and we have added Berkely DB >> support as well. >> >> I'm happy to report that we now believe we are in a position to >> officially support the installation of BioPerl. >> >> Running "install BioPerl" from the CPAN client should now work >> correctly, for the default set of options, and BioPerl-dependant >> packages on the CPAN should recursively install correctly. >> >> Prior to the official release next week, we would appreciate testing >> from the BioPerl community. >> >> Release candidate installers for the October release are available at >> the following URLs >> >> http://strawberryperl.com/download/strawberryperl-5.10.1.0.msi >> >> http://strawberryperl.com/download/strawberryperl-5.8.9.3.msi >> >> Once installed, run Start -> Program Files -> Strawberry Perl -> CPAN >> Client >> >>> From the CPAN client command line, run "install BioPerl" and select >> >> the default options. >> >> Once installed, you should be able to do anything you do normally with >> a BioPerl install. >> >> Assuming all goes well in this release, for the next release January >> 2010 we plan to also produce a "Strawberry Perl Professional" >> distribution that will bundle BioPerl as part of the default >> installation, as well as a Perl IDE and other useful packages. >> >> Success or failure of the release candidate can be reported either >> here or to #win32 on irc.perl.org. >> >> Adam K >> _______________________________________________ >> 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 cjfields at illinois.edu Thu Oct 22 12:21:12 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Oct 2009 11:21:12 -0500 Subject: [Bioperl-l] Testing Needed: Strawberry Perl October 2009 toprovide support for BioPerl In-Reply-To: <5EE2D3A054F144B28A61F4C2337B34F2@NewLife> References: <255d58530910211721k59552dfeod14f3f4c58320196@mail.gmail.com> <5EE2D3A054F144B28A61F4C2337B34F2@NewLife> Message-ID: <7713734A-B262-468B-8822-1A68A5D73213@illinois.edu> If you run 'install CJFIELDS/BioPerl-1.6.1.tar.gz' it works (at least for perl 5.10.1), but it's a bit noisy. Kept having missing dll issues (expat, libxml, etc). chris On Oct 22, 2009, at 9:45 AM, Mark A. Jensen wrote: > Also for the 5.8.9 dist, at this moment, plain "install BioPerl" > yields a 'don't know what it is error' on Vista. > MAJ > > ----- Original Message ----- From: "Adam Kennedy" > > To: "Chris Fields" > Cc: > Sent: Thursday, October 22, 2009 12:44 AM > Subject: Re: [Bioperl-l] Testing Needed: Strawberry Perl October > 2009 toprovide support for BioPerl > > > My apologies, there's a hyphen missing in there. > > > http://strawberryperl.com/download/strawberry-perl-5.10.1.0.msi > > http://strawberryperl.com/download/strawberry-perl-5.8.9.3.msi > > Adam K > > 2009/10/22 Chris Fields : >> Adam, >> >> I can test this using Remote Desktop on a couple PC's here running >> XP (don't >> have access to Vista). The links didn't work for me, though. >> >> chris >> >> On Oct 21, 2009, at 7:21 PM, Adam Kennedy wrote: >> >>> Dear BioPeople >>> >>> Since we added a "Live Support Chat" link to the frontpage of the >>> Strawberry Perl website ( http://strawberryperl.com/ ) we've noticed >>> that one of the main types of visitors that we see in the IRC >>> channel >>> ( #win32 on irc.perl.org ) is biologists trying to install various >>> things. >>> >>> As a result, for the October 2009 release of Strawberry Perl, we've >>> prioritised adding support for CPAN-installation of BioPerl. >>> >>> Changes include a major improvement to crypto support which provides >>> OpenSSL and support for https:// URL, we now ship Postgres and MySQL >>> DBI drivers in the default installation, and we have added Berkely >>> DB >>> support as well. >>> >>> I'm happy to report that we now believe we are in a position to >>> officially support the installation of BioPerl. >>> >>> Running "install BioPerl" from the CPAN client should now work >>> correctly, for the default set of options, and BioPerl-dependant >>> packages on the CPAN should recursively install correctly. >>> >>> Prior to the official release next week, we would appreciate testing >>> from the BioPerl community. >>> >>> Release candidate installers for the October release are available >>> at >>> the following URLs >>> >>> http://strawberryperl.com/download/strawberryperl-5.10.1.0.msi >>> >>> http://strawberryperl.com/download/strawberryperl-5.8.9.3.msi >>> >>> Once installed, run Start -> Program Files -> Strawberry Perl -> >>> CPAN >>> Client >>> >>>> From the CPAN client command line, run "install BioPerl" and select >>> >>> the default options. >>> >>> Once installed, you should be able to do anything you do normally >>> with >>> a BioPerl install. >>> >>> Assuming all goes well in this release, for the next release January >>> 2010 we plan to also produce a "Strawberry Perl Professional" >>> distribution that will bundle BioPerl as part of the default >>> installation, as well as a Perl IDE and other useful packages. >>> >>> Success or failure of the release candidate can be reported either >>> here or to #win32 on irc.perl.org. >>> >>> Adam K >>> _______________________________________________ >>> 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 > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From j_martin at lbl.gov Thu Oct 22 12:55:25 2009 From: j_martin at lbl.gov (Joel Martin) Date: Thu, 22 Oct 2009 09:55:25 -0700 Subject: [Bioperl-l] Testing Needed: Strawberry Perl October 2009 toprovide support for BioPerl In-Reply-To: <5EE2D3A054F144B28A61F4C2337B34F2@NewLife> References: <255d58530910211721k59552dfeod14f3f4c58320196@mail.gmail.com> <5EE2D3A054F144B28A61F4C2337B34F2@NewLife> Message-ID: <20091022165525.GA3318@eniac.jgi-psf.org> Hello, you can install CJFIELDS/BioPerl-1.6.1.tar.gz Joel On Thu, Oct 22, 2009 at 10:45:30AM -0400, Mark A. Jensen wrote: > Also for the 5.8.9 dist, at this moment, plain "install BioPerl" > yields a 'don't know what it is error' on Vista. > MAJ > > ----- Original Message ----- From: "Adam Kennedy" > > To: "Chris Fields" > Cc: > Sent: Thursday, October 22, 2009 12:44 AM > Subject: Re: [Bioperl-l] Testing Needed: Strawberry Perl October 2009 > toprovide support for BioPerl > > > My apologies, there's a hyphen missing in there. > > > http://strawberryperl.com/download/strawberry-perl-5.10.1.0.msi > > http://strawberryperl.com/download/strawberry-perl-5.8.9.3.msi > > Adam K > > 2009/10/22 Chris Fields : >> Adam, >> >> I can test this using Remote Desktop on a couple PC's here running XP >> (don't >> have access to Vista). The links didn't work for me, though. >> >> chris >> >> On Oct 21, 2009, at 7:21 PM, Adam Kennedy wrote: >> >>> Dear BioPeople >>> >>> Since we added a "Live Support Chat" link to the frontpage of the >>> Strawberry Perl website ( http://strawberryperl.com/ ) we've noticed >>> that one of the main types of visitors that we see in the IRC channel >>> ( #win32 on irc.perl.org ) is biologists trying to install various >>> things. >>> >>> As a result, for the October 2009 release of Strawberry Perl, we've >>> prioritised adding support for CPAN-installation of BioPerl. >>> >>> Changes include a major improvement to crypto support which provides >>> OpenSSL and support for https:// URL, we now ship Postgres and MySQL >>> DBI drivers in the default installation, and we have added Berkely DB >>> support as well. >>> >>> I'm happy to report that we now believe we are in a position to >>> officially support the installation of BioPerl. >>> >>> Running "install BioPerl" from the CPAN client should now work >>> correctly, for the default set of options, and BioPerl-dependant >>> packages on the CPAN should recursively install correctly. >>> >>> Prior to the official release next week, we would appreciate testing >>> from the BioPerl community. >>> >>> Release candidate installers for the October release are available at >>> the following URLs >>> >>> http://strawberryperl.com/download/strawberryperl-5.10.1.0.msi >>> >>> http://strawberryperl.com/download/strawberryperl-5.8.9.3.msi >>> >>> Once installed, run Start -> Program Files -> Strawberry Perl -> CPAN >>> Client >>> >>>> From the CPAN client command line, run "install BioPerl" and select >>> >>> the default options. >>> >>> Once installed, you should be able to do anything you do normally with >>> a BioPerl install. >>> >>> Assuming all goes well in this release, for the next release January >>> 2010 we plan to also produce a "Strawberry Perl Professional" >>> distribution that will bundle BioPerl as part of the default >>> installation, as well as a Perl IDE and other useful packages. >>> >>> Success or failure of the release candidate can be reported either >>> here or to #win32 on irc.perl.org. >>> >>> Adam K >>> _______________________________________________ >>> 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 > > > _______________________________________________ > 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 Thu Oct 22 18:23:30 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Thu, 22 Oct 2009 18:23:30 -0400 Subject: [Bioperl-l] a PerlIO layer for Bio::SeqIO Message-ID: Hi All: Have you ever wanted to do this? open($f, "<:via(SeqIO)", "my.fas"); open($g, ">:via(SeqIO::embl)", "my.fas.embl"); while (<$f>) { print $g $_; } Or this? open($f, "<:via(SeqIO)", "my.fas"); open(STDOUT, ">:via(SeqIO::fasta)"); $seq = <$f>; print "The following is an example of FASTA format:", $seq; Or even this? (tied *STDOUT)->set_write_format('gcg'); print "While this is an example of GCG:", $seq; Now you can, and much more. See http://search.cpan.org/search?query=PerlIO::via::SeqIO Send me the bugs. cheers, MAJ From Russell.Smithies at agresearch.co.nz Thu Oct 22 18:57:01 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Fri, 23 Oct 2009 11:57:01 +1300 Subject: [Bioperl-l] a PerlIO layer for Bio::SeqIO In-Reply-To: References: Message-ID: <18DF7D20DFEC044098A1062202F5FFF32B62D67492@exchsth.agresearch.co.nz> Why anyone would want to do it this way is the only thing that's bugging me ;-) Maybe I'm a bit dense this morning but what's the advantage? --Russell (I need more coffee) > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Mark A. Jensen > Sent: Friday, 23 October 2009 11:24 a.m. > To: BioPerl List > Subject: [Bioperl-l] a PerlIO layer for Bio::SeqIO > > Hi All: > > Have you ever wanted to do this? > > open($f, "<:via(SeqIO)", "my.fas"); > open($g, ">:via(SeqIO::embl)", "my.fas.embl"); > while (<$f>) { print $g $_; } > > Or this? > > open($f, "<:via(SeqIO)", "my.fas"); > open(STDOUT, ">:via(SeqIO::fasta)"); > $seq = <$f>; > print "The following is an example of FASTA format:", $seq; > > Or even this? > > (tied *STDOUT)->set_write_format('gcg'); > print "While this is an example of GCG:", $seq; > > Now you can, and much more. See > http://search.cpan.org/search?query=PerlIO::via::SeqIO > > Send me the bugs. > cheers, > MAJ > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From maj at fortinbras.us Thu Oct 22 19:03:52 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Thu, 22 Oct 2009 19:03:52 -0400 Subject: [Bioperl-l] a PerlIO layer for Bio::SeqIO In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF32B62D67492@exchsth.agresearch.co.nz> References: <18DF7D20DFEC044098A1062202F5FFF32B62D67492@exchsth.agresearch.co.nz> Message-ID: <1DD55DFD52CE4A658652907BE02B30AE@NewLife> Because it's fun! Also: use CGI; use PerlIO::via::SeqIO; use strict; use warnings; my $q = new CGI; my ($seqfh, $dup); open($seqfh, "<:via(SeqIO)", 'test.fas'); open(STDOUT, ">:via(SeqIO::fasta)"); my $s = <$seqfh>; print ( $q->start_html, "Copy the desired format from the boxes below:

", $q->div({-style=>"border:solid 1px black"}, $q->h3("FASTA\n"), $q->pre($s)) ); (tied *STDOUT)->set_write_format('embl'); print ( $q->div({-style=>"border:solid 1px black"}, $q->h3("EMBL"), $q->pre($s)) ); (tied *STDOUT)->set_write_format('gcg'); print ( $q->div({-style=>"border:solid 1px black"}, $q->h3("GCG"), $q->pre($s)), $q->end_html ); 1; ----- Original Message ----- From: "Smithies, Russell" To: "'Mark A. Jensen'" ; "'BioPerl List'" Sent: Thursday, October 22, 2009 6:57 PM Subject: RE: [Bioperl-l] a PerlIO layer for Bio::SeqIO Why anyone would want to do it this way is the only thing that's bugging me ;-) Maybe I'm a bit dense this morning but what's the advantage? --Russell (I need more coffee) > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Mark A. Jensen > Sent: Friday, 23 October 2009 11:24 a.m. > To: BioPerl List > Subject: [Bioperl-l] a PerlIO layer for Bio::SeqIO > > Hi All: > > Have you ever wanted to do this? > > open($f, "<:via(SeqIO)", "my.fas"); > open($g, ">:via(SeqIO::embl)", "my.fas.embl"); > while (<$f>) { print $g $_; } > > Or this? > > open($f, "<:via(SeqIO)", "my.fas"); > open(STDOUT, ">:via(SeqIO::fasta)"); > $seq = <$f>; > print "The following is an example of FASTA format:", $seq; > > Or even this? > > (tied *STDOUT)->set_write_format('gcg'); > print "While this is an example of GCG:", $seq; > > Now you can, and much more. See > http://search.cpan.org/search?query=PerlIO::via::SeqIO > > Send me the bugs. > cheers, > MAJ > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From florent.angly at gmail.com Thu Oct 22 19:14:25 2009 From: florent.angly at gmail.com (Florent Angly) Date: Thu, 22 Oct 2009 16:14:25 -0700 Subject: [Bioperl-l] a PerlIO layer for Bio::SeqIO In-Reply-To: <1DD55DFD52CE4A658652907BE02B30AE@NewLife> References: <18DF7D20DFEC044098A1062202F5FFF32B62D67492@exchsth.agresearch.co.nz> <1DD55DFD52CE4A658652907BE02B30AE@NewLife> Message-ID: <4AE0E751.8070300@gmail.com> Sounds cool Mark! After all, UNIX is based on the notion on piping data from one program to another using filehandles. Any chance that this could also work for compressed files like *.gz ?? I don't think that Bio::Root::Utilities::compress and uncompress can deal with filehandles, can it? Florent Mark A. Jensen wrote: > Because it's fun! Also: > > use CGI; > use PerlIO::via::SeqIO; > use strict; > use warnings; > my $q = new CGI; > my ($seqfh, $dup); > open($seqfh, "<:via(SeqIO)", 'test.fas'); > open(STDOUT, ">:via(SeqIO::fasta)"); > > my $s = <$seqfh>; > > print ( > $q->start_html, > "Copy the desired format from the boxes below:

", > $q->div({-style=>"border:solid 1px black"}, > $q->h3("FASTA\n"), > $q->pre($s)) > ); > (tied *STDOUT)->set_write_format('embl'); > print ( > $q->div({-style=>"border:solid 1px black"}, > $q->h3("EMBL"), > $q->pre($s)) > ); > (tied *STDOUT)->set_write_format('gcg'); > print ( > $q->div({-style=>"border:solid 1px black"}, > $q->h3("GCG"), > $q->pre($s)), > $q->end_html > ); > 1; > > ----- Original Message ----- From: "Smithies, Russell" > > To: "'Mark A. Jensen'" ; "'BioPerl List'" > > Sent: Thursday, October 22, 2009 6:57 PM > Subject: RE: [Bioperl-l] a PerlIO layer for Bio::SeqIO > > > Why anyone would want to do it this way is the only thing that's > bugging me ;-) > Maybe I'm a bit dense this morning but what's the advantage? > > --Russell > (I need more coffee) > >> -----Original Message----- >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >> bounces at lists.open-bio.org] On Behalf Of Mark A. Jensen >> Sent: Friday, 23 October 2009 11:24 a.m. >> To: BioPerl List >> Subject: [Bioperl-l] a PerlIO layer for Bio::SeqIO >> >> Hi All: >> >> Have you ever wanted to do this? >> >> open($f, "<:via(SeqIO)", "my.fas"); >> open($g, ">:via(SeqIO::embl)", "my.fas.embl"); >> while (<$f>) { print $g $_; } >> >> Or this? >> >> open($f, "<:via(SeqIO)", "my.fas"); >> open(STDOUT, ">:via(SeqIO::fasta)"); >> $seq = <$f>; >> print "The following is an example of FASTA format:", $seq; >> >> Or even this? >> >> (tied *STDOUT)->set_write_format('gcg'); >> print "While this is an example of GCG:", $seq; >> >> Now you can, and much more. See >> http://search.cpan.org/search?query=PerlIO::via::SeqIO >> >> Send me the bugs. >> cheers, >> MAJ >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From Russell.Smithies at agresearch.co.nz Thu Oct 22 19:40:35 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Fri, 23 Oct 2009 12:40:35 +1300 Subject: [Bioperl-l] a PerlIO layer for Bio::SeqIO In-Reply-To: <1DD55DFD52CE4A658652907BE02B30AE@NewLife> References: <18DF7D20DFEC044098A1062202F5FFF32B62D67492@exchsth.agresearch.co.nz> <1DD55DFD52CE4A658652907BE02B30AE@NewLife> Message-ID: <18DF7D20DFEC044098A1062202F5FFF32B62D674CE@exchsth.agresearch.co.nz> In a Statistics seminar I attended recently, the presenter pointed out that Statisticians aren't boring people, they just get excited by boring things. I think the same applies to Bioinformaticians and Perl programmers ;-) --Russell > -----Original Message----- > From: Mark A. Jensen [mailto:maj at fortinbras.us] > Sent: Friday, 23 October 2009 12:04 p.m. > To: Smithies, Russell; 'BioPerl List' > Subject: Re: [Bioperl-l] a PerlIO layer for Bio::SeqIO > > Because it's fun! Also: > > use CGI; > use PerlIO::via::SeqIO; > use strict; > use warnings; > my $q = new CGI; > my ($seqfh, $dup); > open($seqfh, "<:via(SeqIO)", 'test.fas'); > open(STDOUT, ">:via(SeqIO::fasta)"); > > my $s = <$seqfh>; > > print ( > $q->start_html, > "Copy the desired format from the boxes below:

", > $q->div({-style=>"border:solid 1px black"}, > $q->h3("FASTA\n"), > $q->pre($s)) > ); > (tied *STDOUT)->set_write_format('embl'); > print ( > $q->div({-style=>"border:solid 1px black"}, > $q->h3("EMBL"), > $q->pre($s)) > ); > (tied *STDOUT)->set_write_format('gcg'); > print ( > $q->div({-style=>"border:solid 1px black"}, > $q->h3("GCG"), > $q->pre($s)), > $q->end_html > ); > 1; > > ----- Original Message ----- > From: "Smithies, Russell" > To: "'Mark A. Jensen'" ; "'BioPerl List'" > > Sent: Thursday, October 22, 2009 6:57 PM > Subject: RE: [Bioperl-l] a PerlIO layer for Bio::SeqIO > > > Why anyone would want to do it this way is the only thing that's bugging me > ;-) > Maybe I'm a bit dense this morning but what's the advantage? > > --Russell > (I need more coffee) > > > -----Original Message----- > > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > > bounces at lists.open-bio.org] On Behalf Of Mark A. Jensen > > Sent: Friday, 23 October 2009 11:24 a.m. > > To: BioPerl List > > Subject: [Bioperl-l] a PerlIO layer for Bio::SeqIO > > > > Hi All: > > > > Have you ever wanted to do this? > > > > open($f, "<:via(SeqIO)", "my.fas"); > > open($g, ">:via(SeqIO::embl)", "my.fas.embl"); > > while (<$f>) { print $g $_; } > > > > Or this? > > > > open($f, "<:via(SeqIO)", "my.fas"); > > open(STDOUT, ">:via(SeqIO::fasta)"); > > $seq = <$f>; > > print "The following is an example of FASTA format:", $seq; > > > > Or even this? > > > > (tied *STDOUT)->set_write_format('gcg'); > > print "While this is an example of GCG:", $seq; > > > > Now you can, and much more. See > > http://search.cpan.org/search?query=PerlIO::via::SeqIO > > > > Send me the bugs. > > cheers, > > MAJ > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > From maj at fortinbras.us Thu Oct 22 19:54:51 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Thu, 22 Oct 2009 19:54:51 -0400 Subject: [Bioperl-l] a PerlIO layer for Bio::SeqIO In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF32B62D674CE@exchsth.agresearch.co.nz> References: <18DF7D20DFEC044098A1062202F5FFF32B62D67492@exchsth.agresearch.co.nz> <1DD55DFD52CE4A658652907BE02B30AE@NewLife> <18DF7D20DFEC044098A1062202F5FFF32B62D674CE@exchsth.agresearch.co.nz> Message-ID: True that! ----- Original Message ----- From: "Smithies, Russell" To: "'Mark A. Jensen'" ; "'BioPerl List'" Sent: Thursday, October 22, 2009 7:40 PM Subject: RE: [Bioperl-l] a PerlIO layer for Bio::SeqIO In a Statistics seminar I attended recently, the presenter pointed out that Statisticians aren't boring people, they just get excited by boring things. I think the same applies to Bioinformaticians and Perl programmers ;-) --Russell > -----Original Message----- > From: Mark A. Jensen [mailto:maj at fortinbras.us] > Sent: Friday, 23 October 2009 12:04 p.m. > To: Smithies, Russell; 'BioPerl List' > Subject: Re: [Bioperl-l] a PerlIO layer for Bio::SeqIO > > Because it's fun! Also: > > use CGI; > use PerlIO::via::SeqIO; > use strict; > use warnings; > my $q = new CGI; > my ($seqfh, $dup); > open($seqfh, "<:via(SeqIO)", 'test.fas'); > open(STDOUT, ">:via(SeqIO::fasta)"); > > my $s = <$seqfh>; > > print ( > $q->start_html, > "Copy the desired format from the boxes below:

", > $q->div({-style=>"border:solid 1px black"}, > $q->h3("FASTA\n"), > $q->pre($s)) > ); > (tied *STDOUT)->set_write_format('embl'); > print ( > $q->div({-style=>"border:solid 1px black"}, > $q->h3("EMBL"), > $q->pre($s)) > ); > (tied *STDOUT)->set_write_format('gcg'); > print ( > $q->div({-style=>"border:solid 1px black"}, > $q->h3("GCG"), > $q->pre($s)), > $q->end_html > ); > 1; > > ----- Original Message ----- > From: "Smithies, Russell" > To: "'Mark A. Jensen'" ; "'BioPerl List'" > > Sent: Thursday, October 22, 2009 6:57 PM > Subject: RE: [Bioperl-l] a PerlIO layer for Bio::SeqIO > > > Why anyone would want to do it this way is the only thing that's bugging me > ;-) > Maybe I'm a bit dense this morning but what's the advantage? > > --Russell > (I need more coffee) > > > -----Original Message----- > > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > > bounces at lists.open-bio.org] On Behalf Of Mark A. Jensen > > Sent: Friday, 23 October 2009 11:24 a.m. > > To: BioPerl List > > Subject: [Bioperl-l] a PerlIO layer for Bio::SeqIO > > > > Hi All: > > > > Have you ever wanted to do this? > > > > open($f, "<:via(SeqIO)", "my.fas"); > > open($g, ">:via(SeqIO::embl)", "my.fas.embl"); > > while (<$f>) { print $g $_; } > > > > Or this? > > > > open($f, "<:via(SeqIO)", "my.fas"); > > open(STDOUT, ">:via(SeqIO::fasta)"); > > $seq = <$f>; > > print "The following is an example of FASTA format:", $seq; > > > > Or even this? > > > > (tied *STDOUT)->set_write_format('gcg'); > > print "While this is an example of GCG:", $seq; > > > > Now you can, and much more. See > > http://search.cpan.org/search?query=PerlIO::via::SeqIO > > > > Send me the bugs. > > cheers, > > MAJ > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > From maj at fortinbras.us Thu Oct 22 19:44:10 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Thu, 22 Oct 2009 19:44:10 -0400 Subject: [Bioperl-l] a PerlIO layer for Bio::SeqIO In-Reply-To: <4AE0E751.8070300@gmail.com> References: <18DF7D20DFEC044098A1062202F5FFF32B62D67492@exchsth.agresearch.co.nz> <1DD55DFD52CE4A658652907BE02B30AE@NewLife> <4AE0E751.8070300@gmail.com> Message-ID: This is definitely doable. I will investigate. There is at least one PerlIO via layer for compression (bzip2); the cool thing about layers is you should be able to do something like open($cfh, '>:via(SeqIO::embl):via(bzip2)', 'my.embl.bz2') A quick test of passing an IO::Compress handle to via(SeqIO) indicates I have more a little more work to do. (Gotta fill that spare time,RS!) cheers MAJ ----- Original Message ----- From: "Florent Angly" To: "Mark A. Jensen" Cc: "Smithies, Russell" ; "'BioPerl List'" Sent: Thursday, October 22, 2009 7:14 PM Subject: Re: [Bioperl-l] a PerlIO layer for Bio::SeqIO > Sounds cool Mark! After all, UNIX is based on the notion on piping data from > one program to another using filehandles. > Any chance that this could also work for compressed files like *.gz ?? I don't > think that Bio::Root::Utilities::compress and uncompress can deal with > filehandles, can it? > Florent > > Mark A. Jensen wrote: >> Because it's fun! Also: >> >> use CGI; >> use PerlIO::via::SeqIO; >> use strict; >> use warnings; >> my $q = new CGI; >> my ($seqfh, $dup); >> open($seqfh, "<:via(SeqIO)", 'test.fas'); >> open(STDOUT, ">:via(SeqIO::fasta)"); >> >> my $s = <$seqfh>; >> >> print ( >> $q->start_html, >> "Copy the desired format from the boxes below:

", >> $q->div({-style=>"border:solid 1px black"}, >> $q->h3("FASTA\n"), >> $q->pre($s)) >> ); >> (tied *STDOUT)->set_write_format('embl'); >> print ( >> $q->div({-style=>"border:solid 1px black"}, >> $q->h3("EMBL"), >> $q->pre($s)) >> ); >> (tied *STDOUT)->set_write_format('gcg'); >> print ( >> $q->div({-style=>"border:solid 1px black"}, >> $q->h3("GCG"), >> $q->pre($s)), >> $q->end_html >> ); >> 1; >> >> ----- Original Message ----- From: "Smithies, Russell" >> >> To: "'Mark A. Jensen'" ; "'BioPerl List'" >> >> Sent: Thursday, October 22, 2009 6:57 PM >> Subject: RE: [Bioperl-l] a PerlIO layer for Bio::SeqIO >> >> >> Why anyone would want to do it this way is the only thing that's bugging me >> ;-) >> Maybe I'm a bit dense this morning but what's the advantage? >> >> --Russell >> (I need more coffee) >> >>> -----Original Message----- >>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>> bounces at lists.open-bio.org] On Behalf Of Mark A. Jensen >>> Sent: Friday, 23 October 2009 11:24 a.m. >>> To: BioPerl List >>> Subject: [Bioperl-l] a PerlIO layer for Bio::SeqIO >>> >>> Hi All: >>> >>> Have you ever wanted to do this? >>> >>> open($f, "<:via(SeqIO)", "my.fas"); >>> open($g, ">:via(SeqIO::embl)", "my.fas.embl"); >>> while (<$f>) { print $g $_; } >>> >>> Or this? >>> >>> open($f, "<:via(SeqIO)", "my.fas"); >>> open(STDOUT, ">:via(SeqIO::fasta)"); >>> $seq = <$f>; >>> print "The following is an example of FASTA format:", $seq; >>> >>> Or even this? >>> >>> (tied *STDOUT)->set_write_format('gcg'); >>> print "While this is an example of GCG:", $seq; >>> >>> Now you can, and much more. See >>> http://search.cpan.org/search?query=PerlIO::via::SeqIO >>> >>> Send me the bugs. >>> cheers, >>> MAJ >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> ======================================================================= >> Attention: The information contained in this message and/or attachments >> from AgResearch Limited is intended only for the persons or entities >> to which it is addressed and may contain confidential and/or privileged >> material. Any review, retransmission, dissemination or other use of, or >> taking of any action in reliance upon, this information by persons or >> entities other than the intended recipients is prohibited by AgResearch >> Limited. If you have received this message in error, please notify the >> sender immediately. >> ======================================================================= >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > From coldmeadow at gmail.com Fri Oct 23 01:10:12 2009 From: coldmeadow at gmail.com (Chris) Date: Fri, 23 Oct 2009 15:10:12 +1000 Subject: [Bioperl-l] Bio::Tree:Statistics parsimony question Message-ID: Hello, I have been able to use the ps() method in Bio::Tree::Statistics to calulate the parsimony for tag values from a tree if they are strings. This is the way I have been implementing the method: my $obj = Bio::Tree::Statistics->new(); my $pars = $obj->ps($tree,'seq'); print "Parsimony = $pars \n"; Is it possible to do so if they are an array? say I have an array @seq = qw(A,A,C,G), I can add these as values to a leaf node of a tree using; foreach my $char (@seq){ $node->add_tag_value('seq',$char); } Does anybody have a suggestion to get the parsimony for each label of the array of labels for such a tree ? Thanks in advance, Chris. From maj at fortinbras.us Fri Oct 23 08:27:54 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Fri, 23 Oct 2009 08:27:54 -0400 Subject: [Bioperl-l] Bio::PopGen::PopStats In-Reply-To: <1677ba770910201020i4039360emdc7962854dd7be3f@mail.gmail.com> References: <1677ba770910201020i4039360emdc7962854dd7be3f@mail.gmail.com> Message-ID: Hi Rob, Don't forget to use strict; use warnings; There's an omission and a typo in your script that these would have caught. You need my $stat = Bio::PopGen::PopStats->new() and > my $fst = $stats->Fst(\@pop,\@marker); should be my $fst = $stats->Fst(\@pop,\@markers); cheers MAJ ----- Original Message ----- From: "Robin Runyowa" To: Cc: Sent: Tuesday, October 20, 2009 1:20 PM Subject: [Bioperl-l] Bio::PopGen::PopStats > Hi, I am a newbie in bioperl and I am trying to use to > Bio::PopGen::PopStats. > Unfortunately, I am not sure how to create arrays of objects so I keep > getting an error message. > My input files are below: > testpop3.cvs: > SAMPLE,rs0001 > Person1,A T > Person2,T T > Person3,A A > Person4,T A > Person5,A A > > > testpop4.cvs > SAMPLE,rs0001 > Per1,A T > Per2,T T > Per3,A A > Per4,T A > Per5,A A > > > My script: > use Bio::PopGen::PopStats; > use Bio::PopGen::Individual; > use Bio::PopGen::Genotype; > use Bio::PopGen::Population; > use Bio::PopGen::IO; > > my $handle = new Bio::PopGen::IO (-format => 'csv', > -file => 'testpop3.cvs'); > my $handle2 = new Bio::PopGen::IO (-format => 'csv', > -file => 'testpop4.cvs'); > > my $YRI = $handle ->next_population; > my $CEU = $handle2 ->next_population; > my @pop = (); > push @pop, $YRI; > push @pop, $CEU; > @markers = $YRI->get_marker_names; > my $fst = $stats->Fst(\@pop,\@marker); > > Thanks, Rob > _______________________________________________ > 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 Fri Oct 23 09:12:31 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Fri, 23 Oct 2009 09:12:31 -0400 Subject: [Bioperl-l] Bio::Tree:Statistics parsimony question Message-ID: up to list... ----- Original Message ----- From: "Mark A. Jensen" To: "Chris" Sent: Friday, October 23, 2009 8:14 AM Subject: Re: [Bioperl-l] Bio::Tree:Statistics parsimony question > Hi Chris, > > looks like you could simply do > > @ps = map { $obj->ps($tree, $_) } @seq; > > or into a hash %ps with tags as keys: > > @ps{@seq} = map { $obj->ps($tree,$_) } @seq; > > cheers MAJ > ----- Original Message ----- > From: "Chris" > To: > Sent: Friday, October 23, 2009 1:10 AM > Subject: [Bioperl-l] Bio::Tree:Statistics parsimony question > > >> Hello, >> I have been able to use the ps() method in Bio::Tree::Statistics to calulate >> the parsimony for tag values from a tree if they are strings. >> >> This is the way I have been implementing the method: >> >> my $obj = Bio::Tree::Statistics->new(); >> my $pars = $obj->ps($tree,'seq'); >> print "Parsimony = $pars \n"; >> >> Is it possible to do so if they are an array? >> >> say I have an array @seq = qw(A,A,C,G), I can add these as values to a leaf >> node of a tree using; >> >> foreach my $char (@seq){ >> $node->add_tag_value('seq',$char); >> } >> >> Does anybody have a suggestion to get the parsimony for each label of the >> array of labels for such a tree ? >> >> Thanks in advance, >> Chris. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> From MEC at stowers.org Fri Oct 23 12:16:57 2009 From: MEC at stowers.org (Cook, Malcolm) Date: Fri, 23 Oct 2009 11:16:57 -0500 Subject: [Bioperl-l] Next-gen modules Message-ID: Lincoln? Scot? Hi there! How do I get the permissions I need if Lincoln wants me to submit the patch below which fixes this bug: http://rt.cpan.org/Public/Bug/Display.html?id=50532 % cvs -d :pserver:anonymous at gmod.cvs.sourceforge.net:/cvsroot/gmod co gbrowse-adaptors/Bio-SamTools Cheers, --Malcolm Cook - Stowers Institute for Medical Research *** Sam.pm.~1.18.~ Thu Sep 24 14:57:53 2009 --- Sam.pm Fri Oct 23 11:05:14 2009 *************** *** 1219,1230 **** my $expand_flags = $args{-expand_flags}; my $split_splices = $args{-split} || $args{-split_splices}; ! -e $bam_path && -r _ or croak "$fa_path does not exist or is not readable"; my $bam = Bio::DB::Bam->open($bam_path) or croak "$bam_path open: $!"; my $fai; if ($fa_path) { ! -e $fa_path && -r _ or croak "$fa_path does not exist or is not readable"; $fai = Bio::DB::Sam::Fai->open($fa_path) or croak "$fa_path open: $!"; } --- 1219,1232 ---- my $expand_flags = $args{-expand_flags}; my $split_splices = $args{-split} || $args{-split_splices}; ! -e $bam_path or croak "$bam_path does not exist"; ! -r _ or croak "is not readable"; my $bam = Bio::DB::Bam->open($bam_path) or croak "$bam_path open: $!"; my $fai; if ($fa_path) { ! -e $fa_path or croak "$fa_path does not exist"; ! -r _ or croak "$fa_path is not readable"; $fai = Bio::DB::Sam::Fai->open($fa_path) or croak "$fa_path open: $!"; } From scott at scottcain.net Fri Oct 23 14:17:33 2009 From: scott at scottcain.net (Scott Cain) Date: Fri, 23 Oct 2009 14:17:33 -0400 Subject: [Bioperl-l] [Gmod-gbrowse] Next-gen modules In-Reply-To: References: Message-ID: <4536f7700910231117y1b8a819fq9916760080ce50aa@mail.gmail.com> Hi Malcolm, You need a SourceForge user account that you'll tell me, so I can give you developer permissions, and then get an svn checkout of the gbrowse-adaptors repo (we switched to svn last month). Scott On Fri, Oct 23, 2009 at 12:16 PM, Cook, Malcolm wrote: > Lincoln?? Scot? > > Hi there! > > How do I get the permissions I need if Lincoln wants me to submit the patch > below which fixes this bug: > http://rt.cpan.org/Public/Bug/Display.html?id=50532 > > % cvs -d :pserver:anonymous at gmod.cvs.sourceforge.net:/cvsroot/gmod co > gbrowse-adaptors/Bio-SamTools > > Cheers, > > --Malcolm Cook - Stowers Institute for Medical Research > > > > *** Sam.pm.~1.18.~????? Thu Sep 24 14:57:53 2009 > --- Sam.pm????? Fri Oct 23 11:05:14 2009 > *************** > *** 1219,1230 **** > ????? my $expand_flags? = $args{-expand_flags}; > ????? my $split_splices = $args{-split} || $args{-split_splices}; > > !???? -e $bam_path && -r _? or croak "$fa_path does not exist or is not > readable"; > ????? my $bam = Bio::DB::Bam->open($bam_path)????? or croak "$bam_path open: > $!"; > > ????? my $fai; > ????? if ($fa_path) { > !??????? -e $fa_path? && -r _? or croak "$fa_path does not exist or is not > readable"; > ???????? $fai = Bio::DB::Sam::Fai->open($fa_path)? or croak "$fa_path open: > $!"; > ????? } > > --- 1219,1232 ---- > ????? my $expand_flags? = $args{-expand_flags}; > ????? my $split_splices = $args{-split} || $args{-split_splices}; > > !???? -e $bam_path or croak "$bam_path does not exist"; > !???? -r _? or croak "is not readable"; > ????? my $bam = Bio::DB::Bam->open($bam_path)????? or croak "$bam_path open: > $!"; > > ????? my $fai; > ????? if ($fa_path) { > !??????? -e $fa_path or croak "$fa_path does not exist"; > !??????? -r _? or croak "$fa_path is not readable"; > ???????? $fai = Bio::DB::Sam::Fai->open($fa_path)? or croak "$fa_path open: > $!"; > ????? } > > > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart your > developing skills, take BlackBerry mobile applications to market and stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse at lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From coldmeadow at gmail.com Fri Oct 23 17:00:49 2009 From: coldmeadow at gmail.com (Chris) Date: Sat, 24 Oct 2009 07:00:49 +1000 Subject: [Bioperl-l] Bio::Tree:Statistics parsimony question In-Reply-To: References: Message-ID: Hi Mark, I might be missing something, but I cant see how that will work. ps() takes as input a tree with the tags already in the leaf nodes and the key for those tags. I think your suggested solution places the tags from the @seq array into ps() which throws an exception error. Maybe another explanaition; I would like to calculate the parsimony score at each position of an alignment. Consider 1 block with only 1 character in for each species; species1 A species 2 G species 3 G species 4 G I can do this for 1 position, by adding the tag (which Ive named 'seq') value pair to each leaf node of the phylogeny tree for the 4 species, where the tag is a single character. Then calculating the parsimony for that column is simply my $obj = Bio::Tree::Statistics->new(); my $pars = $obj->ps($tree,'seq'); print "Parsimony = $pars \n"; Now consider an alignment block with more than 1 character species1 ACG species 2 GCT species 3 GGG species 4 GGT I see it is possible to add an array of values as a tag, now, instead of a single character as a tag on each leaf node, I have an array of nucleotides as tags at each leaf node. I was hoping for a way to calculate the parsimony given a tree with such tag value pairs. Regards, Chris. On Fri, Oct 23, 2009 at 11:12 PM, Mark A. Jensen wrote: > up to list... > ----- Original Message ----- From: "Mark A. Jensen" > To: "Chris" > Sent: Friday, October 23, 2009 8:14 AM > Subject: Re: [Bioperl-l] Bio::Tree:Statistics parsimony question > > > > Hi Chris, >> looks like you could simply do >> >> @ps = map { $obj->ps($tree, $_) } @seq; >> >> or into a hash %ps with tags as keys: >> >> @ps{@seq} = map { $obj->ps($tree,$_) } @seq; >> >> cheers MAJ >> ----- Original Message ----- From: "Chris" >> To: >> Sent: Friday, October 23, 2009 1:10 AM >> Subject: [Bioperl-l] Bio::Tree:Statistics parsimony question >> >> >> Hello, >>> I have been able to use the ps() method in Bio::Tree::Statistics to >>> calulate >>> the parsimony for tag values from a tree if they are strings. >>> >>> This is the way I have been implementing the method: >>> >>> my $obj = Bio::Tree::Statistics->new(); >>> my $pars = $obj->ps($tree,'seq'); >>> print "Parsimony = $pars \n"; >>> >>> Is it possible to do so if they are an array? >>> >>> say I have an array @seq = qw(A,A,C,G), I can add these as values to a >>> leaf >>> node of a tree using; >>> >>> foreach my $char (@seq){ >>> $node->add_tag_value('seq',$char); >>> } >>> >>> Does anybody have a suggestion to get the parsimony for each label of the >>> array of labels for such a tree ? >>> >>> Thanks in advance, >>> 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 maj at fortinbras.us Fri Oct 23 19:11:30 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Fri, 23 Oct 2009 19:11:30 -0400 Subject: [Bioperl-l] Bio::Tree:Statistics parsimony question In-Reply-To: References: Message-ID: I see. You can use the add_trait method on the tree object; to this, you provide a file containing a table of nodes X traits. The following code works; it creates a trait table on the fly, according to seq data given in the DATA section (after __END__). Then in a loop, add_traits is used to add each position and calculate the ps. There's probably a better way, but this could get you started. use Bio::Tree::Statistics; use Bio::TreeIO; use strict; use warnings; # tree file can be found in t/data... my $in = Bio::TreeIO->new(-format => 'nexus', -file => 'traittree.nexus'); my $obj = Bio::Tree::Statistics->new(); my $tree = $in->next_tree; # make a trait table from the sequences open(my $tmpf, ">seq.dat"); my $len = ; chomp $len; print $tmpf join("\t", "id", map { "pos".$_ } (1..$len)), "\n"; while () { chomp; my ($id, $seq) = split /\s+/; print $tmpf join( "\t", $id, split('', $seq) ), "\n"; } close($tmpf); # cycle through my @pars; for (1..