From cjfields at uiuc.edu Fri Feb 1 14:03:36 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 1 Feb 2008 13:03:36 -0600 Subject: [Bioperl-l] Odd issue with HSP::seq_inds() Message-ID: Apologies ahead of time for the longish post! While working on a recent bug (http://bugzilla.open-bio.org/show_bug.cgi?id=2436 ) I found a pretty significant bug. It appears that seq_inds() is giving some bad return values tied specifically to reports where either or both query or hit are translated. I'll file a full bug report but I felt it might be worth bringing up here to discuss specifically what values should be expected when these reports are parsed (all three nucleotide positions or only the first for each nonmatching translated position, etc). I used the following script to track the total HSPs as well as those where seq_inds() returns positions within the HSP bounds for query and hit: ------------------------------------------- use Bio::SearchIO; use Test::More qw(no_plan); my $file = shift || die; my $io = Bio::SearchIO->new(-format => 'blast', -file => $file); my ($hsp_co, $correctq, $correcth) = (0,0,0); while (my $res = $io->next_result) { while (my $hit = $res->next_hit) { while (my $hsp = $hit->next_hsp) { $hsp_co++; my ($qs, $qe, $hs, $he) = ($hsp->start('query'),$hsp- >end('query'), $hsp->start('hit'),$hsp- >end('hit')); my @pos = $hsp->seq_inds('query','nomatch'); my @pos2 = grep {$_ >= $qs && $_ <= $qe} @pos; # should always be true if (scalar(@pos2) == scalar(@pos)) { $correctq++; } @pos = $hsp->seq_inds('hit','nomatch'); @pos2 = grep {$_ >= $hs && $_ <= $he} @pos; # should always be true if (scalar(@pos2) == scalar(@pos)) { $correcth++; } } } } is($correctq, $hsp_co, 'Query seq_inds() positions fall within HSP bounds'); is($correcth, $hsp_co, 'Subject seq_inds() positions fall within HSP bounds'); ------------------------------------------- Here are the results for the following BLAST report types (culled from test reports used in SearchIO.t): BLASTN : both pass TBLASTN : query passes, subject fails BLASTX : query fails, subject passes TBLASTX : both fail When looking at the failed query seq_inds() data for the first HSP in the TBLASTX report used in SearchIO.t (HUMBETGLOA.tblastx), I get these positions for the query: 355 364 365 367 368 370 371 373 374 375 and for the hit: 1941 1942 1943 1945 1946 1948 1949 1951 1952 1961 This is the actual first HSP for that report: ------------------------------------------- >gb|AE000479.1|AE000479 Escherichia coli K-12 MG1655 section 369 of 400 of the complete genome Length = 10934 Score = 33.6 bits (67), Expect = 0.13 Identities = 11/26 (42%), Positives = 16/26 (61%) Frame = +1 / -2 Query: 1057 SAYWSIFPPLGCWWSTLGPRGSLSPL 1134 +A W++FPP+G W L + SPL Sbjct: 5893 AAVWALFPPVGSQWGCLASQWRTSPL 5816 ------------------------------------------- It looks like it has something to do with the positions getting divided by 3 but not converted back to correspond to the nucleotide position. When fixing this (and as mentioned above), do we want to only report the first nucleotide position where the mismatch occurs, or report the three positions corresponding to that codon region? Any thoughts? chris From tthmok at gmail.com Sun Feb 3 16:54:49 2008 From: tthmok at gmail.com (Terrance Mok) Date: Sun, 3 Feb 2008 14:54:49 -0700 Subject: [Bioperl-l] Problems Installing Bioperl 1.5.2 - Windows Message-ID: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> Hi I've been trying to install bioperl on a fresh install of ActivePerl on Windows. Following the installation guide using the GUI Perl Package Manager, I add the 4 locations and all of them list 0 packages except for "Bribes http://www.Bribes.org/perl/ppm ". Then when searching for bioperl (with all package view), nothing shows up since no packages are found for all the other locations I added. I've also had problems installing on Ubuntu (helping a friend), when using CPAN and following exactly the guide on the bioperl installation it will not work. When doing the install command in CPAN, install S/SE/SENDU/bioperl- 1.5.2_102.tar.gz she gets an error that "/home/username/.cpan/build/bioperl-1.5.2_102: No such file or directory at Makefile.PL line 25." From anjan.purkayastha at gmail.com Sun Feb 3 12:10:49 2008 From: anjan.purkayastha at gmail.com (ANJAN PURKAYASTHA) Date: Sun, 3 Feb 2008 12:10:49 -0500 Subject: [Bioperl-l] sequence object question Message-ID: hi, here is the problem i'm facing. i parse a genbank file with the statement: my $gb_stream = Bio::SeqIO->new( -file => 'gb_test_file', -format => 'GenBank'); while (my $seq_obj= $gb_stream->next_seq){ ..... } presumably $seq_obj is a Bio::Seq::RichSeq object. now, when I try: my $feat_obj($seq_obj->getSeqFeatures){ ..... } i get an error message: Can't locate object method "getSeqFeatures" via package "Bio::Seq::RichSeq" at gb_file_reader.pl line 11. on reading docs I find that Bio::Seq::RichSeq does not have a getSeqFeatures method. but, RIchSeq is a child of the Seq class, which HAS a getSeqFeatures method (i presume this method is also inherited by the RichSeq class). so, why am i getting an error message and how do i go about getting the features within each genbank file? appreciate any pointers. TIA. anjan -- ANJAN PURKAYASTHA, PhD. Senior Computational Biologist ========================== 1101 King Street, Suite 310, Alexandria, VA 22314. 703.518.8040 (office) 703.740.6939 (mobile) email: anjan at vbi.vt.edu; anjan.purkayastha at gmail.com http://www.vbi.vt.edu ========================== From jason at bioperl.org Sun Feb 3 18:51:21 2008 From: jason at bioperl.org (Jason Stajich) Date: Sun, 3 Feb 2008 15:51:21 -0800 Subject: [Bioperl-l] sequence object question In-Reply-To: References: Message-ID: <212091BA-2942-4A95-9329-AB76D8F102A5@bioperl.org> It is 'get_SeqFeatures' http://doc.bioperl.org/bioperl-live/Bio/FeatureHolderI.html#POD1 Deobfuscator: http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio %3A%3ASeq&sort_order=by+method&search_string=Bio%3A%3ASeq http://bioperl.org/cgi-bin/deob_detail.cgi? method=Bio::Seq::get_SeqFeatures HOWTO: http://bioperl.org/wiki/HOWTO:Feature-Annotation On Feb 3, 2008, at 9:10 AM, ANJAN PURKAYASTHA wrote: > hi, > here is the problem i'm facing. > > i parse a genbank file with the statement: > my $gb_stream = Bio::SeqIO->new( -file => 'gb_test_file', -format => > 'GenBank'); > while (my $seq_obj= $gb_stream->next_seq){ > ..... > > } > > presumably $seq_obj is a Bio::Seq::RichSeq object. > > now, when I try: > my $feat_obj($seq_obj->getSeqFeatures){ > ..... > } > i get an error message: Can't locate object method "getSeqFeatures" > via > package "Bio::Seq::RichSeq" at gb_file_reader.pl line 11. > > > on reading docs I find that Bio::Seq::RichSeq does not have a > getSeqFeatures > method. > but, RIchSeq is a child of the Seq class, which HAS a > getSeqFeatures method > (i presume this method is also inherited by the RichSeq class). > > so, why am i getting an error message and how do i go about getting > the > features within each genbank file? > > appreciate any pointers. > > TIA. > > anjan > > -- > ANJAN PURKAYASTHA, PhD. > Senior Computational Biologist > ========================== > > 1101 King Street, Suite 310, > Alexandria, VA 22314. > 703.518.8040 (office) > 703.740.6939 (mobile) > > email: > anjan at vbi.vt.edu; > anjan.purkayastha at gmail.com > > http://www.vbi.vt.edu > > ========================== > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From anjan.purkayastha at gmail.com Sun Feb 3 23:00:33 2008 From: anjan.purkayastha at gmail.com (ANJAN PURKAYASTHA) Date: Sun, 3 Feb 2008 23:00:33 -0500 Subject: [Bioperl-l] sequence object question In-Reply-To: <212091BA-2942-4A95-9329-AB76D8F102A5@bioperl.org> References: <212091BA-2942-4A95-9329-AB76D8F102A5@bioperl.org> Message-ID: Thanks a lot! On Feb 3, 2008 6:51 PM, Jason Stajich wrote: > It is 'get_SeqFeatures' > http://doc.bioperl.org/bioperl-live/Bio/FeatureHolderI.html#POD1 > > Deobfuscator: > http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio > %3A%3ASeq&sort_order=by+method&search_string=Bio%3A%3ASeq > http://bioperl.org/cgi-bin/deob_detail.cgi? > method=Bio::Seq::get_SeqFeatures > > HOWTO: > http://bioperl.org/wiki/HOWTO:Feature-Annotation > > > On Feb 3, 2008, at 9:10 AM, ANJAN PURKAYASTHA wrote: > > > hi, > > here is the problem i'm facing. > > > > i parse a genbank file with the statement: > > my $gb_stream = Bio::SeqIO->new( -file => 'gb_test_file', -format => > > 'GenBank'); > > while (my $seq_obj= $gb_stream->next_seq){ > > ..... > > > > } > > > > presumably $seq_obj is a Bio::Seq::RichSeq object. > > > > now, when I try: > > my $feat_obj($seq_obj->getSeqFeatures){ > > ..... > > } > > i get an error message: Can't locate object method "getSeqFeatures" > > via > > package "Bio::Seq::RichSeq" at gb_file_reader.pl line 11. > > > > > > on reading docs I find that Bio::Seq::RichSeq does not have a > > getSeqFeatures > > method. > > but, RIchSeq is a child of the Seq class, which HAS a > > getSeqFeatures method > > (i presume this method is also inherited by the RichSeq class). > > > > so, why am i getting an error message and how do i go about getting > > the > > features within each genbank file? > > > > appreciate any pointers. > > > > TIA. > > > > anjan > > > > -- > > ANJAN PURKAYASTHA, PhD. > > Senior Computational Biologist > > ========================== > > > > 1101 King Street, Suite 310, > > Alexandria, VA 22314. > > 703.518.8040 (office) > > 703.740.6939 (mobile) > > > > email: > > anjan at vbi.vt.edu; > > anjan.purkayastha at gmail.com > > > > http://www.vbi.vt.edu > > > > ========================== > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- ANJAN PURKAYASTHA, PhD. Senior Computational Biologist ========================== 1101 King Street, Suite 310, Alexandria, VA 22314. 703.518.8040 (office) 703.740.6939 (mobile) email: anjan at vbi.vt.edu; anjan.purkayastha at gmail.com http://www.vbi.vt.edu ========================== From bix at sendu.me.uk Mon Feb 4 03:45:31 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 04 Feb 2008 08:45:31 +0000 Subject: [Bioperl-l] Problems Installing Bioperl 1.5.2 - Windows In-Reply-To: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> References: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> Message-ID: <47A6D0AB.7050702@sendu.me.uk> Terrance Mok wrote: > Hi I've been trying to install bioperl on a fresh install of ActivePerl on > Windows. > Following the installation guide using the GUI Perl Package Manager, I add > the 4 locations and all of them list 0 packages except for "Bribes > http://www.Bribes.org/perl/ppm ". > Then when searching for bioperl (with all package view), nothing shows up > since no packages are found for all the other locations I added. Hopefully someone else will chime in, but perhaps there's something wrong with the server? Can anyone else confirm? > I've also had problems installing on Ubuntu (helping a friend), when using > CPAN and following exactly the guide on the bioperl installation it will not > work. When doing the install command in CPAN, install S/SE/SENDU/bioperl- > 1.5.2_102.tar.gz she gets an error that > "/home/username/.cpan/build/bioperl-1.5.2_102: No such file or directory at > Makefile.PL line 25." Hard to figure out what might be wrong without complete details. Can she install anything else via CPAN? Has she run out of disc space? From darren.obbard at ed.ac.uk Mon Feb 4 03:56:06 2008 From: darren.obbard at ed.ac.uk (Darren Obbard) Date: Mon, 04 Feb 2008 08:56:06 +0000 Subject: [Bioperl-l] Problems Installing Bioperl 1.5.2 - Windows In-Reply-To: <47A6D0AB.7050702@sendu.me.uk> References: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> <47A6D0AB.7050702@sendu.me.uk> Message-ID: <47A6D326.40103@ed.ac.uk> Hi, > Terrance Mok wrote: >> Then when searching for bioperl (with all package view), nothing >> shows up >> since no packages are found for all the other locations I added. > Hopefully someone else will chime in, but perhaps there's something > wrong with the server? Can anyone else confirm? Just to note that I too have had the same problem. From ca. 2 weeks ago I could see no packages on the recommended bioperl repository. I just assumed I was doing something wrong, and thought I'd wait until my need became urgent. -- Darren Obbard University of Edinburgh, UK From darren.obbard at ed.ac.uk Mon Feb 4 06:07:23 2008 From: darren.obbard at ed.ac.uk (Darren Obbard) Date: Mon, 04 Feb 2008 11:07:23 +0000 Subject: [Bioperl-l] Problems Installing Bioperl 1.5.2 - Windows In-Reply-To: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> References: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> Message-ID: <47A6F1EB.8060806@ed.ac.uk> Hi again, Having just looked, it seems fine on this machine (XP proffessional, sp2). The problem I was (and am) having are on a clean install of Vista (ultimate). Perhaps this is a vista/activestate issue? What versions of windows/activeperl are people having problems with? From cjfields at uiuc.edu Mon Feb 4 12:53:08 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 4 Feb 2008 11:53:08 -0600 Subject: [Bioperl-l] Problems Installing Bioperl 1.5.2 - Windows In-Reply-To: <47A6D0AB.7050702@sendu.me.uk> References: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> <47A6D0AB.7050702@sendu.me.uk> Message-ID: <8863D982-5CEF-4E0E-8840-FC8850D96F06@uiuc.edu> On Feb 4, 2008, at 2:45 AM, Sendu Bala wrote: > Terrance Mok wrote: >> Hi I've been trying to install bioperl on a fresh install of >> ActivePerl on >> Windows. >> Following the installation guide using the GUI Perl Package >> Manager, I add >> the 4 locations and all of them list 0 packages except for "Bribes >> http://www.Bribes.org/perl/ppm ". >> Then when searching for bioperl (with all package view), nothing >> shows up >> since no packages are found for all the other locations I added. > > Hopefully someone else will chime in, but perhaps there's something > wrong with the server? Can anyone else confirm? I haven't used ActivePerl in a while personally since switching to OS X (even when using perl 5.10). Terrance, did you follow the ActivePerl instructions or our installation instructions? Also, we don't guarantee that it will work with AtcivePerl's 5.10 port but it's worth a try; if not downgrade to the latest 5.8 build. >> I've also had problems installing on Ubuntu (helping a friend), >> when using >> CPAN and following exactly the guide on the bioperl installation it >> will not >> work. When doing the install command in CPAN, install S/SE/SENDU/ >> bioperl- >> 1.5.2_102.tar.gz she gets an error that >> "/home/username/.cpan/build/bioperl-1.5.2_102: No such file or >> directory at >> Makefile.PL line 25." > > Hard to figure out what might be wrong without complete details. Can > she install anything else via CPAN? Has she run out of disc space? Haven't seen that before but it works for me using cpan and perl 5.8 and perl 5.10. chris From jay at jays.net Mon Feb 4 14:42:17 2008 From: jay at jays.net (Jay Hannah) Date: Mon, 04 Feb 2008 13:42:17 -0600 Subject: [Bioperl-l] SVN server trouble? Message-ID: <47A76A99.2080307@jays.net> I'm getting this error trying to check out trunk, from 2 different servers on 2 different networks: $ svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk bioperl-live svn: Can't find a temporary directory: Error string not specified yet Is this an SVN server problem of some sort, or is it just me somehow? ( Oh, and come hang out with us: irc.freenode.net #bioperl ) Thanks, Jay Hannah http://clab.ist.unomaha.edu/CLAB/index.php/User:Jhannah From David.Messina at sbc.su.se Mon Feb 4 16:35:42 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Mon, 4 Feb 2008 22:35:42 +0100 Subject: [Bioperl-l] SVN server trouble? In-Reply-To: <47A76A99.2080307@jays.net> References: <47A76A99.2080307@jays.net> Message-ID: <628aabb70802041335o300dca9dha7b75d4e0037ef54@mail.gmail.com> Not just you, Jay. I'm getting the same error trying to 'svn update' on a previously-checked-out working copy. Dave From cjfields at uiuc.edu Mon Feb 4 16:48:00 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 4 Feb 2008 15:48:00 -0600 Subject: [Bioperl-l] SVN server trouble? In-Reply-To: <628aabb70802041335o300dca9dha7b75d4e0037ef54@mail.gmail.com> References: <47A76A99.2080307@jays.net> <628aabb70802041335o300dca9dha7b75d4e0037ef54@mail.gmail.com> Message-ID: I went ahead and reported it to support. It's an odd issue, but a checkout works from dev (for those with dev accounts), so it has to be something wonky on code.open-bio.org. chris On Feb 4, 2008, at 3:35 PM, Dave Messina wrote: > Not just you, Jay. I'm getting the same error trying to 'svn update' > on a > previously-checked-out working copy. > Dave From jason at bioperl.org Mon Feb 4 17:11:14 2008 From: jason at bioperl.org (Jason Stajich) Date: Mon, 4 Feb 2008 14:11:14 -0800 Subject: [Bioperl-l] SVN server trouble? In-Reply-To: References: <47A76A99.2080307@jays.net> <628aabb70802041335o300dca9dha7b75d4e0037ef54@mail.gmail.com> Message-ID: ChrisD says that something with is eating up free space on the host so /tmp is full causing the problem(s). Will report in when it's been fixed and we can figure out whether the SVNweb runaway svn diffs are creating the glut of big files. -jason On Feb 4, 2008, at 1:48 PM, Chris Fields wrote: > I went ahead and reported it to support. It's an odd issue, but a > checkout works from dev (for those with dev accounts), so it has to > be something wonky on code.open-bio.org. > > chris > > On Feb 4, 2008, at 3:35 PM, Dave Messina wrote: > >> Not just you, Jay. I'm getting the same error trying to 'svn >> update' on a >> previously-checked-out working copy. >> Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From luisecarracedo at hotmail.com Tue Feb 5 12:59:33 2008 From: luisecarracedo at hotmail.com (luis esteban) Date: Tue, 5 Feb 2008 19:59:33 +0200 Subject: [Bioperl-l] Eland report Message-ID: Hi to everibody!! Is there anybody working in any project tryng to convert Blat or Blast reports in Eland reports. Any Idea, any sugestions would be apreciated. Thanks a Lot Luis Esteban PhD _________________________________________________________________ ?Aburrido? Ingres? ya y divertite como nunca en MSN Juegos. http://juegos.ar.msn.com/ From jason at bioperl.org Tue Feb 5 14:22:14 2008 From: jason at bioperl.org (Jason Stajich) Date: Tue, 5 Feb 2008 11:22:14 -0800 Subject: [Bioperl-l] Eland report In-Reply-To: References: Message-ID: You mean print out eland reports from a BLAST/BLAT/table report? I really hope eland report doesn't become the standard though... -jason On Feb 5, 2008, at 9:59 AM, luis esteban wrote: > > Hi to everibody!! > Is there anybody working in any project tryng to convert Blat or > Blast reports in Eland reports. > Any Idea, any sugestions would be apreciated. > Thanks a Lot > Luis Esteban PhD > _________________________________________________________________ > ?Aburrido? Ingres? ya y divertite como nunca en MSN Juegos. > http://juegos.ar.msn.com/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From sjmiller at email.arizona.edu Tue Feb 5 15:23:28 2008 From: sjmiller at email.arizona.edu (Susan J. Miller) Date: Tue, 05 Feb 2008 13:23:28 -0700 Subject: [Bioperl-l] Bioperl-l Digest, Vol 57, Issue 10 In-Reply-To: References: Message-ID: <47A8C5C0.7040401@email.arizona.edu> bioperl-l-request at lists.open-bio.org wrote: > > Message: 2 > Date: Thu, 31 Jan 2008 10:34:31 +0100 > From: Georg Otto > Subject: Re: [Bioperl-l] Bio::DB::GenBank and large number of requests > To: bioperl-l at bioperl.org > Message-ID: > Content-Type: text/plain; charset=us-ascii > > Hi, > > I succeeded with a similar task using the seqhound database. I had a > list of > 200,000 gid numbers, but I guess it can work in a similar > fashion using accession numbers. Hi Georg, How recently have you used the SeqHound database? We installed it from CPAN but when we try to run the following test script this error occurs: MSG: HTTP::Request error: 500 Can't connect to seqhound.blueprint.org:80 (Bad hostname 'seqhound.blueprint.org') Script: #!/usr/local/bin/perl use warnings; use Bio::SeqIO; use Bio::DB::SeqHound; my $sh = Bio::DB::SeqHound->new(); my $seq = $sh->get_Seq_by_acc("CAA28783"); print $seq->display_name, "\n"; Do you know if SeqHound has moved? Is there a way to comfigure it so that it works? Thanks, -susan Susan J. Miller Manager, Scientific Data Analysis Biotechnology Computing Facility Arizona Research Laboratories (520) 626-2597 From cjfields at uiuc.edu Tue Feb 5 16:38:31 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 5 Feb 2008 15:38:31 -0600 Subject: [Bioperl-l] SeqHound In-Reply-To: <47A8C5C0.7040401@email.arizona.edu> References: <47A8C5C0.7040401@email.arizona.edu> Message-ID: <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> The URL has changed. I'll fix this in bioperl-live. You can fix this in your script directly for now (though I hate globals): use Bio::DB::SeqHound; $Bio::DB::SeqHound::HOSTBASE = 'http://dogboxonline.unleashedinformatics.com/' ; my $sh = Bio::DB::SeqHound->new(); my $seq = $sh->get_Seq_by_acc("CAA28783"); print $seq->display_name, "\n"; chris On Feb 5, 2008, at 2:23 PM, Susan J. Miller wrote: > bioperl-l-request at lists.open-bio.org wrote: >> >> Message: 2 >> Date: Thu, 31 Jan 2008 10:34:31 +0100 >> From: Georg Otto >> Subject: Re: [Bioperl-l] Bio::DB::GenBank and large number of >> requests >> To: bioperl-l at bioperl.org >> Message-ID: >> Content-Type: text/plain; charset=us-ascii >> Hi, >> I succeeded with a similar task using the seqhound database. I had a >> list of > 200,000 gid numbers, but I guess it can work in a similar >> fashion using accession numbers. > > Hi Georg, > > How recently have you used the SeqHound database? We installed it > from CPAN but when we try to run the following test script this > error occurs: > > MSG: HTTP::Request error: 500 Can't connect to > seqhound.blueprint.org:80 (Bad hostname 'seqhound.blueprint.org') > > Script: > #!/usr/local/bin/perl > use warnings; > use Bio::SeqIO; > use Bio::DB::SeqHound; > > my $sh = Bio::DB::SeqHound->new(); > my $seq = $sh->get_Seq_by_acc("CAA28783"); > print $seq->display_name, "\n"; > > > Do you know if SeqHound has moved? Is there a way to comfigure it > so that it works? > > Thanks, > -susan > > Susan J. Miller > Manager, Scientific Data Analysis > Biotechnology Computing Facility > Arizona Research Laboratories > (520) 626-2597 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Tue Feb 5 17:59:48 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 5 Feb 2008 16:59:48 -0600 Subject: [Bioperl-l] SeqHound In-Reply-To: <47A8E3BF.7000308@email.arizona.edu> References: <47A8C5C0.7040401@email.arizona.edu> <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> <47A8E3BF.7000308@email.arizona.edu> Message-ID: <025C4E5C-CD77-442F-AEB1-ACC265B36017@uiuc.edu> On Feb 5, 2008, at 4:31 PM, Susan J. Miller wrote: > Chris Fields wrote: >> The URL has changed. I'll fix this in bioperl-live. >> You can fix this in your script directly for now (though I hate >> globals): >> use Bio::DB::SeqHound; >> $Bio::DB::SeqHound::HOSTBASE = 'http://dogboxonline.unleashedinformatics.com/' >> ; > > Thanks Chris, that helps a little bit, but I'm still not having much > luck with the SeqHound DB. The CPAN SeqHound.pm documentation for > the get_Stream_by_Query method says: > ... No problem. It was an easy fix. ... > I get the error: > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Id list has been truncated even after maxids requested > STACK: Error::throw > STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/ > Root/Root.pm:359 > STACK: Bio::DB::Query::WebQuery::_fetch_ids /usr/lib/perl5/site_perl/ > 5.8.8/Bio/DB/Query/WebQuery.pm:236 > STACK: Bio::DB::Query::WebQuery::ids /usr/lib/perl5/site_perl/5.8.8/ > Bio/DB/Query/WebQuery.pm:200 > STACK: Bio::DB::SeqHound::get_Stream_by_query /usr/lib/perl5/ > site_perl/5.8.8/Bio/DB/SeqHound.pm:314 > STACK: SeqHoundQuery.pl:21 > > There are only 5013 sequences that match this query so it seems odd > that the Id list is too long...or am I using SeqHound improperly? > > (My reason for trying SeqHound is that I want to set up a monthly > cron job to download nucest fasta sequences for drosphila > melanogaster, and I've tried NCBI E-Utilities and the script > generated by the NCBI ebot and in both cases some of the 570828 > records get dropped, even after running repeated attempts.) > > > Thanks, > -susan The URL is likely way too long (a common problem when using a GET as opposed to a POST with LWP). NCBI's efetch has the same problem, which is why using epost is a good idea (except it only takes GI's!). You will have to loop through the IDs in bunches of 250-500 max to get what you want. Don't know if there is a way to post to SeqHound but it might be worth investigating at some point. I also see they have a SOAP interface up. chris From sjmiller at email.arizona.edu Tue Feb 5 17:31:27 2008 From: sjmiller at email.arizona.edu (Susan J. Miller) Date: Tue, 05 Feb 2008 15:31:27 -0700 Subject: [Bioperl-l] SeqHound In-Reply-To: <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> References: <47A8C5C0.7040401@email.arizona.edu> <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> Message-ID: <47A8E3BF.7000308@email.arizona.edu> Chris Fields wrote: > The URL has changed. I'll fix this in bioperl-live. > > You can fix this in your script directly for now (though I hate globals): > > use Bio::DB::SeqHound; > > $Bio::DB::SeqHound::HOSTBASE = > 'http://dogboxonline.unleashedinformatics.com/'; > Thanks Chris, that helps a little bit, but I'm still not having much luck with the SeqHound DB. The CPAN SeqHound.pm documentation for the get_Stream_by_Query method says: Title : get_Stream_by_query Usage : $seq = $db->get_Stream_by_query($query); Function: Retrieves Seq objects from Entrez 'en masse', rather than one at a time. For large numbers of sequences, this is far superior than get_Stream_by_[id/acc](). Example : $query_string = 'Candida maltosa 26S ribosomal RNA gene'; However, when I try: $query_string = 'drosophila simulans[orgn]'; $query = Bio::DB::Query::GenBank->new(-db=>'nucest', -query=>$query_string); $stream = $sh->get_Stream_by_query($query); I get the error: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Id list has been truncated even after maxids requested STACK: Error::throw STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359 STACK: Bio::DB::Query::WebQuery::_fetch_ids /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Query/WebQuery.pm:236 STACK: Bio::DB::Query::WebQuery::ids /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Query/WebQuery.pm:200 STACK: Bio::DB::SeqHound::get_Stream_by_query /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqHound.pm:314 STACK: SeqHoundQuery.pl:21 There are only 5013 sequences that match this query so it seems odd that the Id list is too long...or am I using SeqHound improperly? (My reason for trying SeqHound is that I want to set up a monthly cron job to download nucest fasta sequences for drosphila melanogaster, and I've tried NCBI E-Utilities and the script generated by the NCBI ebot and in both cases some of the 570828 records get dropped, even after running repeated attempts.) Thanks, -susan Susan J. Miller Manager, Scientific Data Analysis Biotechnology Computing Facility Arizona Research Laboratories (520) 626-2597 From lincoln.stein at gmail.com Tue Feb 5 18:43:06 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 5 Feb 2008 18:43:06 -0500 Subject: [Bioperl-l] ActiveState Perl problems Message-ID: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> Hi Scott, Bioperl folk, I'm afraid that the ActiveState ppm install of BioPerl no longer works. Using the current ActiveState (perl version 5.10), I added the Bribes, Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates repositories. However, when I synched up, all but the Bribes reps showed up empty in the ppm tool. In addition, there's nothing in the release candidate rep any longer. I used to use this to get at Bioperl 1.5. Perhaps the architecture needs to be changed? Lincoln -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From cjfields at uiuc.edu Tue Feb 5 19:13:29 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 5 Feb 2008 18:13:29 -0600 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> Message-ID: I'll try changing out package.xml on portal. The one in RC appears to be blank now (which explains why you can't use that one). chris On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: > Hi Scott, Bioperl folk, > > I'm afraid that the ActiveState ppm install of BioPerl no longer > works. > Using the current ActiveState (perl version 5.10), I added the Bribes, > Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates > repositories. However, when I synched up, all but the Bribes reps > showed up > empty in the ppm tool. > > In addition, there's nothing in the release candidate rep any > longer. I used > to use this to get at Bioperl 1.5. > > Perhaps the architecture needs to be changed? > > Lincoln > > > > -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > (516) 367-8380 (voice) > (516) 367-8389 (fax) > FOR URGENT MESSAGES & SCHEDULING, > PLEASE CONTACT MY ASSISTANT, > SANDRA MICHELSEN, AT michelse at cshl.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From golharam at umdnj.edu Tue Feb 5 18:15:43 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Tue, 05 Feb 2008 18:15:43 -0500 Subject: [Bioperl-l] Bio::SeqIO object for GenBank XML format? Message-ID: <47A8EE1F.7050100@umdnj.edu> Is there a SeqIO module for the XML format for GenBank records? The "http://www.bioperl.org/wiki/HOWTO:SeqIO" page doesn't show one listed. From Kevin.M.Brown at asu.edu Tue Feb 5 19:25:58 2008 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Tue, 5 Feb 2008 17:25:58 -0700 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> Message-ID: <1A4207F8295607498283FE9E93B775B4045AA97F@EX02.asurite.ad.asu.edu> Well, Kobes seems to have two different ppm repos. One for 8xx builds of activestate perl and one for 10xx builds. So, Bioperl probably needs to be rebuilt for 5.10 to get it to show in the 5.10 repos. I just opened up Activestate perl 5.8 and I see 1.5.2_100 listed in it from the Regular Release site. > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Lincoln Stein > Sent: Tuesday, February 05, 2008 4:43 PM > To: Scott Cain > Cc: bioperl-l > Subject: [Bioperl-l] ActiveState Perl problems > > Hi Scott, Bioperl folk, > > I'm afraid that the ActiveState ppm install of BioPerl no > longer works. > Using the current ActiveState (perl version 5.10), I added the Bribes, > Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates > repositories. However, when I synched up, all but the Bribes > reps showed up > empty in the ppm tool. > > In addition, there's nothing in the release candidate rep any > longer. I used > to use this to get at Bioperl 1.5. > > Perhaps the architecture needs to be changed? > > Lincoln > > > > -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > (516) 367-8380 (voice) > (516) 367-8389 (fax) > FOR URGENT MESSAGES & SCHEDULING, > PLEASE CONTACT MY ASSISTANT, > SANDRA MICHELSEN, AT michelse at cshl.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From jason at bioperl.org Tue Feb 5 19:45:35 2008 From: jason at bioperl.org (Jason Stajich) Date: Tue, 5 Feb 2008 16:45:35 -0800 Subject: [Bioperl-l] Bio::SeqIO object for GenBank XML format? In-Reply-To: <47A8EE1F.7050100@umdnj.edu> References: <47A8EE1F.7050100@umdnj.edu> Message-ID: <67216BC0-8F2F-432C-B94F-C9A92640E01A@bioperl.org> Then there probably isn't - the codebase Bo/SeqIO directory would tell you otherwise I guess. Does anyone use the format and want to write one? On Feb 5, 2008, at 3:15 PM, Ryan Golhar wrote: > Is there a SeqIO module for the XML format for GenBank records? > The "http://www.bioperl.org/wiki/HOWTO:SeqIO" page doesn't show one > listed. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bosborne11 at verizon.net Tue Feb 5 18:52:57 2008 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 05 Feb 2008 18:52:57 -0500 Subject: [Bioperl-l] SeqHound In-Reply-To: <47A8E3BF.7000308@email.arizona.edu> References: <47A8C5C0.7040401@email.arizona.edu> <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> <47A8E3BF.7000308@email.arizona.edu> Message-ID: <4D3A27D3-D535-4F34-8A7F-966F30B51F86@verizon.net> Susan, It sounds like you could use rsync though perhaps there's some detail that I missed. A typical command would look something like this: rsync -av ftp.ncbi.nlm.nih.gov::blast/db/FASTA/ /local/data/FASTA/ Brian O. On Feb 5, 2008, at 5:31 PM, Susan J. Miller wrote: > (My reason for trying SeqHound is that I want to set up a monthly > cron job to download nucest fasta sequences for drosphila > melanogaster, and I've tried NCBI E-Utilities and the script > generated by the NCBI ebot and in both cases some of the 570828 > records get dropped, even after running repeated attempts.) From barry.moore at genetics.utah.edu Tue Feb 5 20:09:56 2008 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Tue, 5 Feb 2008 18:09:56 -0700 Subject: [Bioperl-l] SeqHound In-Reply-To: <47A8E3BF.7000308@email.arizona.edu> References: <47A8C5C0.7040401@email.arizona.edu> <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> <47A8E3BF.7000308@email.arizona.edu> Message-ID: Susan, I'm joining this discussion late so my apologies if I'm missing the original point. If you're trying to routinely download thousands of sequences from GenBank or SeqHound you probably want to be using ftp to download the flat files and query/parse locally. If you're trying to stay on top of the latest Drosophila ESTs, then how about setting up a nightly cron job to download the incremental updates from NCBIs ftp (ftp://ftp.ncbi.nih.gov/genbank/daily-nc) and parse that for Drosophila EST sequences. The EST division is huge, but I would think nightly incrementals should be manageable. Barry On Feb 5, 2008, at 3:31 PM, Susan J. Miller wrote: > Chris Fields wrote: >> The URL has changed. I'll fix this in bioperl-live. >> >> You can fix this in your script directly for now (though I hate >> globals): >> >> use Bio::DB::SeqHound; >> >> $Bio::DB::SeqHound::HOSTBASE = >> 'http://dogboxonline.unleashedinformatics.com/'; >> > > Thanks Chris, that helps a little bit, but I'm still not having much > luck with the SeqHound DB. The CPAN SeqHound.pm documentation for the > get_Stream_by_Query method says: > > Title : get_Stream_by_query > Usage : $seq = $db->get_Stream_by_query($query); > Function: Retrieves Seq objects from Entrez 'en masse', rather than > one at a time. For large numbers of sequences, this is far superior > than get_Stream_by_[id/acc](). > Example : $query_string = 'Candida maltosa 26S ribosomal RNA gene'; > > However, when I try: > > $query_string = 'drosophila simulans[orgn]'; > $query = Bio::DB::Query::GenBank->new(-db=>'nucest', > -query=>$query_string); > $stream = $sh->get_Stream_by_query($query); > > I get the error: > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Id list has been truncated even after maxids requested > STACK: Error::throw > STACK: Bio::Root::Root::throw > /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359 > STACK: Bio::DB::Query::WebQuery::_fetch_ids > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Query/WebQuery.pm:236 > STACK: Bio::DB::Query::WebQuery::ids > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Query/WebQuery.pm:200 > STACK: Bio::DB::SeqHound::get_Stream_by_query > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqHound.pm:314 > STACK: SeqHoundQuery.pl:21 > > There are only 5013 sequences that match this query so it seems odd > that > the Id list is too long...or am I using SeqHound improperly? > > (My reason for trying SeqHound is that I want to set up a monthly cron > job to download nucest fasta sequences for drosphila melanogaster, and > I've tried NCBI E-Utilities and the script generated by the NCBI ebot > and in both cases some of the 570828 records get dropped, even after > running repeated attempts.) > > > Thanks, > -susan > > Susan J. Miller > Manager, Scientific Data Analysis > Biotechnology Computing Facility > Arizona Research Laboratories > (520) 626-2597 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at uiuc.edu Tue Feb 5 20:19:16 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 5 Feb 2008 19:19:16 -0600 Subject: [Bioperl-l] Bio::SeqIO object for GenBank XML format? In-Reply-To: <67216BC0-8F2F-432C-B94F-C9A92640E01A@bioperl.org> References: <47A8EE1F.7050100@umdnj.edu> <67216BC0-8F2F-432C-B94F-C9A92640E01A@bioperl.org> Message-ID: <9F54378C-9905-4E90-88B9-F539B1E933DF@uiuc.edu> Could probably base it off of the BSML parser. Might be better to write up a general INSDC XML parser, which GenBank/EMBL/DDBJ all use now: http://www.insdc.org/page.php?page=documents&sid=fa24a7d177ab7a687e87a85db6822c01 chris On Feb 5, 2008, at 6:45 PM, Jason Stajich wrote: > Then there probably isn't - the codebase Bo/SeqIO directory would > tell you otherwise I guess. > Does anyone use the format and want to write one? > > On Feb 5, 2008, at 3:15 PM, Ryan Golhar wrote: > >> Is there a SeqIO module for the XML format for GenBank records? >> The "http://www.bioperl.org/wiki/HOWTO:SeqIO" page doesn't show one >> listed. >> >> _______________________________________________ >> 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 Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Tue Feb 5 20:32:52 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 5 Feb 2008 19:32:52 -0600 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <1A4207F8295607498283FE9E93B775B4045AA97F@EX02.asurite.ad.asu.edu> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> <1A4207F8295607498283FE9E93B775B4045AA97F@EX02.asurite.ad.asu.edu> Message-ID: <3BFD59BB-152C-4D43-B8E7-96DC293D8C34@uiuc.edu> Kobes keeps two separate repos because there are several binary-only modules (DBD::mysql, GD, etc) which are incompatible with older major perl releases (5.6, 5.8, 5.10). If the modules are pure perl then there shouldn't be a problem. Saying that, there is one issue which tanks Bio::SeqIO::entrezgene parsing (which mistakenly made pseudohashes) which Stefan and I fixed recently; that'll tank in perl 5.10. chris On Feb 5, 2008, at 6:25 PM, Kevin Brown wrote: > Well, Kobes seems to have two different ppm repos. One for 8xx builds > of activestate perl and one for 10xx builds. So, Bioperl probably > needs > to be rebuilt for 5.10 to get it to show in the 5.10 repos. I just > opened up Activestate perl 5.8 and I see 1.5.2_100 listed in it from > the > Regular Release site. > >> -----Original Message----- >> From: bioperl-l-bounces at lists.open-bio.org >> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of >> Lincoln Stein >> Sent: Tuesday, February 05, 2008 4:43 PM >> To: Scott Cain >> Cc: bioperl-l >> Subject: [Bioperl-l] ActiveState Perl problems >> >> Hi Scott, Bioperl folk, >> >> I'm afraid that the ActiveState ppm install of BioPerl no >> longer works. >> Using the current ActiveState (perl version 5.10), I added the >> Bribes, >> Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates >> repositories. However, when I synched up, all but the Bribes >> reps showed up >> empty in the ppm tool. >> >> In addition, there's nothing in the release candidate rep any >> longer. I used >> to use this to get at Bioperl 1.5. >> >> Perhaps the architecture needs to be changed? >> >> Lincoln >> >> >> >> -- >> Lincoln D. Stein >> Cold Spring Harbor Laboratory >> 1 Bungtown Road >> Cold Spring Harbor, NY 11724 >> (516) 367-8380 (voice) >> (516) 367-8389 (fax) >> FOR URGENT MESSAGES & SCHEDULING, >> PLEASE CONTACT MY ASSISTANT, >> SANDRA MICHELSEN, AT michelse at cshl.edu >> _______________________________________________ >> 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 Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From golharam at umdnj.edu Tue Feb 5 19:54:24 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Tue, 05 Feb 2008 19:54:24 -0500 Subject: [Bioperl-l] Bio::SeqIO object for GenBank XML format? In-Reply-To: <67216BC0-8F2F-432C-B94F-C9A92640E01A@bioperl.org> References: <47A8EE1F.7050100@umdnj.edu> <67216BC0-8F2F-432C-B94F-C9A92640E01A@bioperl.org> Message-ID: <47A90540.9060002@umdnj.edu> If no one else has already built one, then I'd be happy to based on the genbank and chaosxml/tigrxml modules. Ryan Jason Stajich wrote: > Then there probably isn't - the codebase Bo/SeqIO directory would tell > you otherwise I guess. > Does anyone use the format and want to write one? > > On Feb 5, 2008, at 3:15 PM, Ryan Golhar wrote: > >> Is there a SeqIO module for the XML format for GenBank records? The >> "http://www.bioperl.org/wiki/HOWTO:SeqIO" page doesn't show one listed. >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > From cjfields at uiuc.edu Tue Feb 5 22:06:06 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 5 Feb 2008 21:06:06 -0600 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> Message-ID: <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> According to this page you can remove the tags and it will assume the files are for any OS: http://aspn.activestate.com/ASPN/docs/ActivePerl/5.10/lib/ActivePerl/PPM/PPD.html#ppd_xml_format I have moved the old package.xml to package.bak and replaced it with one w/o those tags; I can now pick it up on Mac OS X using ActiveState perl 5.10: ppm> search * Downloading bioperl.org packlist...not modified 1: Bio-ASN1-EntrezGene v1.09 2: Bundle-BioPerl-Core v1.5.2_100 3: Bundle-BioPerl-Db v1.5.2_100 4: Bundle-BioPerl-Network v1.5.2_100 5: Bundle-BioPerl-Run v1.5.2_100 6: Class-AutoClass v1.01 7: GD-SVG v0.25 8: Graph v0.80 9: SVG-Graph v0.01 10: bioperl v1.5.2_100 11: bioperl-db v1.5.2_100 12: bioperl-network v1.5.2_100 13: bioperl-run v1.5.2_100 I'll add ARCHITECTURE versioning tags back when we know it's working (maybe tomorrow, when I can get on to WinXP to test it). chris On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: > Hi Scott, Bioperl folk, > > I'm afraid that the ActiveState ppm install of BioPerl no longer > works. > Using the current ActiveState (perl version 5.10), I added the Bribes, > Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates > repositories. However, when I synched up, all but the Bribes reps > showed up > empty in the ppm tool. > > In addition, there's nothing in the release candidate rep any > longer. I used > to use this to get at Bioperl 1.5. > > Perhaps the architecture needs to be changed? > > Lincoln > > > > -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > (516) 367-8380 (voice) > (516) 367-8389 (fax) > FOR URGENT MESSAGES & SCHEDULING, > PLEASE CONTACT MY ASSISTANT, > SANDRA MICHELSEN, AT michelse at cshl.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From lincoln.stein at gmail.com Tue Feb 5 23:25:27 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 5 Feb 2008 23:25:27 -0500 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> Message-ID: <6dce9a0b0802052025y1243b7den4d19ed4dd1d71ff9@mail.gmail.com> Wow, nice fast work! Thanks all. Lincoln On Feb 5, 2008 10:06 PM, Chris Fields wrote: > According to this page you can remove the tags and it > will assume the files are for any OS: > > > http://aspn.activestate.com/ASPN/docs/ActivePerl/5.10/lib/ActivePerl/PPM/PPD.html#ppd_xml_format > > I have moved the old package.xml to package.bak and replaced it with > one w/o those tags; I can now pick it up on Mac OS X using ActiveState > perl 5.10: > > ppm> search * > Downloading bioperl.org packlist...not modified > 1: Bio-ASN1-EntrezGene v1.09 > 2: Bundle-BioPerl-Core v1.5.2_100 > 3: Bundle-BioPerl-Db v1.5.2_100 > 4: Bundle-BioPerl-Network v1.5.2_100 > 5: Bundle-BioPerl-Run v1.5.2_100 > 6: Class-AutoClass v1.01 > 7: GD-SVG v0.25 > 8: Graph v0.80 > 9: SVG-Graph v0.01 > 10: bioperl v1.5.2_100 > 11: bioperl-db v1.5.2_100 > 12: bioperl-network v1.5.2_100 > 13: bioperl-run v1.5.2_100 > > I'll add ARCHITECTURE versioning tags back when we know it's working > (maybe tomorrow, when I can get on to WinXP to test it). > > chris > > On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: > > > Hi Scott, Bioperl folk, > > > > I'm afraid that the ActiveState ppm install of BioPerl no longer > > works. > > Using the current ActiveState (perl version 5.10), I added the Bribes, > > Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates > > repositories. However, when I synched up, all but the Bribes reps > > showed up > > empty in the ppm tool. > > > > In addition, there's nothing in the release candidate rep any > > longer. I used > > to use this to get at Bioperl 1.5. > > > > Perhaps the architecture needs to be changed? > > > > Lincoln > > > > > > > > -- > > Lincoln D. Stein > > Cold Spring Harbor Laboratory > > 1 Bungtown Road > > Cold Spring Harbor, NY 11724 > > (516) 367-8380 (voice) > > (516) 367-8389 (fax) > > FOR URGENT MESSAGES & SCHEDULING, > > PLEASE CONTACT MY ASSISTANT, > > SANDRA MICHELSEN, AT michelse at cshl.edu > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From bioinfo21 at gmail.com Wed Feb 6 02:04:37 2008 From: bioinfo21 at gmail.com (Priya) Date: Wed, 6 Feb 2008 12:34:37 +0530 Subject: [Bioperl-l] Bioperl Message-ID: <98af6e260802052304y66add58fi65e289cb4b9069f7@mail.gmail.com> Hi all I am new to Bioperl. I have installed Bioperl in Linux. I am trying to use one of the sample programs in bioperl. I couldnt figure out where to set the http proxy authentication. I tried to follow the manual for installation. Still I am not getting it right . Let me know how to set the proxy authentication and where exactly it should be set. I tried to set env variables for http in .bashrc. Still its not working. Help me out. Thanks in advance. Regards Priya.. From lincoln.stein at gmail.com Wed Feb 6 10:03:31 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Wed, 6 Feb 2008 10:03:31 -0500 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> Message-ID: <6dce9a0b0802060703j231704acta813715265f1fab5@mail.gmail.com> Sadly, bioperl still won't install under ActiveState 5.10 because it can't find a repository with the SOAP::Lite prerequisite. Lincoln On Feb 5, 2008 10:06 PM, Chris Fields wrote: > According to this page you can remove the tags and it > will assume the files are for any OS: > > > http://aspn.activestate.com/ASPN/docs/ActivePerl/5.10/lib/ActivePerl/PPM/PPD.html#ppd_xml_format > > I have moved the old package.xml to package.bak and replaced it with > one w/o those tags; I can now pick it up on Mac OS X using ActiveState > perl 5.10: > > ppm> search * > Downloading bioperl.org packlist...not modified > 1: Bio-ASN1-EntrezGene v1.09 > 2: Bundle-BioPerl-Core v1.5.2_100 > 3: Bundle-BioPerl-Db v1.5.2_100 > 4: Bundle-BioPerl-Network v1.5.2_100 > 5: Bundle-BioPerl-Run v1.5.2_100 > 6: Class-AutoClass v1.01 > 7: GD-SVG v0.25 > 8: Graph v0.80 > 9: SVG-Graph v0.01 > 10: bioperl v1.5.2_100 > 11: bioperl-db v1.5.2_100 > 12: bioperl-network v1.5.2_100 > 13: bioperl-run v1.5.2_100 > > I'll add ARCHITECTURE versioning tags back when we know it's working > (maybe tomorrow, when I can get on to WinXP to test it). > > chris > > On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: > > > Hi Scott, Bioperl folk, > > > > I'm afraid that the ActiveState ppm install of BioPerl no longer > > works. > > Using the current ActiveState (perl version 5.10), I added the Bribes, > > Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates > > repositories. However, when I synched up, all but the Bribes reps > > showed up > > empty in the ppm tool. > > > > In addition, there's nothing in the release candidate rep any > > longer. I used > > to use this to get at Bioperl 1.5. > > > > Perhaps the architecture needs to be changed? > > > > Lincoln > > > > > > > > -- > > Lincoln D. Stein > > Cold Spring Harbor Laboratory > > 1 Bungtown Road > > Cold Spring Harbor, NY 11724 > > (516) 367-8380 (voice) > > (516) 367-8389 (fax) > > FOR URGENT MESSAGES & SCHEDULING, > > PLEASE CONTACT MY ASSISTANT, > > SANDRA MICHELSEN, AT michelse at cshl.edu > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From cjfields at uiuc.edu Wed Feb 6 10:55:00 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 6 Feb 2008 09:55:00 -0600 Subject: [Bioperl-l] BOSC 2008? Message-ID: <1182EAB9-7A75-498F-B91B-C14771DFD607@uiuc.edu> Anyone have information on the where/when for BOSC 2008? chris From n.haigh at sheffield.ac.uk Wed Feb 6 11:36:19 2008 From: n.haigh at sheffield.ac.uk (Nathan S Haigh) Date: Wed, 06 Feb 2008 16:36:19 +0000 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <6dce9a0b0802060703j231704acta813715265f1fab5@mail.gmail.com> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> <6dce9a0b0802060703j231704acta813715265f1fab5@mail.gmail.com> Message-ID: <47A9E203.3080008@sheffield.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Last time I was playing with Windows PPM packages, I seem to remember having to build some packages for inclusion in the BioPerl repo so that all dependencies were satisfied. Unfortunately, I don't have time to do this myself, but it's a work around if someone has time to do it? Alternatively, contact one of the other repo's and see if they can do something about it as it will/should be available for at least an older version of ActivePerl. Sorry I can't be more help. Nath Lincoln Stein wrote: > Sadly, bioperl still won't install under ActiveState 5.10 because it can't > find a repository with the SOAP::Lite prerequisite. > > Lincoln > > On Feb 5, 2008 10:06 PM, Chris Fields wrote: > >> According to this page you can remove the tags and it >> will assume the files are for any OS: >> >> >> http://aspn.activestate.com/ASPN/docs/ActivePerl/5.10/lib/ActivePerl/PPM/PPD.html#ppd_xml_format >> >> I have moved the old package.xml to package.bak and replaced it with >> one w/o those tags; I can now pick it up on Mac OS X using ActiveState >> perl 5.10: >> >> ppm> search * >> Downloading bioperl.org packlist...not modified >> 1: Bio-ASN1-EntrezGene v1.09 >> 2: Bundle-BioPerl-Core v1.5.2_100 >> 3: Bundle-BioPerl-Db v1.5.2_100 >> 4: Bundle-BioPerl-Network v1.5.2_100 >> 5: Bundle-BioPerl-Run v1.5.2_100 >> 6: Class-AutoClass v1.01 >> 7: GD-SVG v0.25 >> 8: Graph v0.80 >> 9: SVG-Graph v0.01 >> 10: bioperl v1.5.2_100 >> 11: bioperl-db v1.5.2_100 >> 12: bioperl-network v1.5.2_100 >> 13: bioperl-run v1.5.2_100 >> >> I'll add ARCHITECTURE versioning tags back when we know it's working >> (maybe tomorrow, when I can get on to WinXP to test it). >> >> chris >> >> On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: >> >>> Hi Scott, Bioperl folk, >>> >>> I'm afraid that the ActiveState ppm install of BioPerl no longer >>> works. >>> Using the current ActiveState (perl version 5.10), I added the Bribes, >>> Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates >>> repositories. However, when I synched up, all but the Bribes reps >>> showed up >>> empty in the ppm tool. >>> >>> In addition, there's nothing in the release candidate rep any >>> longer. I used >>> to use this to get at Bioperl 1.5. >>> >>> Perhaps the architecture needs to be changed? >>> >>> Lincoln >>> >>> >>> >>> -- >>> Lincoln D. Stein >>> Cold Spring Harbor Laboratory >>> 1 Bungtown Road >>> Cold Spring Harbor, NY 11724 >>> (516) 367-8380 (voice) >>> (516) 367-8389 (fax) >>> FOR URGENT MESSAGES & SCHEDULING, >>> PLEASE CONTACT MY ASSISTANT, >>> SANDRA MICHELSEN, AT michelse at cshl.edu >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> >> > > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHqeID9gTv6QYzVL4RAsyqAJ0XkCJgdKu6SHzci4XGww4OofRBzgCfQqCL MxylCxJflKjtscupJ5cRHKk= =Brpe -----END PGP SIGNATURE----- From cjfields at uiuc.edu Wed Feb 6 12:09:40 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 6 Feb 2008 11:09:40 -0600 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <47A9E203.3080008@sheffield.ac.uk> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> <6dce9a0b0802060703j231704acta813715265f1fab5@mail.gmail.com> <47A9E203.3080008@sheffield.ac.uk> Message-ID: <0E379930-B25F-42F5-8706-B39C64D6D2EB@uiuc.edu> SOAP::Lite is pretty complicated; I'm not sure if it is pure perl either (which makes it problematic for WinXP). I'll do some checking around to see if there is a perl 5.10 build for Windows. I'm toying around with the idea of setting up a nightly PPM archives of the bioperl distributions in their own directory, along with nightly tar balls. Just need to get time to work on it! chris On Feb 6, 2008, at 10:36 AM, Nathan S Haigh wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Last time I was playing with Windows PPM packages, I seem to > remember having to build some packages for inclusion in the BioPerl > repo so that all > dependencies were satisfied. Unfortunately, I don't have time to do > this myself, but it's a work around if someone has time to do it? > Alternatively, > contact one of the other repo's and see if they can do something > about it as it will/should be available for at least an older > version of ActivePerl. > > Sorry I can't be more help. > Nath > > > Lincoln Stein wrote: >> Sadly, bioperl still won't install under ActiveState 5.10 because >> it can't >> find a repository with the SOAP::Lite prerequisite. >> >> Lincoln >> >> On Feb 5, 2008 10:06 PM, Chris Fields wrote: >> >>> According to this page you can remove the tags and it >>> will assume the files are for any OS: >>> >>> >>> http://aspn.activestate.com/ASPN/docs/ActivePerl/5.10/lib/ActivePerl/PPM/PPD.html#ppd_xml_format >>> >>> I have moved the old package.xml to package.bak and replaced it with >>> one w/o those tags; I can now pick it up on Mac OS X using >>> ActiveState >>> perl 5.10: >>> >>> ppm> search * >>> Downloading bioperl.org packlist...not modified >>> 1: Bio-ASN1-EntrezGene v1.09 >>> 2: Bundle-BioPerl-Core v1.5.2_100 >>> 3: Bundle-BioPerl-Db v1.5.2_100 >>> 4: Bundle-BioPerl-Network v1.5.2_100 >>> 5: Bundle-BioPerl-Run v1.5.2_100 >>> 6: Class-AutoClass v1.01 >>> 7: GD-SVG v0.25 >>> 8: Graph v0.80 >>> 9: SVG-Graph v0.01 >>> 10: bioperl v1.5.2_100 >>> 11: bioperl-db v1.5.2_100 >>> 12: bioperl-network v1.5.2_100 >>> 13: bioperl-run v1.5.2_100 >>> >>> I'll add ARCHITECTURE versioning tags back when we know it's working >>> (maybe tomorrow, when I can get on to WinXP to test it). >>> >>> chris >>> >>> On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: >>> >>>> Hi Scott, Bioperl folk, >>>> >>>> I'm afraid that the ActiveState ppm install of BioPerl no longer >>>> works. >>>> Using the current ActiveState (perl version 5.10), I added the >>>> Bribes, >>>> Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates >>>> repositories. However, when I synched up, all but the Bribes reps >>>> showed up >>>> empty in the ppm tool. >>>> >>>> In addition, there's nothing in the release candidate rep any >>>> longer. I used >>>> to use this to get at Bioperl 1.5. >>>> >>>> Perhaps the architecture needs to be changed? >>>> >>>> Lincoln >>>> >>>> >>>> >>>> -- >>>> Lincoln D. Stein >>>> Cold Spring Harbor Laboratory >>>> 1 Bungtown Road >>>> Cold Spring Harbor, NY 11724 >>>> (516) 367-8380 (voice) >>>> (516) 367-8389 (fax) >>>> FOR URGENT MESSAGES & SCHEDULING, >>>> PLEASE CONTACT MY ASSISTANT, >>>> SANDRA MICHELSEN, AT michelse at cshl.edu >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> Christopher Fields >>> Postdoctoral Researcher >>> Lab of Dr. Robert Switzer >>> Dept of Biochemistry >>> University of Illinois Urbana-Champaign >>> >>> >>> >>> >> >> > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.6 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFHqeID9gTv6QYzVL4RAsyqAJ0XkCJgdKu6SHzci4XGww4OofRBzgCfQqCL > MxylCxJflKjtscupJ5cRHKk= > =Brpe > -----END PGP SIGNATURE----- Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Feb 6 12:54:16 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 6 Feb 2008 11:54:16 -0600 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <47A9E203.3080008@sheffield.ac.uk> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> <6dce9a0b0802060703j231704acta813715265f1fab5@mail.gmail.com> <47A9E203.3080008@sheffield.ac.uk> Message-ID: <48143927-C57B-4525-9025-A6FDC5A49070@uiuc.edu> Just an update: I have installed ActivePerl 5.10 on my WinXP box and added the following repos to PPM4 (in the following order, just in case it matters): Kobes: http://cpan.uwinnipeg.ca/PPMPackages/10xx/ Bribes: http://www.bribes.org/perl/ppm BioPerl: http://bioperl.org/DIST Note that the above Kobes repo is 5.10-specific. SOAP::Lite is in both Kobes and Bribes for perl 5.10. I then ran into issues with XML::SAX::ExpatXS and XML::SAX::Writer (the former is a binary-only, so likely failed with the ActiveState autobuild process; the latter should work though, so it might be worth hosting a version in BioPerl). I removed both dependencies from package.xml on the server and everything appears to install fine now using PPM4. I'll see if Randy Kobes can get an XML::SAX::ExpatXS version up. It is only required for 1.5.2; bioperl-live no longer requires it (just XML::SAX). chris On Feb 6, 2008, at 10:36 AM, Nathan S Haigh wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Last time I was playing with Windows PPM packages, I seem to > remember having to build some packages for inclusion in the BioPerl > repo so that all > dependencies were satisfied. Unfortunately, I don't have time to do > this myself, but it's a work around if someone has time to do it? > Alternatively, > contact one of the other repo's and see if they can do something > about it as it will/should be available for at least an older > version of ActivePerl. > > Sorry I can't be more help. > Nath > > > Lincoln Stein wrote: >> Sadly, bioperl still won't install under ActiveState 5.10 because >> it can't >> find a repository with the SOAP::Lite prerequisite. >> >> Lincoln >> >> On Feb 5, 2008 10:06 PM, Chris Fields wrote: >> >>> According to this page you can remove the tags and it >>> will assume the files are for any OS: >>> >>> >>> http://aspn.activestate.com/ASPN/docs/ActivePerl/5.10/lib/ActivePerl/PPM/PPD.html#ppd_xml_format >>> >>> I have moved the old package.xml to package.bak and replaced it with >>> one w/o those tags; I can now pick it up on Mac OS X using >>> ActiveState >>> perl 5.10: >>> >>> ppm> search * >>> Downloading bioperl.org packlist...not modified >>> 1: Bio-ASN1-EntrezGene v1.09 >>> 2: Bundle-BioPerl-Core v1.5.2_100 >>> 3: Bundle-BioPerl-Db v1.5.2_100 >>> 4: Bundle-BioPerl-Network v1.5.2_100 >>> 5: Bundle-BioPerl-Run v1.5.2_100 >>> 6: Class-AutoClass v1.01 >>> 7: GD-SVG v0.25 >>> 8: Graph v0.80 >>> 9: SVG-Graph v0.01 >>> 10: bioperl v1.5.2_100 >>> 11: bioperl-db v1.5.2_100 >>> 12: bioperl-network v1.5.2_100 >>> 13: bioperl-run v1.5.2_100 >>> >>> I'll add ARCHITECTURE versioning tags back when we know it's working >>> (maybe tomorrow, when I can get on to WinXP to test it). >>> >>> chris >>> >>> On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: >>> >>>> Hi Scott, Bioperl folk, >>>> >>>> I'm afraid that the ActiveState ppm install of BioPerl no longer >>>> works. >>>> Using the current ActiveState (perl version 5.10), I added the >>>> Bribes, >>>> Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates >>>> repositories. However, when I synched up, all but the Bribes reps >>>> showed up >>>> empty in the ppm tool. >>>> >>>> In addition, there's nothing in the release candidate rep any >>>> longer. I used >>>> to use this to get at Bioperl 1.5. >>>> >>>> Perhaps the architecture needs to be changed? >>>> >>>> Lincoln >>>> >>>> >>>> >>>> -- >>>> Lincoln D. Stein >>>> Cold Spring Harbor Laboratory >>>> 1 Bungtown Road >>>> Cold Spring Harbor, NY 11724 >>>> (516) 367-8380 (voice) >>>> (516) 367-8389 (fax) >>>> FOR URGENT MESSAGES & SCHEDULING, >>>> PLEASE CONTACT MY ASSISTANT, >>>> SANDRA MICHELSEN, AT michelse at cshl.edu >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> Christopher Fields >>> Postdoctoral Researcher >>> Lab of Dr. Robert Switzer >>> Dept of Biochemistry >>> University of Illinois Urbana-Champaign >>> >>> >>> >>> >> >> > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.6 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFHqeID9gTv6QYzVL4RAsyqAJ0XkCJgdKu6SHzci4XGww4OofRBzgCfQqCL > MxylCxJflKjtscupJ5cRHKk= > =Brpe > -----END PGP SIGNATURE----- > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From sjmiller at email.arizona.edu Wed Feb 6 15:57:35 2008 From: sjmiller at email.arizona.edu (Susan J. Miller) Date: Wed, 06 Feb 2008 13:57:35 -0700 Subject: [Bioperl-l] SeqHound In-Reply-To: References: <47A8C5C0.7040401@email.arizona.edu> <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> <47A8E3BF.7000308@email.arizona.edu> Message-ID: <47AA1F3F.9000404@email.arizona.edu> Barry Moore wrote: > Susan, > > I'm joining this discussion late so my apologies if I'm missing the > original point. If you're trying to routinely download thousands of > sequences from GenBank or SeqHound you probably want to be using ftp to > download the flat files and query/parse locally. If you're trying to > stay on top of the latest Drosophila ESTs, then how about setting up a > nightly cron job to download the incremental updates from NCBIs ftp > (ftp://ftp.ncbi.nih.gov/genbank/daily-nc) and parse that for Drosophila > EST sequences. The EST division is huge, but I would think nightly > incrementals should be manageable. Hi Barry, I'll try your suggestion. I guess my interpretation of the documentation for SeqHound was erroneous. (Who knows what 'large numbers of sequences' means?) I tried using SeqHound's get_Stream_by_id method to fetch 10000 sequences, 500 at a time, and got a timeout error. -- Regards, -susan Susan J. Miller Manager, Scientific Data Analysis Biotechnology Computing Facility Arizona Research Laboratories (520) 626-2597 From David.Messina at sbc.su.se Wed Feb 6 16:17:46 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 6 Feb 2008 22:17:46 +0100 Subject: [Bioperl-l] BOSC 2008? In-Reply-To: <1182EAB9-7A75-498F-B91B-C14771DFD607@uiuc.edu> References: <1182EAB9-7A75-498F-B91B-C14771DFD607@uiuc.edu> Message-ID: <628aabb70802061317n2f0d1103w9367346166bf8c3f@mail.gmail.com> Hey Chris, Isn't it usually in conjunction with ISMB (which is Toronto 7/19-23 this year)? From cjfields at uiuc.edu Wed Feb 6 16:22:20 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 6 Feb 2008 15:22:20 -0600 Subject: [Bioperl-l] BOSC 2008? In-Reply-To: <628aabb70802061317n2f0d1103w9367346166bf8c3f@mail.gmail.com> References: <1182EAB9-7A75-498F-B91B-C14771DFD607@uiuc.edu> <628aabb70802061317n2f0d1103w9367346166bf8c3f@mail.gmail.com> Message-ID: <9C6A22B1-9E84-4F17-8459-CBBDCB2110D4@uiuc.edu> Yep. I found this out earlier from Darin London. Just trying to plan for it ahead of time! chris On Feb 6, 2008, at 3:17 PM, Dave Messina wrote: > Hey Chris, > > Isn't it usually in conjunction with ISMB (which is Toronto 7/19-23 > this year)? > > Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Feb 6 16:48:45 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 6 Feb 2008 15:48:45 -0600 Subject: [Bioperl-l] SeqHound In-Reply-To: <47AA1F3F.9000404@email.arizona.edu> References: <47A8C5C0.7040401@email.arizona.edu> <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> <47A8E3BF.7000308@email.arizona.edu> <47AA1F3F.9000404@email.arizona.edu> Message-ID: <78824D84-B8B7-4A5C-BD81-7224F26D32E9@uiuc.edu> On Feb 6, 2008, at 2:57 PM, Susan J. Miller wrote: > Barry Moore wrote: >> Susan, >> I'm joining this discussion late so my apologies if I'm missing the >> original point. If you're trying to routinely download thousands >> of sequences from GenBank or SeqHound you probably want to be using >> ftp to download the flat files and query/parse locally. If you're >> trying to stay on top of the latest Drosophila ESTs, then how about >> setting up a nightly cron job to download the incremental updates >> from NCBIs ftp (ftp://ftp.ncbi.nih.gov/genbank/daily-nc) and parse >> that for Drosophila EST sequences. The EST division is huge, but I >> would think nightly incrementals should be manageable. > > > Hi Barry, > > I'll try your suggestion. I guess my interpretation of the > documentation for SeqHound was erroneous. (Who knows what 'large > numbers of sequences' means?) I tried using SeqHound's > get_Stream_by_id method to fetch 10000 sequences, 500 at a time, and > got a timeout error. > > > -- > Regards, > -susan Barry's and Brian's suggestions make more sense. You could also possibly automate a Entrez query to limit retrievals to a period of time instead of munging through the last releases; it all depends on how many sequences you need to parse through. The SeqHound timeout may be set up on their end to prevent a single server from spamming them with tons of requests. NCBI is a bit more tolerant but can be brittle with busy server traffic. chris From barry.moore at genetics.utah.edu Wed Feb 6 16:50:53 2008 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Wed, 6 Feb 2008 14:50:53 -0700 Subject: [Bioperl-l] Fwd: SeqHound References: <6CA6C310-E23C-47ED-9206-7F914BCA689E@genetics.utah.edu> Message-ID: <7167DD26-92F7-4D44-B111-E6CAA30BFB1E@genetics.utah.edu> Susan- Yeah, I used them several years ago, and it seemed like quite a good project at the time. I see that it has recently moved to a new location with a start up company, and I couldn't make heads or tails of their new sight. I wonder if the SeqHound side of their work hasn't suffered - perhaps only temporarily - from their recent move from academia to the brave new world of .com start-up. B On Feb 6, 2008, at 1:57 PM, Susan J. Miller wrote: > Barry Moore wrote: >> Susan, >> >> I'm joining this discussion late so my apologies if I'm missing the >> original point. If you're trying to routinely download thousands of >> sequences from GenBank or SeqHound you probably want to be using >> ftp to >> download the flat files and query/parse locally. If you're trying to >> stay on top of the latest Drosophila ESTs, then how about setting >> up a >> nightly cron job to download the incremental updates from NCBIs ftp >> (ftp://ftp.ncbi.nih.gov/genbank/daily-nc) and parse that for >> Drosophila >> EST sequences. The EST division is huge, but I would think nightly >> incrementals should be manageable. > > > Hi Barry, > > I'll try your suggestion. I guess my interpretation of the > documentation for SeqHound was erroneous. (Who knows what 'large > numbers of sequences' means?) I tried using SeqHound's > get_Stream_by_id > method to fetch 10000 sequences, 500 at a time, and got a timeout > error. > > > -- > Regards, > -susan > > Susan J. Miller > Manager, Scientific Data Analysis > Biotechnology Computing Facility > Arizona Research Laboratories > (520) 626-2597 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From oliverpelz at googlemail.com Thu Feb 7 12:24:38 2008 From: oliverpelz at googlemail.com (Oliver Pelz) Date: Thu, 7 Feb 2008 18:24:38 +0100 Subject: [Bioperl-l] Found dead links in PDoc and a little improvement Message-ID: Hello everybody, I am a beginner in bioperl and currently working heavily with the PDoc's. In this doc here: http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Variation/IO/flat.html the two links to the EBI in the description field are dead. I have looked to find other information but there is nothing available about this pseudo embl format. Has someone the old descriptions and can edit/paste them in this documentation. Another thing would help beginners. At the Bio::SeqIO documentation there are those examples for world fastest ... converter. It would be cool to add a $out->close() to those examples because I was very frustrated in the beginning when the outfiles were empty after the script had finished. Thanks for reading Oliver From bosborne11 at verizon.net Thu Feb 7 13:41:48 2008 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 07 Feb 2008 13:41:48 -0500 Subject: [Bioperl-l] Found dead links in PDoc and a little improvement In-Reply-To: References: Message-ID: Oliver, Removed those dead links, thank you for that. The reason there's no close() in most code examples is that Perl programmers don't usually use this function. The filehandle is closed automatically when open() is called again or when the Perl script finishes. Brian O. On Feb 7, 2008, at 12:24 PM, Oliver Pelz wrote: > Hello everybody, > I am a beginner in bioperl and currently working heavily with the > PDoc's. > > In this doc here: > http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Variation/IO/flat.html > > the two links to the EBI in the description field are dead. I have > looked to > find other information > but there is nothing available about this pseudo embl format. > Has someone the old descriptions and can edit/paste them in this > documentation. > > Another thing would help beginners. > At the Bio::SeqIO documentation there are those examples for world > fastest > ... converter. > It would be cool to add a $out->close() to those examples because I > was very > frustrated in the > beginning when the outfiles were empty after the script had finished. > > Thanks for reading > > Oliver > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From golharam at umdnj.edu Thu Feb 7 16:24:16 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 07 Feb 2008 16:24:16 -0500 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser Message-ID: <47AB7700.8030801@umdnj.edu> Is there a SeqIO parser module for GenBank ASN.1 format? I thought it would have been genbank or entrezgene, but neither of them work. From cjfields at uiuc.edu Thu Feb 7 16:48:25 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 7 Feb 2008 15:48:25 -0600 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <47AB7700.8030801@umdnj.edu> References: <47AB7700.8030801@umdnj.edu> Message-ID: No. The only ASN.1 parser is entrezgene. You could probably try building one using the same ASN.1 parser that SeqIO::entrezgene uses (Bio::ASN1::EntrezGene); it includes a parser for sequences: http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm chris On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: > Is there a SeqIO parser module for GenBank ASN.1 format? I thought > it would have been genbank or entrezgene, but neither of them work. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jason at bioperl.org Thu Feb 7 17:46:41 2008 From: jason at bioperl.org (Jason Stajich) Date: Thu, 7 Feb 2008 14:46:41 -0800 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: References: <47AB7700.8030801@umdnj.edu> Message-ID: <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> ugh - why parse ASN.1? NCBI provides converter application in the ncbi toolkit to many formats : genbank, XML, etc. On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: > No. The only ASN.1 parser is entrezgene. You could probably try > building one using the same ASN.1 parser that SeqIO::entrezgene > uses (Bio::ASN1::EntrezGene); it includes a parser for sequences: > > http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ > ASN1/Sequence.pm > > chris > > On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: > >> Is there a SeqIO parser module for GenBank ASN.1 format? I >> thought it would have been genbank or entrezgene, but neither of >> them work. >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From golharam at umdnj.edu Thu Feb 7 18:00:33 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 07 Feb 2008 18:00:33 -0500 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> Message-ID: <47AB8D91.9080201@umdnj.edu> That I can use from Perl? Such as???? I need to retrieve Gene Ontology information (classification and GO id) from the Entrez Gene record. I thought it would be easiest using BioPerl to do this. BioPerl only has an ASN.1 parser, entrezgene. When I use this to load the Gene record, I'm using: my $io = Bio::SeqIO->new(-file => ' "entrezgene" ); my $seq_obj = $io->next_seq; Something is not working with the second line. I get an error: "Use of uninitialized value in string eq at /home/golharam/bioperl/bioperl-1.5.1//Bio/SeqIO/entrezgene.pm line 244" It sort of makes sense because, well, the Entrez Gene record doesn't have a sequence...it has information about a gene. I figure I must be doing something wrong but I haven't seen anything in BioPerl about parsing entrez gene records any other way. Ryan Jason Stajich wrote: > ugh - why parse ASN.1? NCBI provides converter application in the ncbi > toolkit to many formats : genbank, XML, etc. > On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: > >> No. The only ASN.1 parser is entrezgene. You could probably try >> building one using the same ASN.1 parser that SeqIO::entrezgene uses >> (Bio::ASN1::EntrezGene); it includes a parser for sequences: >> >> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm >> >> >> chris >> >> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >> >>> Is there a SeqIO parser module for GenBank ASN.1 format? I thought >>> it would have been genbank or entrezgene, but neither of them work. >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > From luciap at sas.upenn.edu Thu Feb 7 17:37:46 2008 From: luciap at sas.upenn.edu (Lucia Peixoto) Date: Thu, 07 Feb 2008 17:37:46 -0500 Subject: [Bioperl-l] How to add branch labels for PAML codeml branch models Message-ID: <1202423866.47ab883ab02a3@webmail.sas.upenn.edu> Just a small question in order to label the branches to use model 2 of PAML branch models can I use add_tag_value of Bio::Tree Node? or there's some other way to do it with bioperl? thanks Lucia Peixoto Department of Biology,SAS University of Pennsylvania From cjfields at uiuc.edu Thu Feb 7 18:39:11 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 7 Feb 2008 17:39:11 -0600 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <47AB8E92.4000307@umdnj.edu> References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8E92.4000307@umdnj.edu> Message-ID: Bio::SeqIO::entrezgene should do this. Any dbxrefs (including GO IDs) should be stored in the annotation collection, but I'm not sure how it is parsed; you'll have to test it out. I agree with Jason; ASN.1 isn't a very friendly format. Don't know why NCBI sticks with it, but I'm sure they have their reasons (I think this may have been discussed before on the list). chris On Feb 7, 2008, at 5:04 PM, Ryan Golhar wrote: > Let me re-phrase then - I want to parse an entry such as this: > > http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 > > to retrieve the text of the Gene Ontology entries and the associated > GO IDs for those entries. Is this possible with BioPerl? If so, > how can I do this with BioPerl? > > Ryan > > > > Jason Stajich wrote: >> ugh - why parse ASN.1? NCBI provides converter application in the >> ncbi toolkit to many formats : genbank, XML, etc. >> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: >>> No. The only ASN.1 parser is entrezgene. You could probably try >>> building one using the same ASN.1 parser that SeqIO::entrezgene >>> uses (Bio::ASN1::EntrezGene); it includes a parser for sequences: >>> >>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm >>> >>> chris >>> >>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >>> >>>> Is there a SeqIO parser module for GenBank ASN.1 format? I >>>> thought it would have been genbank or entrezgene, but neither of >>>> them work. >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> Christopher Fields >>> Postdoctoral Researcher >>> Lab of Dr. Robert Switzer >>> Dept of Biochemistry >>> University of Illinois Urbana-Champaign >>> >>> >>> >>> _______________________________________________ >>> 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 > Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From golharam at umdnj.edu Thu Feb 7 18:04:50 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 07 Feb 2008 18:04:50 -0500 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> Message-ID: <47AB8E92.4000307@umdnj.edu> Let me re-phrase then - I want to parse an entry such as this: http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 to retrieve the text of the Gene Ontology entries and the associated GO IDs for those entries. Is this possible with BioPerl? If so, how can I do this with BioPerl? Ryan Jason Stajich wrote: > ugh - why parse ASN.1? NCBI provides converter application in the ncbi > toolkit to many formats : genbank, XML, etc. > On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: > >> No. The only ASN.1 parser is entrezgene. You could probably try >> building one using the same ASN.1 parser that SeqIO::entrezgene uses >> (Bio::ASN1::EntrezGene); it includes a parser for sequences: >> >> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm >> >> >> chris >> >> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >> >>> Is there a SeqIO parser module for GenBank ASN.1 format? I thought >>> it would have been genbank or entrezgene, but neither of them work. >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> >> _______________________________________________ >> 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 golharam at umdnj.edu Thu Feb 7 18:09:06 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 07 Feb 2008 18:09:06 -0500 Subject: [Bioperl-l] BioPipe links don't work Message-ID: <47AB8F92.2030006@umdnj.edu> The links to BioPipe on the HOWTO page do not work. They all lead to http://www.sedoparking.com/biopipe.org From barry.moore at genetics.utah.edu Thu Feb 7 19:31:53 2008 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Thu, 7 Feb 2008 17:31:53 -0700 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <47AB8E92.4000307@umdnj.edu> References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8E92.4000307@umdnj.edu> Message-ID: Ryan, I you have a list of NCBI Gene IDs then you can grab the flatfile gene2go from NCBIs ftp site ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2go.gz. That will give you tax_id, gene_id, go_id, evidence code, qualifier, category etc. From there you can get the description from the GO OBO file http://www.geneontology.org/ontology/ gene_ontology_edit.obo. If all you need is the description then the file is pretty easy to parse on the fly, but if you need to traverse the graphs or if you want an already written parser then add go-perl http://search.cpan.org/~cmungall/go-perl/go-perl.pod Barry On Feb 7, 2008, at 4:04 PM, Ryan Golhar wrote: > Let me re-phrase then - I want to parse an entry such as this: > > http://www.ncbi.nlm.nih.gov/sites/entrez? > db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 > > to retrieve the text of the Gene Ontology entries and the > associated GO > IDs for those entries. Is this possible with BioPerl? If so, how > can I > do this with BioPerl? > > Ryan > > > > Jason Stajich wrote: >> ugh - why parse ASN.1? NCBI provides converter application in the >> ncbi >> toolkit to many formats : genbank, XML, etc. >> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: >> >>> No. The only ASN.1 parser is entrezgene. You could probably try >>> building one using the same ASN.1 parser that SeqIO::entrezgene uses >>> (Bio::ASN1::EntrezGene); it includes a parser for sequences: >>> >>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/ >>> Bio/ASN1/Sequence.pm >>> >>> >>> chris >>> >>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >>> >>>> Is there a SeqIO parser module for GenBank ASN.1 format? I thought >>>> it would have been genbank or entrezgene, but neither of them work. >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> Christopher Fields >>> Postdoctoral Researcher >>> Lab of Dr. Robert Switzer >>> Dept of Biochemistry >>> University of Illinois Urbana-Champaign >>> >>> >>> >>> _______________________________________________ >>> 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 golharam at umdnj.edu Thu Feb 7 19:46:21 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 07 Feb 2008 19:46:21 -0500 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8E92.4000307@umdnj.edu> Message-ID: <47ABA65D.1000705@umdnj.edu> Thank Barry. I did try using go-perl but it is slow when processing queries. I didn't know about ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz. I think that is exactly what I'm looking for. Ryan Barry Moore wrote: > Ryan, > > I you have a list of NCBI Gene IDs then you can grab the flatfile > gene2go from NCBIs ftp site > ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz. That will give you > tax_id, gene_id, go_id, evidence code, qualifier, category etc. From > there you can get the description from the GO OBO file > http://www.geneontology.org/ontology/gene_ontology_edit.obo. If all you > need is the description then the file is pretty easy to parse on the > fly, but if you need to traverse the graphs or if you want an already > written parser then add go-perl > http://search.cpan.org/~cmungall/go-perl/go-perl.pod > > Barry > > > > On Feb 7, 2008, at 4:04 PM, Ryan Golhar wrote: > >> Let me re-phrase then - I want to parse an entry such as this: >> >> http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 >> >> >> to retrieve the text of the Gene Ontology entries and the associated GO >> IDs for those entries. Is this possible with BioPerl? If so, how can I >> do this with BioPerl? >> >> Ryan >> >> >> >> Jason Stajich wrote: >>> ugh - why parse ASN.1? NCBI provides converter application in the ncbi >>> toolkit to many formats : genbank, XML, etc. >>> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: >>> >>>> No. The only ASN.1 parser is entrezgene. You could probably try >>>> building one using the same ASN.1 parser that SeqIO::entrezgene uses >>>> (Bio::ASN1::EntrezGene); it includes a parser for sequences: >>>> >>>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm >>>> >>>> >>>> >>>> chris >>>> >>>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >>>> >>>>> Is there a SeqIO parser module for GenBank ASN.1 format? I thought >>>>> it would have been genbank or entrezgene, but neither of them work. >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> Christopher Fields >>>> Postdoctoral Researcher >>>> Lab of Dr. Robert Switzer >>>> Dept of Biochemistry >>>> University of Illinois Urbana-Champaign >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 golharam at umdnj.edu Thu Feb 7 18:59:52 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 07 Feb 2008 18:59:52 -0500 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8E92.4000307@umdnj.edu> Message-ID: <47AB9B78.5090907@umdnj.edu> That's what I thought too. However, I'm getting errors with a parser. I found Bio::ASN1::EntrezGene online and am using that module outside of Bioperl as it works well for what I'm doing. I've already changed my code and don't want to deal with tracking down the errors I had with BioPerl (I've already spend enough time on this) but they were easy enough to reproduce. Ryan Chris Fields wrote: > Bio::SeqIO::entrezgene should do this. Any dbxrefs (including GO IDs) > should be stored in the annotation collection, but I'm not sure how it > is parsed; you'll have to test it out. > > I agree with Jason; ASN.1 isn't a very friendly format. Don't know why > NCBI sticks with it, but I'm sure they have their reasons (I think this > may have been discussed before on the list). > > chris > > On Feb 7, 2008, at 5:04 PM, Ryan Golhar wrote: > >> Let me re-phrase then - I want to parse an entry such as this: >> >> http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 >> >> >> to retrieve the text of the Gene Ontology entries and the associated >> GO IDs for those entries. Is this possible with BioPerl? If so, how >> can I do this with BioPerl? >> >> Ryan >> >> >> >> Jason Stajich wrote: >>> ugh - why parse ASN.1? NCBI provides converter application in the >>> ncbi toolkit to many formats : genbank, XML, etc. >>> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: >>>> No. The only ASN.1 parser is entrezgene. You could probably try >>>> building one using the same ASN.1 parser that SeqIO::entrezgene uses >>>> (Bio::ASN1::EntrezGene); it includes a parser for sequences: >>>> >>>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm >>>> >>>> >>>> chris >>>> >>>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >>>> >>>>> Is there a SeqIO parser module for GenBank ASN.1 format? I thought >>>>> it would have been genbank or entrezgene, but neither of them work. >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> Christopher Fields >>>> Postdoctoral Researcher >>>> Lab of Dr. Robert Switzer >>>> Dept of Biochemistry >>>> University of Illinois Urbana-Champaign >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >> > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > > From cjfields at uiuc.edu Thu Feb 7 20:32:18 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 7 Feb 2008 19:32:18 -0600 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <47AB9B78.5090907@umdnj.edu> References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8E92.4000307@umdnj.edu> <47AB9B78.5090907@umdnj.edu> Message-ID: <1001C6BB-24D5-4BB8-B135-0E9D2952B49A@uiuc.edu> It's possible that has been fixed in bioperl-live. However, just in case, if you are getting errors could you file a bug report along with the relevant code demonstrating it? chris On Feb 7, 2008, at 5:59 PM, Ryan Golhar wrote: > That's what I thought too. However, I'm getting errors with a parser. > > I found Bio::ASN1::EntrezGene online and am using that module > outside of Bioperl as it works well for what I'm doing. > > I've already changed my code and don't want to deal with tracking > down the errors I had with BioPerl (I've already spend enough time > on this) but they were easy enough to reproduce. > > Ryan > > > Chris Fields wrote: >> Bio::SeqIO::entrezgene should do this. Any dbxrefs (including GO >> IDs) should be stored in the annotation collection, but I'm not >> sure how it is parsed; you'll have to test it out. >> I agree with Jason; ASN.1 isn't a very friendly format. Don't know >> why NCBI sticks with it, but I'm sure they have their reasons (I >> think this may have been discussed before on the list). >> chris >> On Feb 7, 2008, at 5:04 PM, Ryan Golhar wrote: >>> Let me re-phrase then - I want to parse an entry such as this: >>> >>> http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 >>> >>> to retrieve the text of the Gene Ontology entries and the >>> associated GO IDs for those entries. Is this possible with >>> BioPerl? If so, how can I do this with BioPerl? >>> >>> Ryan >>> >>> >>> >>> Jason Stajich wrote: >>>> ugh - why parse ASN.1? NCBI provides converter application in the >>>> ncbi toolkit to many formats : genbank, XML, etc. >>>> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: >>>>> No. The only ASN.1 parser is entrezgene. You could probably >>>>> try building one using the same ASN.1 parser that >>>>> SeqIO::entrezgene uses (Bio::ASN1::EntrezGene); it includes a >>>>> parser for sequences: >>>>> >>>>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm >>>>> >>>>> chris >>>>> >>>>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >>>>> >>>>>> Is there a SeqIO parser module for GenBank ASN.1 format? I >>>>>> thought it would have been genbank or entrezgene, but neither >>>>>> of them work. >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> Christopher Fields >>>>> Postdoctoral Researcher >>>>> Lab of Dr. Robert Switzer >>>>> Dept of Biochemistry >>>>> University of Illinois Urbana-Champaign >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jason at bioperl.org Thu Feb 7 20:52:39 2008 From: jason at bioperl.org (Jason Stajich) Date: Thu, 7 Feb 2008 17:52:39 -0800 Subject: [Bioperl-l] How to add branch labels for PAML codeml branch models In-Reply-To: <1202423866.47ab883ab02a3@webmail.sas.upenn.edu> References: <1202423866.47ab883ab02a3@webmail.sas.upenn.edu> Message-ID: It will work if you just change the node's ID to be something like: 'ID #1' (for tips) and for the internal nodes just set the id to ("#1"), etc... I added some code to demonstrate this one the wiki: http://bioperl.org/wiki/HOWTO:PAML#Setting_up_Branch-specific_labels The format is nonstandard so you have to hack the output some to get what you want, hence the extra part that requires you strip out the " since they are required for escaping space characters. -jason On Feb 7, 2008, at 2:37 PM, Lucia Peixoto wrote: > Just a small question > in order to label the branches to use model 2 of PAML branch models > can I use add_tag_value of Bio::Tree Node? > or there's some other way to do it with bioperl? > > thanks > > Lucia Peixoto > Department of Biology,SAS > University of Pennsylvania > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjm at fruitfly.org Thu Feb 7 21:14:20 2008 From: cjm at fruitfly.org (Chris Mungall) Date: Thu, 7 Feb 2008 18:14:20 -0800 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8E92.4000307@umdnj.edu> Message-ID: Just to add to Barry's suggestions: You can query the database directly: http://www.berkeleybop.org/goose You can also use the go-db-perl API and point it at the mysql port of one of the mirrors; see http://www.geneontology.org/GO.database.shtml On Feb 7, 2008, at 4:31 PM, Barry Moore wrote: > Ryan, > > I you have a list of NCBI Gene IDs then you can grab the flatfile > gene2go from NCBIs ftp site ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ > gene2go.gz. That will give you tax_id, gene_id, go_id, evidence > code, qualifier, category etc. From there you can get the > description from the GO OBO file http://www.geneontology.org/ > ontology/gene_ontology_edit.obo. If all you need is the > description then the file is pretty easy to parse on the fly, but > if you need to traverse the graphs or if you want an already > written parser then add go-perl http://search.cpan.org/~cmungall/go- > perl/go-perl.pod > > Barry > > > > On Feb 7, 2008, at 4:04 PM, Ryan Golhar wrote: > >> Let me re-phrase then - I want to parse an entry such as this: >> >> http://www.ncbi.nlm.nih.gov/sites/entrez? >> db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 >> >> to retrieve the text of the Gene Ontology entries and the >> associated GO >> IDs for those entries. Is