$len) { my $key = $tree->add_trait('seq.dat', $_); push @pars, $obj->ps($tree, $key); } print join("\n", @pars); __END__ 3 1 ACG 2 GCT 3 GGG 4 GGT 5 ACG 6 GCT 7 GGG 8 GGT 9 ACG 10 GCT 11 GGG 12 GGT 13 ACG 14 GCT 15 GGG 16 GGT ----- Original Message ----- From: Chris To: Mark A. Jensen Cc: bioperl List Sent: Friday, October 23, 2009 5:00 PM Subject: Re: [Bioperl-l] Bio::Tree:Statistics parsimony question Hi Mark, I might be missing something, but I cant see how that will work. ps() takes as input a tree with the tags already in the leaf nodes and the key for those tags. I think your suggested solution places the tags from the @seq array into ps() which throws an exception error. Maybe another explanaition; I would like to calculate the parsimony score at each position of an alignment. Consider 1 block with only 1 character in for each species; species1 A species 2 G species 3 G species 4 G I can do this for 1 position, by adding the tag (which Ive named 'seq') value pair to each leaf node of the phylogeny tree for the 4 species, where the tag is a single character. Then calculating the parsimony for that column is simply my $obj = Bio::Tree::Statistics->new(); my $pars = $obj->ps($tree,'seq'); print "Parsimony = $pars \n"; Now consider an alignment block with more than 1 character species1 ACG species 2 GCT species 3 GGG species 4 GGT I see it is possible to add an array of values as a tag, now, instead of a single character as a tag on each leaf node, I have an array of nucleotides as tags at each leaf node. I was hoping for a way to calculate the parsimony given a tree with such tag value pairs. Regards, Chris. On Fri, Oct 23, 2009 at 11:12 PM, Mark A. Jensen wrote: up to list... ----- Original Message ----- From: "Mark A. Jensen" To: "Chris" Sent: Friday, October 23, 2009 8:14 AM Subject: Re: [Bioperl-l] Bio::Tree:Statistics parsimony question Hi Chris, looks like you could simply do @ps = map { $obj->ps($tree, $_) } @seq; or into a hash %ps with tags as keys: @ps{@seq} = map { $obj->ps($tree,$_) } @seq; cheers MAJ ----- Original Message ----- From: "Chris" To: Sent: Friday, October 23, 2009 1:10 AM Subject: [Bioperl-l] Bio::Tree:Statistics parsimony question Hello, I have been able to use the ps() method in Bio::Tree::Statistics to calulate the parsimony for tag values from a tree if they are strings. This is the way I have been implementing the method: my $obj = Bio::Tree::Statistics->new(); my $pars = $obj->ps($tree,'seq'); print "Parsimony = $pars \n"; Is it possible to do so if they are an array? say I have an array @seq = qw(A,A,C,G), I can add these as values to a leaf node of a tree using; foreach my $char (@seq){ $node->add_tag_value('seq',$char); } Does anybody have a suggestion to get the parsimony for each label of the array of labels for such a tree ? Thanks in advance, 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 chmille4 at gmail.com Sat Oct 24 09:03:47 2009 From: chmille4 at gmail.com (Chase Miller) Date: Sat, 24 Oct 2009 09:03:47 -0400 Subject: [Bioperl-l] identifying accession number's database Message-ID: <991fb8210910240603n31581140o219ef4c7fa96c0c4@mail.gmail.com> Hi all, I have a list of accession numbers which could be from several databases(e.g. NCBI, UniProt, Ensemble). Does anyone know of a way I can determine which database a particular accession number is from? thanks, Chase From s.denaxas at gmail.com Sat Oct 24 10:16:29 2009 From: s.denaxas at gmail.com (Spiros Denaxas) Date: Sat, 24 Oct 2009 15:16:29 +0100 Subject: [Bioperl-l] MeSH terms Message-ID: Hello, I am trying to build a tool to enable researches perform systematic reviews more easily. One of the functions would be to fetch and present the relevant MeSH headings and MeSH entry terms from text. Is there a module for doing this? The only thing I could find is http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/DB/MeSH.pm but I was after something that could potentially also work with the flat XML files. thanks in advance, Spiros From chmille4 at gmail.com Sat Oct 24 12:59:50 2009 From: chmille4 at gmail.com (Chase Miller) Date: Sat, 24 Oct 2009 12:59:50 -0400 Subject: [Bioperl-l] identifying accession number's database In-Reply-To: References: <991fb8210910240603n31581140o219ef4c7fa96c0c4@mail.gmail.com> Message-ID: <991fb8210910240959x6e8419aai83483e15407d56ef@mail.gmail.com> Hans, thanks that was definitely helpful. Looks like there isn't a perfect solution, so I'll have to do a bit of guessing with my regexs. (sounds like a good project....Bio::DB::GuessDB...) > Mark, I had a feeling my old google mentor wasn't going to let me off the hook that easily once Hans said it was an open problem. :) I'll dust off my commit bit and see what I can do. Cheers, Chase > ----- Original Message ----- From: "Chase Miller" > To: "BioPerl List" > Sent: Saturday, October 24, 2009 9:03 AM > Subject: [Bioperl-l] identifying accession number's database > > > Hi all, >> >> I have a list of accession numbers which could be from several >> databases(e.g. NCBI, UniProt, Ensemble). Does anyone know of a way I can >> determine which database a particular accession number is from? >> >> thanks, >> Chase >> _______________________________________________ >> 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 Oct 24 12:19:51 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 24 Oct 2009 12:19:51 -0400 Subject: [Bioperl-l] identifying accession number's database In-Reply-To: <991fb8210910240603n31581140o219ef4c7fa96c0c4@mail.gmail.com> References: <991fb8210910240603n31581140o219ef4c7fa96c0c4@mail.gmail.com> Message-ID: (sounds like a good project....Bio::DB::GuessDB...) ----- Original Message ----- From: "Chase Miller" To: "BioPerl List" Sent: Saturday, October 24, 2009 9:03 AM Subject: [Bioperl-l] identifying accession number's database > Hi all, > > I have a list of accession numbers which could be from several > databases(e.g. NCBI, UniProt, Ensemble). Does anyone know of a way I can > determine which database a particular accession number is from? > > thanks, > Chase > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From robert.bradbury at gmail.com Sat Oct 24 14:45:01 2009 From: robert.bradbury at gmail.com (Robert Bradbury) Date: Sat, 24 Oct 2009 14:45:01 -0400 Subject: [Bioperl-l] PubMed records (was: MeSH terms) Message-ID: I'm not sure if this is related to the MeSH question question or not, but I've googled the documentation several times and never managed to find "robust" examples for how to manipulate PubMed records. It would seem that there ought to be code lying around which does: Given Genbank ID, Fetch all Pubmed records from that ID Fetch all related records (via NCBI's "related" record IDs) Purge the list of duplicates, then do things like fetch all of the abstracts or fetch all of the MeSH headings, etc. for all of those records. Another example would include fetching all records of relatedness (i.e. a PubMed tree of depth N (or cloud of some max N)). I think that one can use NCBI's fetch interface to do this (one could do it by having NCBI email you all of the PubMed results and have an email harvester collect those results, parse them and setup a new set of queries). Of course this seems like an overhead intensive way to do this. Given the fact that increasing amounts of information is becoming open to the public one could consider even parsing the published papers and supplemental files (e.g. XLS tables) for genes of interest (as it seems the authors of most work as well as the PubMed record processors fail to provide or research the gene name information that is supposed to be in the PubMed records). Now it may simply be that its because I lack sufficient experience with the BioPerl documentation that I am unaware of the functions/tools which do this type of thing. So if anyone has any hints/pointers they would be appreciated. Thanks, Robert Bradbury From bosborne11 at verizon.net Sat Oct 24 15:18:20 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Sat, 24 Oct 2009 15:18:20 -0400 Subject: [Bioperl-l] PubMed records (was: MeSH terms) In-Reply-To: References: Message-ID: <87D07E9A-61D9-4119-B91D-B8A5920461DD@verizon.net> Robert, Not sure what "robust" means - would "working" suffice? Also, you suggested starting with a Genbank id but what I'm about to show you starts with Pubmed ids, at the other end. What I will do is take some of this and make a little script for Bioperl's examples/ directory. In the meantime, here is some code: #!/bin/perl -w use Bio::Biblio; my $pmid = 52; my $biblio = Bio::Biblio->new(-access => "eutils"); my $ref = $biblio->get_by_id($pmid); # $ref contains raw XML print $ref,"\n"; And what it prints is below. Brian O. 52 1976 02 09 1976 02 09 2006 11 15
0006-2960 14 24 1975 Dec 2 Biochemistry Biochemistry Evidence of the involvement of a 50S ribosomal protein in several active sites. 5321-7 The functional role of the Bacillus stearothermophilus 50S ribosomal protein B-L3 (probably homologous to the Escherichia coli protein L2) was examined by chemical modification. The complex [B-L3-23S RNA] was photooxidized in the presence of rose bengal and the modified protein incorporated by reconstitution into 50S ribosomal subunits containing all other unmodified components. Particles containing photooxidized B-L3 are defective in several functional assays, including (1) poly(U)-directed poly(Phe) synthesis, (2) peptidyltransferase activity, (3) ability to associate with a [30S-poly(U)-Phe-tRNA] complex, and (4) binding of elongation factor G and GTP. The rates of loss of the partial functional activities during photooxidation of B-L3 indicate that at least two independent inactivating events are occurring, a faster one, involving oxidation of one or more histidine residues, affecting peptidyltransferase and subunit association activities and a slower one affecting EF-G binding. Therefore the protein B-L3 has one or more histidine residues which are essential for peptidyltransferase and subunit association, and another residue which is essential for EF-G- GTP binding. B-L3 may be the ribosomal peptidyltransferase protein, or a part of the active site, and may contribute functional groups to the other active sites as well. Fahnestock S R SR eng Journal Article Research Support, U.S. Gov't, P.H.S.
UNITED STATES Biochemistry 0370623 0 Macromolecular Substances 0 Ribosomal Proteins IM Bacillus stearothermophilus metabolism Binding Sites Hydrogen-Ion Concentration Kinetics Macromolecular Substances Oxidation-Reduction Photochemistry Protein Binding Ribosomal Proteins metabolism Ribosomes metabolism 1975 12 2 1975 12 2 0 1 1975 12 2 0 0 ppublish 52 On Oct 24, 2009, at 2:45 PM, Robert Bradbury wrote: > > I'm not sure if this is related to the MeSH question question or > not, but > I've googled the documentation several times and never managed to find > "robust" examples for how to manipulate PubMed records. > > It would seem that there ought to be code lying around which does: > Given Genbank ID, > Fetch all Pubmed records from that ID > Fetch all related records (via NCBI's "related" record IDs) > > Purge the list of duplicates, then do things like fetch all of the > abstracts or fetch all of the MeSH headings, etc. for all of those > records. > > Another example would include fetching all records of relatedness > (i.e. a > PubMed tree of depth N (or cloud of some max N)). > > I think that one can use NCBI's fetch interface to do this (one > could do it > by having NCBI email you all of the PubMed results and have an email > harvester collect those results, parse them and setup a new set of > queries). Of course this seems like an overhead intensive way to do > this. > Given the fact that increasing amounts of information is becoming > open to > the public one could consider even parsing the published papers and > supplemental files (e.g. XLS tables) for genes of interest (as it > seems the > authors of most work as well as the PubMed record processors fail to > provide > or research the gene name information that is supposed to be in the > PubMed > records). > > Now it may simply be that its because I lack sufficient experience > with the > BioPerl documentation that I am unaware of the functions/tools which > do this > type of thing. So if anyone has any hints/pointers they would be > appreciated. > > Thanks, > Robert Bradbury > _______________________________________________ > 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 Sat Oct 24 19:17:08 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 24 Oct 2009 17:17:08 -0600 Subject: [Bioperl-l] identifying accession number's database In-Reply-To: References: <991fb8210910240603n31581140o219ef4c7fa96c0c4@mail.gmail.com> Message-ID: <9D1F27C6-3C6C-4FA1-867D-F67630B4150F@gmx.net> I know that a former coworker of mine (Serge, copied) has written Perl code that guesses for quite a number of possible sources. I don't know whether any of it is available somewhere. -hilmar Sent from my iPod On Oct 24, 2009, at 10:19 AM, "Mark A. Jensen" wrote: > (sounds like a good project....Bio::DB::GuessDB...) > ----- Original Message ----- From: "Chase Miller" > To: "BioPerl List" > Sent: Saturday, October 24, 2009 9:03 AM > Subject: [Bioperl-l] identifying accession number's database > > >> Hi all, >> I have a list of accession numbers which could be from several >> databases(e.g. NCBI, UniProt, Ensemble). Does anyone know of a way >> I can >> determine which database a particular accession number is from? >> thanks, >> Chase >> _______________________________________________ >> 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 biopython at maubp.freeserve.co.uk Sun Oct 25 07:12:53 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Sun, 25 Oct 2009 11:12:53 +0000 Subject: [Bioperl-l] PubMed records (was: MeSH terms) In-Reply-To: References: Message-ID: <320fb6e00910250412j7666d17hd62d2b4eda92ad0f@mail.gmail.com> On Sat, Oct 24, 2009 at 6:45 PM, Robert Bradbury wrote: > ? > I'm not sure if this is related to the MeSH question question or not, but > I've googled the documentation several times and never managed to find > "robust" examples for how to manipulate PubMed records. > > It would seem that there ought to be code lying around which does: > ?Given Genbank ID, > ? ? Fetch all Pubmed records from that ID > ? ? ? ? Fetch all related records (via NCBI's "related" record IDs) Isn't this exactly what the NCBI's ELink is for? http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/elink_help.html http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/entrezlinks.html You'd need to work out which of the Entrez databases you are starting from (probably protein or genome), and then the relevant ELink command (maybe genome_pubmed, or protein_pubmed, protein_pubmed or protein_pubmed_weighted look possible). Then for related pubmed articles, the ELink command is just pubmed_pubmed. Peter From robert.bradbury at gmail.com Sun Oct 25 09:03:18 2009 From: robert.bradbury at gmail.com (Robert Bradbury) Date: Sun, 25 Oct 2009 09:03:18 -0400 Subject: [Bioperl-l] PubMed records (was: MeSH terms) In-Reply-To: <320fb6e00910250412j7666d17hd62d2b4eda92ad0f@mail.gmail.com> References: <320fb6e00910250412j7666d17hd62d2b4eda92ad0f@mail.gmail.com> Message-ID: On Sun, Oct 25, 2009 at 7:12 AM, Peter wrote: > > Isn't this exactly what the NCBI's ELink is for? > (snip) > Interesting. I knew they had some of this but I didn't know they had extended it so far (obviously the cloud of computers normally running blast searches is keeping itself busy when there is nothing better to do). [Aside: Does anyone know exactly what NCBI's computing capacity is? Or how this compares with the other major sites (Ensembl, Sanger, Broad, UCSC) capacity?] Now, extending Brian's helpful comment, is there anything within BioPerl or CPAN in general which can take the "link cloud" and extend it into "degree of connectivity cloud". If anyone has ever used the Linux utility "etherape" they will have an idea of what I'm talking about. Etherape displays the local network traffic in a grapical format with nodes for which machines are communicating with each other and colors, sizes and brightness of the links between them representing the traffic type, amount and age of the communications. I'm sure that agencies which shall not be named have similar display programs which deal with the quantity and type of "chatter" between "persons of interest". This is all pretty standard stuff from a "network graph" standpoint. This type of graphical information can be highly useful from a "systems biology" standpoint as well as an educational standpoint when one wants to understand something like the components of a protein complex, the time domain of gene expression, the activity of research in an area, etc. So if the information is available I'm wondering what the tools are to make it useful? With the amount of computing power now available to home users now one could begin to think of very creative ways of using this type of information from a data mining standpoint. Robert From cjfields at illinois.edu Sun Oct 25 10:16:34 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Oct 2009 09:16:34 -0500 Subject: [Bioperl-l] PubMed records (was: MeSH terms) In-Reply-To: <320fb6e00910250412j7666d17hd62d2b4eda92ad0f@mail.gmail.com> References: <320fb6e00910250412j7666d17hd62d2b4eda92ad0f@mail.gmail.com> Message-ID: On Oct 25, 2009, at 6:12 AM, Peter wrote: > On Sat, Oct 24, 2009 at 6:45 PM, Robert Bradbury > wrote: >> >> I'm not sure if this is related to the MeSH question question or >> not, but >> I've googled the documentation several times and never managed to >> find >> "robust" examples for how to manipulate PubMed records. >> >> It would seem that there ought to be code lying around which does: >> Given Genbank ID, >> Fetch all Pubmed records from that ID >> Fetch all related records (via NCBI's "related" record IDs) > > Isn't this exactly what the NCBI's ELink is for? > > http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/elink_help.html > http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/entrezlinks.html > > You'd need to work out which of the Entrez databases you are > starting from (probably protein or genome), and then the relevant > ELink command (maybe genome_pubmed, or protein_pubmed, > protein_pubmed or protein_pubmed_weighted look possible). > Then for related pubmed articles, the ELink command is just > pubmed_pubmed. > > Peter Agreed. This should be possible through BioPerl's Bio::DB::EUtilities. I'll try to post an example up. chris From cjfields at illinois.edu Sun Oct 25 11:08:22 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Oct 2009 10:08:22 -0500 Subject: [Bioperl-l] PubMed records (was: MeSH terms) In-Reply-To: References: <320fb6e00910250412j7666d17hd62d2b4eda92ad0f@mail.gmail.com> Message-ID: <92809DA3-5FDE-4032-B690-707A3B4509C0@illinois.edu> On Oct 25, 2009, at 9:16 AM, Chris Fields wrote: > On Oct 25, 2009, at 6:12 AM, Peter wrote: > >> On Sat, Oct 24, 2009 at 6:45 PM, Robert Bradbury >> wrote: >>> >>> I'm not sure if this is related to the MeSH question question or >>> not, but >>> I've googled the documentation several times and never managed to >>> find >>> "robust" examples for how to manipulate PubMed records. >>> >>> It would seem that there ought to be code lying around which does: >>> Given Genbank ID, >>> Fetch all Pubmed records from that ID >>> Fetch all related records (via NCBI's "related" record IDs) >> >> Isn't this exactly what the NCBI's ELink is for? >> >> http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/elink_help.html >> http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/entrezlinks.html >> >> You'd need to work out which of the Entrez databases you are >> starting from (probably protein or genome), and then the relevant >> ELink command (maybe genome_pubmed, or protein_pubmed, >> protein_pubmed or protein_pubmed_weighted look possible). >> Then for related pubmed articles, the ELink command is just >> pubmed_pubmed. >> >> Peter > > Agreed. This should be possible through BioPerl's > Bio::DB::EUtilities. I'll try to post an example up. > > chris As promised... chris PS. I've been thinking about a couple of small additions: 1) normalizing how one indicates whether or not to use eutil cookies/ history (indicating such currently requires one to be more explicit), 2) adding a pipeline-like utility where one could pass in a series of hashrefs with databases and it will link them all together using eutil history/cookies. If there is a need for this I can start working on it over the next few weeks, after I finally get the next set of alphas out. -------------------------------------- #!