this possible with BioPerl? If so, how >> can I >> do this with BioPerl? >> >> Ryan >> >> >> >> Jason Stajich wrote: >>> ugh - why parse ASN.1? NCBI provides converter application in the >>> ncbi >>> toolkit to many formats : genbank, XML, etc. >>> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: >>> >>>> No. The only ASN.1 parser is entrezgene. You could probably try >>>> building one using the same ASN.1 parser that SeqIO::entrezgene >>>> uses >>>> (Bio::ASN1::EntrezGene); it includes a parser for sequences: >>>> >>>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/ >>>> Bio/ASN1/Sequence.pm >>>> >>>> >>>> chris >>>> >>>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >>>> >>>>> Is there a SeqIO parser module for GenBank ASN.1 format? I >>>>> thought >>>>> it would have been genbank or entrezgene, but neither of them >>>>> work. >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> Christopher Fields >>>> Postdoctoral Researcher >>>> Lab of Dr. Robert Switzer >>>> Dept of Biochemistry >>>> University of Illinois Urbana-Champaign >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 hlapp at gmx.net Thu Feb 7 21:45:48 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 7 Feb 2008 21:45:48 -0500 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <47AB8D91.9080201@umdnj.edu> References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8D91.9080201@umdnj.edu> Message-ID: On Feb 7, 2008, at 6:00 PM, Ryan Golhar wrote: > Something is not working with the second line. I get an error: > > "Use of uninitialized value in string eq at > /home/golharam/bioperl/bioperl-1.5.1//Bio/SeqIO/ > entrezgene.pm line 244" This isn't an error, is it - it's a warning, no? -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Thu Feb 7 22:24:45 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 7 Feb 2008 21:24:45 -0600 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8D91.9080201@umdnj.edu> Message-ID: I agree. I also noticed Ryan's running bioperl 1.5.1. Probably worth trying the latest code from Subversion. chris On Feb 7, 2008, at 8:45 PM, Hilmar Lapp wrote: > > On Feb 7, 2008, at 6:00 PM, Ryan Golhar wrote: > >> Something is not working with the second line. I get an error: >> >> "Use of uninitialized value in string eq at >> /home/golharam/bioperl/bioperl-1.5.1//Bio/SeqIO/ >> entrezgene.pm line 244" > > > This isn't an error, is it - it's a warning, no? > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From David.Messina at sbc.su.se Fri Feb 8 04:00:05 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Fri, 8 Feb 2008 10:00:05 +0100 Subject: [Bioperl-l] BioPipe links don't work In-Reply-To: <47AB8F92.2030006@umdnj.edu> References: <47AB8F92.2030006@umdnj.edu> Message-ID: <628aabb70802080100g43c02f0btdc8c8065c576ff3d@mail.gmail.com> BioPipe, as far as I can tell, is dead, and indeed the HOWTO is no longer active. Therefore I've removed the BioPipe entry entirely. If anyone would prefer it stay, please let me know and I'll revert the change and update the links to point to the GMOD "BioPipe is no longer supported" page. Dave From luciap at sas.upenn.edu Fri Feb 8 10:53:36 2008 From: luciap at sas.upenn.edu (Lucia Peixoto) Date: Fri, 08 Feb 2008 10:53:36 -0500 Subject: [Bioperl-l] How to add branch labels for PAML codeml branch models In-Reply-To: References: <1202423866.47ab883ab02a3@webmail.sas.upenn.edu> Message-ID: <1202486016.47ac7b003b860@webmail.sas.upenn.edu> Hi as I have my trees right now the bootstrap support ends up as the node ID so I guess I have to assign node ID to bootstrap first and then change? Lucia Quoting Jason Stajich : > It will work if you just change the node's ID to be something like: > 'ID #1' (for tips) and for the internal nodes just set the id to > ("#1"), etc... > > I added some code to demonstrate this one the wiki: > http://bioperl.org/wiki/HOWTO:PAML#Setting_up_Branch-specific_labels > > The format is nonstandard so you have to hack the output some to get > what you want, hence the extra part that requires you strip out the " > since they are required for escaping space characters. > > -jason > On Feb 7, 2008, at 2:37 PM, Lucia Peixoto wrote: > > > Just a small question > > in order to label the branches to use model 2 of PAML branch models > > can I use add_tag_value of Bio::Tree Node? > > or there's some other way to do it with bioperl? > > > > thanks > > > > Lucia Peixoto > > Department of Biology,SAS > > University of Pennsylvania > > _______________________________________________ > > 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 > Lucia Peixoto Department of Biology,SAS University of Pennsylvania From jason at bioperl.org Fri Feb 8 13:18:59 2008 From: jason at bioperl.org (Jason Stajich) Date: Fri, 8 Feb 2008 10:18:59 -0800 Subject: [Bioperl-l] How to add branch labels for PAML codeml branch models In-Reply-To: <1202486016.47ac7b003b860@webmail.sas.upenn.edu> References: <1202423866.47ab883ab02a3@webmail.sas.upenn.edu> <1202486016.47ac7b003b860@webmail.sas.upenn.edu> Message-ID: <793E2862-7D2F-4936-93E3-960BD6D74EB3@bioperl.org> http://bioperl.org/wiki/HOWTO:Trees#Reading_and_Writing_Trees Remember that in newick format bootstrap and internal node ids are effectively the same thing - that we store in them separate slots in bioperl is that fact that other formats can separate out this data but there is no standard in newick format. In sometime cases formats do accept the node labels that look like NODEID[BOOTSTRAP] for internal nodes (and BioPerl parses those out nicely) but most programs don't recognize that. On parsing, unless you tell Bioperl that the internal IDs are bootstrap values it is going to store that data as an ID. You will want to clear the bootstraps anyways to write PAML trees anyways. -jason On Feb 8, 2008, at 7:53 AM, Lucia Peixoto wrote: > Hi > as I have my trees right now the bootstrap support ends up as the > node ID > so I guess I have to assign node ID to bootstrap first and then > change? > > > Lucia > > Quoting Jason Stajich : > >> It will work if you just change the node's ID to be something like: >> 'ID #1' (for tips) and for the internal nodes just set the id to >> ("#1"), etc... >> >> I added some code to demonstrate this one the wiki: >> http://bioperl.org/wiki/HOWTO:PAML#Setting_up_Branch- >> specific_labels >> >> The format is nonstandard so you have to hack the output some to get >> what you want, hence the extra part that requires you strip out the " >> since they are required for escaping space characters. >> >> -jason >> On Feb 7, 2008, at 2:37 PM, Lucia Peixoto wrote: >> >>> Just a small question >>> in order to label the branches to use model 2 of PAML branch models >>> can I use add_tag_value of Bio::Tree Node? >>> or there's some other way to do it with bioperl? >>> >>> thanks >>> >>> Lucia Peixoto >>> Department of Biology,SAS >>> University of Pennsylvania >>> _______________________________________________ >>> 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 >> > > > Lucia Peixoto > Department of Biology,SAS > University of Pennsylvania From golharam at umdnj.edu Fri Feb 8 21:01:45 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 08 Feb 2008 21:01:45 -0500 Subject: [Bioperl-l] error in build.pl of bioperl-live Message-ID: <47AD0989.1050904@umdnj.edu> I just obtained the latest build of bioperl from svn. When I run 'perl Build.pl', I get an error "Use of uninitialized value in concatenation (.) or string at Build.PL line 184.". Here's the output I see (The error is at the end): [golharam at hydrogen bioperl-live]$ perl Build.PL Checking prerequisites... Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] * Optional prerequisite Ace is not installed (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF:: Adaptor::ace) * Optional prerequisite Algorithm::Munkres is not installed (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) * Optional prerequisite Math::Random is not installed (wanted for Random Phylogenetic Networks, used by Bio::PhyloNetwork::RandomFactory) * Optional prerequisite GraphViz is not installed (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz) * Class::AutoClass (0.091) is installed, but we prefer to have 1 (wanted for creating objects, used by Bio::Graph::SimpleGraph, Bio::Graph::SimpleGraph::Traversal and Bio::Graph::ProteinGraph) * Optional prerequisite Array::Compare is not installed (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Checking features: Network..................enabled BioDBSeqFeature_mysql....enabled BioDBGFF.................enabled BioDBSeqFeature_BDB......enabled Do you want to run the BioDBGFF or BioDBSeqFeature_mysql live database tests? y/ n [n] n - will not run the BioDBGFF live database tests Use of uninitialized value in concatenation (.) or string at Build.PL line 184. Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] From golharam at umdnj.edu Fri Feb 8 21:08:30 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 08 Feb 2008 21:08:30 -0500 Subject: [Bioperl-l] error in build.pl of bioperl-live In-Reply-To: <47AD0989.1050904@umdnj.edu> References: <47AD0989.1050904@umdnj.edu> Message-ID: <47AD0B1E.3050200@umdnj.edu> In addition, if I continue past the error and run './Build test', I get a bunch of errors like this: BEGIN failed--compilation aborted at t/lib/BioperlTest.pm line 109. Compilation failed in require at t/Allele.t line 9. BEGIN failed--compilation aborted at t/Allele.t line 9. t/Allele.......................... Dubious, test returned 255 (wstat 65280, 0xff00) No subtests run All the tests fail. The last few lines read: Files=257, Tests=0, 19 wallclock secs ( 0.77 usr 0.51 sys + 12.18 cusr 1.75 csys = 15.21 CPU) Result: FAIL Failed 255/257 test programs. 0/0 subtests failed. Am I missing something? This can't be related to the missing prereqs as all the tests are failing. Ryan Golhar wrote: > I just obtained the latest build of bioperl from svn. When I run 'perl > Build.pl', I get an error "Use of uninitialized value in concatenation > (.) or string at Build.PL line 184.". Here's the output I see (The > error is at the end): > > [golharam at hydrogen bioperl-live]$ perl Build.PL > Checking prerequisites... > Install [a]ll optional external modules, [n]one, or choose > [i]nteractively? [n] > * Optional prerequisite Ace is not installed > (wanted for access of ACeDB database, used by Bio::DB::Ace and > Bio::DB::GFF:: > Adaptor::ace) > * Optional prerequisite Algorithm::Munkres is not installed > (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) > * Optional prerequisite Math::Random is not installed > (wanted for Random Phylogenetic Networks, used by > Bio::PhyloNetwork::RandomFactory) > * Optional prerequisite GraphViz is not installed > (wanted for Phylogenetic Network Visulization, used by > Bio::PhyloNetwork::GraphViz) > * Class::AutoClass (0.091) is installed, but we prefer to have 1 > (wanted for creating objects, used by Bio::Graph::SimpleGraph, > Bio::Graph::SimpleGraph::Traversal and Bio::Graph::ProteinGraph) > * Optional prerequisite Array::Compare is not installed > (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) > > ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the > versions > of the modules indicated above before proceeding with this installation > > Checking features: > Network..................enabled > BioDBSeqFeature_mysql....enabled > BioDBGFF.................enabled > BioDBSeqFeature_BDB......enabled > > Do you want to run the BioDBGFF or BioDBSeqFeature_mysql live database > tests? y/ > n [n] n > - will not run the BioDBGFF live database tests > > Use of uninitialized value in concatenation (.) or string at Build.PL > line 184. > Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? > [a] > From hlapp at gmx.net Fri Feb 8 22:33:55 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 8 Feb 2008 22:33:55 -0500 Subject: [Bioperl-l] error in build.pl of bioperl-live In-Reply-To: <47AD0989.1050904@umdnj.edu> References: <47AD0989.1050904@umdnj.edu> Message-ID: Hi Ryan, On Feb 8, 2008, at 9:01 PM, Ryan Golhar wrote: > I get an error "Use of uninitialized value in concatenation (.) or > string at Build.PL line 184.". do keep in mind that this kind of message is almost never an error. It's simply a warning that you wouldn't even see w/o -w. All that it means is that a scalar with an undefined value is being evaluated to a string (which results, by default, in an empty string). Is the build failing or halting at this point for you? That said, it's indeed a good to point those out, as someone either should have initialized a scalar when it wasn't, or that someone was expecting the scalar to always have a value, and so the absence of it may indicate an unexpected condition resulting from an error elsewhere. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From golharam at umdnj.edu Fri Feb 8 22:58:02 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 08 Feb 2008 22:58:02 -0500 Subject: [Bioperl-l] error in build.pl of bioperl-live In-Reply-To: References: <47AD0989.1050904@umdnj.edu> Message-ID: <47AD24CA.2050102@umdnj.edu> Hi Hilmar, The script doesn't halt, but the tests do fail. I sent another message with the errors I am seeing. I do not know if they are related to this or not. Ryan Hilmar Lapp wrote: > Hi Ryan, > > On Feb 8, 2008, at 9:01 PM, Ryan Golhar wrote: > >> I get an error "Use of uninitialized value in concatenation (.) or >> string at Build.PL line 184.". > > > do keep in mind that this kind of message is almost never an error. It's > simply a warning that you wouldn't even see w/o -w. All that it means is > that a scalar with an undefined value is being evaluated to a string > (which results, by default, in an empty string). > > Is the build failing or halting at this point for you? > > That said, it's indeed a good to point those out, as someone either > should have initialized a scalar when it wasn't, or that someone was > expecting the scalar to always have a value, and so the absence of it > may indicate an unexpected condition resulting from an error elsewhere. > > -hilmar From hlapp at gmx.net Fri Feb 8 23:07:31 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 8 Feb 2008 23:07:31 -0500 Subject: [Bioperl-l] error in build.pl of bioperl-live In-Reply-To: <47AD24CA.2050102@umdnj.edu> References: <47AD0989.1050904@umdnj.edu> <47AD24CA.2050102@umdnj.edu> Message-ID: On Feb 8, 2008, at 10:58 PM, Ryan Golhar wrote: > The script doesn't halt, but the tests do fail. I sent another > message with the errors I am seeing. I do not know if they are > related to this or not. Yep I saw that. They might be related if, for example, the issue is related to not finding BioPerl? Can you run one test in verbose mode? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Fri Feb 8 23:47:08 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 8 Feb 2008 22:47:08 -0600 Subject: [Bioperl-l] error in build.pl of bioperl-live In-Reply-To: <47AD24CA.2050102@umdnj.edu> References: <47AD0989.1050904@umdnj.edu> <47AD24CA.2050102@umdnj.edu> Message-ID: Ryan, I don't see either the 'Use of initialized' error or the massive failed test issue using Mac OS X (perl 5.8). I get a different set of warnings using perl 5.10 related to Data::Dumper but not this (and everything runs fine). It might be of help to know what perl version, OS, etc. you are using. It also might be worth upgrading Module::Build and Test::Harness as well (though the Build.PL script should catch that and warn you). chris On Feb 8, 2008, at 9:58 PM, Ryan Golhar wrote: > Hi Hilmar, > > The script doesn't halt, but the tests do fail. I sent another > message with the errors I am seeing. I do not know if they are > related to this or not. > > Ryan > > > Hilmar Lapp wrote: >> Hi Ryan, >> On Feb 8, 2008, at 9:01 PM, Ryan Golhar wrote: >>> I get an error "Use of uninitialized value in concatenation (.) or >>> string at Build.PL line 184.". >> do keep in mind that this kind of message is almost never an error. >> It's simply a warning that you wouldn't even see w/o -w. All that >> it means is that a scalar with an undefined value is being >> evaluated to a string (which results, by default, in an empty >> string). >> Is the build failing or halting at this point for you? >> That said, it's indeed a good to point those out, as someone either >> should have initialized a scalar when it wasn't, or that someone >> was expecting the scalar to always have a value, and so the absence >> of it may indicate an unexpected condition resulting from an error >> elsewhere. >> -hilmar > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Fri Feb 8 23:49:14 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 8 Feb 2008 22:49:14 -0600 Subject: [Bioperl-l] error in build.pl of bioperl-live In-Reply-To: References: <47AD0989.1050904@umdnj.edu> <47AD24CA.2050102@umdnj.edu> Message-ID: <35C30475-6CC6-470E-B40B-DF13E65FC8A3@uiuc.edu> On Feb 8, 2008, at 10:07 PM, Hilmar Lapp wrote: > > On Feb 8, 2008, at 10:58 PM, Ryan Golhar wrote: > >> The script doesn't halt, but the tests do fail. I sent another >> message with the errors I am seeing. I do not know if they are >> related to this or not. > > > Yep I saw that. They might be related if, for example, the issue is > related to not finding BioPerl? > > Can you run one test in verbose mode? > > -hilmar To add to that, 'perl -I. t/SearchIO.t' should also still work for most (but not all). chris From heikki at sanbi.ac.za Tue Feb 12 03:25:32 2008 From: heikki at sanbi.ac.za (Heikki Lehvaslaiho) Date: Tue, 12 Feb 2008 10:25:32 +0200 Subject: [Bioperl-l] BioHackathon 2008 Message-ID: <200802121025.32797.heikki@sanbi.ac.za> Hi all, BioHackathon 2008 is happening right now in Tokyo, Japan. See http://hackathon.dbcls.jp/ The focus is on web services but some direct work on Bio* projects is getting done, too. See page: http://hackathon.dbcls.jp/wiki/OpenBio* for ideas thrown in the air. I just had a look how well the most common sequence file formats survive reading from a flat file into BioPerl objects and writing back into the same format: http://hackathon.dbcls.jp/wiki/BioPerlRoundTripFirstPass -Heikki -- ______ _/ _/_____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za _/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho _/ _/ _/ SANBI, South African National Bioinformatics Institute _/ _/ _/ University of Western Cape, South Africa _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 ___ _/_/_/_/_/________________________________________________________ From lenski at mdc-berlin.de Tue Feb 12 04:54:25 2008 From: lenski at mdc-berlin.de (Ulf Lenski) Date: Tue, 12 Feb 2008 10:54:25 +0100 Subject: [Bioperl-l] fetch protein-na-complexes from pdb Message-ID: <47B16CD1.2060307@mdc-berlin.de> is there a bioperl modul for fetching protein-na-complexes from the pdb? and can i distinguish ss-dna from dna chains without parsing the pdb files and go through the coordinates (calculate distances etc...)? tx - ulf. -------------- next part -------------- A non-text attachment was scrubbed... Name: lenski.vcf Type: text/x-vcard Size: 216 bytes Desc: not available URL: From bernd.web at gmail.com Tue Feb 12 07:45:51 2008 From: bernd.web at gmail.com (Bernd Web) Date: Tue, 12 Feb 2008 13:45:51 +0100 Subject: [Bioperl-l] fetch protein-na-complexes from pdb In-Reply-To: <47B16CD1.2060307@mdc-berlin.de> References: <47B16CD1.2060307@mdc-berlin.de> Message-ID: <716af09c0802120445n6d477c7dj5de7819408eb2c48@mail.gmail.com> Hi Ulf, At rcsb.org you can get a list of PDB IDs for Protein/NA complexes and even download the entries there. See http://www.rcsb.org/pdb/statistics/holdings.do Also see "webdownload" on the RCSB site. Alternatively, you could fetch the files one by one (e.g. with wget). The file "ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_entry_type.txt" contains the entry type of all PDB entries (i.e.: prot/nuc/prot-nuc and diffraction/NMR). Regards, Bernd 2008/2/12 Ulf Lenski : > is there a bioperl modul for fetching protein-na-complexes from the pdb? > and can i distinguish ss-dna from dna chains without parsing the pdb > files and go through the coordinates (calculate distances etc...)? > > tx - ulf. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From lenski at mdc-berlin.de Tue Feb 12 08:43:51 2008 From: lenski at mdc-berlin.de (Ulf Lenski) Date: Tue, 12 Feb 2008 14:43:51 +0100 Subject: [Bioperl-l] fetch protein-na-complexes from pdb In-Reply-To: <716af09c0802120445n6d477c7dj5de7819408eb2c48@mail.gmail.com> References: <47B16CD1.2060307@mdc-berlin.de> <716af09c0802120445n6d477c7dj5de7819408eb2c48@mail.gmail.com> Message-ID: <47B1A297.7030406@mdc-berlin.de> hi bernd, thanks a lot - that helps me for my first question. but how can I distinguish the nuc chains? How I can find out the type of a single chain? ss-rna ss-dna ds-rna ds-dna regards, ulf. Bernd Web schrieb: > Hi Ulf, > > At rcsb.org you can get a list of PDB IDs for Protein/NA complexes and > even download the entries there. See > http://www.rcsb.org/pdb/statistics/holdings.do > Also see "webdownload" on the RCSB site. > > Alternatively, you could fetch the files one by one (e.g. with wget). > The file "ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_entry_type.txt" > contains the entry type of all PDB entries (i.e.: prot/nuc/prot-nuc > and diffraction/NMR). > > Regards, > Bernd > > > 2008/2/12 Ulf Lenski : > >> is there a bioperl modul for fetching protein-na-complexes from the pdb? >> and can i distinguish ss-dna from dna chains without parsing the pdb >> files and go through the coordinates (calculate distances etc...)? >> >> tx - ulf. >> >> _______________________________________________ >> 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 > > -------------- next part -------------- A non-text attachment was scrubbed... Name: lenski.vcf Type: text/x-vcard Size: 216 bytes Desc: not available URL: From cjfields at uiuc.edu Tue Feb 12 12:02:13 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 12 Feb 2008 11:02:13 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release Message-ID: Now that SVN migration is complete and a BioSQL 1.0 release is imminent (congrats Hilmar and Heikki), I would like to get a new bioperl core release out the door soon, preferably by the next BOSC meeting, end of summer by the latest. One major issue that all the core devs have right now is time, or a serious lack thereof. I, for instance, will be moving into a new research position in the next few months or so. I'm assuming Jason, Hilmar, Heikki, Sendu, and the other core developers are facing similar time constraints. In that light, we need to decide whether we are planning a new 1.5 release, or if we want to start a new stable (1.6) release. With the latter, we need to define very specifically what needs to be accomplished for that release, and it needs to be realistic with the timeframe above in mind. I would also like to extend the invitation for anyone who wishes to help to join in. For my vote, I would like to release a new stable 1.6; 1.5.x has been around for too long and the end goals were never really defined clearly (something we need to keep in mind for the next dev release). I also vote for separating out experimental/untested/undocumented/ unmaintained modules into a separate 'bioperl-dev' release (the 'here be dragons' of bioperl). I believe it would help the core release cycle tremendously. Issues raised in the past just off the top of my head (add more as needed): * perl 5.10 compliance (appears to mostly work now) * outstanding bugs (core only) * GFF/GFF3 compliance * BioSQL 1.0 compliance (impending) * POD and test coverage * smoke tests for bioperl-live/db/etc. * smaller, more focused core (less dependencies) * separating out experimental or poorly maintained modules into a separate 'bioperl-dev' distribution * bioperl-db issues with Bio::Species changes * module maintenance * sequence format roundtripping (i.e. genbank, embl, swissetc) * additional sequence parsers (insdcxml, etc) * enhancement requests in bugzilla (Albert?) chris From hangsyin at gmail.com Tue Feb 12 11:50:33 2008 From: hangsyin at gmail.com (Hang) Date: Tue, 12 Feb 2008 08:50:33 -0800 (PST) Subject: [Bioperl-l] BLAT in memory Message-ID: <15435321.post@talk.nabble.com> Dear all, I wonder whether it is a way that allows me to BLAT sequences and retrieve the result without writing to a file. Thank you! Best, Hang -- View this message in context: http://www.nabble.com/BLAT-in-memory-tp15435321p15435321.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From jason at bioperl.org Tue Feb 12 12:49:56 2008 From: jason at bioperl.org (Jason Stajich) Date: Tue, 12 Feb 2008 09:49:56 -0800 Subject: [Bioperl-l] BLAT in memory In-Reply-To: <15435321.post@talk.nabble.com> References: <15435321.post@talk.nabble.com> Message-ID: <63C04F95-2EFB-433B-91F8-7907829E18CB@bioperl.org> Specify 'stdout' as the filename. -jason On Feb 12, 2008, at 8:50 AM, Hang wrote: > > Dear all, > > I wonder whether it is a way that allows me to BLAT sequences and > retrieve > the result without writing to a file. Thank you! > > Best, > Hang > -- > View this message in context: http://www.nabble.com/BLAT-in-memory- > tp15435321p15435321.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 bix at sendu.me.uk Tue Feb 12 13:10:52 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 12 Feb 2008 18:10:52 +0000 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: Message-ID: <47B1E12C.9010708@sendu.me.uk> Chris Fields wrote: > * perl 5.10 compliance (appears to mostly work now) > * outstanding bugs (core only) > * POD and test coverage I'm fine with everything you said, but I'll just say that, at a minimum, the above is what needs to be done. Someone needs to step up and organise that 3rd point, since it will require a lot of work. As I've already done work on the test suite, if no one else expresses an interest I might look into it myself. > Now that SVN migration is complete Speaking of which, is there a way a file (like, oh, I don't know, bioperl-live/trunk/t/lib/BioperlTest.pm) can exist just once in SVN but be seen in other locations (like bioperl-run/trunk/t/lib/BioperlTest.pm)? Such that a commit to the version in bioperl-run also affects the version in bioperl-live? Or is there some appropriate other way to organise where cross-repository files are kept and dealt with? From cjfields at uiuc.edu Tue Feb 12 13:51:57 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 12 Feb 2008 12:51:57 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <47B1E12C.9010708@sendu.me.uk> References: <47B1E12C.9010708@sendu.me.uk> Message-ID: <9424A11E-7541-442C-B53E-C791A2D8C6FB@uiuc.edu> On Feb 12, 2008, at 12:10 PM, Sendu Bala wrote: > Chris Fields wrote: >> * perl 5.10 compliance (appears to mostly work now) >> * outstanding bugs (core only) >> * POD and test coverage > > I'm fine with everything you said, but I'll just say that, at a > minimum, the above is what needs to be done. I think we should also try to get bioperl-db up to speed for the BioSQL 1.0 release (at least Bio::Species-related issues). > Someone needs to step up and organise that 3rd point, since it will > require a lot of work. As I've already done work on the test suite, > if no one else expresses an interest I might look into it myself. Jason and I discussed it off list (along with Nathan Haigh). We also brought up the idea of smoke tests, which should pinpoint how stable bioperl-live distributions are. Having those set up would pinpoint modules we think need to stay in core or should go into a separate 'dev/extras' distribution. We could test smoke/coverage/POD on those as well. >> Now that SVN migration is complete > > Speaking of which, is there a way a file (like, oh, I don't know, > bioperl-live/trunk/t/lib/BioperlTest.pm) can exist just once in SVN > but be seen in other locations (like bioperl-run/trunk/t/lib/ > BioperlTest.pm)? Such that a commit to the version in bioperl-run > also affects the version in bioperl-live? Or is there some > appropriate other way to organise where cross-repository files are > kept and dealt with? Maybe using external definitions, though I haven't messed with it personally. http://svnbook.red-bean.com/en/1.4/svn.advanced.externals.html One of the outstanding issues on SVN migration is the use of aliases for a checkout ('bioperl-all'); that would probably require setting svn:externals in some way. chris From hlapp at gmx.net Tue Feb 12 18:24:31 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 13 Feb 2008 08:24:31 +0900 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <47B1E12C.9010708@sendu.me.uk> References: <47B1E12C.9010708@sendu.me.uk> Message-ID: On Feb 13, 2008, at 3:10 AM, Sendu Bala wrote: > Speaking of which, is there a way a file (like, oh, I don't know, > bioperl-live/trunk/t/lib/BioperlTest.pm) can exist just once in SVN > but be seen in other locations (like bioperl-run/trunk/t/lib/ > BioperlTest.pm)? svn supposedly supports symlinks (though I haven't tested that myself yet), and since bioperl-live and bioperl-run are under the same svn root (aren't they?) you could make a symbolic link. The downside of this is that if someone only checks out bioperl-run the link would presumably be dangling. Though maybe not, not sure how super-smart svn is in this regard. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Tue Feb 12 21:10:23 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 13 Feb 2008 11:10:23 +0900 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <9424A11E-7541-442C-B53E-C791A2D8C6FB@uiuc.edu> References: <47B1E12C.9010708@sendu.me.uk> <9424A11E-7541-442C-B53E-C791A2D8C6FB@uiuc.edu> Message-ID: <66FBC084-74E4-458D-9F46-FCAD124AB8DE@gmx.net> On Feb 13, 2008, at 3:51 AM, Chris Fields wrote: > I think we should also try to get bioperl-db up to speed for the > BioSQL 1.0 release (at least Bio::Species-related issues). I agree. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From n.haigh at sheffield.ac.uk Wed Feb 13 03:46:02 2008 From: n.haigh at sheffield.ac.uk (Nathan S Haigh) Date: Wed, 13 Feb 2008 08:46:02 +0000 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <9424A11E-7541-442C-B53E-C791A2D8C6FB@uiuc.edu> References: <47B1E12C.9010708@sendu.me.uk> <9424A11E-7541-442C-B53E-C791A2D8C6FB@uiuc.edu> Message-ID: <47B2AE4A.3040509@sheffield.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Chris Fields wrote: > On Feb 12, 2008, at 12:10 PM, Sendu Bala wrote: > >> Chris Fields wrote: >>> * perl 5.10 compliance (appears to mostly work now) >>> * outstanding bugs (core only) >>> * POD and test coverage >> >> I'm fine with everything you said, but I'll just say that, at a >> minimum, the above is what needs to be done. > > I think we should also try to get bioperl-db up to speed for the BioSQL > 1.0 release (at least Bio::Species-related issues). > >> Someone needs to step up and organise that 3rd point, since it will >> require a lot of work. As I've already done work on the test suite, if >> no one else expresses an interest I might look into it myself. > > Jason and I discussed it off list (along with Nathan Haigh). We also > brought up the idea of smoke tests, which should pinpoint how stable > bioperl-live distributions are. Having those set up would pinpoint > modules we think need to stay in core or should go into a separate > 'dev/extras' distribution. We could test smoke/coverage/POD on those as > well. > I've moved away from Perl coding over the past 6-12 months but try to keep an eye on the BioPerl mailing list and chip in when I can. The last time the Devel::Cover module came up, it was lacking the ability to sort the coverage report table by each of the coverage metrics - which was a problem for us as we have so many modules and it was time consuming to find those with poor coverage. However, this feature were implemented in Devel::Cover 0.62, so it makes things slightly easier/neater. I'm not sure if the problem of failing tests still mess up the completion of the coverage report or not. >>> Now that SVN migration is complete >> >> Speaking of which, is there a way a file (like, oh, I don't know, >> bioperl-live/trunk/t/lib/BioperlTest.pm) can exist just once in SVN >> but be seen in other locations (like >> bioperl-run/trunk/t/lib/BioperlTest.pm)? Such that a commit to the >> version in bioperl-run also affects the version in bioperl-live? Or is >> there some appropriate other way to organise where cross-repository >> files are kept and dealt with? > See the subversion FAQs: http://subversion.tigris.org/faq.html#symlinks > Maybe using external definitions, though I haven't messed with it > personally. > > http://svnbook.red-bean.com/en/1.4/svn.advanced.externals.html > > One of the outstanding issues on SVN migration is the use of aliases for > a checkout ('bioperl-all'); that would probably require setting > svn:externals in some way. > > chris -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHsq5K9gTv6QYzVL4RAuJWAKCM/eEEXL5LqTsG/fGAmGIM6+dW9QCfe/6w T2a/dKg6d8HHXNXrOnSbdcs= =T8pz -----END PGP SIGNATURE----- From David.Messina at sbc.su.se Wed Feb 13 06:06:58 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 13 Feb 2008 12:06:58 +0100 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: Message-ID: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> I agree with Chris that the next BioPerl release should be 1.6. Shunting abandoned, experimental, and less-developed code to "bioperl-dev" would be extremely beneficial. As Chris stated, not only does it reduce the number of modules needing full test coverage, but the most important core modules are the ones most likely to have good test coverage already. And it would make BioPerl easier to grok for newcomers, too, which is always nice. I've made a first go at dividing the current bioperl core along these lines here: http://www.bioperl.org/wiki/Proposed_1.6_core_modules It's a very rough cut, so those with more familiarity with the bioperl corpus, please go in and rearrange as you see fit. Dave From n.haigh at sheffield.ac.uk Wed Feb 13 07:07:16 2008 From: n.haigh at sheffield.ac.uk (Nathan S Haigh) Date: Wed, 13 Feb 2008 12:07:16 +0000 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> Message-ID: <47B2DD74.5020503@sheffield.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I remember a conversion about how/if to split bioperl modules up in the past. If I remember rightly, there was talk of splitting all modules up and then creating a CPAN bundle for the core modules. I don't know if this make the admin really complex, but this allows people to install just those modules they require rather than the whole bioperl-core. For example, if I write a script or a module that wants to make use of BioPerl's SeqIO abilities, the end user has to download and install a load of modules that he/she may never use. Instead, it would be nicer to simply install SeqIO and it's dependecies. If I want to install all the BioPerl core, I can install a CPAN bundle. Just a thought. Nath Dave Messina wrote: > I agree with Chris that the next BioPerl release should be 1.6. > > Shunting abandoned, experimental, and less-developed code to "bioperl-dev" > would be extremely beneficial. As Chris stated, not only does it reduce the > number of modules needing full test coverage, but the most important core > modules are the ones most likely to have good test coverage already. And it > would make BioPerl easier to grok for newcomers, too, which is always nice. > > I've made a first go at dividing the current bioperl core along these lines > here: > http://www.bioperl.org/wiki/Proposed_1.6_core_modules > > It's a very rough cut, so those with more familiarity with the bioperl > corpus, please go in and rearrange as you see fit. > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHst109gTv6QYzVL4RAvmAAKCmJa5X0dvyPiQ6lADQ0BBk/tu3OQCg1cNC ZZVlnTSKc6dcCbYJ5JgUGjA= =bvUu -----END PGP SIGNATURE----- From bosborne11 at verizon.net Wed Feb 13 10:08:36 2008 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 13 Feb 2008 10:08:36 -0500 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> Message-ID: Dave, A few of those modules are supposed to be removed in 1.6, according to the notes in the DEPRECATED file. I've marked them. Brian O. On Feb 13, 2008, at 6:06 AM, Dave Messina wrote: > I've made a first go at dividing the current bioperl core along > these lines > here: > http://www.bioperl.org/wiki/Proposed_1.6_core_modules From cjfields at uiuc.edu Wed Feb 13 11:58:03 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 13 Feb 2008 10:58:03 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> Message-ID: I've added/modified the page as well; moved Bio::FeatureIO and Bio::SeqFeature::Annotated over to the bioperl-dev for now, along with Bio::Assembly and Bio::Restriction. We'll have to test out removing those modules to see what blows up. chris On Feb 13, 2008, at 9:08 AM, Brian Osborne wrote: > Dave, > > A few of those modules are supposed to be removed in 1.6, according > to the notes in the DEPRECATED file. I've marked them. > > Brian O. > > > On Feb 13, 2008, at 6:06 AM, Dave Messina wrote: > >> I've made a first go at dividing the current bioperl core along >> these lines >> here: >> http://www.bioperl.org/wiki/Proposed_1.6_core_modules > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Feb 13 14:11:34 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 13 Feb 2008 13:11:34 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> Message-ID: <8C98F03E-0424-4383-A08C-F227745DBEF6@uiuc.edu> On Feb 13, 2008, at 12:32 PM, Brian Osborne wrote: > Chris, > > You should be careful about the names of these packages. For > example, Bio::Biblio and Bio::Restriction are not "in development" > as the term bioperl-dev implies. They're tried and true. And there > may be sets of modules that are experimental in "bioperl-dev", of > course. Is it possible to have 2 packages, "dev" and "tools"? Or > something along those lines? > > Calling things by the wrong names leads to confusion, witness the > Bioperl newcomers who would install an antiquated version 1.4 > because it was labelled 'stable'. > > BIO I agree the name 'dev' is misleading. 'tools' or 'extras' sounds better, maybe using 'dev' for experimental implementations, such as Jason's SeqFeature::Slim or my SeqIO driver/handler modules. The problem with the two namespaces you mention is lack of maintenance and documentation, though I agree they're stable (so maybe in those cases maintenance isn't an issue). We do need to clean up documentation issues with those classes as well as many more (mine included); POD/test coverage will help out there. chris From bosborne11 at verizon.net Wed Feb 13 13:32:46 2008 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 13 Feb 2008 13:32:46 -0500 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> Message-ID: <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> Chris, You should be careful about the names of these packages. For example, Bio::Biblio and Bio::Restriction are not "in development" as the term bioperl-dev implies. They're tried and true. And there may be sets of modules that are experimental in "bioperl-dev", of course. Is it possible to have 2 packages, "dev" and "tools"? Or something along those lines? Calling things by the wrong names leads to confusion, witness the Bioperl newcomers who would install an antiquated version 1.4 because it was labelled 'stable'. BIO On Feb 13, 2008, at 11:58 AM, Chris Fields wrote: > I've added/modified the page as well; moved Bio::FeatureIO and > Bio::SeqFeature::Annotated over to the bioperl-dev for now, along > with Bio::Assembly and Bio::Restriction. We'll have to test out > removing those modules to see what blows up. From David.Messina at sbc.su.se Wed Feb 13 14:55:26 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 13 Feb 2008 20:55:26 +0100 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> Message-ID: <628aabb70802131155q73674b72qad547c55c5443e2d@mail.gmail.com> Great, thanks guys. From bix at sendu.me.uk Wed Feb 13 15:19:01 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 13 Feb 2008 20:19:01 +0000 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> Message-ID: <47B350B5.3060501@sendu.me.uk> Brian Osborne wrote: > You should be careful about the names of these packages. For example, > Bio::Biblio and Bio::Restriction are not "in development" as the term > bioperl-dev implies. They're tried and true. And there may be sets of > modules that are experimental in "bioperl-dev", of course. Is it > possible to have 2 packages, "dev" and "tools"? Or something along those > lines? > > Calling things by the wrong names leads to confusion, witness the > Bioperl newcomers who would install an antiquated version 1.4 because it > was labelled 'stable'. On the topic of confusion, I think 'bioperl-tools' is a very bad choice since we have Bio::Tools. Why would Bio::Microarray (for example) be in there? (And then we have Bio::Microarray::Tools ...) Can all of the non Bio::Tools modules currently in the bioperl-tools section of the wiki page be annotated as to why they're there and not in core? Then maybe we can come up with a better name to categorize them all under. Perhaps we could also annotate the things in core to justify why they should be in core? Is anyone good at creating maps so we can easily see what Bioperl modules are most used (by other Bioperl modules)? Or is the split intended to be 'core' == "anything and everything that was in 1.4", '????' == "everything else"? In which case, what's a good name for "modules created after 1.4"? 'crust'? ;) From cjfields at uiuc.edu Wed Feb 13 16:05:16 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 13 Feb 2008 15:05:16 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <47B350B5.3060501@sendu.me.uk> References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> <47B350B5.3060501@sendu.me.uk> Message-ID: <477CF001-FF35-4A08-A360-C9FA2031E353@uiuc.edu> On Feb 13, 2008, at 2:19 PM, Sendu Bala wrote: > Brian Osborne wrote: >> You should be careful about the names of these packages. For >> example, Bio::Biblio and Bio::Restriction are not "in development" >> as the term bioperl-dev implies. They're tried and true. And there >> may be sets of modules that are experimental in "bioperl-dev", of >> course. Is it possible to have 2 packages, "dev" and "tools"? Or >> something along those lines? >> Calling things by the wrong names leads to confusion, witness the >> Bioperl newcomers who would install an antiquated version 1.4 >> because it was labelled 'stable'. > > On the topic of confusion, I think 'bioperl-tools' is a very bad > choice since we have Bio::Tools. Why would Bio::Microarray (for > example) be in there? (And then we have Bio::Microarray::Tools ...) > > Can all of the non Bio::Tools modules currently in the bioperl-tools > section of the wiki page be annotated as to why they're there and > not in core? Then maybe we can come up with a better name to > categorize them all under. > > Perhaps we could also annotate the things in core to justify why > they should be in core? Is anyone good at creating maps so we can > easily see what Bioperl modules are most used (by other Bioperl > modules)? Frankly, it will be hard for a handful of people (Dave, Brian, and I) to justify the existence for every bioperl module or it's placement in bioperl-?, but at least we have a start on it. The page is open for editing by anyone (Dave, Brian, and I have already added quite a bit). There is also a discussion page to add to, which is a good place for proposals and to sketch out ideas. I think we should take some time on this to stew over the options available, maybe a month or two, and set some deadline for starting up. > Or is the split intended to be 'core' == "anything and everything > that was in 1.4", '????' == "everything else"? In which case, what's > a good name for "modules created after 1.4"? 'crust'? ;) I personally take the extreme view of having a very tight core with just the basic sequence, feature, alignment, and annotation classes (just for maintenance sake); everything else just uses those base classes anyway, so I don't necessarily consider them core. I don't think paring down to that level is feasible for a 1.6 release, but moving some of the unmaintained cruft out into a separate installation would be a good start. chris From pengchy at yahoo.com.cn Wed Feb 13 20:26:21 2008 From: pengchy at yahoo.com.cn (Åô³Ì) Date: 14 Feb 2008 01:26:21 -0000 Subject: Åô³ÌÑûÇëÄú¼ÓÈëÈô±ÈÁÚ Message-ID: <20080214012621.30230.qmail@zorpia.com> Hi bioperl! Your friend ???? from ????, just invited you to online photo albums and journals at Zorpia.com. So what is Zorpia? It is an online community that allows you to upload unlimited amount of photos, write journals and make friends. We also have a variety of skins in store for you so that you can customize your homepage freely. Join now for free! Please click the following link to join Zorpia: http://cn.signup.zorpia.com/signup?invitation_key=200802c0d8af2b64f8ef03d6417e4ab4&referral=pengchy This message was delivered with the ????'s initiation. If you wish to discontinue receiving invitations from us, please click the following link: http://cn.signup.zorpia.com/email/optout/bioperl-l at lists.open-bio.org From hangsyin at gmail.com Wed Feb 13 22:10:54 2008 From: hangsyin at gmail.com (Hang) Date: Wed, 13 Feb 2008 19:10:54 -0800 (PST) Subject: [Bioperl-l] Re trieve ID tag in GFF3 Message-ID: <15473188.post@talk.nabble.com> Dear All, I wonder what method I should call to retrieve values of ID tags in GFF3 format. For example, a GFF3 entry in the database is like this: 4 FlyBase gene 24068 25621 . + . ID=FBgn0040037;Name=ABC;Ontology_term=... I'd like to retrieve the scalar value 'FBgn0040037' to compare with another value. Please complete the code below: use Bio::DB::SeqFeature::Store; my $db = Bio::DB::SeqFeature::Store->new(-adaptor => 'DBI::mysql', -dsn => 'dbi:mysql:XXX_gff', -user => 'XXX', -pass => 'XXX')|| die "Database open failed"; ??? Thanks alot! Hang -- View this message in context: http://www.nabble.com/Retrieve-ID-tag-in-GFF3-tp15473188p15473188.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From cjfields at uiuc.edu Thu Feb 14 15:36:27 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 14 Feb 2008 14:36:27 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <47B350B5.3060501@sendu.me.uk> References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> <47B350B5.3060501@sendu.me.uk> Message-ID: <3C0A6ADA-AABC-4D7A-B858-CEB8E87AFDDE@uiuc.edu> On Feb 13, 2008, at 2:19 PM, Sendu Bala wrote: > Brian Osborne wrote: >> You should be careful about the names of these packages. For >> example, Bio::Biblio and Bio::Restriction are not "in development" >> as the term bioperl-dev implies. They're tried and true. And there >> may be sets of modules that are experimental in "bioperl-dev", of >> course. Is it possible to have 2 packages, "dev" and "tools"? Or >> something along those lines? >> Calling things by the wrong names leads to confusion, witness the >> Bioperl newcomers who would install an antiquated version 1.4 >> because it was labelled 'stable'. > > On the topic of confusion, I think 'bioperl-tools' is a very bad > choice since we have Bio::Tools. Why would Bio::Microarray (for > example) be in there? (And then we have Bio::Microarray::Tools ...) > > Can all of the non Bio::Tools modules currently in the bioperl-tools > section of the wiki page be annotated as to why they're there and > not in core? Then maybe we can come up with a better name to > categorize them all under. > > Perhaps we could also annotate the things in core to justify why > they should be in core? Is anyone good at creating maps so we can > easily see what Bioperl modules are most used (by other Bioperl > modules)? > > > Or is the split intended to be 'core' == "anything and everything > that was in 1.4", '????' == "everything else"? In which case, what's > a good name for "modules created after 1.4"? 'crust'? ;) I added a modified proposal to the Talk page for the Release: http://www.bioperl.org/wiki/Talk:Proposed_1.6_core_modules I'm pretty flexible on any of that; it's a proposal only and I think some of it may be wrongheaded, but hey, I'm willing to take a few rotten tomatoes. The key issue is we should try to work out what we mean by 'core' or the core library. I have a rather extreme view of it as being the bare essentials without external, non-perl core dependencies (only SeqI/PrimarySeqI, AlignI, AnnotationI, SeqFeatureI and required modules for those classes) but I'm sure others would lump in parsers, DB functionality, etc. I basically suggest placing those (and any stable but potentially non-core code) in a 'bioperl-main', with any unstable or untested code going into a 'bioperl-unstable'. In essence, bioperl-main would require core and resemble a stable release; bioperl-unstable would require bioperl-main (and core) and resemble a dev release. Not sure how versioning would go or if this is a viable option at all, but it's worth discussing. chris From aaron.j.mackey at gsk.com Fri Feb 15 13:06:58 2008 From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com) Date: Fri, 15 Feb 2008 13:06:58 -0500 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <47B350B5.3060501@sendu.me.uk> Message-ID: > Or is the split intended to be 'core' == "anything and everything that > was in 1.4", '????' == "everything else"? In which case, what's a good > name for "modules created after 1.4"? 'crust'? ;) Nah, "icing". a module "use" map might be very useful to help identify "core" vs. other layers of mantle/crust/icing. http://www.perlmonks.org/?node_id=87329 http://search.cpan.org/src/NEILB/pmusage-1.2/ Some more serious alternatives to "bioperl-dev" and "-tools" might be: "-accessory" or "-optional" or "-other" or "-addons", etc. -Aaron From lincoln.stein at gmail.com Fri Feb 15 15:17:31 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Fri, 15 Feb 2008 15:17:31 -0500 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: Message-ID: <6dce9a0b0802151217t59e41ccq2bcb10c68b8aede1@mail.gmail.com> > * perl 5.10 compliance (appears to mostly work now) > * GFF/GFF3 compliance I've been doing a lot of work on this recently. I think it's much improved. No problems with 5.10 for the modules that I use frequently. Lincoln > > * BioSQL 1.0 compliance (impending) > * POD and test coverage > * smoke tests for bioperl-live/db/etc. > * smaller, more focused core (less dependencies) > * separating out experimental or poorly maintained modules into a > separate 'bioperl-dev' distribution > * bioperl-db issues with Bio::Species changes > * module maintenance > * sequence format roundtripping (i.e. genbank, embl, swissetc) > * additional sequence parsers (insdcxml, etc) > * enhancement requests in bugzilla (Albert?) > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From cjfields at uiuc.edu Fri Feb 15 16:43:42 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 15 Feb 2008 15:43:42 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <6dce9a0b0802151217t59e41ccq2bcb10c68b8aede1@mail.gmail.com> References: <6dce9a0b0802151217t59e41ccq2bcb10c68b8aede1@mail.gmail.com> Message-ID: On Feb 15, 2008, at 2:17 PM, Lincoln Stein wrote: >> * perl 5.10 compliance (appears to mostly work now) >> * GFF/GFF3 compliance > > > I've been doing a lot of work on this recently. I think it's much > improved. > No problems with 5.10 for the modules that I use frequently. > > Lincoln I think bioperl works now for perl 5.10. The only significant issue we ran into were problems with Bio::SeqIO::entrezgene. The parser looped and created a pseudohash under some conditions, which threw all sorts of errors with 5.8. Stefan and I fixed that one in Subversion. There were some odd Data::Dumper-related messages popping up with 'perl Build.PL' using perl 5.10; not sure what's going on there, but it appears harmless: Encountered CODE ref, using dummy placeholder at /opt/perl/lib/5.10.0/ darwin-2level/Data/Dumper.pm line 190. chris From cjfields at uiuc.edu Fri Feb 15 16:49:33 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 15 Feb 2008 15:49:33 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: Message-ID: On Feb 15, 2008, at 12:06 PM, aaron.j.mackey at gsk.com wrote: >> Or is the split intended to be 'core' == "anything and everything >> that >> was in 1.4", '????' == "everything else"? In which case, what's a >> good >> name for "modules created after 1.4"? 'crust'? ;) > > Nah, "icing". > > a module "use" map might be very useful to help identify "core" vs. > other > layers of mantle/crust/icing. > > http://www.perlmonks.org/?node_id=87329 > http://search.cpan.org/src/NEILB/pmusage-1.2/ > > Some more serious alternatives to "bioperl-dev" and "-tools" might be: > "-accessory" or "-optional" or "-other" or "-addons", etc. > > -Aaron 'bioperl-extras' (Ricky Gervais fan myself) chris From hlapp at gmx.net Fri Feb 15 17:14:10 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 16 Feb 2008 07:14:10 +0900 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: Message-ID: <82E17B18-32D9-4858-9245-EEF9D143DA11@gmx.net> On Feb 16, 2008, at 6:49 AM, Chris Fields wrote: >> >> Some more serious alternatives to "bioperl-dev" and "-tools" might >> be: >> "-accessory" or "-optional" or "-other" or "-addons", etc. >> >> -Aaron > > 'bioperl-extras' (Ricky Gervais fan myself) > Actually I like bioperl-opt - sounds somehow reminiscent of the /opt directory we all know (often containing the best things :) -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Sun Feb 17 09:07:20 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 17 Feb 2008 08:07:20 -0600 Subject: [Bioperl-l] [Bioperl-guts-l] [14510] bioperl-live/trunk/Bio/SeqIO/swiss.pm: GN line output now follows the new format. In-Reply-To: <200802171000.m1HA0oGq003135@dev.open-bio.org> References: <200802171000.m1HA0oGq003135@dev.open-bio.org> Message-ID: Heikki, See bug 1825: http://bugzilla.open-bio.org/show_bug.cgi?id=1825 Hilmar's final comments about restructuring Bio::Annotation::StructuredValue using Data::Stag should work. chris On Feb 17, 2008, at 4:00 AM, Heikki Lehvaslaiho wrote: > Revision: 14510 > Author: heikki > Date: 2008-02-17 05:00:50 -0500 (Sun, 17 Feb 2008) > > Log Message: > ----------- > GN line output now follows the new format. BioPerl would need new > objects to store all infomation so for now only the official name > (Name=) and synonym categories are kept. ORFNames and > OrderedLocusNames are treated as synonyms. > > Modified Paths: > -------------- > bioperl-live/trunk/Bio/SeqIO/swiss.pm > > Modified: bioperl-live/trunk/Bio/SeqIO/swiss.pm > =================================================================== > --- bioperl-live/trunk/Bio/SeqIO/swiss.pm 2008-02-17 09:48:07 UTC > (rev 14509) > +++ bioperl-live/trunk/Bio/SeqIO/swiss.pm 2008-02-17 10:00:50 UTC > (rev 14510) > @@ -494,16 +494,13 @@ > #Definition lines > $self->_write_line_swissprot_regex("DE ","DE ",$seq- > >desc(),"\\s\+\|\$",$LINE_LENGTH); > > - #Gene name > - if ((my @genes = $seq->annotation- > >get_Annotations('gene_name') ) ) { > - $self->_print("GN ", > - join(' OR ', > - map { > - $_->isa("Bio::Annotation::StructuredValue") ? > - $_->value(-joins => [" AND ", " OR "]) : > - $_->value(); > - } @genes), > - ".\n"); > + #Gene name; print out new format but only two categories: Name > and Synonyms > + if ( my @genes = $seq->annotation- > >get_Annotations('gene_name') ) { > + my @gene_names = map { $_->get_all_values} @genes; > + my $gn_string = 'Name='. shift(@gene_names). ';'; > + $gn_string .= ' Synonyms='. join(', ', @gene_names). ";" if > scalar @gene_names; > + $self->_write_line_swissprot_regex("GN ","GN ", > $gn_string,"\\s\+\|\$",$LINE_LENGTH); > + > } > > # Organism lines > @@ -1267,7 +1264,6 @@ > } > > my $subl = $length - (length $pre1) -1 ; > - my @lines; > > my $first_line = 1; > while($line =~ m/(.{1,$subl})($regex)/g) { > > > _______________________________________________ > Bioperl-guts-l mailing list > Bioperl-guts-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From heikki at sanbi.ac.za Mon Feb 18 03:12:11 2008 From: heikki at sanbi.ac.za (Heikki Lehvaslaiho) Date: Mon, 18 Feb 2008 10:12:11 +0200 Subject: [Bioperl-l] [Bioperl-guts-l] [14510] bioperl-live/trunk/Bio/SeqIO/swiss.pm: GN line output now follows the new format. In-Reply-To: References: <200802171000.m1HA0oGq003135@dev.open-bio.org> Message-ID: <200802181012.11295.heikki@sanbi.ac.za> Thanks for pointing this out to me. Looks like I've solved the first level: "Problem #1 is to have all the value tokens available from the created object, regardless of their tags." Anybody want to go on to the next level and code in the complete representation of the GN line? -Heikki On Sunday 17 February 2008 16:07:20 Chris Fields wrote: > Heikki, > > See bug 1825: > > http://bugzilla.open-bio.org/show_bug.cgi?id=1825 > > Hilmar's final comments about restructuring > Bio::Annotation::StructuredValue using Data::Stag should work. > > chris > > On Feb 17, 2008, at 4:00 AM, Heikki Lehvaslaiho wrote: > > Revision: 14510 > > Author: heikki > > Date: 2008-02-17 05:00:50 -0500 (Sun, 17 Feb 2008) > > > > Log Message: > > ----------- > > GN line output now follows the new format. BioPerl would need new > > objects to store all infomation so for now only the official name > > (Name=) and synonym categories are kept. ORFNames and > > OrderedLocusNames are treated as synonyms. > > > > Modified Paths: > > -------------- > > bioperl-live/trunk/Bio/SeqIO/swiss.pm > > > > Modified: bioperl-live/trunk/Bio/SeqIO/swiss.pm > > =================================================================== > > --- bioperl-live/trunk/Bio/SeqIO/swiss.pm 2008-02-17 09:48:07 UTC > > (rev 14509) > > +++ bioperl-live/trunk/Bio/SeqIO/swiss.pm 2008-02-17 10:00:50 UTC > > (rev 14510) > > @@ -494,16 +494,13 @@ > > #Definition lines > > $self->_write_line_swissprot_regex("DE ","DE ",$seq- > > > > >desc(),"\\s\+\|\$",$LINE_LENGTH); > > > > - #Gene name > > - if ((my @genes = $seq->annotation- > > > > >get_Annotations('gene_name') ) ) { > > > > - $self->_print("GN ", > > - join(' OR ', > > - map { > > - $_->isa("Bio::Annotation::StructuredValue") ? > > - $_->value(-joins => [" AND ", " OR "]) : > > - $_->value(); > > - } @genes), > > - ".\n"); > > + #Gene name; print out new format but only two categories: Name > > and Synonyms > > + if ( my @genes = $seq->annotation- > > > > >get_Annotations('gene_name') ) { > > > > + my @gene_names = map { $_->get_all_values} @genes; > > + my $gn_string = 'Name='. shift(@gene_names). ';'; > > + $gn_string .= ' Synonyms='. join(', ', @gene_names). ";" if > > scalar @gene_names; > > + $self->_write_line_swissprot_regex("GN ","GN ", > > $gn_string,"\\s\+\|\$",$LINE_LENGTH); > > + > > } > > > > # Organism lines > > @@ -1267,7 +1264,6 @@ > > } > > > > my $subl = $length - (length $pre1) -1 ; > > - my @lines; > > > > my $first_line = 1; > > while($line =~ m/(.{1,$subl})($regex)/g) { > > > > > > _______________________________________________ > > Bioperl-guts-l mailing list > > Bioperl-guts-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za _/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho _/ _/ _/ SANBI, South African National Bioinformatics Institute _/ _/ _/ University of Western Cape, South Africa _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 ___ _/_/_/_/_/________________________________________________________ From cjfields at uiuc.edu Mon Feb 18 13:56:32 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 18 Feb 2008 12:56:32 -0600 Subject: [Bioperl-l] [Bioperl-guts-l] [14510] bioperl-live/trunk/Bio/SeqIO/swiss.pm: GN line output now follows the new format. In-Reply-To: <200802181012.11295.heikki@sanbi.ac.za> References: <200802171000.m1HA0oGq003135@dev.open-bio.org> <200802181012.11295.heikki@sanbi.ac.za> Message-ID: <670A1145-D1A6-4245-A621-750E0F4FFB6E@uiuc.edu> I may try working on the next. I had indicated that I would do this in the past, just never got around to it; time is the enemy of us all. chris On Feb 18, 2008, at 2:12 AM, Heikki Lehvaslaiho wrote: > Thanks for pointing this out to me. Looks like I've solved the first > level: > > "Problem #1 is to have all the value tokens > available from the created object, regardless of their tags." > > Anybody want to go on to the next level and code in the complete > representation of the GN line? > > -Heikki > > > On Sunday 17 February 2008 16:07:20 Chris Fields wrote: >> Heikki, >> >> See bug 1825: >> >> http://bugzilla.open-bio.org/show_bug.cgi?id=1825 >> >> Hilmar's final comments about restructuring >> Bio::Annotation::StructuredValue using Data::Stag should work. >> >> chris >> >> On Feb 17, 2008, at 4:00 AM, Heikki Lehvaslaiho wrote: >>> Revision: 14510 >>> Author: heikki >>> Date: 2008-02-17 05:00:50 -0500 (Sun, 17 Feb 2008) >>> >>> Log Message: >>> ----------- >>> GN line output now follows the new format. BioPerl would need new >>> objects to store all infomation so for now only the official name >>> (Name=) and synonym categories are kept. ORFNames and >>> OrderedLocusNames are treated as synonyms. >>> >>> Modified Paths: >>> -------------- >>> bioperl-live/trunk/Bio/SeqIO/swiss.pm >>> >>> Modified: bioperl-live/trunk/Bio/SeqIO/swiss.pm >>> =================================================================== >>> --- bioperl-live/trunk/Bio/SeqIO/swiss.pm 2008-02-17 09:48:07 UTC >>> (rev 14509) >>> +++ bioperl-live/trunk/Bio/SeqIO/swiss.pm 2008-02-17 10:00:50 UTC >>> (rev 14510) >>> @@ -494,16 +494,13 @@ >>> #Definition lines >>> $self->_write_line_swissprot_regex("DE ","DE ",$seq- >>> >>>> desc(),"\\s\+\|\$",$LINE_LENGTH); >>> >>> - #Gene name >>> - if ((my @genes = $seq->annotation- >>> >>>> get_Annotations('gene_name') ) ) { >>> >>> - $self->_print("GN ", >>> - join(' OR ', >>> - map { >>> - $_->isa("Bio::Annotation::StructuredValue") ? >>> - $_->value(-joins => [" AND ", " OR "]) : >>> - $_->value(); >>> - } @genes), >>> - ".\n"); >>> + #Gene name; print out new format but only two categories: Name >>> and Synonyms >>> + if ( my @genes = $seq->annotation- >>> >>>> get_Annotations('gene_name') ) { >>> >>> + my @gene_names = map { $_->get_all_values} @genes; >>> + my $gn_string = 'Name='. shift(@gene_names). ';'; >>> + $gn_string .= ' Synonyms='. join(', ', @gene_names). ";" if >>> scalar @gene_names; >>> + $self->_write_line_swissprot_regex("GN ","GN ", >>> $gn_string,"\\s\+\|\$",$LINE_LENGTH); >>> + >>> } >>> >>> # Organism lines >>> @@ -1267,7 +1264,6 @@ >>> } >>> >>> my $subl = $length - (length $pre1) -1 ; >>> - my @lines; >>> >>> my $first_line = 1; >>> while($line =~ m/(.{1,$subl})($regex)/g) { >>> >>> >>> _______________________________________________ >>> Bioperl-guts-l mailing list >>> Bioperl-guts-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l >> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > -- > ______ _/ _/_____________________________________________________ > _/ _/ > _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za > _/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho > _/ _/ _/ SANBI, South African National Bioinformatics Institute > _/ _/ _/ University of Western Cape, South Africa > _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 > ___ _/_/_/_/_/________________________________________________________ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From hlapp at gmx.net Mon Feb 18 17:14:33 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 18 Feb 2008 17:14:33 -0500 Subject: [Bioperl-l] BOSC 2008? In-Reply-To: <9C6A22B1-9E84-4F17-8459-CBBDCB2110D4@uiuc.edu> References: <1182EAB9-7A75-498F-B91B-C14771DFD607@uiuc.edu> <628aabb70802061317n2f0d1103w9367346166bf8c3f@mail.gmail.com> <9C6A22B1-9E84-4F17-8459-CBBDCB2110D4@uiuc.edu> Message-ID: As an aside, I've posted the (so far "unofficial") update on the news.open-bio.org blog. -hilmar On Feb 6, 2008, at 4:22 PM, Chris Fields wrote: > Yep. I found this out earlier from Darin London. Just trying to > plan for it ahead of time! > > chris > > On Feb 6, 2008, at 3:17 PM, Dave Messina wrote: > >> Hey Chris, >> >> Isn't it usually in conjunction with ISMB (which is Toronto >> 7/19-23 this year)? >> >> > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From johan.nilsson at sh.se Tue Feb 19 09:42:52 2008 From: johan.nilsson at sh.se (Johan Nilsson) Date: Tue, 19 Feb 2008 15:42:52 +0100 Subject: [Bioperl-l] Dumping a MSA from BLAST results Message-ID: <47BAEAEC.5080203@sh.se> Hello, I have a question regarding the conversion from a Blast search result (PSI-blast using blastpgp, to be more exact) to a multiple sequence alignment file. I'm running the Bio::Tools::Run::StandAloneBlast and I retrieve the HSPs from the resulting Bio::Search::Hit::HitI objects. I have no problems obtaining each HSP alignment using $hit->get_aln. However, rather than dumping many local alignments, I would like to write a single result file where the HSPs are interleaved. I guess this shouldn't be too hard, but nevertheless I haven't found out how to do this in a simple way. Any suggestions would be highly appreciated! Best Regards /Johan Nilsson From jason at bioperl.org Tue Feb 19 11:17:32 2008 From: jason at bioperl.org (Jason Stajich) Date: Tue, 19 Feb 2008 08:17:32 -0800 Subject: [Bioperl-l] Dumping a MSA from BLAST results In-Reply-To: <47BAEAEC.5080203@sh.se> References: <47BAEAEC.5080203@sh.se> Message-ID: <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> All the individual pairwise alignments won't necessarily be an alignment of the same region and the gap insertions can be different in each instance of the query sequence that is participating in the pairwise alns so it won't fit into an MSA. It makes more sense to extract the aligned part of the hit sequences identified and a subsequence of the query which is the min and max region aligned. Run this through a MSA program. -jason On Feb 19, 2008, at 6:42 AM, Johan Nilsson wrote: > Hello, > > I have a question regarding the conversion from a Blast search > result (PSI-blast using blastpgp, to be more exact) to a multiple > sequence alignment file. I'm running the > Bio::Tools::Run::StandAloneBlast and I retrieve the HSPs from the > resulting Bio::Search::Hit::HitI objects. I have no problems > obtaining each HSP alignment using $hit->get_aln. However, rather > than dumping many local alignments, I would like to write a single > result file where the HSPs are interleaved. > > I guess this shouldn't be too hard, but nevertheless I haven't > found out how to do this in a simple way. Any suggestions would be > highly appreciated! > > Best Regards > /Johan Nilsson > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at uiuc.edu Tue Feb 19 12:18:34 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 19 Feb 2008 11:18:34 -0600 Subject: [Bioperl-l] Dumping a MSA from BLAST results In-Reply-To: <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> Message-ID: One could use an alternative blastall output format (like -m1 to -m6), which give various anchored alignments. None of these are parsed via bioperl as far as I know; might be worth getting something up and running if there is enough interest in it. chris PS. Here's example output using 'blastall -p blastp -i test2.faa -d CP000560.faa -m6', which is query-anchored, flat, blunt ends: BLASTP 2.2.16 [Mar-25-2007] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= gi|1373160|gb|AAB57770.1| PyrR (173 letters) Database: CP000560.faa 3693 sequences; 1,147,568 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gb|ABS73893.1| PyrR [Bacillus amyloliquefaciens FZB42] 322 1e-89 gb|ABS75590.1| ComFC [Bacillus amyloliquefaciens FZB42] 37 6e-04 gb|ABS72500.1| Prs [Bacillus amyloliquefaciens FZB42] 28 0.22 gb|ABS72703.1| YcdA [Bacillus amyloliquefaciens FZB42] 27 0.49 gb|ABS74832.1| Apt [Bacillus amyloliquefaciens FZB42] 26 1.1 gb|ABS75734.1| Upp [Bacillus amyloliquefaciens FZB42] 26 1.4 gb|ABS74081.1| NrdE [Bacillus amyloliquefaciens FZB42] 25 1.9 gb|ABS76054.1| RocD [Bacillus amyloliquefaciens FZB42] 24 4.1 gb|ABS74744.1| Gpr [Bacillus amyloliquefaciens FZB42] 24 5.4 gb|ABS74336.1| UvrX [Bacillus amyloliquefaciens FZB42] 23 7.1 gb|ABS74825.1| YrvM [Bacillus amyloliquefaciens FZB42] 23 9.2 gb|ABS72555.1| RpoB [Bacillus amyloliquefaciens FZB42] 23 9.2 1_0 1 MNQKAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKR--- LAER---- 53 ABS73893 1 MNQKAVILDEQAIRRALTRIAHEMIERNKGMNDCILVGIKTRGIYLAKR--- LAER---- 53 ABS75590 116 ------------------------------- NTHTLIPIPLSGERLAERGFNQSEL---- 140 ABS72500 164 ----------------------------KDLKDIVIVSPDHGGVTRARK--- LADR---- 188 ABS72703 55 ----------------------------------------------ALK--- VTVT---- 61 ABS74832 ------------------------------------------------------------ ABS75734 ------------------------------------------------------------ ABS74081 ------------------------------------------------------------ ABS74081 502 -----------------------------------------RSAELAKE--- KGET---- 513 ABS76054 305 ------VLEEEGLAERSLQLGRYFKEELEKIDNPIIKDVRGRGLFIGVE--- LTEAARPY 355 ABS74744 43 -------------------------ERDKG-------GIKVRTVDITKE--- GAEL---- 63 ABS74336 ------------------------------------------------------------ ABS74825 ------------------------------------------------------------ ABS72555 ------------------------------------------------------------ 1_0 54 IEQIEGNPVTVGEIDITLYRDDLSKKTSNDEPLVKGADIP-V--DITD--- QKVILVDDV 107 ABS73893 54 IEQIEGNPVTVGEIDITLYRDDLTKKTSNEEPLVKGADIP-A--DITD--- QKVIVVDDV 107 ABS75590 141 LASLLGMPVISPLIRLNNEKQSKKSKTDRLSAEKKFSAAE-N--SATG--- MNVILIDDI 194 ABS72500 189 LKA----PIAI---------IDKRRPRPNE---VEVMNIV-G--NVEG--- KTAILIDDI 226 ABS72703 62 VKNTGKDPLTVKSSDFSLYQDD--AKTAK-----------------TD--- KEDLMQSGT 99 ABS74832 112 --------------------------------------------------- QRVLITDDL 120 ABS75734 100 ---------------VGLYRDPETLK-----PVEYYVKLP-S--DVEE--- REFIVVDPM 133 ABS74081 386 -----------------LQASQVSAYTDYDEEDEIGLDIS-C--NLGS--- LNILNVMKH 422 ABS74081 514 FEHYEGSTYATGEYFNKYIEKEFSPAYEKIAALFEGMHIP-TIEDWKE--- LKAFVAENG 569 ABS76054 356 CEKLKGEGLLCKETHDTVIR---------------------------------------- 375 ABS74744 64 SGKKQGRYVTIEAQGVREHDSDMQEKVT-------------------------------- 91 ABS74336 109 ----------------------------------KTIDLP-T-- NITMDIYRYCLILFDK 131 ABS74825 199 ------------------- REDVRKEVGNDEAKIRKAQMP-------------------- 219 ABS72555 1090 -----GAAYTLQEI-LTVKSDDVVGRVKTYEAIVKGDNVPEP--GVPE--- SFKVLIKEL 1138 1_0 108 LYTGRTVRAGMDALVDVGRPSSIQLAVLVDRGHRELPIRADYIGKNIPTSKSEKVMVQLD 167 ABS73893 108 LYTGRTVRAAMDALVDVGRPSSIQLAVLVDRGHRELPIRADYIGKNIPTSKAEKVMVQLS 167 ABS75590 195 YTTGATLHQAAEVLLTAGKASSVSSFTLI------------------------------- 223 ABS72500 227 IDTAGTITLAANALVENG------------------------------------------ 244 ABS72703 100 LHAGKTVTGNLYFTADEGK----------------------------------------- 118 ABS74832 121 LATGGTIEATIKLVEELG------------------------------------------ 138 ABS75734 134 LATGGSAVEAINSL---------------------------------------------- 147 ABS74081 423 KSIERTVKLATDSLTHVSETTDIRNAPAVRRANKAM------------------------ 458 ABS74081 570 MY---------------------------------------------------------- 571 ABS76054 374 ------------------------------------------------------------ 375 ABS74744 90 ------------------------------------------------------------ 91 ABS74336 132 FYTGKTVRS--------------------------------------------------- 140 ABS74825 218 ------------------------------------------------------------ 219 ABS72555 1139 ------ QSLGMDVKILSGDEEEIEMRDLED------------------------------ 1162 1_0 168 EVDQND 173 ABS73893 168 EVDQTD 173 ABS75590 222 ------ 223 ABS72500 243 ------ 244 ABS72703 117 ------ 118 ABS74832 137 ------ 138 ABS75734 146 ------ 147 ABS74081 457 ------ 458 ABS74081 570 ------ 571 ABS76054 374 ------ 375 ABS74744 90 ------ 91 ABS74336 139 ------ 140 ABS74825 218 ------ 219 ABS72555 1161 ------ 1162 On Feb 19, 2008, at 10:17 AM, Jason Stajich wrote: > All the individual pairwise alignments won't necessarily be an > alignment of the same region and the gap insertions can be different > in each instance of the query sequence that is participating in the > pairwise alns so it won't fit into an MSA. > > It makes more sense to extract the aligned part of the hit sequences > identified and a subsequence of the query which is the min and max > region aligned. Run this through a MSA program. > > -jason > On Feb 19, 2008, at 6:42 AM, Johan Nilsson wrote: > >> Hello, >> >> I have a question regarding the conversion from a Blast search >> result (PSI-blast using blastpgp, to be more exact) to a multiple >> sequence alignment file. I'm running the >> Bio::Tools::Run::StandAloneBlast and I retrieve the HSPs from the >> resulting Bio::Search::Hit::HitI objects. I have no problems >> obtaining each HSP alignment using $hit->get_aln. However, rather >> than dumping many local alignments, I would like to write a single >> result file where the HSPs are interleaved. >> >> I guess this shouldn't be too hard, but nevertheless I haven't >> found out how to do this in a simple way. Any suggestions would be >> highly appreciated! >> >> Best Regards >> /Johan Nilsson >> _______________________________________________ >> 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 Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From hangsyin at gmail.com Tue Feb 19 19:20:18 2008 From: hangsyin at gmail.com (Hang) Date: Tue, 19 Feb 2008 16:20:18 -0800 (PST) Subject: [Bioperl-l] Bio::SeqIO fastq Message-ID: <15579570.post@talk.nabble.com> Hi, I'd like to read and write fastq entry. I don't know what is wrong with the following code: use Bio::SeqIO; my $in = Bio::SeqIO->new(-format => "fastq", -file => "test.fq"); while( my $seq = $in->next_seq ) { my $qual = $seq->qual; print $qual; } my test.fq file: @test AAAAA +test IIIII I got "Can't locate method 'qual' via package "AAAAA", perhaps you forgot to load "AAAAA?" at line XX ". Thanks Hang -- View this message in context: http://www.nabble.com/Bio%3A%3ASeqIO-fastq-tp15579570p15579570.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From heikki at sanbi.ac.za Wed Feb 20 15:12:40 2008 From: heikki at sanbi.ac.za (Heikki Lehvaslaiho) Date: Wed, 20 Feb 2008 22:12:40 +0200 Subject: [Bioperl-l] Bio::SeqIO fastq In-Reply-To: <15579570.post@talk.nabble.com> References: <15579570.post@talk.nabble.com> Message-ID: <200802202212.40772.heikki@sanbi.ac.za> Hang, It works for me. The last statement should be print "@$qual", "\n"; to print out readable values. Maybe you have an old version of BioPerl? Try: perl -MBio::Perl -le 'print Bio::Perl->VERSION;' I recommend installing the latest from CVS/SVN. -Heikki On Wednesday 20 February 2008 02:20:18 Hang wrote: > Hi, > > I'd like to read and write fastq entry. I don't know what is wrong with the > following code: > > use Bio::SeqIO; > my $in = Bio::SeqIO->new(-format => "fastq", > -file => "test.fq"); > while( my $seq = $in->next_seq ) { > my $qual = $seq->qual; > print $qual; > } > > my test.fq file: > @test > AAAAA > +test > IIIII > > I got "Can't locate method 'qual' via package "AAAAA", perhaps you forgot > to load "AAAAA?" at line XX ". > > Thanks > Hang -- ______ _/ _/_____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za _/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho _/ _/ _/ SANBI, South African National Bioinformatics Institute _/ _/ _/ University of Western Cape, South Africa _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 ___ _/_/_/_/_/________________________________________________________ From j.s.soares at gmail.com Wed Feb 20 18:04:35 2008 From: j.s.soares at gmail.com (Djodja) Date: Wed, 20 Feb 2008 15:04:35 -0800 (PST) Subject: [Bioperl-l] Bio::SeqIO fastq In-Reply-To: <200802202212.40772.heikki@sanbi.ac.za> References: <15579570.post@talk.nabble.com> <200802202212.40772.heikki@sanbi.ac.za> Message-ID: <15601113.post@talk.nabble.com> Hang, It works fine for me as well. My Bioperl version is: djodja at djodja-desktop:~$ perl -MBio::Perl -le 'print Bio::Perl->VERSION;' 1.005002102 djodja at djodja-desktop:~$ Maybe that is the problem. All the best, Djodja -- View this message in context: http://www.nabble.com/Bio%3A%3ASeqIO-fastq-tp15579570p15601113.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From shameer at ncbs.res.in Wed Feb 20 04:35:43 2008 From: shameer at ncbs.res.in (K. Shameer) Date: Wed, 20 Feb 2008 15:05:43 +0530 (IST) Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> Message-ID: <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> Dear All, Is there any module available in Bioperl that can be used to perform clustering of Gene Ontology terms from a set of Gene IDs and its respective Flybase GO annotations. These Gene IDs where hits from a high-throughput experiment. We would like to find the GO-Term enriched areas to get better biological insight irrespective of the experimental parameters. I am extremely sorry if this is off-topic : Can you please point me towards any paper/libraries that had used Gene Ontology based clustering ? Many thanks in advance, -- K. Shameer Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group National Centre for Biological Sciences (TIFR) GKVK Campus, Bangalore - 65, Karnataka - India T - 91-080-23666001 EXT - 6251 W - http://www.ncbs.res.in From sdavis2 at mail.nih.gov Thu Feb 21 06:54:47 2008 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Thu, 21 Feb 2008 06:54:47 -0500 Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> Message-ID: <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> On Wed, Feb 20, 2008 at 4:35 AM, K. Shameer wrote: > Dear All, > > Is there any module available in Bioperl that can be used to perform > clustering of Gene Ontology terms from a set of Gene IDs and its > respective Flybase GO annotations. These Gene IDs where hits from a > high-throughput experiment. We would like to find the GO-Term enriched > areas to get better biological insight irrespective of the experimental > parameters. > > I am extremely sorry if this is off-topic : > Can you please point me towards any paper/libraries that had used Gene > Ontology based clustering ? I'm not sure what you mean by GO clustering. However, there are a number of packages that will look for enriched GO terms given a set of Gene IDs. If you are looking for programmatic support for custom pipelines, you can look at R/Bioconductor. Here is a website that will look for GO enrichment and takes Flybase IDs as the gene identifier: http://niaid.abcc.ncifcrf.gov/home.jsp Sean From thiago.venancio at gmail.com Thu Feb 21 07:00:10 2008 From: thiago.venancio at gmail.com (Thiago M. Venancio) Date: Thu, 21 Feb 2008 09:00:10 -0300 Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> Message-ID: <44255ea80802210400u6e5242fdpae4c724621395f05@mail.gmail.com> Hi, This is off topic, but here we go. For enrichment analysis, I use Ontologizer: http://www.charite.de/ch/medgen/ontologizer/ But I am also not sure what do you mean by clustering. Best. T On Thu, Feb 21, 2008 at 8:54 AM, Sean Davis wrote: > On Wed, Feb 20, 2008 at 4:35 AM, K. Shameer wrote: > > Dear All, > > > > Is there any module available in Bioperl that can be used to perform > > clustering of Gene Ontology terms from a set of Gene IDs and its > > respective Flybase GO annotations. These Gene IDs where hits from a > > high-throughput experiment. We would like to find the GO-Term enriched > > areas to get better biological insight irrespective of the experimental > > parameters. > > > > I am extremely sorry if this is off-topic : > > Can you please point me towards any paper/libraries that had used Gene > > Ontology based clustering ? > > I'm not sure what you mean by GO clustering. However, there are a > number of packages that will look for enriched GO terms given a set of > Gene IDs. If you are looking for programmatic support for custom > pipelines, you can look at R/Bioconductor. > > Here is a website that will look for GO enrichment and takes Flybase > IDs as the gene identifier: > > http://niaid.abcc.ncifcrf.gov/home.jsp > > Sean > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- "At the center of your being you have the answer; You know who you are and you know what you want." Lao Tzu ======================== Thiago Motta Venancio, M.Sc., PhD Laboratory of Bioinformatics University of Sao Paulo ======================== From shameer at ncbs.res.in Thu Feb 21 07:29:01 2008 From: shameer at ncbs.res.in (K. Shameer) Date: Thu, 21 Feb 2008 17:59:01 +0530 (IST) Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> Message-ID: <60630.192.168.1.1.1203596941.squirrel@mail.ncbs.res.in> Dear All, Thanks for your reply. > I'm not sure what you mean by GO clustering. However, there are a > number of packages that will look for enriched GO terms given a set of > Gene IDs. In simple terms I have a list of genes, irrespective of any experimental value I need to cluster them based on their GO-Terms using the Di Acyclic Graph data structure of the Gene ontology databases. I found an interesting package from CPAN : GO::TermFinder . http://search.cpan.org/dist/GO-TermFinder/ I am not sure if this is a part of Bioperl :). I have tried with few examples it is working fine but I got few wrong results. If this is not part of Bioperl project, I may need to write to the authors. > If you are looking for programmatic support for custom > pipelines, you can look at R/Bioconductor. Thanks a lot !! I have seen a couple of R packages related to GO. But, I honestly wanted to do it in Perl :) !!! > > Here is a website that will look for GO enrichment and takes Flybase > IDs as the gene identifier: > http://niaid.abcc.ncifcrf.gov/home.jsp Thanks for the link. But I am specifically for something stand alone due to huge volume of my dataset. Cheers, Shameer NCBS - TIFR From golharam at umdnj.edu Thu Feb 21 07:26:58 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 21 Feb 2008 07:26:58 -0500 Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <44255ea80802210400u6e5242fdpae4c724621395f05@mail.gmail.com> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> <44255ea80802210400u6e5242fdpae4c724621395f05@mail.gmail.com> Message-ID: <47BD6E12.3000808@umdnj.edu> ArrayTrack is a good tool to do this, available from the FDA. It has some nice output and performs some statistical analysis for you. I'm using it now to cluster GO terms. Thiago M. Venancio wrote: > Hi, > This is off topic, but here we go. > For enrichment analysis, I use Ontologizer: > > http://www.charite.de/ch/medgen/ontologizer/ > > But I am also not sure what do you mean by clustering. > > Best. > > T > > On Thu, Feb 21, 2008 at 8:54 AM, Sean Davis wrote: > >> On Wed, Feb 20, 2008 at 4:35 AM, K. Shameer wrote: >>> Dear All, >>> >>> Is there any module available in Bioperl that can be used to perform >>> clustering of Gene Ontology terms from a set of Gene IDs and its >>> respective Flybase GO annotations. These Gene IDs where hits from a >>> high-throughput experiment. We would like to find the GO-Term enriched >>> areas to get better biological insight irrespective of the experimental >>> parameters. >>> >>> I am extremely sorry if this is off-topic : >>> Can you please point me towards any paper/libraries that had used Gene >>> Ontology based clustering ? >> I'm not sure what you mean by GO clustering. However, there are a >> number of packages that will look for enriched GO terms given a set of >> Gene IDs. If you are looking for programmatic support for custom >> pipelines, you can look at R/Bioconductor. >> >> Here is a website that will look for GO enrichment and takes Flybase >> IDs as the gene identifier: >> >> http://niaid.abcc.ncifcrf.gov/home.jsp >> >> Sean >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > From cjfields at uiuc.edu Thu Feb 21 09:21:14 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 21 Feb 2008 08:21:14 -0600 Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <60630.192.168.1.1.1203596941.squirrel@mail.ncbs.res.in> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> <60630.192.168.1.1.1203596941.squirrel@mail.ncbs.res.in> Message-ID: <96A3AC13-1963-4802-8ADA-77D00B393823@uiuc.edu> On Feb 21, 2008, at 6:29 AM, K. Shameer wrote: > Dear All, > > Thanks for your reply. > >> I'm not sure what you mean by GO clustering. However, there are a >> number of packages that will look for enriched GO terms given a set >> of >> Gene IDs. > > In simple terms I have a list of genes, irrespective of any > experimental > value I need to cluster them based on their GO-Terms using the Di > Acyclic > Graph data structure of the Gene ontology databases. > > I found an interesting package from CPAN : GO::TermFinder . > http://search.cpan.org/dist/GO-TermFinder/ > > I am not sure if this is a part of Bioperl :). I have tried with few > examples it is working fine but I got few wrong results. If this is > not > part of Bioperl project, I may need to write to the authors. It's not part of BioPerl, so you should contact the author. >> If you are looking for programmatic support for custom >> pipelines, you can look at R/Bioconductor. > > Thanks a lot !! I have seen a couple of R packages related to GO. > But, I > honestly wanted to do it in Perl :) !!! >> BioPerl's ontology classes are all in Bio::Ontology and Bio::OntologyIO. I would also recommend looking at Chris Mungall's go- perl: http://search.cpan.org/~cmungall/go-perl-0.08/go-perl.pod >> Here is a website that will look for GO enrichment and takes Flybase >> IDs as the gene identifier: >> http://niaid.abcc.ncifcrf.gov/home.jsp > > Thanks for the link. But I am specifically for something stand alone > due > to huge volume of my dataset. > > Cheers, > Shameer > NCBS - TIFR It's always faster to do it locally, I agree, as long as the tools are available to do so. chris From donald.jackson at bms.com Thu Feb 21 09:01:51 2008 From: donald.jackson at bms.com (Donald Jackson (Genomics)) Date: Thu, 21 Feb 2008 09:01:51 -0500 Subject: [Bioperl-l] qury In-Reply-To: <4e5ea6f60802191727x1980d2c8p4783300b4223cd5f@mail.gmail.com> References: <4e5ea6f60802191727x1980d2c8p4783300b4223cd5f@mail.gmail.com> Message-ID: <47BD844F.4070801@bms.com> Hi Somil, I get the same error from my test script. It will be a few days before I can troubleshoot and upload the fix to CVS; I'll let you know when I've posted the fix. Don Jackson Somil Dutt wrote: >Hello > >I used the SiRNA tool which is written below > > >use Bio::Tools::SiRNA; > >* > my $sirna_designer = Bio::Tools::SiRNA->new( -target => $bio_seq, > -rules => 'saigo' > ); > my @pairs = $sirna_designer->design; > > foreach $pair (@pairs) { > my $sense_oligo_sequence = $pair->sense->seq; > my $antisense_oligo_sequence = $pair->antisense->seq; > > # print out results > print join ("\t", $pair->start, $pair->end, $pair->rank, > $sense_oligo_sequence, $antisense_oligo_sequence), "\n";* > } > > >But the following problem > >------------- EXCEPTION Bio::Root::BadParameter ------------- >MSG: Target must be passed as a Bio::Seq object >STACK Bio::Tools::SiRNA::target C:/Perl/site/lib/Bio/Tools/SiRNA.pm:220 >STACK Bio::Tools::SiRNA::new C:/Perl/site/lib/Bio/Tools/SiRNA.pm:198 >STACK toplevel start.pl:32 > >I dont understand why this error is coming. > >Regards > > From shameer at ncbs.res.in Thu Feb 21 14:12:16 2008 From: shameer at ncbs.res.in (K. Shameer) Date: Fri, 22 Feb 2008 00:42:16 +0530 (IST) Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <96A3AC13-1963-4802-8ADA-77D00B393823@uiuc.edu> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> <60630.192.168.1.1.1203596941.squirrel@mail.ncbs.res.in> <96A3AC13-1963-4802-8ADA-77D00B393823@uiuc.edu> Message-ID: <39220.192.168.1.1.1203621136.squirrel@mail.ncbs.res.in> >> I am not sure if this is a part of Bioperl :). I have tried with few >> examples it is working fine but I got few wrong results. If this is >> not part of Bioperl project, I may need to write to the authors. > > It's not part of BioPerl, so you should contact the author. Thanks Chris, Is there any specific way to check installed bioperl modules ? > > BioPerl's ontology classes are all in Bio::Ontology and > Bio::OntologyIO. I would also recommend looking at Chris Mungall's go- > perl: > > http://search.cpan.org/~cmungall/go-perl-0.08/go-perl.pod Thanks for the information. > It's always faster to do it locally, I agree, as long as the tools are > available to do so. :) K. Shameer NCBS - TIFR From cjfields at uiuc.edu Thu Feb 21 23:37:54 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 21 Feb 2008 22:37:54 -0600 Subject: [Bioperl-l] Bio::Graphics and perl 5.10 Message-ID: <25A5CCCB-CE0F-4E12-8C31-451775C7FB4E@uiuc.edu> I'm getting a single failed test for Bio::Graphics in bioperl-live which appears to be perl 5.10-specific and is related to Bio::Graphics::FeatureFile: t/BioGraphics...... 