/usr/bin/perl -w use strict; use warnings; use Bio::DB::EUtilities; my $term = 'Notch3 AND "Mus musculus"[ORGN]'; my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch', -db => 'protein', -term => $term, -usehistory => 'y'); my $hist = $eutil->next_History || die "No queue history returned"; # can stipulate the actual linkname as well using -linkname $eutil->reset_parameters(-eutil => 'elink', -db => 'pubmed', -dbfrom => 'protein', -history => $hist, -cmd => 'neighbor_history'); $hist = $eutil->next_History || die "No queue history returned"; # adjust -retstart/-retmax to get more results $eutil->reset_parameters(-eutil => 'esummary', -db => 'protein', -history => $hist); $eutil->print_all; From ulrik.stervbo at gmail.com Sun Oct 25 11:42:17 2009 From: ulrik.stervbo at gmail.com (Ulrik Stervbo) Date: Sun, 25 Oct 2009 16:42:17 +0100 Subject: [Bioperl-l] Export as HTML Message-ID: <3483f8d50910250842q18099b4w4b39e3a130b25835@mail.gmail.com> Hi List, I am all new to bioperl :-D I have several annotated sequences as sequence objects I would like to print to a HTML file, so that the annotation is highlighted with some colours. For each sequence I would also like to include a short legend describing the colours. Do I have to do this by hand or is there a module that can help me? Ultimately I need to copy the colourful sequences into a word-document, is there a better way that go via html? Best and thanks for any help and suggestions Ulrik From s.denaxas at gmail.com Sun Oct 25 11:48:27 2009 From: s.denaxas at gmail.com (Spiros Denaxas) Date: Sun, 25 Oct 2009 15:48:27 +0000 Subject: [Bioperl-l] Export as HTML In-Reply-To: <3483f8d50910250842q18099b4w4b39e3a130b25835@mail.gmail.com> References: <3483f8d50910250842q18099b4w4b39e3a130b25835@mail.gmail.com> Message-ID: Hi, Data::Table [1] might be pretty handy. Spiros [1] http://search.cpan.org/perldoc?Data::Table On Sun, Oct 25, 2009 at 3:42 PM, Ulrik Stervbo wrote: > Hi List, > > I am all new to bioperl :-D > > I have several annotated sequences as sequence objects I would like to print > to a HTML file, so that the annotation is highlighted with some colours. For > each sequence I would also like to include a short legend describing the > colours. > > Do I have to do this by hand or is there a module that can help me? > > Ultimately I need to copy the colourful sequences into a word-document, is > there a better way that go via html? > > Best and thanks for any help and suggestions > Ulrik > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From ulrik.stervbo at gmail.com Sun Oct 25 11:58:42 2009 From: ulrik.stervbo at gmail.com (Ulrik Stervbo) Date: Sun, 25 Oct 2009 16:58:42 +0100 Subject: [Bioperl-l] Export as HTML In-Reply-To: References: <3483f8d50910250842q18099b4w4b39e3a130b25835@mail.gmail.com> Message-ID: <3483f8d50910250858h6b0a1869xc92a09da6f996ab7@mail.gmail.com> Hi, Thanks - but I do not want is as a table. I would like something like: Test1 Gene1 Mismatch >test1 GTGCTGGGATTCTGTaaGTGCAGATTTGCTGGGTGAGCGGAG Test2 Gene2 >test2 GTGCTGGGATTCTGTaaGTGCAGATTTGCTGGGTGAGCGGAG as HTML so it is easy to paste into the word document Ulrik 2009/10/25 Spiros Denaxas > Hi, > > Data::Table [1] might be pretty handy. > > Spiros > > [1] http://search.cpan.org/perldoc?Data::Table > > On Sun, Oct 25, 2009 at 3:42 PM, Ulrik Stervbo > wrote: > > Hi List, > > > > I am all new to bioperl :-D > > > > I have several annotated sequences as sequence objects I would like to > print > > to a HTML file, so that the annotation is highlighted with some colours. > For > > each sequence I would also like to include a short legend describing the > > colours. > > > > Do I have to do this by hand or is there a module that can help me? > > > > Ultimately I need to copy the colourful sequences into a word-document, > is > > there a better way that go via html? > > > > Best and thanks for any help and suggestions > > Ulrik > > _______________________________________________ > > 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 Oct 25 14:07:21 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Sun, 25 Oct 2009 14:07:21 -0400 Subject: [Bioperl-l] broken link on bioperl.org main page Message-ID: <628aabb70910251107s7e236fc5jea1139e7015b8a6d@mail.gmail.com> Hi, The "...install Bioperl?" link under "How do I...?" is broken. I believe it should point to: http://www.bioperl.org/wiki/Installing_BioPerl If someone with write access to the wiki front page has a moment, could you please update the link? Thanks, Dave From maj at fortinbras.us Sun Oct 25 15:26:40 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 25 Oct 2009 15:26:40 -0400 Subject: [Bioperl-l] broken link on bioperl.org main page In-Reply-To: <628aabb70910251107s7e236fc5jea1139e7015b8a6d@mail.gmail.com> References: <628aabb70910251107s7e236fc5jea1139e7015b8a6d@mail.gmail.com> Message-ID: done--thanks Dave ----- Original Message ----- From: "Dave Messina" To: "bioperl-l" Sent: Sunday, October 25, 2009 2:07 PM Subject: [Bioperl-l] broken link on bioperl.org main page > Hi, > > The "...install Bioperl?" link under "How do I...?" is broken. I believe it > should point to: > http://www.bioperl.org/wiki/Installing_BioPerl > > If someone with write access to the wiki front page has a moment, could you > please update the link? > > > Thanks, > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From michael.watson at bbsrc.ac.uk Mon Oct 26 13:04:08 2009 From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C)) Date: Mon, 26 Oct 2009 17:04:08 +0000 Subject: [Bioperl-l] strand in Bio::SearchIO when parsing fasta35 output Message-ID: <8D08960C647E64438CE5740657CBBDC501487319AE@iahcexch1.iah.bbsrc.ac.uk> Dear all Where does this go? Perhaps I am doing something wrong. Fasta35 output puts the strand in the hit list at the top: cluster_99033:3 ( 23) [r] 115 37.9 0.0011 cluster_79238:1 ( 27) [f] 126 38.0 0.00097 0.963 0.963 27 The [r] stands for reverse and the [f] stands for forward. There is also the text "rev-comp" after the hit line further down. However, when I parse fasta35 output using SearchIO and output the strand of the HSP: print $hsp->strand('hit'), ","; print $hsp->strand('query'), "\n"; This simply prints out 0, 0 (I assume 0 is the default in BioPerl for "I don't know which strand it's on"). So the information is there, but it's not getting parsed. Alternatively, I've missed something and will feel a bit foolish. Currently using BioPerl 1.6.0 Thanks Mick From jason at bioperl.org Mon Oct 26 14:45:47 2009 From: jason at bioperl.org (Jason Stajich) Date: Mon, 26 Oct 2009 11:45:47 -0700 Subject: [Bioperl-l] strand in Bio::SearchIO when parsing fasta35 output In-Reply-To: <8D08960C647E64438CE5740657CBBDC501487319AE@iahcexch1.iah.bbsrc.ac.uk> References: <8D08960C647E64438CE5740657CBBDC501487319AE@iahcexch1.iah.bbsrc.ac.uk> Message-ID: <9994F70B-AE92-4425-9AAC-E9A2DC26964E@bioperl.org> Is this -m9 -d 0 output or standard default? I think the strand is parsed in the HSP parsing. Can you double check what $hsp->query->strand and $hsp->hit->strand prints? A full example report as a bug request will be next step if that doesn't resolve. -jason On Oct 26, 2009, at 10:04 AM, michael watson (IAH-C) wrote: > Dear all > > Where does this go? Perhaps I am doing something wrong. > > Fasta35 output puts the strand in the hit list at the top: > > cluster_99033:3 ( 23) [r] 115 37.9 > 0.0011 > cluster_79238:1 ( 27) [f] 126 38.0 0.00097 0.963 > 0.963 27 > > The [r] stands for reverse and the [f] stands for forward. > > There is also the text "rev-comp" after the hit line further down. > > However, when I parse fasta35 output using SearchIO and output the > strand of the HSP: > > print $hsp->strand('hit'), ","; > print $hsp->strand('query'), "\n"; > > This simply prints out 0, 0 (I assume 0 is the default in BioPerl > for "I don't know which strand it's on"). > > So the information is there, but it's not getting parsed. > Alternatively, I've missed something and will feel a bit foolish. > > Currently using BioPerl 1.6.0 > > Thanks > Mick > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich jason.stajich at gmail.com jason at bioperl.org From michael.watson at bbsrc.ac.uk Tue Oct 27 05:01:12 2009 From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C)) Date: Tue, 27 Oct 2009 09:01:12 +0000 Subject: [Bioperl-l] strand in Bio::SearchIO when parsing fasta35 output In-Reply-To: <9994F70B-AE92-4425-9AAC-E9A2DC26964E@bioperl.org> References: <8D08960C647E64438CE5740657CBBDC501487319AE@iahcexch1.iah.bbsrc.ac.uk> <9994F70B-AE92-4425-9AAC-E9A2DC26964E@bioperl.org> Message-ID: <8D08960C647E64438CE5740657CBBDC501487319B6@iahcexch1.iah.bbsrc.ac.uk> Hi Jason They both print 0 also. A bug report it is Mick -----Original Message----- From: Jason Stajich [mailto:jason.stajich at gmail.com] On Behalf Of Jason Stajich Sent: 26 October 2009 18:46 To: michael watson (IAH-C) Cc: bioperl-l Subject: Re: [Bioperl-l] strand in Bio::SearchIO when parsing fasta35 output Is this -m9 -d 0 output or standard default? I think the strand is parsed in the HSP parsing. Can you double check what $hsp->query->strand and $hsp->hit->strand prints? A full example report as a bug request will be next step if that doesn't resolve. -jason On Oct 26, 2009, at 10:04 AM, michael watson (IAH-C) wrote: > Dear all > > Where does this go? Perhaps I am doing something wrong. > > Fasta35 output puts the strand in the hit list at the top: > > cluster_99033:3 ( 23) [r] 115 37.9 > 0.0011 > cluster_79238:1 ( 27) [f] 126 38.0 0.00097 0.963 > 0.963 27 > > The [r] stands for reverse and the [f] stands for forward. > > There is also the text "rev-comp" after the hit line further down. > > However, when I parse fasta35 output using SearchIO and output the > strand of the HSP: > > print $hsp->strand('hit'), ","; > print $hsp->strand('query'), "\n"; > > This simply prints out 0, 0 (I assume 0 is the default in BioPerl > for "I don't know which strand it's on"). > > So the information is there, but it's not getting parsed. > Alternatively, I've missed something and will feel a bit foolish. > > Currently using BioPerl 1.6.0 > > Thanks > Mick > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich jason.stajich at gmail.com jason at bioperl.org From clarsen at vecna.com Tue Oct 27 12:33:01 2009 From: clarsen at vecna.com (Chris Larsen) Date: Tue, 27 Oct 2009 12:33:01 -0400 Subject: [Bioperl-l] Polyproteins, ribo slippage, and mat_peptide in viruses? Message-ID: All, I am attempting to find some solutions to a DB loading problem we are encountering in viruses. It is multifold: Some viruses churn out a polyprotein rather than individual peptides; further they also slip the ribosome, so a source nucleotide is used more than once in translation (ribosome halts, backs up one nucleotide, and continues in a new frame); and finally we have post translational processing into mature peptides. The main thing is that the mature peptide is contained a a subset of the whole parent polyprotein, but is not provided as a single file in GBK for each mat_peptide CDS. We have to get that in order to run algorithms on the relevant processed proteins. Therefore we cannot directly load into GUS, but rather have to choose how to get the mat_peptide sequence. Actually I think the viruses know that, and are just messing with us out of spite, since we have iPods and they dont. Anyway.. from anyone who has encountered this I seek guidance. We have as choices: 1. Get the locations of mature peptide children in /Protein/ carve the mat_peptide sequence out of the whole polyprotein translation check that the mat_peptide is infact an identical subset of the translated protein load that OR 2. Use the locations of starts and stops in /Nucleotide/ translate that, using the slippage information get mature peptides that line up exactly to the parent polyprotein If you know of BioPerl sequence handling support for this, I would love to hear more. Clearly this is a nonstandard thingamabob. Stupid viruses Chris -- Christopher Larsen, Ph.D. Sr. Scientist / Grants Manager Vecna Technologies 6404 Ivy Lane #500 Greenbelt, MD 20770 Phone: (240) 965-4525 Fax: (240) 547-6133 240-737-4525 From biopython at maubp.freeserve.co.uk Tue Oct 27 13:29:08 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 27 Oct 2009 17:29:08 +0000 Subject: [Bioperl-l] Polyproteins, ribo slippage, and mat_peptide in viruses? In-Reply-To: References: Message-ID: <320fb6e00910271029m26f07564l727fb78adae81c11@mail.gmail.com> On Tue, Oct 27, 2009 at 4:33 PM, Chris Larsen wrote: > All, > > I am attempting to find some solutions to a DB loading problem we are > encountering in viruses. It is multifold: > > Some viruses churn out a polyprotein rather than individual peptides; > further they also slip the ribosome, so a source nucleotide is used more > than once ?in translation (ribosome halts, backs up one nucleotide, and > continues in a new frame); and finally we have post translational processing > into mature peptides. The main thing is that the mature peptide is contained > a a subset of the whole parent polyprotein, but is not provided as a single > file in GBK for each mat_peptide CDS. We have to get that in order to run > algorithms on the relevant processed proteins. Therefore we cannot directly > load into GUS, but rather have to choose how to get the mat_peptide > sequence. Actually I think the viruses know that, and are just messing with > us out of spite, since we have iPods and they dont. Anyway.. from anyone who > has encountered this I seek guidance. > > We have as choices: > > 1. Get the locations of mature peptide children in /Protein/ > carve the mat_peptide sequence out of the whole polyprotein translation > check that the mat_peptide is infact an identical subset of the translated > protein > load that > > OR > > 2. Use the locations of starts and stops in /Nucleotide/ > translate that, using the slippage information > get mature peptides that line up exactly to the parent polyprotein > > If you know of BioPerl sequence handling support for this, I would love to > hear more. Clearly this is a nonstandard thingamabob. > > Stupid viruses > > Chris Cool viruses :) Do you have some specific examples from GenBank? I'm starting to deal with virus annotation in my work, so this is of interest. Peter P.S. As you might guess from my email address, I'm actually more interested in Biopython than BioPerl, but the same algorithmic approach could be tested in either. From jay at jays.net Tue Oct 27 14:12:38 2009 From: jay at jays.net (Jay Hannah) Date: Tue, 27 Oct 2009 13:12:38 -0500 Subject: [Bioperl-l] svn: Decompression of svndiff data failed Message-ID: <9EA21BF4-C7C9-4347-AB5D-1AF5CB2F1EE2@jays.net> Hmm... Anyone else hitting this? I'm getting this on Linux and OSX... $ svn co -r16285 svn://code.open-bio.org/bioperl/bioperl-live/trunk ... A trunk/Bio/Structure/SecStr/STRIDE/Res.pm A trunk/Bio/Structure/StructureI.pm A trunk/Bio/Structure/IO svn: Decompression of svndiff data failed ------ svn version 1.4.4 on OSX 10.6.1. svn version 1.5.1 Linux version 2.6.24-24-generic (buildd at rothera) (gcc version 4.2.4 (Ubuntu 4.2.4-1ubuntu4)) #1 SMP Wed Apr 15 15:54:25 UTC 2009 ------ Thanks, j From tristan.lefebure at gmail.com Tue Oct 27 15:31:03 2009 From: tristan.lefebure at gmail.com (Tristan Lefebure) Date: Tue, 27 Oct 2009 15:31:03 -0400 Subject: [Bioperl-l] hacking BlastTable.pm to support blast -m 8 Message-ID: <200910271531.03337.tristan.lefebure@gmail.com> Hello, As far as I understand, Bio::Index::BlastTable only supports the -m 9 blast format. Another popular and more compact format is -m 8, the main difference being that the blast program, the query and database, and the different field names are not reported between each search, i.e. you get a much cleaner table (which looks much easier to parse). By looking at BlastTable.pm, it looks like the main hack would be in the sub _index_file. Right now it is: sub _index_file { my( $self, $file, # File name $i, # Index-number of file being indexed ) = @_; my( $begin, # Offset from start of file of the start # of the last found record. ); open(my $BLAST, '<', $file) or $self->throw("cannot open file $file\n"); my $indexpoint = 0; my $lastline = 0; while( <$BLAST> ) { if(m{^#\s+T?BLAST[PNX]} ) { my $len = length $_; $indexpoint = tell($BLAST)-$len; } if(m{^#\s+Query:\s+([^\n]+)}) { foreach my $id ($self->id_parser()->($1)) { $self->debug("id is $id, begin is $indexpoint\n"); $self->add_record($id, $i, $indexpoint); } } } } Using the -m 8 format, is it me or this could be done by getting the query name from the first row of the blast table, find when the hits for this query starts and stop, and give this to add_record()? I'm kind of not sure to get all the details regarding the $i and $indexpoint... so well, if an expert eye could give me some advice or hack the code that would be nice ;) --Tristan From clarsen at vecna.com Tue Oct 27 15:47:27 2009 From: clarsen at vecna.com (Chris Larsen) Date: Tue, 27 Oct 2009 15:47:27 -0400 Subject: [Bioperl-l] EXAMPLE: Polyproteins, ribo slippage, and mat_peptide in viruses? In-Reply-To: References: Message-ID: My bad...thanks everyone. An example of a virus that does this is in order so we don't have to do this in our heads. There's no slippage in this isolate per se, however the main problem of generating component *.faa from polyprotein still exists. Chris > For instance, check this: > http://www.ncbi.nlm.nih.gov/nuccore/NC_001959 > > You may recall some cruise where half the ship threw up. YAY > norovirus. Lets take that as a useful problem to address solutions to. > > No mat_peptide sequence is given. How to get that? From biopython at maubp.freeserve.co.uk Tue Oct 27 15:54:04 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 27 Oct 2009 19:54:04 +0000 Subject: [Bioperl-l] Polyproteins, ribo slippage, and mat_peptide in viruses? In-Reply-To: <0B39B25C-802B-4F8A-B1BF-2A9E95E0CD18@vecna.com> References: <320fb6e00910271029m26f07564l727fb78adae81c11@mail.gmail.com> <0B39B25C-802B-4F8A-B1BF-2A9E95E0CD18@vecna.com> Message-ID: <320fb6e00910271254k5aab61cdo5b2b22eb6ff462f9@mail.gmail.com> On Tue, Oct 27, 2009 at 7:15 PM, Chris Larsen wrote: > > Hello Peter! > > For instance, check this: > http://www.ncbi.nlm.nih.gov/nuccore/NC_001959 > ... > > No mat_peptide sequence is given. We want that... Looking at the GenBank file displayed, the mat_peptide features (mature peptides) do not include a translation entry (like the parent CDS feature does). However, they do have protein IDs - which are actually links in the HTML version. This leads me to suggest a third option as an alternative to the two ideas you outlined. You could parse the GenBank file(s), and for each mat_peptide feature look up the protein ID via Entrez EFetch (e.g. as a FASTA file, or a GenPept file). If you only have a relatively small number of viruses and proteins this is probably going to be pretty easy. At least, I could do it in Biopython and I am sure the same is true with the BioPerl GenBank parser and their EFetch interface. However, for a large dataset, handling it all locally (your options (1) and (2) sound best). Peter From tristan.lefebure at gmail.com Tue Oct 27 15:59:02 2009 From: tristan.lefebure at gmail.com (Tristan Lefebure) Date: Tue, 27 Oct 2009 15:59:02 -0400 Subject: [Bioperl-l] hacking BlastTable.pm to support blast -m 8 In-Reply-To: References: <200910271531.03337.tristan.lefebure@gmail.com> Message-ID: <200910271559.02219.tristan.lefebure@gmail.com> On