1..35 ok 1 - use Bio::Graphics::FeatureFile; ok 2 - use Bio::Graphics::Panel; ok 3 not ok 4 # Failed test at t/BioGraphics.t line 49. # got: '7' # expected: '5' ok 5 ok 6 ok 7 ok 8 ... It appears to be coming from render() passing two extra tracks under perl 5.10 over what is passed in perl 5.8. If anyone is running perl 5.10, can they test this out? chris From cjfields at uiuc.edu Fri Feb 22 11:28:01 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 22 Feb 2008 10:28:01 -0600 Subject: [Bioperl-l] Bio::Graphics and perl 5.10 In-Reply-To: <25A5CCCB-CE0F-4E12-8C31-451775C7FB4E@uiuc.edu> References: <25A5CCCB-CE0F-4E12-8C31-451775C7FB4E@uiuc.edu> Message-ID: <116A7145-55FD-4254-AA94-1D1AAD8D7853@uiuc.edu> (cc'ing to gbrowse list as this pertains somewhat...) Just added a bioperl bug report for this along with the png file output from perl 5.8 and perl 5.10: http://bugzilla.open-bio.org/show_bug.cgi?id=2457 Lincoln's recent commits to Bio::Graphics::FeatureFile didn't fix the issue. However, it is now pinpointing the problem for both perl 5.8 and perl 5.10 (same warning for both, with only perl 5.10 failing): 1..35 ok 1 - use Bio::Graphics::FeatureFile; ok 2 - use Bio::Graphics::Panel; ok 3 Cosmid EST FGENESH SwissProt P-element / yk53c10.3 yk53c10.5 at Bio/ Graphics/FeatureFile.pm line 285. not ok 4 # Failed test at t/BioGraphics.t line 49. # got: '7' # expected: '5' ok 5 ok 6 ok 7 ok 8 ... chris On Feb 21, 2008, at 10:37 PM, Chris Fields wrote: > I'm getting a single failed test for Bio::Graphics in bioperl-live > which appears to be perl 5.10-specific and is related to > Bio::Graphics::FeatureFile: > > t/BioGraphics...... > 1..35 > ok 1 - use Bio::Graphics::FeatureFile; > ok 2 - use Bio::Graphics::Panel; > ok 3 > not ok 4 > > # Failed test at t/BioGraphics.t line 49. > # got: '7' > # expected: '5' > ok 5 > ok 6 > ok 7 > ok 8 > ... > > It appears to be coming from render() passing two extra tracks under > perl 5.10 over what is passed in perl 5.8. If anyone is running > perl 5.10, can they test this out? > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From heikki at sanbi.ac.za Mon Feb 25 01:18:33 2008 From: heikki at sanbi.ac.za (Heikki Lehvaslaiho) Date: Mon, 25 Feb 2008 08:18:33 +0200 Subject: [Bioperl-l] GN line parsing from Uniprot/Swiss-Prot Message-ID: <200802250818.33345.heikki@sanbi.ac.za> There has been an longstanding problem with GN (gene name) line parsing in SwissProt format. It has solved in a way that deals with all the complexity in that line but unfortunately is not backward compatible. You have to upgrade your scripts if you use bioperl-live. This documentation is now part of Bio::SeqIO::swiss.pm: =head2 GN (Gene name) line management details A Uniprot/Swiss-Prot entry holds information on one protein sequence. If that sequence is identical across genes and species, they are all merged into one entry. This creates complex needs for several annotation fields in swiss-prot format. The latest syntax for GN line is described in the user manual: http://www.expasy.ch/sprot/userman.html#GN_line Each of the possibly multiple genes in an entry can have Name, Synonyms (only if there is a name), OrderedLocusNames (names from genomic sequences) and ORFNames (temporary or cosmid names). "Name" here really means "symbol". This complexity is now dealth with the following way: Each gene is an Bio::Annotation::Collection object that is accessed like all other annotations. The tag name is 'gene_name': my @genes = $seq->annotation->get_Annotations('gene_name'); Note that if you are not interested in the complexity of multiple genes, you can easily just take the first value: my ($gene) = $seq->annotation->get_Annotations('gene_name'); None of the four categories for gene_names are obligatory, so you have to test returned objects for existence before using them: my ($name) = $gene->get_Annotations('name'); if ($name) { print "The official gene symbol is: ". $name->value. "\n"; } The can be only one name, so $name is a Bio::Annotation::SimpleValue object. In other categories (tags: synonyms, orderedlocusnames, orfnames; all lower case) there can be more than one value, so they are stored in Bio::Annotation::StructuredValue objects. There can be only one object with a given tag within a given gene. All values for that category are stored in an ordered list within the StructureValue object. e.g: if ( my ($synonyms) = $gene->get_Annotations('synonyms') ) { print "Synonyms: ". join(', ', $synonyms->get_all_values). "\n"; } Since Uniprot/Swiss-Prot format have been around for quite some time, the parser is also able to read in the older GN line syntax where genes are separated by AND and various symbols by OR. The first symbol is taken to be the name and the remaining ones are stored as synonyms. Thanks for Chris Fields for helping out, Enjoy, -Heikki -- ______ _/ _/_____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za _/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho _/ _/ _/ SANBI, South African National Bioinformatics Institute _/ _/ _/ University of Western Cape, South Africa _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 ___ _/_/_/_/_/________________________________________________________ From hangsyin at gmail.com Thu Feb 21 16:14:05 2008 From: hangsyin at gmail.com (Hang) Date: Thu, 21 Feb 2008 13:14:05 -0800 (PST) Subject: [Bioperl-l] Bio::SeqIO fastq In-Reply-To: <15601113.post@talk.nabble.com> References: <15579570.post@talk.nabble.com> <200802202212.40772.heikki@sanbi.ac.za> <15601113.post@talk.nabble.com> Message-ID: <15618960.post@talk.nabble.com> Heikki and Djodja, Many thanks for you guys' help! That code is working right now. Hang Djodja wrote: > > Hang, > > It works fine for me as well. > > My Bioperl version is: > > djodja at djodja-desktop:~$ perl -MBio::Perl -le 'print Bio::Perl->VERSION;' > > 1.005002102 > > djodja at djodja-desktop:~$ > > Maybe that is the problem. > > All the best, > > Djodja > > > -- View this message in context: http://www.nabble.com/Bio%3A%3ASeqIO-fastq-tp15579570p15618960.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From sheila.zuniga at sistemasgenomicos.com Mon Feb 25 10:48:18 2008 From: sheila.zuniga at sistemasgenomicos.com (=?iso-8859-1?Q?Sheila_Zu=F1iga_Trejos?=) Date: Mon, 25 Feb 2008 16:48:18 +0100 Subject: [Bioperl-l] bioperl installation problems with CPAN Message-ID: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Dear Sir, I'm trying to install Bioperl using CPAN but it seems impossible. I get several error messages when running cpan > install Bundle::CPAN. Please find attached a file containing these error messages. Any idea of what is happening? Thanks very much for your help, Sheila -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: error.txt URL: From rchu at coh.org Mon Feb 25 16:33:10 2008 From: rchu at coh.org (Roy) Date: Mon, 25 Feb 2008 21:33:10 +0000 (UTC) Subject: [Bioperl-l] SeqIO and large GenBank files Message-ID: Hi everyone, I want to parse some of the .gbk RefSeq files from ncbi, more specifically, ref_chr*.gbk. My script seems to open the sequence stream okay, but when I try to get the next sequence in the stream, my script spits out a lot of warnings of subroutine redefinitions. Is this file incompatible with SeqIO genbank reader? Any insight is appreciated, thanks. Roy test file: ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_01 ===start_code=== #!/usr/bin/perl -w use strict; use warnings; use Bio::Perl; use Bio::SeqIO; my $USAGE = "usage: $0 \n\n"; unless (@ARGV) { print $USAGE; exit; } my $stream = Bio::SeqIO->new(-file => $ARGV[0], -format => "genbank"); my $seq_obj = $stream->next_seq; exit; ===end_code=== ===start warnings=== Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 80, line 36. Subroutine start redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 102, line 36. Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 128, line 36. Subroutine length redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 165, line 36. Subroutine location_type redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 256, line 36. Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 303, line 36. Subroutine trunc redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 334, line 36. Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 91, line 49. Subroutine each_Location redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 123, line 49. Subroutine sub_Location redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 152, line 49. Subroutine add_sub_Location redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 221, line 49. Subroutine splittype redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 245, line 49. Subroutine is_single_sequence redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 273, line 49. Subroutine guide_strand redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 298, line 49. Subroutine strand redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 326, line 49. Subroutine flip_strand redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 367, line 49. Subroutine start redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 388, line 49. Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 407, line 49. Subroutine min_start redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 426, line 49. Subroutine max_start redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 448, line 49. Subroutine start_pos_type redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 471, line 49. Subroutine min_end redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 492, line 49. Subroutine max_end redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 515, line 49. Subroutine end_pos_type redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 539, line 49. Subroutine seq_id redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 565, line 49. Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 611, line 49. Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 134, line 747. Subroutine location_type redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 161, line 747. Subroutine start redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 223, line 747. Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 250, line 747. Subroutine min_start redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 277, line 747. Subroutine max_start redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 296, line 747. Subroutine start_pos_type redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 316, line 747. Subroutine min_end redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 346, line 747. Subroutine max_end redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 365, line 747. Subroutine end_pos_type redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 385, line 747. Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 456, line 747. Subroutine _fuzzypointdecode redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 557, line 747. ==end warnings== From cjfields at uiuc.edu Mon Feb 25 17:17:49 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 25 Feb 2008 16:17:49 -0600 Subject: [Bioperl-l] SeqIO and large GenBank files In-Reply-To: References: Message-ID: <4F9A56D3-1EAE-4916-A2F6-E10DB4CE3C18@uiuc.edu> The perl executable is overly paranoid on Windows for some reason when the '-w' flag is set on the shebang line ('#!/usr/bin/perl -w'); it doesn't like method overloading for some reason. Remove it and the warnings should go away (note: you should still leave 'use strict' and 'use warnings'). chris On Feb 25, 2008, at 3:33 PM, Roy wrote: > Hi everyone, > > I want to parse some of the .gbk RefSeq files from ncbi, more > specifically, > ref_chr*.gbk. My script seems to open the sequence stream okay, but > when I try > to get the next sequence in the stream, my script spits out a lot of > warnings of > subroutine redefinitions. Is this file incompatible with SeqIO > genbank reader? > Any insight is appreciated, thanks. > > Roy > > test file: > > ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_01 > > ===start_code=== > #!/usr/bin/perl -w > use strict; > use warnings; > use Bio::Perl; > use Bio::SeqIO; > my $USAGE = "usage: $0 \n\n"; > unless (@ARGV) { > print $USAGE; > exit; > } > my $stream = Bio::SeqIO->new(-file => $ARGV[0], -format => "genbank"); > my $seq_obj = $stream->next_seq; > exit; > ===end_code=== > > ===start warnings=== > Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Simple.pm > line 80, > line 36. > Subroutine start redefined at C:/Perl/site/lib/Bio\Location > \Simple.pm line 102, > line 36. > Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Simple.pm > line 128, > line 36. > Subroutine length redefined at C:/Perl/site/lib/Bio\Location > \Simple.pm line 165, > line 36. > Subroutine location_type redefined at C:/Perl/site/lib/Bio\Location > \Simple.pm > line 256, line 36. > Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location > \Simple.pm line > 303, line 36. > Subroutine trunc redefined at C:/Perl/site/lib/Bio\Location > \Simple.pm line 334, > line 36. > Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Split.pm > line 91, > line 49. > Subroutine each_Location redefined at C:/Perl/site/lib/Bio\Location > \Split.pm > line 123, line 49. > Subroutine sub_Location redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 152, line 49. > Subroutine add_sub_Location redefined at C:/Perl/site/lib/Bio > \Location\Split.pm > line 221, line 49. > Subroutine splittype redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 245, line 49. > Subroutine is_single_sequence redefined at > C:/Perl/site/lib/Bio\Location\Split.pm line 273, line 49. > Subroutine guide_strand redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 298, line 49. > Subroutine strand redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line 326, > line 49. > Subroutine flip_strand redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 367, line 49. > Subroutine start redefined at C:/Perl/site/lib/Bio\Location\Split.pm > line 388, > line 49. > Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Split.pm > line 407, > line 49. > Subroutine min_start redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 426, line 49. > Subroutine max_start redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 448, line 49. > Subroutine start_pos_type redefined at C:/Perl/site/lib/Bio\Location > \Split.pm > line 471, line 49. > Subroutine min_end redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line 492, > line 49. > Subroutine max_end redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line 515, > line 49. > Subroutine end_pos_type redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 539, line 49. > Subroutine seq_id redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line 565, > line 49. > Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 611, line 49. > Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm > line 134, > line 747. > Subroutine location_type redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm > line 161, line 747. > Subroutine start redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm > line 223, > line 747. > Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm > line 250, > line 747. > Subroutine min_start redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm line > 277, line 747. > Subroutine max_start redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm line > 296, line 747. > Subroutine start_pos_type redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm > line 316, line 747. > Subroutine min_end redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm line 346, > line 747. > Subroutine max_end redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm line 365, > line 747. > Subroutine end_pos_type redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm line > 385, line 747. > Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm line > 456, line 747. > Subroutine _fuzzypointdecode redefined at C:/Perl/site/lib/Bio > \Location\Fuzzy.pm > line 557, line 747. > ==end warnings== > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From Russell.Smithies at agresearch.co.nz Mon Feb 25 17:12:39 2008 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 26 Feb 2008 11:12:39 +1300 Subject: [Bioperl-l] Bio::Assembly::IO problems In-Reply-To: <000001c877c5$d8dc2d70$7000000a@sistemas.local> References: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Message-ID: Is the Bio::Assembly::IO stuff working? I want to parse some .ace files but keep getting errors: [smithiesr at impala ace_phrap]$ perl 454_read_ace.pl Can't call method "get_consensus_sequence" on an undefined value at /usr/lib/perl5/site_perl/5.8.8/Bio/Assembly/IO/ace.pm line 169, line 20. My code is: #!perl -w use Bio::Assembly::IO; use Data::Dumper; my $in = "454Contigs.ace"; $io = new Bio::Assembly::IO(-file=>$in,-format=>"ace"); $ass = $io->next_assembly; print Dumper $ass; exit; any ideas? Thanx, Russell Smithies Bioinformatics Software Developer T +64 3 489 9085 E? russell.smithies at agresearch.co.nz Invermay? Research Centre Puddle Alley, Mosgiel, New Zealand T? +64 3 489 3809?? F? +64 3 489 9174? www.agresearch.co.nz ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From cjfields at uiuc.edu Mon Feb 25 18:01:42 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 25 Feb 2008 17:01:42 -0600 Subject: [Bioperl-l] Bio::Assembly::IO problems In-Reply-To: References: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Message-ID: <5827D6E2-B798-4001-84DB-8C38586D3CF2@uiuc.edu> Russell, Using the test data from the bioperl installation appears to work, but I wouldn't be surprised if this is a bug. Can you file this as a bug along with some test data? http://bugzilla.open-bio.org/ chris On Feb 25, 2008, at 4:12 PM, Smithies, Russell wrote: > Is the Bio::Assembly::IO stuff working? > I want to parse some .ace files but keep getting errors: > > [smithiesr at impala ace_phrap]$ perl 454_read_ace.pl > Can't call method "get_consensus_sequence" on an undefined value > at /usr/lib/perl5/site_perl/5.8.8/Bio/Assembly/IO/ace.pm line 169, > line 20. > > My code is: > > #!perl -w > > use Bio::Assembly::IO; > use Data::Dumper; > > my $in = "454Contigs.ace"; > > $io = new Bio::Assembly::IO(-file=>$in,-format=>"ace"); > $ass = $io->next_assembly; > > print Dumper $ass; > exit; > > any ideas? > > Thanx, > > Russell Smithies > > Bioinformatics Software 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 > > > = > ====================================================================== > 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 Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From rchu at coh.org Mon Feb 25 18:21:26 2008 From: rchu at coh.org (Roy) Date: Mon, 25 Feb 2008 23:21:26 +0000 (UTC) Subject: [Bioperl-l] SeqIO and large GenBank files References: <4F9A56D3-1EAE-4916-A2F6-E10DB4CE3C18@uiuc.edu> Message-ID: Chris Fields uiuc.edu> writes: > > The perl executable is overly paranoid on Windows for some reason when > the '-w' flag is set on the shebang line ('#!/usr/bin/perl -w'); it > doesn't like method overloading for some reason. Remove it and the > warnings should go away (note: you should still leave 'use strict' and > 'use warnings'). > > chris Thanks Chris. Your suggestion worked. I was concerned that there may be some other error because it was taking an ungodly amount of time to process, but that resolved the problems. -Roy From Russell.Smithies at agresearch.co.nz Mon Feb 25 18:23:06 2008 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 26 Feb 2008 12:23:06 +1300 Subject: [Bioperl-l] Bio::Assembly::IO problems - FIXED! In-Reply-To: References: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Message-ID: I solved the problem :-) The contig lines in our .ace files have a lower-case 'c' in the contig name instead of upper-case so weren't being found by this regex in ace.pm line 142: (/^CO Contig(\d+) (\d+) (\d+) (\d+) (\w+)/) && do { # New contig found! e.g: CO contig00001 711 12 6 U instead of: CO Contig00001 711 12 6 U Our contigs were generated with Newbler version 1.1.01.20. so might be something to watch out for in future. Russell Smithies Bioinformatics Software Developer T +64 3 489 9085 E? russell.smithies at agresearch.co.nz Invermay? Research Centre Puddle Alley, Mosgiel, New Zealand T? +64 3 489 3809?? F? +64 3 489 9174? www.agresearch.co.nz > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open- > bio.org] On Behalf Of Smithies, Russell > Sent: Tuesday, 26 February 2008 11:13 a.m. > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] Bio::Assembly::IO problems > > Is the Bio::Assembly::IO stuff working? > I want to parse some .ace files but keep getting errors: > > [smithiesr at impala ace_phrap]$ perl 454_read_ace.pl > Can't call method "get_consensus_sequence" on an undefined value at > /usr/lib/perl5/site_perl/5.8.8/Bio/Assembly/IO/ace.pm line 169, line 20. > > My code is: > > #!perl -w > > use Bio::Assembly::IO; > use Data::Dumper; > > my $in = "454Contigs.ace"; > > $io = new Bio::Assembly::IO(-file=>$in,-format=>"ace"); > $ass = $io->next_assembly; > > print Dumper $ass; > exit; > > any ideas? > > Thanx, > > Russell Smithies > > Bioinformatics Software 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 > > > ============================================================= > ========== > 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 ======================================================================= 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 David.Messina at sbc.su.se Mon Feb 25 18:46:44 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 26 Feb 2008 00:46:44 +0100 Subject: [Bioperl-l] bioperl installation problems with CPAN In-Reply-To: <000001c877c5$d8dc2d70$7000000a@sistemas.local> References: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Message-ID: <628aabb70802251546i3f43212eo705e762bf34ec27a@mail.gmail.com> Hi Sheila, It looks like your cpan configuration has gotten messed up. It's giving invalid parameters to the make command: make: *** No hay ninguna regla para construir el objetivo `dual'. Alto. /usr/bin/make dual processor system -- NOT OK Go to the command line on your system. Enter the cpan shell: % cpan Type the following: cpan> o conf makepl_arg "" cpan> o conf commit That should reset the arguments that cpan adds to the make command. If that doesn't fix your problem, reset everything by typing cpan> o conf defaults cpan> o conf commit and see if that does it. Dave From schaffer at scripps.edu Mon Feb 25 20:04:50 2008 From: schaffer at scripps.edu (Lana Schaffer) Date: Mon, 25 Feb 2008 17:04:50 -0800 Subject: [Bioperl-l] statistics Message-ID: <8F897BD2B0EB714CB79B96D84911B30209E543@EXCHV1.lj.ad.scripps.edu> Hi, I want to know if Bioperl does t-tests and how to do it? Also, I need to get a chi-squared statistic. Thanks, Lana Schaffer Biostatistics/Informatics The Scripps Research Institute DNA Array Core Facility La Jolla, CA 92037 (858) 784-2263 (858) 784-2994 schaffer at scripps.edu From sdavis2 at mail.nih.gov Mon Feb 25 21:45:00 2008 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Mon, 25 Feb 2008 21:45:00 -0500 Subject: [Bioperl-l] statistics In-Reply-To: <8F897BD2B0EB714CB79B96D84911B30209E543@EXCHV1.lj.ad.scripps.edu> References: <8F897BD2B0EB714CB79B96D84911B30209E543@EXCHV1.lj.ad.scripps.edu> Message-ID: <264855a00802251845p25130950q5dbdc4228dbb2b93@mail.gmail.com> On Mon, Feb 25, 2008 at 8:04 PM, Lana Schaffer wrote: > Hi, > I want to know if Bioperl does t-tests and how to do it? > Also, I need to get a chi-squared statistic. Hi, Lana. I don't think bioperl offers this functionality. However, a quick search of cpan (http://search.cpan.org) turns up: http://search.cpan.org/~yunfang/Statistics-TTest-1.1.0/TTest.pm http://search.cpan.org/~dcantrell/Statistics-ChiSquare-0.5/lib/Statistics/ChiSquare.pm That said, I know you are an R user. I generally stick to R for any numerics. If you need both a parsing/data munging language and statistics, consider python, where the rpy package allows you access R from python and even does data conversion, etc. Sean From florent.angly at gmail.com Tue Feb 26 00:37:20 2008 From: florent.angly at gmail.com (Florent Angly) Date: Mon, 25 Feb 2008 21:37:20 -0800 Subject: [Bioperl-l] Bio::Assembly::IO problems - FIXED! In-Reply-To: References: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Message-ID: <47C3A590.4070204@gmail.com> As far as I know, there really isn't a specification of the ACE file format, that would rule if it is legal to have the kind of contig name (non capitalized), other that its original implementation in Phrap. According to the spirit of the ACE file format, my guess is that any contig name should be allowed. For example, on this webpage http://www.cbcb.umd.edu/research/contig_representation.shtml, the contig name is just a number. So please Russel file this as a bug so that the developers can keep track of this bug, Regards, Florent Smithies, Russell wrote: > I solved the problem :-) > The contig lines in our .ace files have a lower-case 'c' in the contig name instead of upper-case so weren't being found by this regex in ace.pm line 142: > (/^CO Contig(\d+) (\d+) (\d+) (\d+) (\w+)/) && do { # New contig found! > > e.g: > CO contig00001 711 12 6 U > instead of: > CO Contig00001 711 12 6 U > > Our contigs were generated with Newbler version 1.1.01.20. so might be something to watch out for in future. > > > Russell Smithies > > Bioinformatics Software Developer > T +64 3 489 9085 > E russell.smithies at agresearch.co.nz > > Invermay Research Centre > Puddle Alley, > Mosgiel, > New Zealand > T +64 3 489 3809 > F +64 3 489 9174 > www.agresearch.co.nz > > > > > > > > > >> -----Original Message----- >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open- >> bio.org] On Behalf Of Smithies, Russell >> Sent: Tuesday, 26 February 2008 11:13 a.m. >> To: bioperl-l at lists.open-bio.org >> Subject: [Bioperl-l] Bio::Assembly::IO problems >> >> Is the Bio::Assembly::IO stuff working? >> I want to parse some .ace files but keep getting errors: >> >> [smithiesr at impala ace_phrap]$ perl 454_read_ace.pl >> Can't call method "get_consensus_sequence" on an undefined value at >> /usr/lib/perl5/site_perl/5.8.8/Bio/Assembly/IO/ace.pm line 169, line 20. >> >> My code is: >> >> #!perl -w >> >> use Bio::Assembly::IO; >> use Data::Dumper; >> >> my $in = "454Contigs.ace"; >> >> $io = new Bio::Assembly::IO(-file=>$in,-format=>"ace"); >> $ass = $io->next_assembly; >> >> print Dumper $ass; >> exit; >> >> any ideas? >> >> Thanx, >> >> Russell Smithies >> >> Bioinformatics Software 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 >> >> >> ============================================================= >> ========== >> 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 >> > ======================================================================= > 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 David.Messina at sbc.su.se Tue Feb 26 05:47:36 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 26 Feb 2008 11:47:36 +0100 Subject: [Bioperl-l] bioperl installation problems with CPAN In-Reply-To: <000701c87857$15dd6d60$7000000a@sistemas.local> References: <628aabb70802251546i3f43212eo705e762bf34ec27a@mail.gmail.com> <000701c87857$15dd6d60$7000000a@sistemas.local> Message-ID: <628aabb70802260247h2d063d4ah489318aad66c4e6a@mail.gmail.com> Hi Sheila, Please be sure to keep bioperl-l on the Cc so that everyone can follow along the discussion. I don't think this is a BioPerl-specific problem. Can you successfully install other modules from CPAN? Could you type "o conf" in cpan and paste the results into your reply to this message? Dave On 2/26/08, Sheila Zu?iga Trejos wrote: > > Hi Dave, > I've tried the two options and in both cases I got the same error message. > I even restart the server both times in case it could make any difference > but nothing changed. > First attempt: > > Type: cpan> o conf makepl_arg "" > Return: makepl_arg > Type: cpan> o conf commit > Return: commit: wrote /etc/perl/CPAN/Config.pm > Type: cpan> install Bundle::CPAN > Return: error message attached (same as before) > > Second attempt: > > Type: cpan> o conf defaults > (did not return anything) > Type: cpan> o conf commit > Return: commit: wrote /etc/perl/CPAN/Config.pm > Type: cpan> install Bundle::CPAN > Return: error message attached (same as before) > > I installed Bioperl in Debian Sarge before and I never had any problem with CPAN but with Debian Etch...Well, I hope you have other ideas. > > Thanks very much for your help. > > Sheila > > ------------------------------ > *De:* dave at davemessina.com [mailto:dave at davemessina.com] *En nombre de *Dave > Messina > *Enviado el:* martes, 26 de febrero de 2008 0:47 > *Para:* Sheila Zu?iga Trejos > *CC:* bioperl-l at bioperl.org > *Asunto:* Re: [Bioperl-l] bioperl installation problems with CPAN > > Hi Sheila, > > It looks like your cpan configuration has gotten messed up. It's giving > invalid parameters to the make command: > > make: *** No hay ninguna regla para construir el objetivo `dual'. Alto. > > /usr/bin/make dual processor system -- NOT OK > > > > Go to the command line on your system. Enter the cpan shell: > > % cpan > > Type the following: > > cpan> o conf makepl_arg "" > cpan> o conf commit > > > That should reset the arguments that cpan adds to the make command. If > that doesn't fix your problem, reset everything by typing > > cpan> o conf defaults > cpan> o conf commit > > and see if that does it. > > > Dave > > > From David.Messina at sbc.su.se Tue Feb 26 06:43:35 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 26 Feb 2008 12:43:35 +0100 Subject: [Bioperl-l] bioperl installation problems with CPAN In-Reply-To: <001001c87868$4e11cb20$7000000a@sistemas.local> References: <628aabb70802260247h2d063d4ah489318aad66c4e6a@mail.gmail.com> <001001c87868$4e11cb20$7000000a@sistemas.local> Message-ID: <628aabb70802260343n43b216a2q580827e26266c8b6@mail.gmail.com> The following two lines show the problem: > make_arg dual processor system > make_install_arg to always uninstall potentially conflicting files > The configuration parameters are key-value pairs. So here the parameter "make_arg" is set to the value "dual processor system". "dual processor system" is not a valid command-line argument for the make program, so that's why cpan can't install BioPerl (or anything else, I would suspect). Type the following in cpan: cpan> o conf make_arg "" cpan> o conf make_install_arg "" cpan> o conf commit Then type cpan> o conf and verify that those two parameters have indeed been changed successfully. If so, then try installing BioPerl again. I think it should work, but let me know if not. Dave From sheila.zuniga at sistemasgenomicos.com Tue Feb 26 06:11:09 2008 From: sheila.zuniga at sistemasgenomicos.com (=?iso-8859-1?Q?Sheila_Zu=F1iga_Trejos?