Tuesday 27 October 2009 15:50:24 Chris Fields wrote: > I'll go ahead and do this based on your suggestion, > unless you have a patch ready. Also, it looks like > the module is missing tests, so I can work on adding > those for both -m8 and -m9 output. > Great! I did nothing, you can go ahead. I bet you can do this 100x faster than me... From cjfields at illinois.edu Tue Oct 27 15:50:24 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 27 Oct 2009 14:50:24 -0500 Subject: [Bioperl-l] hacking BlastTable.pm to support blast -m 8 In-Reply-To: <200910271531.03337.tristan.lefebure@gmail.com> References: <200910271531.03337.tristan.lefebure@gmail.com> Message-ID: On Oct 27, 2009, at 2:31 PM, Tristan Lefebure wrote: > Hello, > As far as I understand, Bio::Index::BlastTable only supports > the -m 9 blast format. Another popular and more compact > format is -m 8, the main difference being that the blast > program, the query and database, and the different field > names are not reported between each search, i.e. you get > a much cleaner table (which looks much easier to parse). > > By looking at BlastTable.pm, it looks like the main > hack would be in the sub _index_file. Right now it is: > > sub _index_file { > my( $self, > $file, # File name > $i, # Index-number of file being indexed > ) = @_; > > my( $begin, # Offset from start of file of the start > # of the last found record. > ); > > open(my $BLAST, '<', $file) or $self->throw("cannot open file > $file\n"); > my $indexpoint = 0; > my $lastline = 0; > while( <$BLAST> ) { > if(m{^#\s+T?BLAST[PNX]} ) { > my $len = length $_; > $indexpoint = tell($BLAST)-$len; > } > if(m{^#\s+Query:\s+([^\n]+)}) { > foreach my $id ($self->id_parser()->($1)) { > $self->debug("id is $id, begin is > $indexpoint\n"); > $self->add_record($id, $i, > $indexpoint); > } > } > } > } > > Using the -m 8 format, is it me or this could be > done by getting the query name from the first row > of the blast table, find when the hits for this query > starts and stop, and give this to add_record()? > > I'm kind of not sure to get all the details > regarding the $i and $indexpoint... so well, if an > expert eye could give me some advice or hack the code > that would be nice ;) > > --Tristan That should be feasible, yes, and you are correct. The main thing to make sure of is to retain the '#' for -m9, so the parser catches the BLAST executable and other info. I'll go ahead and do this based on your suggestion, unless you have a patch ready. Also, it looks like the module is missing tests, so I can work on adding those for both -m8 and -m9 output. chris From clarsen at vecna.com Tue Oct 27 16:07:55 2009 From: clarsen at vecna.com (Chris Larsen) Date: Tue, 27 Oct 2009 16:07:55 -0400 Subject: [Bioperl-l] Polyproteins, ribo slippage, and mat_peptide in viruses? In-Reply-To: <320fb6e00910271254k5aab61cdo5b2b22eb6ff462f9@mail.gmail.com> References: <320fb6e00910271029m26f07564l727fb78adae81c11@mail.gmail.com> <0B39B25C-802B-4F8A-B1BF-2A9E95E0CD18@vecna.com> <320fb6e00910271254k5aab61cdo5b2b22eb6ff462f9@mail.gmail.com> Message-ID: <67E6A22C-6968-460D-B192-E129773A0BA5@vecna.com> Peter, This is a good strategy when the gi is given. However I failed to mention that we are finding the example I gave is unusual (15%?)--- most virus 'mature peptides' we will apply this analysis to do not in fact have a gi number or unique identifier associated with them. There are thousands of dengue virus files to be processed to give mature proteins. Should have mentioned this...Hence the problem--we cant look it up because only the parent polyprotein has a gi. Theres nothing to look up /by/ in most cases. So we still have to build a set of proteins that are cleaved out of every polyprotein, by local and high throughput methods, by building it out of the available information (sadly, kind of a run around-- it should be in the genbank entry). Chris On Oct 27, 2009, at 3:54 PM, Peter wrote: > On Tue, Oct 27, 2009 at 7:15 PM, Chris Larsen > wrote: >> >> Hello Peter! >> >> For instance, check this: >> http://www.ncbi.nlm.nih.gov/nuccore/NC_001959 >> ... >> >> No mat_peptide sequence is given. We want that... > > Looking at the GenBank file displayed, the mat_peptide features > (mature peptides) do not include a translation entry (like the parent > CDS feature does). However, they do have protein IDs - which are > actually links in the HTML version. > > This leads me to suggest a third option as an alternative to the two > ideas you outlined. You could parse the GenBank file(s), and for each > mat_peptide feature look up the protein ID via Entrez EFetch (e.g. as > a FASTA file, or a GenPept file). If you only have a relatively small > number of viruses and proteins this is probably going to be pretty > easy. At least, I could do it in Biopython and I am sure the same is > true with the BioPerl GenBank parser and their EFetch interface. > > However, for a large dataset, handling it all locally (your options > (1) and (2) sound best). > > Peter -- Christopher Larsen, Ph.D. Sr. Scientist / Grants Manager Vecna Technologies 6404 Ivy Lane #500 Greenbelt, MD 20770 Phone: (240) 965-4525 Fax: (240) 547-6133 240-737-4525 From biopython at maubp.freeserve.co.uk Tue Oct 27 16:17:19 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 27 Oct 2009 20:17:19 +0000 Subject: [Bioperl-l] Polyproteins, ribo slippage, and mat_peptide in viruses? In-Reply-To: <67E6A22C-6968-460D-B192-E129773A0BA5@vecna.com> References: <320fb6e00910271029m26f07564l727fb78adae81c11@mail.gmail.com> <0B39B25C-802B-4F8A-B1BF-2A9E95E0CD18@vecna.com> <320fb6e00910271254k5aab61cdo5b2b22eb6ff462f9@mail.gmail.com> <67E6A22C-6968-460D-B192-E129773A0BA5@vecna.com> Message-ID: <320fb6e00910271317y56d37bcfk28d351dc41d437e9@mail.gmail.com> On Tue, Oct 27, 2009 at 8:07 PM, Chris Larsen wrote: > > Peter, > > This is a good strategy when the gi is given. However I failed to mention > that we are finding the example I gave is unusual (15%?)---most virus > 'mature peptides' we will apply this analysis to do not in fact have a gi > number or unique identifier associated with them. There are thousands of > dengue virus files to be processed to give mature proteins. > > Should have mentioned this...Hence the problem--we cant look it up because > only the parent polyprotein has a gi. Theres nothing to look up /by/ in most > cases. So we still have to build a set of proteins that are cleaved out of > every polyprotein, by local and high throughput methods, by building it out > of the available information (sadly, kind of a run around-- it should be in > the genbank entry). > > Chris Ah. That's a shame. I did just take a few minutes to try out the EFetch idea (using Biopython) and it does work beautifully for this "nice" example virus which the NCBI have annotated. I also note that in the example given, all the mature peptides have nice and simple locations (in terms of their co-ordindates for the nucleotides), no ribosomal slippages etc. This means grabbing the relevant bits of the genome and translating it is also pretty easy (option 2 in your original email). Have you got a more typical entry you can point us at? If there is nothing publicly available, I wouldn't mind you emailing me one or two to look at off list (and if don't mind, they might make good examples for Bio* project unit tests or examples). Peter From cjfields at illinois.edu Tue Oct 27 16:46:05 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 27 Oct 2009 15:46:05 -0500 Subject: [Bioperl-l] Polyproteins, ribo slippage, and mat_peptide in viruses? In-Reply-To: <320fb6e00910271317y56d37bcfk28d351dc41d437e9@mail.gmail.com> References: <320fb6e00910271029m26f07564l727fb78adae81c11@mail.gmail.com> <0B39B25C-802B-4F8A-B1BF-2A9E95E0CD18@vecna.com> <320fb6e00910271254k5aab61cdo5b2b22eb6ff462f9@mail.gmail.com> <67E6A22C-6968-460D-B192-E129773A0BA5@vecna.com> <320fb6e00910271317y56d37bcfk28d351dc41d437e9@mail.gmail.com> Message-ID: <32287667-F06D-4BA4-B116-FDFC62B46EF2@illinois.edu> On Oct 27, 2009, at 3:17 PM, Peter wrote: > On Tue, Oct 27, 2009 at 8:07 PM, Chris Larsen > wrote: >> >> Peter, >> >> This is a good strategy when the gi is given. However I failed to >> mention >> that we are finding the example I gave is unusual (15%?)---most virus >> 'mature peptides' we will apply this analysis to do not in fact >> have a gi >> number or unique identifier associated with them. There are >> thousands of >> dengue virus files to be processed to give mature proteins. >> >> Should have mentioned this...Hence the problem--we cant look it up >> because >> only the parent polyprotein has a gi. Theres nothing to look up / >> by/ in most >> cases. So we still have to build a set of proteins that are cleaved >> out of >> every polyprotein, by local and high throughput methods, by >> building it out >> of the available information (sadly, kind of a run around-- it >> should be in >> the genbank entry). >> >> Chris > > Ah. That's a shame. I did just take a few minutes to try out the > EFetch idea (using Biopython) and it does work beautifully for > this "nice" example virus which the NCBI have annotated. Interesting thing about that example: if you follow the hyperlinks for the mat_peptide feature key, they relate back to the full protein sequence with from/to, not to the protein_id for the feature. Example: # link from the first mat_peptide http://www.ncbi.nlm.nih.gov/protein/9630804?from=1&to=398&report=gpwithparts # protein_id http://www.ncbi.nlm.nih.gov/protein/28416959 This record doesn't appear to contain any mapping information along those lines, which makes me think this is an autogenerated record using the Gene record, which does have those mappings: http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=1491970 > I also note that in the example given, all the mature peptides > have nice and simple locations (in terms of their co-ordindates > for the nucleotides), no ribosomal slippages etc. This means > grabbing the relevant bits of the genome and translating it is > also pretty easy (option 2 in your original email). > > Have you got a more typical entry you can point us at? > > If there is nothing publicly available, I wouldn't mind you > emailing me one or two to look at off list (and if don't mind, > they might make good examples for Bio* project unit tests > or examples). > > Peter I think one could use the full-length protein and run TFASTX (which allows frameshifts) against the nucleotide sequence. The output will have the frameshifts designated with '/' or '\', so it would then be a matter of splitting the sequence based on the midline, then mapping those protein fragments back to the original sequence coordinates. Is this along the lines of what you mean? chris From biopython at maubp.freeserve.co.uk Tue Oct 27 17:31:55 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 27 Oct 2009 21:31:55 +0000 Subject: [Bioperl-l] Polyproteins, ribo slippage, and mat_peptide in viruses? In-Reply-To: <32287667-F06D-4BA4-B116-FDFC62B46EF2@illinois.edu> References: <320fb6e00910271029m26f07564l727fb78adae81c11@mail.gmail.com> <0B39B25C-802B-4F8A-B1BF-2A9E95E0CD18@vecna.com> <320fb6e00910271254k5aab61cdo5b2b22eb6ff462f9@mail.gmail.com> <67E6A22C-6968-460D-B192-E129773A0BA5@vecna.com> <320fb6e00910271317y56d37bcfk28d351dc41d437e9@mail.gmail.com> <32287667-F06D-4BA4-B116-FDFC62B46EF2@illinois.edu> Message-ID: <320fb6e00910271431w7a56c2b7w3eda8e60adcabef2@mail.gmail.com> On Tue, Oct 27, 2009 at 8:46 PM, Chris Fields wrote: >> >> Ah. That's a shame. I did just take a few minutes to try out the >> EFetch idea (using Biopython) and it does work beautifully for >> this "nice" example virus which the NCBI have annotated. > > Interesting thing about that example: if you follow the hyperlinks for the > mat_peptide feature key, they relate back to the full protein sequence with > from/to, not to the protein_id for the feature. ?Example: > > # link from the first mat_peptide > http://www.ncbi.nlm.nih.gov/protein/9630804?from=1&to=398&report=gpwithparts > > # protein_id > http://www.ncbi.nlm.nih.gov/protein/28416959 Right - the protein ID link is just based on the GI number, 28416959. This link (or EFetch) gives you the (short) mature peptide. > This record doesn't appear to contain any mapping information along those > lines, which makes me think this is an autogenerated record using the Gene > record, which does have those mappings: > > http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=1491970 Are you suggesting one option is (if the mat_peptide annotation is lacking a protein or GI number) to go online to the Gene database using the gene ID of the precursor (parent) protein to find the IDs of the mature (child) peptides? Peter From bill at genenformics.com Tue Oct 27 17:47:02 2009 From: bill at genenformics.com (bill at genenformics.com) Date: Tue, 27 Oct 2009 14:47:02 -0700 Subject: [Bioperl-l] Polyproteins, ribo slippage, and mat_peptide in viruses? In-Reply-To: <320fb6e00910271431w7a56c2b7w3eda8e60adcabef2@mail.gmail.com> References: <320fb6e00910271029m26f07564l727fb78adae81c11@mail.gmail.com> <0B39B25C-802B-4F8A-B1BF-2A9E95E0CD18@vecna.com> <320fb6e00910271254k5aab61cdo5b2b22eb6ff462f9@mail.gmail.com> <67E6A22C-6968-460D-B192-E129773A0BA5@vecna.com> <320fb6e00910271317y56d37bcfk28d351dc41d437e9@mail.gmail.com> <32287667-F06D-4BA4-B116-FDFC62B46EF2@illinois.edu> <320fb6e00910271431w7a56c2b7w3eda8e60adcabef2@mail.gmail.com> Message-ID: These mature proteins do have gi. ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2accession.gz >grep NC_001959 gene2accession 11983 1491970 REVIEWED - - NP_786945.1 28416959 NC_001959.2 106060735 4 5373 + - 11983 1491970 REVIEWED - - NP_786946.1 28416960 NC_001959.2 106060735 4 5373 + - 11983 1491970 REVIEWED - - NP_786947.1 28416961 NC_001959.2 106060735 4 5373 + - 11983 1491970 REVIEWED - - NP_786948.1 28416962 NC_001959.2 106060735 4 5373 + - 11983 1491970 REVIEWED - - NP_786949.1 28416963 NC_001959.2 106060735 4 5373 + - 11983 1491970 REVIEWED - - NP_786950.1 28416964 NC_001959.2 106060735 4 5373 + - 11983 1491971 PROVISIONAL - - NP_056822.1 9630806 NC_001959.2 106060735 6949 7587 + - 11983 1491972 PROVISIONAL - - NP_056821.2 106060736 NC_001959.2 106060735 5357 6949 + - Bill > On Tue, Oct 27, 2009 at 8:46 PM, Chris Fields > wrote: >>> >>> Ah. That's a shame. I did just take a few minutes to try out the >>> EFetch idea (using Biopython) and it does work beautifully for >>> this "nice" example virus which the NCBI have annotated. >> >> Interesting thing about that example: if you follow the hyperlinks for >> the >> mat_peptide feature key, they relate back to the full protein sequence >> with >> from/to, not to the protein_id for the feature. ?Example: >> >> # link from the first mat_peptide >> http://www.ncbi.nlm.nih.gov/protein/9630804?from=1&to=398&report=gpwithparts >> >> # protein_id >> http://www.ncbi.nlm.nih.gov/protein/28416959 > > Right - the protein ID link is just based on the GI number, 28416959. > This link (or EFetch) gives you the (short) mature peptide. > >> This record doesn't appear to contain any mapping information along >> those >> lines, which makes me think this is an autogenerated record using the >> Gene >> record, which does have those mappings: >> >> http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=1491970 > > Are you suggesting one option is (if the mat_peptide annotation > is lacking a protein or GI number) to go online to the Gene > database using the gene ID of the precursor (parent) protein > to find the IDs of the mature (child) peptides? > > Peter > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From biopython at maubp.freeserve.co.uk Tue Oct 27 18:03:12 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 27 Oct 2009 22:03:12 +0000 Subject: [Bioperl-l] Polyproteins, ribo slippage, and mat_peptide in viruses? In-Reply-To: References: <320fb6e00910271029m26f07564l727fb78adae81c11@mail.gmail.com> <0B39B25C-802B-4F8A-B1BF-2A9E95E0CD18@vecna.com> <320fb6e00910271254k5aab61cdo5b2b22eb6ff462f9@mail.gmail.com> <67E6A22C-6968-460D-B192-E129773A0BA5@vecna.com> <320fb6e00910271317y56d37bcfk28d351dc41d437e9@mail.gmail.com> <32287667-F06D-4BA4-B116-FDFC62B46EF2@illinois.edu> <320fb6e00910271431w7a56c2b7w3eda8e60adcabef2@mail.gmail.com> Message-ID: <320fb6e00910271503m7070ac5s2facf6346be9dbba@mail.gmail.com> On Tue, Oct 27, 2009 at 9:47 PM, wrote: > These mature proteins do have gi. Yes, they are in the original GenBank file too. The problem is Chris said he picked a poor example - this one is well annotated, but in general his GenBank files lack these cross references. Which is why I asked for a more realistic example if he can share one ;) Peter From clarsen at vecna.com Tue Oct 27 18:13:22 2009 From: clarsen at vecna.com (Chris Larsen) Date: Tue, 27 Oct 2009 18:13:22 -0400 Subject: [Bioperl-l] Polyproteins, ribo slippage, and mat_peptide in viruses? In-Reply-To: <32287667-F06D-4BA4-B116-FDFC62B46EF2@illinois.edu> References: <320fb6e00910271029m26f07564l727fb78adae81c11@mail.gmail.com> <0B39B25C-802B-4F8A-B1BF-2A9E95E0CD18@vecna.com> <320fb6e00910271254k5aab61cdo5b2b22eb6ff462f9@mail.gmail.com> <67E6A22C-6968-460D-B192-E129773A0BA5@vecna.com> <320fb6e00910271317y56d37bcfk28d351dc41d437e9@mail.gmail.com> <32287667-F06D-4BA4-B116-FDFC62B46EF2@illinois.edu> Message-ID: <26672E4E-7868-4B46-B951-6176443084D9@vecna.com> Peter, Chris, Thank you muchly for your expert and well presented dialog. Yes here is an actual and typical problem in generating protein seq from viral polyproteins, in the absence of mat_peptide Seq and unique ID: For record: http://www.ncbi.nlm.nih.gov/nuccore/112253723?report=genbank this is the coronavirus: LOCUS DQ848678 29277 bp RNA linear VRL 12- SEP-2006 DEFINITION Feline coronavirus strain FCoV C1Je, complete genome. ACCESSION DQ848678 VERSION DQ848678.1 GI:112253723 Containing a poly protein 1ab where the ribosome stalls at 12358, backs up one nuc, changes frame, and then continues: CDS join(311..12358,12358..20391) /ribosomal_slippage /codon_start=1 /product="polyprotein 1ab" and which has multiple, gigantic polyproteins, the child peptides towards whom we would actually love to focus our comparative bioinformatic scrutiny, but none of which have mappable IDs or seqs below the polyprotein level as can be seen: mat_peptide 15118..16914 <=== /product="nsp13" <=== /note="helicase" <==these are all we have to go on and where are given no ID below the polyprotein level, no protein sequence...just positions. They are nuc positions at that, but we are given the complete polyprotein seq and have the components to do this on paper, but no code. In summary we would like to dump in genbank files to a method, and get out fasta protein files which have some IDs and seqs. You guys are forcing me (thank god) to think critically and clearly about it too, so let me extend the proposed module or method as best I can: Input offending Virus Genbank file For each mat_peptide in a CDS get nuc coords e.g. 15118..161914 translate it to aa if slippage then stop translating at end of frame 1 and hold for later now translate frame 2 $full_translation = $translation_part_1 . $translation_part_2 compare $full_translation to CDS translation e.g "/ translation="MSSKHFKILVNE..." if identical subsequence then admit as the real, valid mat_peptide sequence Annotate with parent Unique ID+product name e.g. 112253723_helicase go to next mat_peptide concatenate products to a fasta amino acid file for whole virus isolate or CDS set for your virus PHEW. Chris L ========== > > I think one could use the full-length protein and run TFASTX (which > allows frameshifts) against the nucleotide sequence. The output > will have the frameshifts designated with '/' or '\', so it would > then be a matter of splitting the sequence based on the midline, > then mapping those protein fragments back to the original sequence > coordinates. Is this along the lines of what you mean? > > chris Let me look into this thank you CF, I have not used that in the past. From cjfields at illinois.edu Tue Oct 27 19:39:26 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 27 Oct 2009 18:39:26 -0500 Subject: [Bioperl-l] hacking BlastTable.pm to support blast -m 8 In-Reply-To: <200910271559.02219.tristan.lefebure@gmail.com> References: <200910271531.03337.tristan.lefebure@gmail.com> <200910271559.02219.tristan.lefebure@gmail.com> Message-ID: <43050E9D-DAAA-4EEB-8AE9-91696D98E5F0@illinois.edu> On Oct 27, 2009, at 2:59 PM, Tristan Lefebure wrote: > On Tuesday 27 October 2009 15:50:24 Chris Fields wrote: >> I'll go ahead and do this based on your suggestion, >> unless you have a patch ready. Also, it looks like >> the module is missing tests, so I can work on adding >> those for both -m8 and -m9 output. >> > > Great! I did nothing, you can go ahead. I bet you can do > this 100x faster than me... Committed to svn in r16301, along with some tests. Let me know if this doesn't work. chris From bill at genenformics.com Tue Oct 27 19:39:56 2009 From: bill at genenformics.com (bill at genenformics.com) Date: Tue, 27 Oct 2009 16:39:56 -0700 Subject: [Bioperl-l] Polyproteins, ribo slippage, and mat_peptide in viruses? In-Reply-To: <26672E4E-7868-4B46-B951-6176443084D9@vecna.com> References: <320fb6e00910271029m26f07564l727fb78adae81c11@mail.gmail.com> <0B39B25C-802B-4F8A-B1BF-2A9E95E0CD18@vecna.com> <320fb6e00910271254k5aab61cdo5b2b22eb6ff462f9@mail.gmail.com> <67E6A22C-6968-460D-B192-E129773A0BA5@vecna.com> <320fb6e00910271317y56d37bcfk28d351dc41d437e9@mail.gmail.com> <32287667-F06D-4BA4-B116-FDFC62B46EF2@illinois.edu> <26672E4E-7868-4B46-B951-6176443084D9@vecna.com> Message-ID: It appears that acc/gi is not required for mat_peptide. Your solution should work fine. http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objmgr/util/create_defline.cpp#L870 Bill > Peter, Chris, > > Thank you muchly for your expert and well presented dialog. Yes here > is an actual and typical problem in generating protein seq from viral > polyproteins, in the absence of mat_peptide Seq and unique ID: > > For record: > > http://www.ncbi.nlm.nih.gov/nuccore/112253723?report=genbank > > this is the coronavirus: > LOCUS DQ848678 29277 bp RNA linear VRL 12- > SEP-2006 > DEFINITION Feline coronavirus strain FCoV C1Je, complete genome. > ACCESSION DQ848678 > VERSION DQ848678.1 GI:112253723 > Containing a poly protein 1ab where the ribosome stalls at 12358, > backs up one nuc, changes frame, and then continues: > CDS join(311..12358,12358..20391) > /ribosomal_slippage > /codon_start=1 > /product="polyprotein 1ab" > and which has multiple, gigantic polyproteins, the child peptides > towards whom we would actually love to focus our comparative > bioinformatic scrutiny, but none of which have mappable IDs or seqs > below the polyprotein level as can be seen: > mat_peptide 15118..16914 <=== > /product="nsp13" <=== > /note="helicase" <==these are all we have to go > on > and where are given no ID below the polyprotein level, no protein > sequence...just positions. They are nuc positions at that, but we are > given the complete polyprotein seq and have the components to do this > on paper, but no code. In summary we would like to dump in genbank > files to a method, and get out fasta protein files which have some IDs > and seqs. > > You guys are forcing me (thank god) to think critically and clearly > about it too, so let me extend the proposed module or method as best I > can: > > Input offending Virus Genbank file > For each mat_peptide in a CDS > get nuc coords e.g. 15118..161914 > translate it to aa > if slippage then stop translating at end of frame 1 and hold for later > now translate frame 2 > $full_translation = $translation_part_1 . $translation_part_2 > compare $full_translation to CDS translation e.g "/ > translation="MSSKHFKILVNE..." > if identical subsequence then admit as the real, valid mat_peptide > sequence > Annotate with parent Unique ID+product name e.g. 112253723_helicase > go to next mat_peptide > concatenate products to a fasta amino acid file for whole virus > isolate or CDS set for your virus > > PHEW. > > Chris L > > ========== >> >> I think one could use the full-length protein and run TFASTX (which >> allows frameshifts) against the nucleotide sequence. The output >> will have the frameshifts designated with '/' or '\', so it would >> then be a matter of splitting the sequence based on the midline, >> then mapping those protein fragments back to the original sequence >> coordinates. Is this along the lines of what you mean? >> >> chris > > Let me look into this thank you CF, I have not used that in the past. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From tristan.lefebure at gmail.com Tue Oct 27 23:31:29 2009 From: tristan.lefebure at gmail.com (Tristan Lefebure) Date: Tue, 27 Oct 2009 23:31:29 -0400 Subject: [Bioperl-l] hacking BlastTable.pm to support blast -m 8 In-Reply-To: <43050E9D-DAAA-4EEB-8AE9-91696D98E5F0@illinois.edu> References: <200910271531.03337.tristan.lefebure@gmail.com> <200910271559.02219.tristan.lefebure@gmail.com> <43050E9D-DAAA-4EEB-8AE9-91696D98E5F0@illinois.edu> Message-ID: <200910272331.29893.tristan.lefebure@gmail.com> Works perfectly, thanks Chris. On Tuesday 27 October 2009 19:39:26 Chris Fields wrote: > On Oct 27, 2009, at 2:59 PM, Tristan Lefebure wrote: > > On Tuesday 27 October 2009 15:50:24 Chris Fields wrote: > >> I'll go ahead and do this based on your suggestion, > >> unless you have a patch ready. Also, it looks like > >> the module is missing tests, so I can work on adding > >> those for both -m8 and -m9 output. > > > > Great! I did nothing, you can go ahead. I bet you can > > do this 100x faster than me... > > Committed to svn in r16301, along with some tests. Let > me know if this doesn't work. > > chris > From simonstudy at 163.com Wed Oct 28 07:43:30 2009 From: simonstudy at 163.com (=?gb2312?B?0OzP4A==?=) Date: Wed, 28 Oct 2009 19:43:30 +0800 Subject: [Bioperl-l] problem in installation of bioperl Message-ID: <200910281943302654039@163.com> Hi all, I got a problem when I installed Bioperl with activeperl ppm on Windows platform. When I marked the Bioperl package for install in ppm, I got a warning message which said "WARNING: Can't find any package that provides Apache:: for SOAP-Lite". I had added all the repository links to ppm, which is suggested on the Bioperl wiki web. Is there anyone who knows what is the problem and how to fix it? Thanks in advance. Xiang 2009-10-28 ???? From cjfields at illinois.edu Wed Oct 28 08:04:31 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Oct 2009 07:04:31 -0500 Subject: [Bioperl-l] problem in installation of bioperl In-Reply-To: <200910281943302654039@163.com> References: <200910281943302654039@163.com> Message-ID: This should only be a warning (the ActiveState SOAP-Lite package has this dependency). It should still install. chris On Oct 28, 2009, at 6:43 AM, ???? wrote: > Hi all, > > I got a problem when I installed Bioperl with activeperl ppm on > Windows platform. When I marked the Bioperl package for install in > ppm, I got a warning message which said "WARNING: Can't find any > package that provides Apache:: for SOAP-Lite". I had added all the > repository links to ppm, which is suggested on the Bioperl wiki web. > Is there anyone who knows what is the problem and how to fix it? > Thanks in advance. > > Xiang > > 2009-10-28 > > > > ???? > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From simonstudy at 163.com Wed Oct 28 09:43:10 2009 From: simonstudy at 163.com (=?gb2312?B?0OzP4A==?=) Date: Wed, 28 Oct 2009 21:43:10 +0800 Subject: [Bioperl-l] problem in installation of bioperl References: <200910281943302654039@163.com> Message-ID: <200910282143091718810@163.com> Hi Chris, Thanks for your answer. I know that the reason may be the dependency, but I still don't know where to find the needed package to install. It is not in the repositories which are said on the Bioperl website. Could you help me to figure it out. Xiang 2009-10-28 ???? ???????? Chris Fields ?????????? 2009-10-28 20:10:52 ???????? ???? ?????? bioperl-l ?????? Re: [Bioperl-l] problem in installation of bioperl This should only be a warning (the ActiveState SOAP-Lite package has this dependency). It should still install. chris On Oct 28, 2009, at 6:43 AM, ???? wrote: > Hi all, > > I got a problem when I installed Bioperl with activeperl ppm on > Windows platform. When I marked the Bioperl package for install in > ppm, I got a warning message which said "WARNING: Can't find any > package that provides Apache:: for SOAP-Lite". I had added all the > repository links to ppm, which is suggested on the Bioperl wiki web. > Is there anyone who knows what is the problem and how to fix it? > Thanks in advance. > > Xiang > > 2009-10-28 > > > > ???? > > _______________________________________________ > 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 maj at fortinbras.us Wed Oct 28 10:02:49 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 28 Oct 2009 10:02:49 -0400 Subject: [Bioperl-l] problem in installation of bioperl In-Reply-To: <200910282143091718810@163.com> References: <200910281943302654039@163.com> <200910282143091718810@163.com> Message-ID: Xiang- Here's a procedure I know will get around this. Make sure you have the module PPM-Repositories installed. Run ppm-shell, then do ppm> repo add http://bioperl.org/DIST ppm> repo add uwinnipeg ppm> repo add trouchelle If you do ppm> repo you should see something like You should see something like ?? id ?? pkgs ?? name ?? ?? 1 ?? 11431 ?? ActiveState Package Repository ?? ?? 2 ?? 14 ?? bioperl.org ?? ?? 3 ?? 291 ?? uwinnipeg ?? ?? 4 ?? 11755 ?? trouchelle ?? Now do # turn off ActiveState, trouchelle repos ppm> repo off 1 ppm> repo off 4 # to get SOAP-Lite-0.69 from uwinnipeg... ppm> install SOAP-Lite # turn ActiveState, trouchelle back on... ppm> repo on 1 ppm> repo on 4 # now try... ppm> install BioPerl cheers MAJ ----- Original Message ----- From: "????" To: "Chris Fields" Cc: "bioperl-l" Sent: Wednesday, October 28, 2009 9:43 AM Subject: Re: [Bioperl-l] problem in installation of bioperl > Hi Chris, > Thanks for your answer. I know that the reason may be the dependency, but I > still don't know where to find the needed package to install. It is not in the > repositories which are said on the Bioperl website. Could you help me to > figure it out. > > Xiang > 2009-10-28 > > > > ???? > > > > ???????? Chris Fields > ?????????? 2009-10-28 20:10:52 > ???????? ???? > ?????? bioperl-l > ?????? Re: [Bioperl-l] problem in installation of bioperl > > This should only be a warning (the ActiveState SOAP-Lite package has > this dependency). It should still install. > chris > On Oct 28, 2009, at 6:43 AM, ???? wrote: >> Hi all, >> >> I got a problem when I installed Bioperl with activeperl ppm on >> Windows platform. When I marked the Bioperl package for install in >> ppm, I got a warning message which said "WARNING: Can't find any >> package that provides Apache:: for SOAP-Lite". I had added all the >> repository links to ppm, which is suggested on the Bioperl wiki web. >> Is there anyone who knows what is the problem and how to fix it? >> Thanks in advance. >> >> Xiang >> >> 2009-10-28 >> >> >> >> ???? >> >> _______________________________________________ >> 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 simonstudy at 163.com Wed Oct 28 10:47:21 2009 From: simonstudy at 163.com (=?gb2312?B?0OzP4A==?=) Date: Wed, 28 Oct 2009 22:47:21 +0800 Subject: [Bioperl-l] problem in installation of bioperl References: <200910281943302654039@163.com>, <200910282143091718810@163.com>, Message-ID: <200910282247203758086@163.com> Hi Mark, Thanks for your help. It works. Xiang 2009-10-28 ???? ???????? Mark A. Jensen ?????????? 2009-10-28 22:02:49 ???????? ????; Chris Fields ?????? bioperl-l ?????? Re: [Bioperl-l] problem in installation of bioperl Xiang- Here's a procedure I know will get around this. Make sure you have the module PPM-Repositories installed. Run ppm-shell, then do ppm> repo add http://bioperl.org/DIST ppm> repo add uwinnipeg ppm> repo add trouchelle If you do ppm> repo you should see something like You should see something like ?? id ?? pkgs ?? name ?? ?? 1 ?? 11431 ?? ActiveState Package Repository ?? ?? 2 ?? 14 ?? bioperl.org ?? ?? 3 ?? 291 ?? uwinnipeg ?? ?? 4 ?? 11755 ?? trouchelle ?? Now do # turn off ActiveState, trouchelle repos ppm> repo off 1 ppm> repo off 4 # to get SOAP-Lite-0.69 from uwinnipeg... ppm> install SOAP-Lite # turn ActiveState, trouchelle back on... ppm> repo on 1 ppm> repo on 4 # now try... ppm> install BioPerl cheers MAJ ----- Original Message ----- From: "????" To: "Chris Fields" Cc: "bioperl-l" Sent: Wednesday, October 28, 2009 9:43 AM Subject: Re: [Bioperl-l] problem in installation of bioperl > Hi Chris, > Thanks for your answer. I know that the reason may be the dependency, but I > still don't know where to find the needed package to install. It is not in the > repositories which are said on the Bioperl website. Could you help me to > figure it out. > > Xiang > 2009-10-28 > > > > ???? > > > > ???????? Chris Fields > ?????????? 2009-10-28 20:10:52 > ???????? ???? > ?????? bioperl-l > ?????? Re: [Bioperl-l] problem in installation of bioperl > > This should only be a warning (the ActiveState SOAP-Lite package has > this dependency). It should still install. > chris > On Oct 28, 2009, at 6:43 AM, ???? wrote: >> Hi all, >> >> I got a problem when I installed Bioperl with activeperl ppm on >> Windows platform. When I marked the Bioperl package for install in >> ppm, I got a warning message which said "WARNING: Can't find any >> package that provides Apache:: for SOAP-Lite". I had added all the >> repository links to ppm, which is suggested on the Bioperl wiki web. >> Is there anyone who knows what is the problem and how to fix it? >> Thanks in advance. >> >> Xiang >> >> 2009-10-28 >> >> >> >> ???? >> >> _______________________________________________ >> 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 cjfields at illinois.edu Wed Oct 28 11:47:02 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Oct 2009 10:47:02 -0500 Subject: [Bioperl-l] problem in installation of bioperl In-Reply-To: <200910282247203758086@163.com> References: <200910281943302654039@163.com>, <200910282143091718810@163.com>, <200910282247203758086@163.com> Message-ID: <0D90ADF7-48B3-46E7-A6DC-0182875FBE4B@illinois.edu> Mark, do we need to modify those instructions on the wiki? chris PS - I am working on a way to centralize things a bit and autogenerate certain pages that are replicated in both the distribution and the wiki (README, INSTALL, DEPENDENCIES, BioPerl.pm, etc). ATM I'm thinking these will be POD in svn that will be wikified and auto- updated, or vice versa. On Oct 28, 2009, at 9:47 AM, ???? wrote: > Hi Mark, > > Thanks for your help. It works. > > Xiang > > > 2009-10-28 > > > > ???? > > > > ???????? Mark A. Jensen > ?????????? 2009-10-28 22:02:49 > ???????? ????; Chris Fields > ?????? bioperl-l > ?????? Re: [Bioperl-l] problem in installation of bioperl > > Xiang- > Here's a procedure I know will get around this. Make sure you > have the module PPM-Repositories installed. > Run ppm-shell, then do > ppm> repo add http://bioperl.org/DIST > ppm> repo add uwinnipeg > ppm> repo add trouchelle > If you do > ppm> repo > you should see something like > You should see something like > ?? id ?? pkgs ?? name ?? > ?? 1 ?? 11431 ?? ActiveState Package Repository ?? > ?? 2 ?? 14 ?? bioperl.org ?? > ?? 3 ?? 291 ?? uwinnipeg ?? > ?? 4 ?? 11755 ?? trouchelle ?? > Now do > # turn off ActiveState, trouchelle repos > ppm> repo off 1 > ppm> repo off 4 > # to get SOAP-Lite-0.69 from uwinnipeg... > ppm> install SOAP-Lite > # turn ActiveState, trouchelle back on... > ppm> repo on 1 > ppm> repo on 4 > # now try... > ppm> install BioPerl > cheers MAJ > ----- Original Message ----- > From: "????" > To: "Chris Fields" > Cc: "bioperl-l" > Sent: Wednesday, October 28, 2009 9:43 AM > Subject: Re: [Bioperl-l] problem in installation of bioperl >> Hi Chris, >> Thanks for your answer. I know that the reason may be the >> dependency, but I >> still don't know where to find the needed package to install. It is >> not in the >> repositories which are said on the Bioperl website. Could you help >> me to >> figure it out. >> >> Xiang >> 2009-10-28 >> >> >> >> ???? >> >> >> >> ???????? Chris Fields >> ?????????? 2009-10-28 20:10:52 >> ???????? ???? >> ?????? bioperl-l >> ?????? Re: [Bioperl-l] problem in installation of bioperl >> >> This should only be a warning (the ActiveState SOAP-Lite package has >> this dependency). It should still install. >> chris >> On Oct 28, 2009, at 6:43 AM, ???? wrote: >>> Hi all, >>> >>> I got a problem when I installed Bioperl with activeperl ppm on >>> Windows platform. When I marked the Bioperl package for install in >>> ppm, I got a warning message which said "WARNING: Can't find any >>> package that provides Apache:: for SOAP-Lite". I had added all the >>> repository links to ppm, which is suggested on the Bioperl wiki web. >>> Is there anyone who knows what is the problem and how to fix it? >>> Thanks in advance. >>> >>> Xiang >>> >>> 2009-10-28 >>> >>> >>> >>> ???? >>> >>> _______________________________________________ >>> 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 > > _______________________________________________ > 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 Oct 28 11:59:44 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 28 Oct 2009 11:59:44 -0400 Subject: [Bioperl-l] problem in installation of bioperl In-Reply-To: <0D90ADF7-48B3-46E7-A6DC-0182875FBE4B@illinois.edu> References: <200910281943302654039@163.com>, <200910282143091718810@163.com>, <200910282247203758086@163.com> <0D90ADF7-48B3-46E7-A6DC-0182875FBE4B@illinois.edu> Message-ID: I thought about it, but it seems like such a kludge--- I think the key is to get SOAP-Lite-0.69; (I think the problem arose because 0.71 uses the Apache module...But this was an issue only for 5.10, IIRC) -- should we change the dependency instead? ----- Original Message ----- From: "Chris Fields" To: ""????"" Cc: "Mark A. Jensen" ; "bioperl-l" Sent: Wednesday, October 28, 2009 11:47 AM Subject: Re: [Bioperl-l] problem in installation of bioperl Mark, do we need to modify those instructions on the wiki? chris PS - I am working on a way to centralize things a bit and autogenerate certain pages that are replicated in both the distribution and the wiki (README, INSTALL, DEPENDENCIES, BioPerl.pm, etc). ATM I'm thinking these will be POD in svn that will be wikified and auto- updated, or vice versa. On Oct 28, 2009, at 9:47 AM, ???? wrote: > Hi Mark, > > Thanks for your help. It works. > > Xiang > > > 2009-10-28 > > > > ???? > > > > ???????? Mark A. Jensen > ?????????? 2009-10-28 22:02:49 > ???????? ????; Chris Fields > ?????? bioperl-l > ?????? Re: [Bioperl-l] problem in installation of bioperl > > Xiang- > Here's a procedure I know will get around this. Make sure you > have the module PPM-Repositories installed. > Run ppm-shell, then do > ppm> repo add http://bioperl.org/DIST > ppm> repo add uwinnipeg > ppm> repo add trouchelle > If you do > ppm> repo > you should see something like > You should see something like > ?? id ?? pkgs ?? name ?? > ?? 1 ?? 11431 ?? ActiveState Package Repository ?? > ?? 2 ?? 14 ?? bioperl.org ?? > ?? 3 ?? 291 ?? uwinnipeg ?? > ?? 4 ?? 11755 ?? trouchelle ?? > Now do > # turn off ActiveState, trouchelle repos > ppm> repo off 1 > ppm> repo off 4 > # to get SOAP-Lite-0.69 from uwinnipeg... > ppm> install SOAP-Lite > # turn ActiveState, trouchelle back on... > ppm> repo on 1 > ppm> repo on 4 > # now try... > ppm> install BioPerl > cheers MAJ > ----- Original Message ----- > From: "????" > To: "Chris Fields" > Cc: "bioperl-l" > Sent: Wednesday, October 28, 2009 9:43 AM > Subject: Re: [Bioperl-l] problem in installation of bioperl >> Hi Chris, >> Thanks for your answer. I know that the reason may be the dependency, but I >> still don't know where to find the needed package to install. It is not in >> the >> repositories which are said on the Bioperl website. Could you help me to >> figure it out. >> >> Xiang >> 2009-10-28 >> >> >> >> ???? >> >> >> >> ???????? Chris Fields >> ?????????? 2009-10-28 20:10:52 >> ???????? ???? >> ?????? bioperl-l >> ?????? Re: [Bioperl-l] problem in installation of bioperl >> >> This should only be a warning (the ActiveState SOAP-Lite package has >> this dependency). It should still install. >> chris >> On Oct 28, 2009, at 6:43 AM, ???? wrote: >>> Hi all, >>> >>> I got a problem when I installed Bioperl with activeperl ppm on >>> Windows platform. When I marked the Bioperl package for install in >>> ppm, I got a warning message which said "WARNING: Can't find any >>> package that provides Apache:: for SOAP-Lite". I had added all the >>> repository links to ppm, which is suggested on the Bioperl wiki web. >>> Is there anyone who knows what is the problem and how to fix it? >>> Thanks in advance. >>> >>> Xiang >>> >>> 2009-10-28 >>> >>> >>> >>> ???? >>> >>> _______________________________________________ >>> 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 > > _______________________________________________ > 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 Oct 28 12:47:17 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Oct 2009 11:47:17 -0500 Subject: [Bioperl-l] problem in installation of bioperl In-Reply-To: References: <200910281943302654039@163.com>, <200910282143091718810@163.com>, <200910282247203758086@163.com> <0D90ADF7-48B3-46E7-A6DC-0182875FBE4B@illinois.edu> Message-ID: I would rather leave it, as it restricts any install on any OS to using that version, not just ActiveState/Windows. The module dependency is on ActiveState's end (it's their PPM that's listing the dependency), not ours, and everything installs fine. I'll check with the ActiveState bug db and see if this has been filed. Also, just to note, I don't recall this being a problem with Strawberry Perl. The installation there was much simpler and direct, straight from CPAN. chris On Oct 28, 2009, at 10:59 AM, Mark A. Jensen wrote: > I thought about it, but it seems like such a kludge--- I think the > key is to get SOAP-Lite-0.69; (I think the problem arose because 0.71 > uses the Apache module...But this was an issue only for 5.10, IIRC) -- > should we change the dependency instead? > ----- Original Message ----- From: "Chris Fields" > > To: ""????"" > Cc: "Mark A. Jensen" ; "bioperl-l" > > Sent: Wednesday, October 28, 2009 11:47 AM > Subject: Re: [Bioperl-l] problem in installation of bioperl > > > Mark, do we need to modify those instructions on the wiki? > > chris > > PS - I am working on a way to centralize things a bit and autogenerate > certain pages that are replicated in both the distribution and the > wiki (README, INSTALL, DEPENDENCIES, BioPerl.pm, etc). ATM I'm > thinking these will be POD in svn that will be wikified and auto- > updated, or vice versa. > > On Oct 28, 2009, at 9:47 AM, ???? wrote: > >> Hi Mark, >> >> Thanks for your help. It works. >> >> Xiang >> >> >> 2009-10-28 >> >> >> >> ???? >> >> >> >> ???????? Mark A. Jensen >> ?????????? 2009-10-28 22:02:49 >> ???????? ????; Chris Fields >> ?????? bioperl-l >> ?????? Re: [Bioperl-l] problem in installation of bioperl >> >> Xiang- >> Here's a procedure I know will get around this. Make sure you >> have the module PPM-Repositories installed. >> Run ppm-shell, then do >> ppm> repo add http://bioperl.org/DIST >> ppm> repo add uwinnipeg >> ppm> repo add trouchelle >> If you do >> ppm> repo >> you should see something like >> You should see something like >> ?? id ?? pkgs ?? name ?? >> ?? 1 ?? 11431 ?? ActiveState Package Repository ?? >> ?? 2 ?? 14 ?? bioperl.org ?? >> ?? 3 ?? 291 ?? uwinnipeg ?? >> ?? 4 ?? 11755 ?? trouchelle ?? >> Now do >> # turn off ActiveState, trouchelle repos >> ppm> repo off 1 >> ppm> repo off 4 >> # to get SOAP-Lite-0.69 from uwinnipeg... >> ppm> install SOAP-Lite >> # turn ActiveState, trouchelle back on... >> ppm> repo on 1 >> ppm> repo on 4 >> # now try... >> ppm> install BioPerl >> cheers MAJ >> ----- Original Message ----- >> From: "????" >> To: "Chris Fields" >> Cc: "bioperl-l" >> Sent: Wednesday, October 28, 2009 9:43 AM >> Subject: Re: [Bioperl-l] problem in installation of bioperl >>> Hi Chris, >>> Thanks for your answer. I know that the reason may be the >>> dependency, but I >>> still don't know where to find the needed package to install. It >>> is not in the >>> repositories which are said on the Bioperl website. Could you >>> help me to >>> figure it out. >>> >>> Xiang >>> 2009-10-28 >>> >>> >>> >>> ???? >>> >>> >>> >>> ???????? Chris Fields >>> ?????????? 2009-10-28 20:10:52 >>> ???????? ???? >>> ?????? bioperl-l >>> ?????? Re: [Bioperl-l] problem in installation of bioperl >>> >>> This should only be a warning (the ActiveState SOAP-Lite package has >>> this dependency). It should still install. >>> chris >>> On Oct 28, 2009, at 6:43 AM, ???? wrote: >>>> Hi all, >>>> >>>> I got a problem when I installed Bioperl with activeperl ppm on >>>> Windows platform. When I marked the Bioperl package for install in >>>> ppm, I got a warning message which said "WARNING: Can't find any >>>> package that provides Apache:: for SOAP-Lite". I had added all the >>>> repository links to ppm, which is suggested on the Bioperl wiki >>>> web. >>>> Is there anyone who knows what is the problem and how to fix it? >>>> Thanks in advance. >>>> >>>> Xiang >>>> >>>> 2009-10-28 >>>> >>>> >>>> >>>> ???? >>>> >>>> _______________________________________________ >>>> 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 >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > From coldmeadow at gmail.com Wed Oct 28 20:03:39 2009 From: coldmeadow at gmail.com (Chris) Date: Thu, 29 Oct 2009 11:03:39 +1100 Subject: [Bioperl-l] translate DNA whith unkown ORF Message-ID: Hello, I have a fasta file of coding exon DNA. The problem is each sequence is not a full coding exon, but may be only a segment of an exon. I would like to translate this DNA to protein, but the ORF is unknown. I can see the actual protein sequence on the UCSC browser but when I only have segments of exons there is no way to download the protein sequence segments, just the sequence for the whole gene. Does anybody know a way I can access this protein sequence, given a bed file of the coordinates of the coding sequence segments? I have tried the script "longorf.pl" on the fasta file of the DNA sequence but this does not work (or I cannot get it to) - I think it looks for an atg in the sequence and assumes that is the start codon.. Thanks, Chris. From adam at ali.as Wed Oct 28 23:11:00 2009 From: adam at ali.as (Adam Kennedy) Date: Thu, 29 Oct 2009 14:11:00 +1100 Subject: [Bioperl-l] Strawberry Perl October 2009 released, with BioPerl as headline feature Message-ID: <255d58530910282011v4a9de0dfhde859eea799a6a28@mail.gmail.com> Dear BioPeople I'm happy to announce to the final release of Strawberry Perl October 2009. It can be downloaded at http://strawberryperl.com/ The three headline improvements for this release are: - Inclusion of the DBD::Pg PostgreSQL client in the default install - Inclusion of libdb.dll and a working DB_File in the default install, allowing installation of BioPerl from the CPAN. - Inclusion of OpenSSL and a number of other crypto packages, allowing support for HTTPS and signed CPAN modules. The installation of BioPerl 1.6.1 with default Makefile.PL options (i.e. just hitting enter for everything) should now work relatively reliably, albeit with some fairly noisy warnings during testing. Anyone having installation difficulties can click on the "Live Chat" support link at the top of the Strawberry Perl front page or join #win32 on irc.perl.org, and we'll do our best to help you out. Please note the channel is staffed by volunteers in an imperfect mix of timezones, if you do not get an immediate response to your question please lurk in the channel and you'll get an answer when someone wakes up. Over the few releases, our intention is to become and default and obvious choice for running BioPerl applications on Windows (and to improve BioPerl windows support generally). To help achieve this, we have formed a partnership with Microsoft to help with Windows testing. Strawberry Perl is the founding member of Microsoft's Open Source Network, which provides us access to a wide variety of different Windows virtual machine environments, hosted, managed and paid for by Microsoft. These Windows virtual machines (covering XP, Vista, Server 2003 32bit, Server 2003 64bit, Server 2008 32bit, Server 2008 64bit, and shortly Windows 7) are completely free to access and use for testing and debugging, and are available for use by anyone with a register CPAN login. Login accounts and coordination of access to the VMs are managed in irc.perl.org #msopensource. Please contact someone there for access to the environments. In addition to this, for the January 2010 release of the new Strawberry Perl Professional distribution we intend to include BioPerl in the default install, along with the Padre Perl IDE and many other distributions such as SDL for mathematical programming, Imager and GD for graphics, and many other popular CPAN modules. Suggestions for CPAN modules that the BioPerl community would like to see included on top of the core BioPerl package are welcome. Bug reports can be filed against the Perl-Dist- Strawberry package on rt.cpan.org. Thank you all for your time, and look forward to working with you guys to make the installation of BioPerl better, easier, and more reliable. Adam Kennedy Strawberry Perl Team From dan.kortschak at adelaide.edu.au Thu Oct 29 16:27:21 2009 From: dan.kortschak at adelaide.edu.au (Dan Kortschak) Date: Fri, 30 Oct 2009 06:57:21 +1030 Subject: [Bioperl-l] Bioperl-l Digest, Vol 78, Issue 26 In-Reply-To: References: Message-ID: <1256848041.5161.15.camel@epistle> Hi, longorf by default requires an ATG, but can be asked to ignore that with the notstrict option, it naturally runs translation off the end if no stop is found. You may have problems though with the 3' end if there is a stop in the adjacent intron (you'll end up with a bit of translated intron until then next inframe stop - this may or may not be a problem for you); longorf makes no attempt to be intelligent with respect to intron/exon boundaries as it was designed for cDNA sets in mind. Also, if the biologically relevant frame is not the longest, it will not be found (this should be an obvious caveat). If these criteria aren't met, you may want to look at writing something that makes use of Bio::Tools:Genscan (I haven't tried this, so can't vouch for it) or try out run_genscan.pl in the examples/tools directory. I hope this helps Dan On Thu, 2009-10-29 at 12:00 -0400, bioperl-l-request at lists.open-bio.org wrote: > Date: Thu, 29 Oct 2009 11:03:39 +1100 > From: Chris > Subject: [Bioperl-l] translate DNA whith unkown ORF > To: bioperl List > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > Hello, > > I have a fasta file of coding exon DNA. The problem is each sequence is not > a full coding exon, but may be only a segment of an exon. I would like to > translate this DNA to protein, but the ORF is unknown. I can see the actual > protein sequence on the UCSC browser but when I only have segments of exons > there is no way to download the protein sequence segments, just the sequence > for the whole gene. Does anybody know a way I can access this protein > sequence, given a bed file of the coordinates of the coding sequence > segments? I have tried the script "longorf.pl" on the fasta file of the DNA > sequence but this does not work (or I cannot get it to) - I think it looks > for an atg in the sequence and assumes that is the start codon.. > > Thanks, > Chris. From maj at fortinbras.us Thu Oct 29 21:27:27 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Thu, 29 Oct 2009 21:27:27 -0400 Subject: [Bioperl-l] a PerlIO layer for Bio::SeqIO In-Reply-To: <4AE0E751.8070300@gmail.com> References: <18DF7D20DFEC044098A1062202F5FFF32B62D67492@exchsth.agresearch.co.nz><1DD55DFD52CE4A658652907BE02B30AE@NewLife> <4AE0E751.8070300@gmail.com> Message-ID: <9897BD6F61FB4D0EB232A503DB81661B@NewLife> Hey Florent -- Got gzip working now. On CPAN, get the current PerlIO::via::gzip (0.021) and the current PerlIO::via::SeqIO (0.03). Then one can do the following: compressed, converted output: open(my $tfh,"<:via(SeqIO)", "test.fas"); open(my $zfh,'>:via(SeqIO::embl):via(gzip)', 'test.embl.gz'); while (<$tfh>) { print $zfh $_; } close($zfh); decompressed, converted input open($tfh,"<:via(gzip):via(SeqIO::fasta)", "test.fas.gz"); open(my $zfh,'>:via(SeqIO::embl)', 'test.embl'); while (<$tfh>) { print $zfh $_; } gzip-to-gzip conversion: open(my $tfh, "<:via(gzip):via(SeqIO::fasta)", "test.fas.gz"); open(my $zfh, ">:via(gzip):via(SeqIO::embl)", "test.embl.gz"); local $/; print $zfh <$tfh>; close($zfh); have fun-- MAJ ----- Original Message ----- From: "Florent Angly" To: "Mark A. Jensen" Cc: "'BioPerl List'" ; "Smithies,Russell" Sent: Thursday, October 22, 2009 7:14 PM Subject: Re: [Bioperl-l] a PerlIO layer for Bio::SeqIO > Sounds cool Mark! After all, UNIX is based on the notion on piping data from > one program to another using filehandles. > Any chance that this could also work for compressed files like *.gz ?? I don't > think that Bio::Root::Utilities::compress and uncompress can deal with > filehandles, can it? > Florent > > Mark A. Jensen wrote: >> Because it's fun! Also: >> >> use CGI; >> use PerlIO::via::SeqIO; >> use strict; >> use warnings; >> my $q = new CGI; >> my ($seqfh, $dup); >> open($seqfh, "<:via(SeqIO)", 'test.fas'); >> open(STDOUT, ">:via(SeqIO::fasta)"); >> >> my $s = <$seqfh>; >> >> print ( >> $q->start_html, >> "Copy the desired format from the boxes below:

", >> $q->div({-style=>"border:solid 1px black"}, >> $q->h3("FASTA\n"), >> $q->pre($s)) >> ); >> (tied *STDOUT)->set_write_format('embl'); >> print ( >> $q->div({-style=>"border:solid 1px black"}, >> $q->h3("EMBL"), >> $q->pre($s)) >> ); >> (tied *STDOUT)->set_write_format('gcg'); >> print ( >> $q->div({-style=>"border:solid 1px black"}, >> $q->h3("GCG"), >> $q->pre($s)), >> $q->end_html >> ); >> 1; >> >> ----- Original Message ----- From: "Smithies, Russell" >> >> To: "'Mark A. Jensen'" ; "'BioPerl List'" >> >> Sent: Thursday, October 22, 2009 6:57 PM >> Subject: RE: [Bioperl-l] a PerlIO layer for Bio::SeqIO >> >> >> Why anyone would want to do it this way is the only thing that's bugging me >> ;-) >> Maybe I'm a bit dense this morning but what's the advantage? >> >> --Russell >> (I need more coffee) >> >>> -----Original Message----- >>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>> bounces at lists.open-bio.org] On Behalf Of Mark A. Jensen >>> Sent: Friday, 23 October 2009 11:24 a.m. >>> To: BioPerl List >>> Subject: [Bioperl-l] a PerlIO layer for Bio::SeqIO >>> >>> Hi All: >>> >>> Have you ever wanted to do this? >>> >>> open($f, "<:via(SeqIO)", "my.fas"); >>> open($g, ">:via(SeqIO::embl)", "my.fas.embl"); >>> while (<$f>) { print $g $_; } >>> >>> Or this? >>> >>> open($f, "<:via(SeqIO)", "my.fas"); >>> open(STDOUT, ">:via(SeqIO::fasta)"); >>> $seq = <$f>; >>> print "The following is an example of FASTA format:", $seq; >>> >>> Or even this? >>> >>> (tied *STDOUT)->set_write_format('gcg'); >>> print "While this is an example of GCG:", $seq; >>> >>> Now you can, and much more. See >>> http://search.cpan.org/search?query=PerlIO::via::SeqIO >>> >>> Send me the bugs. >>> cheers, >>> MAJ >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> ======================================================================= >> Attention: The information contained in this message and/or attachments >> from AgResearch Limited is intended only for the persons or entities >> to which it is addressed and may contain confidential and/or privileged >> material. Any review, retransmission, dissemination or other use of, or >> taking of any action in reliance upon, this information by persons or >> entities other than the intended recipients is prohibited by AgResearch >> Limited. If you have received this message in error, please notify the >> sender immediately. >> ======================================================================= >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l 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 dfog22 at hotmail.com Fri Oct 30 11:23:41 2009 From: dfog22 at hotmail.com (MathGon) Date: Fri, 30 Oct 2009 08:23:41 -0700 (PDT) Subject: [Bioperl-l] Problem about slashes and backslahes in library paths Message-ID: <26131931.post@talk.nabble.com> I installed Perl on Windows and I have problem to access Bioperl libraries. My scripts are ok, I tried them on an other computer. The error message is: Can't locate Bio/PrimarySeq.pm in @INC (@INC contains H:/Perl64/site/lib/ H:Perl64/site.lib .) at H:\script.pl line 10 I tried to solve this problem by mining posts on forums but I didn't manage. Have you an idea please? -- View this message in context: http://old.nabble.com/Problem-about-slashes-and-backslahes-in-library-paths-tp26131931p26131931.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From Frederic.SAPET at biogemma.com Fri Oct 30 06:10:31 2009 From: Frederic.SAPET at biogemma.com (Frederic.SAPET at biogemma.com) Date: Fri, 30 Oct 2009 11:10:31 +0100 Subject: [Bioperl-l] Bio::Search::Tiling::MapTiling and BlastX report. Message-ID: Hello I'm trying to use the new Bio::Search::Tiling::MapTiling (I have tried both BioPerl 1.6.1 and the last nightly build) module on a WuBlastX report after reading the documentation (http://www.bioperl.org/wiki/HOWTO:Tiling). Please find in attachment the sample file I used for my test. Here is the code I have tried : use Bio::SearchIO; use Bio::Search::Tiling::MapTiling; my $blio = Bio::SearchIO->new( -format => 'blast', -file => 'WuBlastX.txt' ); my $result = $blio->next_result; while (my $hit = $result->next_hit) { my $tiling = Bio::Search::Tiling::MapTiling->new($hit); my @contextsQ = $tiling->contexts('query'); for my $contextQ ( @contextsQ ) { my ($min, $max) = $tiling->range('query', $contextQ); my $tLengthQ = $tiling->length('query', 'exact', $contextQ); print "QUERY range in *$contextQ* => $min, $max (length=$tLengthQ)\n"; } my @contextsS = $tiling->contexts('subject'); for my $contextS ( @contextsS ) { my ($min2, $max2) = $tiling->range('subject', $contextS); print "SUBJECT range in *$contextS* => $min2, $max2\n"; } } exit; Results printed on my terminal are : QUERY range in *m1* => 4065, 10571 (length=7038) QUERY range in *m0* => 7, 11037 (length=2577) QUERY range in *m2* => 2462, 14599 (length=327) SUBJECT range in *all* => 435, 270 I think that the right query range in m1 context should be 1170 to 10571 (and length 6828 ?) and subject range has to be 231 to 3563 no ? The m1 context seems to be the best one, with 2271 amino acid aligned (in 4 HSP )between MySampleSeq and the Protein B9GCX0. Could you please help me to point what is wrong ? Thank you. Fred -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: WuBlastX.txt URL: From djibrilo at yahoo.fr Fri Oct 30 09:00:32 2009 From: djibrilo at yahoo.fr (djibrilo) Date: Fri, 30 Oct 2009 13:00:32 +0000 (GMT) Subject: [Bioperl-l] About Bioperl - patch - installation Windows Message-ID: <763635.66569.qm@web23006.mail.ird.yahoo.com> Dear, There are some problems about bioperl installation on Windows. I am using bioperl on Windows XP, Vista, ... and I use activeperl 5.8 and some times 5.10. for module installation , I use ppm on Windows system and sometimes I use cpan or build via compilation. The problem now is about ppm. There are 2 repositories to install bioperl : 1- trouchelle, there are : - bioperl 1.4, 1.5.2_100 - bioperl-db 0.01, 1.5.2_100 - bioperl-run 1.2.2 ... 2- BioPerl ( http://bioperl.org/DIST), there are : - BioPerl 1.6.1 - bioperl-db 1.5.2_100 - bioperl-network 1.5.2_100 - bioperl-run 1.5.2_100 - Bundle-BioPerl-Core 1.6.1 .... I have seen the package.XML of BioPerl repository : ... ... The file have been updated at 10 October 2009 but some files are old. Then, it is impossible to many people using bioperl on Windows to update correctly bioperl. And, it is difficult to me to send you a patch about clustalw and primer3 modules because I can not install BioPerl-run-1.6.1 on my Windows PC. I have seen another BioPerl repository ( http://bioperl.org/DIST/RC) and there are the same problems. BioPerl-Run.ppd BioPerl-Run BioPerl-Run - wrapper toolkit BioPerl Team <bioperl-l at bioperl.org> BioPerl-DB.ppd BioPerl-DB BioPerl-DB - package for biological databases BioPerl Team <bioperl-l at bioperl.org> BioPerl-Network.ppd BioPerl-Network BioPerl-Network - package for biological networks BioPerl Team <bioperl-l at bioperl.org> Nevertheless there are PPM-BioPerl-Run-1.6.1_001.tar.gz, PPM-BioPerl-DB-1.6.0_001.tar.gz, PPM-BioPerl-Network-1.6.0_001.tar.gz files. Can you try to update all your ppd files on your repositories because it is a real problem to many lab and user wich try to updated bioperl and use it on Windows server. Best Regards, Djibril Ousmanou From robert.bradbury at gmail.com Sat Oct 31 09:55:24 2009 From: robert.bradbury at gmail.com (Robert Bradbury) Date: Sat, 31 Oct 2009 09:55:24 -0400 Subject: [Bioperl-l] Problem about slashes and backslahes in library paths In-Reply-To: <26131931.post@talk.nabble.com> References: <26131931.post@talk.nabble.com> Message-ID: On Fri, Oct 30, 2009 at 11:23 AM, MathGon wrote: > > Can't locate Bio/PrimarySeq.pm in @INC (@INC contains H:/Perl64/site/lib/ > H:Perl64/site.lib .) at H:\script.pl line 10 > > Well, you've got a "mixed" pathname in @INC. Anything that starts with L: would be a windows path while the use of forward slashes (/) is a Linux path. I'd suggest changing the script (or the environment which sets @INC) so it uses only Windows or Linux paths. There may be some Perl scripts that one is supposed to run to setup the @INC variable correctly for ones current system (presumably depends on the supplier of Perl for your Windows installation). Or you could switch to Linux which I would consider to be a much more Perl/BioPerl friendly environment. Because, IMO, sticking with Windows is like boarding the Titanic as it is about to sail out of the harbor. Robert From cjfields at illinois.edu Sat Oct 31 10:10:16 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 31 Oct 2009 09:10:16 -0500 Subject: [Bioperl-l] Problem about slashes and backslahes in library paths In-Reply-To: References: <26131931.post@talk.nabble.com> Message-ID: On Oct 31, 2009, at 8:55 AM, Robert Bradbury wrote: > On Fri, Oct 30, 2009 at 11:23 AM, MathGon wrote: > >> >> Can't locate Bio/PrimarySeq.pm in @INC (@INC contains H:/Perl64/ >> site/lib/ >> H:Perl64/site.lib .) at H:\script.pl line 10 >> >> > Well, you've got a "mixed" pathname in @INC. Anything that starts > with L: > would be a windows path while the use of forward slashes (/) is a > Linux > path. I'd suggest changing the script (or the environment which > sets @INC) > so it uses only Windows or Linux paths. Also, that last directory is a bit odd: H:Perl64/site.lib Regardless, the message means the perl executable used from command line or called from the shebang line can't find BioPerl in @INC. Another way to check is using 'perldoc -l Bio::Root::Root'; replace Bio::Root::Root with any BioPerl module. You can set PERL5LIB to point at your local BioPerl directory, but for Windows you really should install it. It should work using PPM or CPAN with ActivePerl and CPAN with Strawberry Perl. > There may be some Perl scripts that one is supposed to run to setup > the @INC > variable correctly for ones current system (presumably depends on the > supplier of Perl for your Windows installation). > > Or you could switch to Linux which I would consider to be a much more > Perl/BioPerl friendly environment. Because, IMO, sticking with > Windows is > like boarding the Titanic as it is about to sail out of the harbor. > > Robert Ah, let's not start that up here, please? The more users we have the better. I much prefer to use Ubuntu 9.10 and OS X, but some of the devs (me included) have put a decent amount of work trying to get things working on WinXP (to the point of having a local VM). chris From maj at fortinbras.us Sat Oct 31 10:53:38 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 31 Oct 2009 10:53:38 -0400 Subject: [Bioperl-l] Bio::Search::Tiling::MapTiling and BlastX report. In-Reply-To: References: Message-ID: <78B26E0032E84437BBCD7923F8B976FA@NewLife> Hi Fred- I've been looking hard at this; my guess is it's a bug in relating strand/frame contexts to the 'all' AA-only context. Would be kind enough to submit a bug report to http://bugzilla.bioperl.org and attach your script and the blast report? I will work on this ASAP. Thanks Mark ----- Original Message ----- From: To: Sent: Friday, October 30, 2009 6:10 AM Subject: [Bioperl-l] Bio::Search::Tiling::MapTiling and BlastX report. > Hello > > I'm trying to use the new Bio::Search::Tiling::MapTiling (I have tried > both BioPerl 1.6.1 and the last nightly build) module on a WuBlastX > report after reading the documentation > (http://www.bioperl.org/wiki/HOWTO:Tiling). > Please find in attachment the sample file I used for my test. > > > > > Here is the code I have tried : > > use Bio::SearchIO; > use Bio::Search::Tiling::MapTiling; > > my $blio = Bio::SearchIO->new( -format => 'blast', > -file => 'WuBlastX.txt' > ); > > my $result = $blio->next_result; > > while (my $hit = $result->next_hit) { > my $tiling = Bio::Search::Tiling::MapTiling->new($hit); > my @contextsQ = $tiling->contexts('query'); > for my $contextQ ( @contextsQ ) { > my ($min, $max) = $tiling->range('query', $contextQ); > my $tLengthQ = $tiling->length('query', 'exact', $contextQ); > print "QUERY range in *$contextQ* => $min, $max > (length=$tLengthQ)\n"; > } > my @contextsS = $tiling->contexts('subject'); > for my $contextS ( @contextsS ) { > my ($min2, $max2) = $tiling->range('subject', $contextS); > print "SUBJECT range in *$contextS* => $min2, $max2\n"; > } > } > > exit; > > Results printed on my terminal are : > > QUERY range in *m1* => 4065, 10571 (length=7038) > QUERY range in *m0* => 7, 11037 (length=2577) > QUERY range in *m2* => 2462, 14599 (length=327) > SUBJECT range in *all* => 435, 270 > > I think that the right query range in m1 context should be 1170 to 10571 > (and length 6828 ?) > and subject range has to be 231 to 3563 no ? > > The m1 context seems to be the best one, with 2271 amino acid aligned (in > 4 HSP )between MySampleSeq and the Protein B9GCX0. > > Could you please help me to point what is wrong ? > > Thank you. > > Fred -------------------------------------------------------------------------------- > _______________________________________________ > 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 Oct 31 11:11:06 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 31 Oct 2009 10:11:06 -0500 Subject: [Bioperl-l] About Bioperl - patch - installation Windows In-Reply-To: <763635.66569.qm@web23006.mail.ird.yahoo.com> References: <763635.66569.qm@web23006.mail.ird.yahoo.com> Message-ID: <1D7DE491-987E-4FA9-80AA-217E86B2A15A@illinois.edu> Djibril, (Comments interspersed) On Oct 30, 2009, at 8:00 AM, djibrilo wrote: > Dear, > > There are some problems about bioperl installation on Windows. > I am using bioperl on Windows XP, Vista, ... and I use activeperl > 5.8 and some times 5.10. for module installation > , I use ppm on Windows system and sometimes I use cpan or build via > compilation. > > The problem now is about ppm. In general, I understand that mixing perl versions on Windows is NOT recommended unless you know what you are doing. Not sure about upgrading, but this is problematic through PPM for many reasons, first being PPMs are missing (DB_File is a dummy PPM on ActivePerl) and others are problematic (SOAP::Lite is apparently an issue). > There are 2 repositories to install bioperl : > 1- trouchelle, there are : > - bioperl 1.4, 1.5.2_100 > - bioperl-db 0.01, 1.5.2_100 > - bioperl-run 1.2.2 > ... > > 2- BioPerl ( http://bioperl.org/DIST), there are : > - BioPerl 1.6.1 > - bioperl-db 1.5.2_100 > - bioperl-network 1.5.2_100 > - bioperl-run 1.5.2_100 > - Bundle-BioPerl-Core 1.6.1 > .... > > I have seen the package.XML of BioPerl repository : > > ... > > > > > > > > DATE="2006-12-6"> > > DATE="2006-12-6"> > > DATE="2006-12-6"> > > > ... > > The file have been updated at 10 October 2009 but some files are > old. Then, it is impossible to many people using bioperl on Windows to > update correctly bioperl. And, it is difficult to me to send you a > patch about clustalw and primer3 modules because I can not install > BioPerl-run-1.6.1 on my Windows PC. I'll remove the older ones. Just to note, I haven't uploaded the final CPAN releases and the PPMs for BioPerl-DB, BioPerl-Run, and BioPerl-Network to the repo yet, for many various reasons (I haven't had a chance to test them on Win being one of them). To acknowledge something Robert said in another post, Perl is generally configured to work best with UNIX'y flavors, but support for a UNIX-like Perl on Windows is growing, particularly with Strawberry Perl. > I have seen another BioPerl repository ( http://bioperl.org/DIST/RC) > and there are the same problems. Those are release candidates, and should be removed (they haven't been tested yet). The package.xml In the meantime, you can try out code very easily by setting your local PERL5LIB, or having a 'use lib' directive (this also works for bioperl-live). > Nevertheless there are PPM-BioPerl-Run-1.6.1_001.tar.gz, PPM- > BioPerl-DB-1.6.0_001.tar.gz, PPM-BioPerl-Network-1.6.0_001.tar.gz > files. > > Can you try to update all your ppd files on your repositories > because it is a real problem > to many lab and user wich try to updated bioperl and use it on > Windows server. > > Best Regards, > > Djibril Ousmanou We appreciate pointing these things out, I'll file them as a bug for tracking. This is probably the best way to address problems in the future. Also, realize this is a completely volunteer project. It takes an inordinate amount of our (not so free) time to work on BioPerl and related projects, so any help towards this end would be greatly appreciated, including contributing back. Personally, I am a Linux/OS X user and generally avoid anything Win-related (my preference) unless needed. I believe a large number of users here fall in the same category; we only have a couple of active Win users who have time to work on portability issues. I myself managed to get PPM and CPAN installation working by testing via Remote Desktop and (soonish) VM, but that's hardly optimal and is based on my schedule, which has been very busy as of late. To that end, we would really appreciate anyone volunteering and dedicating some time towards getting the Windows bits to work, otherwise Windows support will always be determined on how much time we dedicate to it (at the moment, that being very little). chris From maj at fortinbras.us Sat Oct 31 11:47:44 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 31 Oct 2009 11:47:44 -0400 Subject: [Bioperl-l] About Bioperl - patch - installation Windows In-Reply-To: <1D7DE491-987E-4FA9-80AA-217E86B2A15A@illinois.edu> References: <763635.66569.qm@web23006.mail.ird.yahoo.com> <1D7DE491-987E-4FA9-80AA-217E86B2A15A@illinois.edu> Message-ID: Re: PPM issues-- If you are experiencing a problem with "Apache ... SOAP::Lite", or other module gaps, see the workaround recently posted under http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows#Comand-line_Installation > In general, I understand that mixing perl versions on Windows is NOT > recommended unless you know what you are doing. Even if you do, I wouldn't recommend it (except that you can learn a lot!) MAJ ----- Original Message ----- From: "Chris Fields" To: "djibrilo" Cc: ; Sent: Saturday, October 31, 2009 11:11 AM Subject: Re: [Bioperl-l] About Bioperl - patch - installation Windows > Djibril, > > (Comments interspersed) > > On Oct 30, 2009, at 8:00 AM, djibrilo wrote: > >> Dear, >> >> There are some problems about bioperl installation on Windows. >> I am using bioperl on Windows XP, Vista, ... and I use activeperl 5.8 and >> some times 5.10. for module installation >> , I use ppm on Windows system and sometimes I use cpan or build via >> compilation. >> >> The problem now is about ppm. > > In general, I understand that mixing perl versions on Windows is NOT > recommended unless you know what you are doing. Not sure about upgrading, > but this is problematic through PPM for many reasons, first being PPMs are > missing (DB_File is a dummy PPM on ActivePerl) and others are problematic > (SOAP::Lite is apparently an issue). > >> There are 2 repositories to install bioperl : >> 1- trouchelle, there are : >> - bioperl 1.4, 1.5.2_100 >> - bioperl-db 0.01, 1.5.2_100 >> - bioperl-run 1.2.2 >> ... >> >> 2- BioPerl ( http://bioperl.org/DIST), there are : >> - BioPerl 1.6.1 >> - bioperl-db 1.5.2_100 >> - bioperl-network 1.5.2_100 >> - bioperl-run 1.5.2_100 >> - Bundle-BioPerl-Core 1.6.1 >> .... >> >> I have seen the package.XML of BioPerl repository : >> >> ... >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ... >> >> The file have been updated at 10 October 2009 but some files are old. Then, >> it is impossible to many people using bioperl on Windows to >> update correctly bioperl. And, it is difficult to me to send you a patch >> about clustalw and primer3 modules because I can not install >> BioPerl-run-1.6.1 on my Windows PC. > > I'll remove the older ones. Just to note, I haven't uploaded the final CPAN > releases and the PPMs for BioPerl-DB, BioPerl-Run, and BioPerl-Network to the > repo yet, for many various reasons (I haven't had a chance to test them on > Win being one of them). > > To acknowledge something Robert said in another post, Perl is generally > configured to work best with UNIX'y flavors, but support for a UNIX-like Perl > on Windows is growing, particularly with Strawberry Perl. > >> I have seen another BioPerl repository ( http://bioperl.org/DIST/RC) and >> there are the same problems. > > Those are release candidates, and should be removed (they haven't been tested > yet). The package.xml In the meantime, you can try out code very easily by > setting your local PERL5LIB, or having a 'use lib' directive (this also works > for bioperl-live). > >> Nevertheless there are PPM-BioPerl-Run-1.6.1_001.tar.gz, PPM- >> BioPerl-DB-1.6.0_001.tar.gz, PPM-BioPerl-Network-1.6.0_001.tar.gz >> files. >> >> Can you try to update all your ppd files on your repositories because it is >> a real problem >> to many lab and user wich try to updated bioperl and use it on Windows >> server. >> >> Best Regards, >> >> Djibril Ousmanou > > > We appreciate pointing these things out, I'll file them as a bug for > tracking. This is probably the best way to address problems in the future. > > Also, realize this is a completely volunteer project. It takes an inordinate > amount of our (not so free) time to work on BioPerl and related projects, so > any help towards this end would be greatly appreciated, including > contributing back. Personally, I am a Linux/OS X user and generally avoid > anything Win-related (my preference) unless needed. I believe a large number > of users here fall in the same category; we only have a couple of active Win > users who have time to work on portability issues. > > I myself managed to get PPM and CPAN installation working by testing via > Remote Desktop and (soonish) VM, but that's hardly optimal and is based on my > schedule, which has been very busy as of late. To that end, we would really > appreciate anyone volunteering and dedicating some time towards getting the > Windows bits to work, otherwise Windows support will always be determined on > how much time we dedicate to it (at the moment, that being very little). > > chris > _______________________________________________ > 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 Oct 31 12:59:51 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 31 Oct 2009 12:59:51 -0400 Subject: [Bioperl-l] Bio::Search::Tiling::MapTiling and BlastX report. In-Reply-To: References: Message-ID: <86E01826B55C4789924F5CFAD4A10674@NewLife> Patch committed (r16305); details under Bug#2942. Will add new test case. Users be advised that this was a range problem only; lengths have been correctly calculated. thanks Fred-- MAJ ----- Original Message ----- From: To: Sent: Friday, October 30, 2009 6:10 AM Subject: [Bioperl-l] Bio::Search::Tiling::MapTiling and BlastX report. > Hello > > I'm trying to use the new Bio::Search::Tiling::MapTiling (I have tried > both BioPerl 1.6.1 and the last nightly build) module on a WuBlastX > report after reading the documentation > (http://www.bioperl.org/wiki/HOWTO:Tiling). > Please find in attachment the sample file I used for my test. > > > > > Here is the code I have tried : > > use Bio::SearchIO; > use Bio::Search::Tiling::MapTiling; > > my $blio = Bio::SearchIO->new( -format => 'blast', > -file => 'WuBlastX.txt' > ); > > my $result = $blio->next_result; > > while (my $hit = $result->next_hit) { > my $tiling = Bio::Search::Tiling::MapTiling->new($hit); > my @contextsQ = $tiling->contexts('query'); > for my $contextQ ( @contextsQ ) { > my ($min, $max) = $tiling->range('query', $contextQ); > my $tLengthQ = $tiling->length('query', 'exact', $contextQ); > print "QUERY range in *$contextQ* => $min, $max > (length=$tLengthQ)\n"; > } > my @contextsS = $tiling->contexts('subject'); > for my $contextS ( @contextsS ) { > my ($min2, $max2) = $tiling->range('subject', $contextS); > print "SUBJECT range in *$contextS* => $min2, $max2\n"; > } > } > > exit; > > Results printed on my terminal are : > > QUERY range in *m1* => 4065, 10571 (length=7038) > QUERY range in *m0* => 7, 11037 (length=2577) > QUERY range in *m2* => 2462, 14599 (length=327) > SUBJECT range in *all* => 435, 270 > > I think that the right query range in m1 context should be 1170 to 10571 > (and length 6828 ?) > and subject range has to be 231 to 3563 no ? > > The m1 context seems to be the best one, with 2271 amino acid aligned (in > 4 HSP )between MySampleSeq and the Protein B9GCX0. > > Could you please help me to point what is wrong ? > > Thank you. > > Fred -------------------------------------------------------------------------------- > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l