=) Date: Tue, 26 Feb 2008 12:11:09 +0100 Subject: [Bioperl-l] bioperl installation problems with CPAN In-Reply-To: <628aabb70802260247h2d063d4ah489318aad66c4e6a@mail.gmail.com> Message-ID: <001001c87868$4e11cb20$7000000a@sistemas.local> Hi Dave, Thanks for your quick reply. Here is the output: cpan> o conf CPAN::Config options from /etc/perl/CPAN/Config.pm: commit Commit changes to disk defaults Reload defaults from disk init Interactive setting of all options build_cache 10 build_dir /root/.cpan/build cache_metadata 1 cpan_home /root/.cpan cpan_version_check 1 dontload_hash ftp /usr/bin/ftp ftp_proxy getcwd cwd gpg /usr/bin/gpg gzip /bin/gzip histfile /root/.cpan/histfile histsize 100 http_proxy inactivity_timeout 0 index_expire 1 inhibit_startup_message 0 keep_source_where /root/.cpan/sources lynx make /usr/bin/make make_arg dual processor system make_install_arg to always uninstall potentially conflicting files makepl_arg ncftpget /usr/bin/ncftpget no_proxy pager /usr/bin/less prefer_installer MB prerequisites_policy ask scan_cache atstart shell /bin/bash tar /bin/tar term_is_latin 1 unzip /usr/bin/unzip urllist ftp://ftp.rediris.es/mirror/CPAN/ wget /usr/bin/wget Sheila _____ De: dave at davemessina.com [mailto:dave at davemessina.com] En nombre de Dave Messina Enviado el: martes, 26 de febrero de 2008 11:48 Para: Sheila Zu?iga Trejos CC: bioperl-l at bioperl.org Asunto: Re: [Bioperl-l] bioperl installation problems with CPAN Hi Sheila, Please be sure to keep bioperl-l on the Cc so that everyone can follow along the discussion. I don't think this is a BioPerl-specific problem. Can you successfully install other modules from CPAN? Could you type "o conf" in cpan and paste the results into your reply to this message? Dave On 2/26/08, Sheila Zu?iga Trejos wrote: Hi Dave, I've tried the two options and in both cases I got the same error message. I even restart the server both times in case it could make any difference but nothing changed. First attempt: Type: cpan> o conf makepl_arg "" Return: makepl_arg Type: cpan> o conf commit Return: commit: wrote /etc/perl/CPAN/Config.pm Type: cpan> install Bundle::CPAN Return: error message attached (same as before) Second attempt: Type: cpan> o conf defaults (did not return anything) Type: cpan> o conf commit Return: commit: wrote /etc/perl/CPAN/Config.pm Type: cpan> install Bundle::CPAN Return: error message attached (same as before) I installed Bioperl in Debian Sarge before and I never had any problem with CPAN but with Debian Etch... Well, I hope you have other ideas. Thanks very much for your help. Sheila _____ De: dave at davemessina.com [mailto:dave at davemessina.com] En nombre de Dave Messina Enviado el: martes, 26 de febrero de 2008 0:47 Para: Sheila Zu?iga Trejos CC: bioperl-l at bioperl.org Asunto: Re: [Bioperl-l] bioperl installation problems with CPAN Hi Sheila, It looks like your cpan configuration has gotten messed up. It's giving invalid parameters to the make command: make: *** No hay ninguna regla para construir el objetivo `dual'. Alto. /usr/bin/make dual processor system -- NOT OK Go to the command line on your system. Enter the cpan shell: % cpan Type the following: cpan> o conf makepl_arg "" cpan> o conf commit That should reset the arguments that cpan adds to the make command. If that doesn't fix your problem, reset everything by typing cpan> o conf defaults cpan> o conf commit and see if that does it. Dave From sheila.zuniga at sistemasgenomicos.com Tue Feb 26 06:54:53 2008 From: sheila.zuniga at sistemasgenomicos.com (=?iso-8859-1?Q?Sheila_Zu=F1iga_Trejos?=) Date: Tue, 26 Feb 2008 12:54:53 +0100 Subject: [Bioperl-l] bioperl installation problems with CPAN In-Reply-To: <628aabb70802260343n43b216a2q580827e26266c8b6@mail.gmail.com> Message-ID: <001801c8786e$6a04bc10$7000000a@sistemas.local> Hi Dave, You're right! It works! Thanks very much for your help. Sheila _____ De: dave at davemessina.com [mailto:dave at davemessina.com] En nombre de Dave Messina Enviado el: martes, 26 de febrero de 2008 12:44 Para: Sheila Zu?iga Trejos CC: bioperl-l at bioperl.org Asunto: Re: [Bioperl-l] bioperl installation problems with CPAN The following two lines show the problem: make_arg dual processor system make_install_arg to always uninstall potentially conflicting files The configuration parameters are key-value pairs. So here the parameter "make_arg" is set to the value "dual processor system". "dual processor system" is not a valid command-line argument for the make program, so that's why cpan can't install BioPerl (or anything else, I would suspect). Type the following in cpan: cpan> o conf make_arg "" cpan> o conf make_install_arg "" cpan> o conf commit Then type cpan> o conf and verify that those two parameters have indeed been changed successfully. If so, then try installing BioPerl again. I think it should work, but let me know if not. Dave From bix at sendu.me.uk Mon Feb 25 17:35:18 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 25 Feb 2008 22:35:18 +0000 Subject: [Bioperl-l] bioperl installation problems with CPAN In-Reply-To: <000001c877c5$d8dc2d70$7000000a@sistemas.local> References: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Message-ID: <47C342A6.7090009@sendu.me.uk> Sheila Zu?iga Trejos wrote: > Dear Sir, > I'm trying to install Bioperl using CPAN but it seems impossible. I get > several error messages when running cpan > install Bundle::CPAN. Please find > attached a file containing these error messages. > Any idea of what is happening? Looks like you've given one of the CPAN options (when you first ran CPAN it asked a bunch of questions) a dodgy value: 'dual processor system'. The easiest thing to do would be to delete your .cpan directory and start over, making sure to answer all the questions carefully and correctly. From bix at sendu.me.uk Tue Feb 26 05:34:04 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 26 Feb 2008 10:34:04 +0000 Subject: [Bioperl-l] statistics In-Reply-To: <264855a00802251845p25130950q5dbdc4228dbb2b93@mail.gmail.com> References: <8F897BD2B0EB714CB79B96D84911B30209E543@EXCHV1.lj.ad.scripps.edu> <264855a00802251845p25130950q5dbdc4228dbb2b93@mail.gmail.com> Message-ID: <47C3EB1C.2000407@sendu.me.uk> Sean Davis wrote: > On Mon, Feb 25, 2008 at 8:04 PM, Lana Schaffer wrote: >> Hi, >> I want to know if Bioperl does t-tests and how to do it? >> Also, I need to get a chi-squared statistic. > > Hi, Lana. I don't think bioperl offers this functionality. However, > a quick search of cpan (http://search.cpan.org) turns up: > > http://search.cpan.org/~yunfang/Statistics-TTest-1.1.0/TTest.pm > http://search.cpan.org/~dcantrell/Statistics-ChiSquare-0.5/lib/Statistics/ChiSquare.pm > > That said, I know you are an R user. I generally stick to R for any > numerics. If you need both a parsing/data munging language and > statistics, consider python, where the rpy package allows you access R > from python and even does data conversion, etc. There's also an R interface for perl: http://www.omegahat.org/RSPerl/ From johnsonm at gmail.com Tue Feb 26 19:47:02 2008 From: johnsonm at gmail.com (Mark Johnson) Date: Tue, 26 Feb 2008 18:47:02 -0600 Subject: [Bioperl-l] Bio::Tools::Run::Fgenesh anyone? Message-ID: We've got fgenesh/fgenesh+ installed locally and I'm going to need Bio::Tools::Run::Fgenesh for a nematode annotation pipeline. Does Bio::Tools::Fgenesh still need unit tests as well? Throw 'em in genpred.t with everything else? From jay at jays.net Thu Feb 28 15:25:29 2008 From: jay at jays.net (Jay Hannah) Date: Thu, 28 Feb 2008 14:25:29 -0600 Subject: [Bioperl-l] helpdesk@open-bio.org ... User unknown References: <200802281949.m1SJnIeD000744@ferret.jays.net> Message-ID: <78E7CE4E-9633-4015-B37C-A097D7F5B411@jays.net> Did I remember that address incorrectly? I'd look it up, but... :) j Begin forwarded message: > From: Mail Delivery Subsystem > Date: February 28, 2008 1:49:18 PM CST > To: > Subject: Returned mail: see transcript for details > > The original message was received at Thu, 28 Feb 2008 13:10:05 -0600 > from host-137-197-64-194.unmc.edu [137.197.64.194] > > ----- The following addresses had permanent fatal errors ----- > > (reason: 550 5.1.1 ... User unknown) > > ----- Transcript of session follows ----- > ... while talking to open-bio.org.: >>>> DATA > <<< 550 5.1.1 ... User unknown > 550 5.1.1 ... User unknown > <<< 503 5.0.0 Need RCPT (recipient) > Reporting-MTA: dns; ferret.jays.net > Arrival-Date: Thu, 28 Feb 2008 13:10:05 -0600 > > Final-Recipient: RFC822; helpdesk at open-bio.org > Action: failed > Status: 5.1.1 > Remote-MTA: DNS; open-bio.org > Diagnostic-Code: SMTP; 550 5.1.1 ... User > unknown > Last-Attempt-Date: Thu, 28 Feb 2008 13:49:18 -0600 > > From: Jay Hannah > Date: February 28, 2008 1:09:57 PM CST > To: helpdesk at open-bio.org > Subject: Websites are down? > > > Is this the right email address to report this to? > > I can't reach: > > http://bioperl.org > http://open-bio.org > > Thanks, > > j > > > > From David.Messina at sbc.su.se Thu Feb 28 16:56:46 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Thu, 28 Feb 2008 22:56:46 +0100 Subject: [Bioperl-l] helpdesk@open-bio.org ... User unknown In-Reply-To: <78E7CE4E-9633-4015-B37C-A097D7F5B411@jays.net> References: <200802281949.m1SJnIeD000744@ferret.jays.net> <78E7CE4E-9633-4015-B37C-A097D7F5B411@jays.net> Message-ID: <628aabb70802281356w693787e0r19aa80b56079182d@mail.gmail.com> Close. :) support at helpdesk.open-bio.org > I can't reach: > > > > http://bioperl.org > > http://open-bio.org Both work for me at the moment, by the way. Perhaps 'twas transient? Dave From cjfields at uiuc.edu Fri Feb 1 14:03:36 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 1 Feb 2008 13:03:36 -0600 Subject: [Bioperl-l] Odd issue with HSP::seq_inds() Message-ID: Apologies ahead of time for the longish post! While working on a recent bug (http://bugzilla.open-bio.org/show_bug.cgi?id=2436 ) I found a pretty significant bug. It appears that seq_inds() is giving some bad return values tied specifically to reports where either or both query or hit are translated. I'll file a full bug report but I felt it might be worth bringing up here to discuss specifically what values should be expected when these reports are parsed (all three nucleotide positions or only the first for each nonmatching translated position, etc). I used the following script to track the total HSPs as well as those where seq_inds() returns positions within the HSP bounds for query and hit: ------------------------------------------- use Bio::SearchIO; use Test::More qw(no_plan); my $file = shift || die; my $io = Bio::SearchIO->new(-format => 'blast', -file => $file); my ($hsp_co, $correctq, $correcth) = (0,0,0); while (my $res = $io->next_result) { while (my $hit = $res->next_hit) { while (my $hsp = $hit->next_hsp) { $hsp_co++; my ($qs, $qe, $hs, $he) = ($hsp->start('query'),$hsp- >end('query'), $hsp->start('hit'),$hsp- >end('hit')); my @pos = $hsp->seq_inds('query','nomatch'); my @pos2 = grep {$_ >= $qs && $_ <= $qe} @pos; # should always be true if (scalar(@pos2) == scalar(@pos)) { $correctq++; } @pos = $hsp->seq_inds('hit','nomatch'); @pos2 = grep {$_ >= $hs && $_ <= $he} @pos; # should always be true if (scalar(@pos2) == scalar(@pos)) { $correcth++; } } } } is($correctq, $hsp_co, 'Query seq_inds() positions fall within HSP bounds'); is($correcth, $hsp_co, 'Subject seq_inds() positions fall within HSP bounds'); ------------------------------------------- Here are the results for the following BLAST report types (culled from test reports used in SearchIO.t): BLASTN : both pass TBLASTN : query passes, subject fails BLASTX : query fails, subject passes TBLASTX : both fail When looking at the failed query seq_inds() data for the first HSP in the TBLASTX report used in SearchIO.t (HUMBETGLOA.tblastx), I get these positions for the query: 355 364 365 367 368 370 371 373 374 375 and for the hit: 1941 1942 1943 1945 1946 1948 1949 1951 1952 1961 This is the actual first HSP for that report: ------------------------------------------- >gb|AE000479.1|AE000479 Escherichia coli K-12 MG1655 section 369 of 400 of the complete genome Length = 10934 Score = 33.6 bits (67), Expect = 0.13 Identities = 11/26 (42%), Positives = 16/26 (61%) Frame = +1 / -2 Query: 1057 SAYWSIFPPLGCWWSTLGPRGSLSPL 1134 +A W++FPP+G W L + SPL Sbjct: 5893 AAVWALFPPVGSQWGCLASQWRTSPL 5816 ------------------------------------------- It looks like it has something to do with the positions getting divided by 3 but not converted back to correspond to the nucleotide position. When fixing this (and as mentioned above), do we want to only report the first nucleotide position where the mismatch occurs, or report the three positions corresponding to that codon region? Any thoughts? chris From tthmok at gmail.com Sun Feb 3 16:54:49 2008 From: tthmok at gmail.com (Terrance Mok) Date: Sun, 3 Feb 2008 14:54:49 -0700 Subject: [Bioperl-l] Problems Installing Bioperl 1.5.2 - Windows Message-ID: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> Hi I've been trying to install bioperl on a fresh install of ActivePerl on Windows. Following the installation guide using the GUI Perl Package Manager, I add the 4 locations and all of them list 0 packages except for "Bribes http://www.Bribes.org/perl/ppm ". Then when searching for bioperl (with all package view), nothing shows up since no packages are found for all the other locations I added. I've also had problems installing on Ubuntu (helping a friend), when using CPAN and following exactly the guide on the bioperl installation it will not work. When doing the install command in CPAN, install S/SE/SENDU/bioperl- 1.5.2_102.tar.gz she gets an error that "/home/username/.cpan/build/bioperl-1.5.2_102: No such file or directory at Makefile.PL line 25." From anjan.purkayastha at gmail.com Sun Feb 3 12:10:49 2008 From: anjan.purkayastha at gmail.com (ANJAN PURKAYASTHA) Date: Sun, 3 Feb 2008 12:10:49 -0500 Subject: [Bioperl-l] sequence object question Message-ID: hi, here is the problem i'm facing. i parse a genbank file with the statement: my $gb_stream = Bio::SeqIO->new( -file => 'gb_test_file', -format => 'GenBank'); while (my $seq_obj= $gb_stream->next_seq){ ..... } presumably $seq_obj is a Bio::Seq::RichSeq object. now, when I try: my $feat_obj($seq_obj->getSeqFeatures){ ..... } i get an error message: Can't locate object method "getSeqFeatures" via package "Bio::Seq::RichSeq" at gb_file_reader.pl line 11. on reading docs I find that Bio::Seq::RichSeq does not have a getSeqFeatures method. but, RIchSeq is a child of the Seq class, which HAS a getSeqFeatures method (i presume this method is also inherited by the RichSeq class). so, why am i getting an error message and how do i go about getting the features within each genbank file? appreciate any pointers. TIA. anjan -- ANJAN PURKAYASTHA, PhD. Senior Computational Biologist ========================== 1101 King Street, Suite 310, Alexandria, VA 22314. 703.518.8040 (office) 703.740.6939 (mobile) email: anjan at vbi.vt.edu; anjan.purkayastha at gmail.com http://www.vbi.vt.edu ========================== From jason at bioperl.org Sun Feb 3 18:51:21 2008 From: jason at bioperl.org (Jason Stajich) Date: Sun, 3 Feb 2008 15:51:21 -0800 Subject: [Bioperl-l] sequence object question In-Reply-To: References: Message-ID: <212091BA-2942-4A95-9329-AB76D8F102A5@bioperl.org> It is 'get_SeqFeatures' http://doc.bioperl.org/bioperl-live/Bio/FeatureHolderI.html#POD1 Deobfuscator: http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio %3A%3ASeq&sort_order=by+method&search_string=Bio%3A%3ASeq http://bioperl.org/cgi-bin/deob_detail.cgi? method=Bio::Seq::get_SeqFeatures HOWTO: http://bioperl.org/wiki/HOWTO:Feature-Annotation On Feb 3, 2008, at 9:10 AM, ANJAN PURKAYASTHA wrote: > hi, > here is the problem i'm facing. > > i parse a genbank file with the statement: > my $gb_stream = Bio::SeqIO->new( -file => 'gb_test_file', -format => > 'GenBank'); > while (my $seq_obj= $gb_stream->next_seq){ > ..... > > } > > presumably $seq_obj is a Bio::Seq::RichSeq object. > > now, when I try: > my $feat_obj($seq_obj->getSeqFeatures){ > ..... > } > i get an error message: Can't locate object method "getSeqFeatures" > via > package "Bio::Seq::RichSeq" at gb_file_reader.pl line 11. > > > on reading docs I find that Bio::Seq::RichSeq does not have a > getSeqFeatures > method. > but, RIchSeq is a child of the Seq class, which HAS a > getSeqFeatures method > (i presume this method is also inherited by the RichSeq class). > > so, why am i getting an error message and how do i go about getting > the > features within each genbank file? > > appreciate any pointers. > > TIA. > > anjan > > -- > ANJAN PURKAYASTHA, PhD. > Senior Computational Biologist > ========================== > > 1101 King Street, Suite 310, > Alexandria, VA 22314. > 703.518.8040 (office) > 703.740.6939 (mobile) > > email: > anjan at vbi.vt.edu; > anjan.purkayastha at gmail.com > > http://www.vbi.vt.edu > > ========================== > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From anjan.purkayastha at gmail.com Sun Feb 3 23:00:33 2008 From: anjan.purkayastha at gmail.com (ANJAN PURKAYASTHA) Date: Sun, 3 Feb 2008 23:00:33 -0500 Subject: [Bioperl-l] sequence object question In-Reply-To: <212091BA-2942-4A95-9329-AB76D8F102A5@bioperl.org> References: <212091BA-2942-4A95-9329-AB76D8F102A5@bioperl.org> Message-ID: Thanks a lot! On Feb 3, 2008 6:51 PM, Jason Stajich wrote: > It is 'get_SeqFeatures' > http://doc.bioperl.org/bioperl-live/Bio/FeatureHolderI.html#POD1 > > Deobfuscator: > http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio > %3A%3ASeq&sort_order=by+method&search_string=Bio%3A%3ASeq > http://bioperl.org/cgi-bin/deob_detail.cgi? > method=Bio::Seq::get_SeqFeatures > > HOWTO: > http://bioperl.org/wiki/HOWTO:Feature-Annotation > > > On Feb 3, 2008, at 9:10 AM, ANJAN PURKAYASTHA wrote: > > > hi, > > here is the problem i'm facing. > > > > i parse a genbank file with the statement: > > my $gb_stream = Bio::SeqIO->new( -file => 'gb_test_file', -format => > > 'GenBank'); > > while (my $seq_obj= $gb_stream->next_seq){ > > ..... > > > > } > > > > presumably $seq_obj is a Bio::Seq::RichSeq object. > > > > now, when I try: > > my $feat_obj($seq_obj->getSeqFeatures){ > > ..... > > } > > i get an error message: Can't locate object method "getSeqFeatures" > > via > > package "Bio::Seq::RichSeq" at gb_file_reader.pl line 11. > > > > > > on reading docs I find that Bio::Seq::RichSeq does not have a > > getSeqFeatures > > method. > > but, RIchSeq is a child of the Seq class, which HAS a > > getSeqFeatures method > > (i presume this method is also inherited by the RichSeq class). > > > > so, why am i getting an error message and how do i go about getting > > the > > features within each genbank file? > > > > appreciate any pointers. > > > > TIA. > > > > anjan > > > > -- > > ANJAN PURKAYASTHA, PhD. > > Senior Computational Biologist > > ========================== > > > > 1101 King Street, Suite 310, > > Alexandria, VA 22314. > > 703.518.8040 (office) > > 703.740.6939 (mobile) > > > > email: > > anjan at vbi.vt.edu; > > anjan.purkayastha at gmail.com > > > > http://www.vbi.vt.edu > > > > ========================== > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- ANJAN PURKAYASTHA, PhD. Senior Computational Biologist ========================== 1101 King Street, Suite 310, Alexandria, VA 22314. 703.518.8040 (office) 703.740.6939 (mobile) email: anjan at vbi.vt.edu; anjan.purkayastha at gmail.com http://www.vbi.vt.edu ========================== From bix at sendu.me.uk Mon Feb 4 03:45:31 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 04 Feb 2008 08:45:31 +0000 Subject: [Bioperl-l] Problems Installing Bioperl 1.5.2 - Windows In-Reply-To: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> References: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> Message-ID: <47A6D0AB.7050702@sendu.me.uk> Terrance Mok wrote: > Hi I've been trying to install bioperl on a fresh install of ActivePerl on > Windows. > Following the installation guide using the GUI Perl Package Manager, I add > the 4 locations and all of them list 0 packages except for "Bribes > http://www.Bribes.org/perl/ppm ". > Then when searching for bioperl (with all package view), nothing shows up > since no packages are found for all the other locations I added. Hopefully someone else will chime in, but perhaps there's something wrong with the server? Can anyone else confirm? > I've also had problems installing on Ubuntu (helping a friend), when using > CPAN and following exactly the guide on the bioperl installation it will not > work. When doing the install command in CPAN, install S/SE/SENDU/bioperl- > 1.5.2_102.tar.gz she gets an error that > "/home/username/.cpan/build/bioperl-1.5.2_102: No such file or directory at > Makefile.PL line 25." Hard to figure out what might be wrong without complete details. Can she install anything else via CPAN? Has she run out of disc space? From darren.obbard at ed.ac.uk Mon Feb 4 03:56:06 2008 From: darren.obbard at ed.ac.uk (Darren Obbard) Date: Mon, 04 Feb 2008 08:56:06 +0000 Subject: [Bioperl-l] Problems Installing Bioperl 1.5.2 - Windows In-Reply-To: <47A6D0AB.7050702@sendu.me.uk> References: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> <47A6D0AB.7050702@sendu.me.uk> Message-ID: <47A6D326.40103@ed.ac.uk> Hi, > Terrance Mok wrote: >> Then when searching for bioperl (with all package view), nothing >> shows up >> since no packages are found for all the other locations I added. > Hopefully someone else will chime in, but perhaps there's something > wrong with the server? Can anyone else confirm? Just to note that I too have had the same problem. From ca. 2 weeks ago I could see no packages on the recommended bioperl repository. I just assumed I was doing something wrong, and thought I'd wait until my need became urgent. -- Darren Obbard University of Edinburgh, UK From darren.obbard at ed.ac.uk Mon Feb 4 06:07:23 2008 From: darren.obbard at ed.ac.uk (Darren Obbard) Date: Mon, 04 Feb 2008 11:07:23 +0000 Subject: [Bioperl-l] Problems Installing Bioperl 1.5.2 - Windows In-Reply-To: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> References: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> Message-ID: <47A6F1EB.8060806@ed.ac.uk> Hi again, Having just looked, it seems fine on this machine (XP proffessional, sp2). The problem I was (and am) having are on a clean install of Vista (ultimate). Perhaps this is a vista/activestate issue? What versions of windows/activeperl are people having problems with? From cjfields at uiuc.edu Mon Feb 4 12:53:08 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 4 Feb 2008 11:53:08 -0600 Subject: [Bioperl-l] Problems Installing Bioperl 1.5.2 - Windows In-Reply-To: <47A6D0AB.7050702@sendu.me.uk> References: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> <47A6D0AB.7050702@sendu.me.uk> Message-ID: <8863D982-5CEF-4E0E-8840-FC8850D96F06@uiuc.edu> On Feb 4, 2008, at 2:45 AM, Sendu Bala wrote: > Terrance Mok wrote: >> Hi I've been trying to install bioperl on a fresh install of >> ActivePerl on >> Windows. >> Following the installation guide using the GUI Perl Package >> Manager, I add >> the 4 locations and all of them list 0 packages except for "Bribes >> http://www.Bribes.org/perl/ppm ". >> Then when searching for bioperl (with all package view), nothing >> shows up >> since no packages are found for all the other locations I added. > > Hopefully someone else will chime in, but perhaps there's something > wrong with the server? Can anyone else confirm? I haven't used ActivePerl in a while personally since switching to OS X (even when using perl 5.10). Terrance, did you follow the ActivePerl instructions or our installation instructions? Also, we don't guarantee that it will work with AtcivePerl's 5.10 port but it's worth a try; if not downgrade to the latest 5.8 build. >> I've also had problems installing on Ubuntu (helping a friend), >> when using >> CPAN and following exactly the guide on the bioperl installation it >> will not >> work. When doing the install command in CPAN, install S/SE/SENDU/ >> bioperl- >> 1.5.2_102.tar.gz she gets an error that >> "/home/username/.cpan/build/bioperl-1.5.2_102: No such file or >> directory at >> Makefile.PL line 25." > > Hard to figure out what might be wrong without complete details. Can > she install anything else via CPAN? Has she run out of disc space? Haven't seen that before but it works for me using cpan and perl 5.8 and perl 5.10. chris From jay at jays.net Mon Feb 4 14:42:17 2008 From: jay at jays.net (Jay Hannah) Date: Mon, 04 Feb 2008 13:42:17 -0600 Subject: [Bioperl-l] SVN server trouble? Message-ID: <47A76A99.2080307@jays.net> I'm getting this error trying to check out trunk, from 2 different servers on 2 different networks: $ svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk bioperl-live svn: Can't find a temporary directory: Error string not specified yet Is this an SVN server problem of some sort, or is it just me somehow? ( Oh, and come hang out with us: irc.freenode.net #bioperl ) Thanks, Jay Hannah http://clab.ist.unomaha.edu/CLAB/index.php/User:Jhannah From David.Messina at sbc.su.se Mon Feb 4 16:35:42 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Mon, 4 Feb 2008 22:35:42 +0100 Subject: [Bioperl-l] SVN server trouble? In-Reply-To: <47A76A99.2080307@jays.net> References: <47A76A99.2080307@jays.net> Message-ID: <628aabb70802041335o300dca9dha7b75d4e0037ef54@mail.gmail.com> Not just you, Jay. I'm getting the same error trying to 'svn update' on a previously-checked-out working copy. Dave From cjfields at uiuc.edu Mon Feb 4 16:48:00 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 4 Feb 2008 15:48:00 -0600 Subject: [Bioperl-l] SVN server trouble? In-Reply-To: <628aabb70802041335o300dca9dha7b75d4e0037ef54@mail.gmail.com> References: <47A76A99.2080307@jays.net> <628aabb70802041335o300dca9dha7b75d4e0037ef54@mail.gmail.com> Message-ID: I went ahead and reported it to support. It's an odd issue, but a checkout works from dev (for those with dev accounts), so it has to be something wonky on code.open-bio.org. chris On Feb 4, 2008, at 3:35 PM, Dave Messina wrote: > Not just you, Jay. I'm getting the same error trying to 'svn update' > on a > previously-checked-out working copy. > Dave From jason at bioperl.org Mon Feb 4 17:11:14 2008 From: jason at bioperl.org (Jason Stajich) Date: Mon, 4 Feb 2008 14:11:14 -0800 Subject: [Bioperl-l] SVN server trouble? In-Reply-To: References: <47A76A99.2080307@jays.net> <628aabb70802041335o300dca9dha7b75d4e0037ef54@mail.gmail.com> Message-ID: ChrisD says that something with is eating up free space on the host so /tmp is full causing the problem(s). Will report in when it's been fixed and we can figure out whether the SVNweb runaway svn diffs are creating the glut of big files. -jason On Feb 4, 2008, at 1:48 PM, Chris Fields wrote: > I went ahead and reported it to support. It's an odd issue, but a > checkout works from dev (for those with dev accounts), so it has to > be something wonky on code.open-bio.org. > > chris > > On Feb 4, 2008, at 3:35 PM, Dave Messina wrote: > >> Not just you, Jay. I'm getting the same error trying to 'svn >> update' on a >> previously-checked-out working copy. >> Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From luisecarracedo at hotmail.com Tue Feb 5 12:59:33 2008 From: luisecarracedo at hotmail.com (luis esteban) Date: Tue, 5 Feb 2008 19:59:33 +0200 Subject: [Bioperl-l] Eland report Message-ID: Hi to everibody!! Is there anybody working in any project tryng to convert Blat or Blast reports in Eland reports. Any Idea, any sugestions would be apreciated. Thanks a Lot Luis Esteban PhD _________________________________________________________________ ?Aburrido? Ingres? ya y divertite como nunca en MSN Juegos. http://juegos.ar.msn.com/ From jason at bioperl.org Tue Feb 5 14:22:14 2008 From: jason at bioperl.org (Jason Stajich) Date: Tue, 5 Feb 2008 11:22:14 -0800 Subject: [Bioperl-l] Eland report In-Reply-To: References: Message-ID: You mean print out eland reports from a BLAST/BLAT/table report? I really hope eland report doesn't become the standard though... -jason On Feb 5, 2008, at 9:59 AM, luis esteban wrote: > > Hi to everibody!! > Is there anybody working in any project tryng to convert Blat or > Blast reports in Eland reports. > Any Idea, any sugestions would be apreciated. > Thanks a Lot > Luis Esteban PhD > _________________________________________________________________ > ?Aburrido? Ingres? ya y divertite como nunca en MSN Juegos. > http://juegos.ar.msn.com/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From sjmiller at email.arizona.edu Tue Feb 5 15:23:28 2008 From: sjmiller at email.arizona.edu (Susan J. Miller) Date: Tue, 05 Feb 2008 13:23:28 -0700 Subject: [Bioperl-l] Bioperl-l Digest, Vol 57, Issue 10 In-Reply-To: References: Message-ID: <47A8C5C0.7040401@email.arizona.edu> bioperl-l-request at lists.open-bio.org wrote: > > Message: 2 > Date: Thu, 31 Jan 2008 10:34:31 +0100 > From: Georg Otto > Subject: Re: [Bioperl-l] Bio::DB::GenBank and large number of requests > To: bioperl-l at bioperl.org > Message-ID: > Content-Type: text/plain; charset=us-ascii > > Hi, > > I succeeded with a similar task using the seqhound database. I had a > list of > 200,000 gid numbers, but I guess it can work in a similar > fashion using accession numbers. Hi Georg, How recently have you used the SeqHound database? We installed it from CPAN but when we try to run the following test script this error occurs: MSG: HTTP::Request error: 500 Can't connect to seqhound.blueprint.org:80 (Bad hostname 'seqhound.blueprint.org') Script: #!/usr/local/bin/perl use warnings; use Bio::SeqIO; use Bio::DB::SeqHound; my $sh = Bio::DB::SeqHound->new(); my $seq = $sh->get_Seq_by_acc("CAA28783"); print $seq->display_name, "\n"; Do you know if SeqHound has moved? Is there a way to comfigure it so that it works? Thanks, -susan Susan J. Miller Manager, Scientific Data Analysis Biotechnology Computing Facility Arizona Research Laboratories (520) 626-2597 From cjfields at uiuc.edu Tue Feb 5 16:38:31 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 5 Feb 2008 15:38:31 -0600 Subject: [Bioperl-l] SeqHound In-Reply-To: <47A8C5C0.7040401@email.arizona.edu> References: <47A8C5C0.7040401@email.arizona.edu> Message-ID: <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> The URL has changed. I'll fix this in bioperl-live. You can fix this in your script directly for now (though I hate globals): use Bio::DB::SeqHound; $Bio::DB::SeqHound::HOSTBASE = 'http://dogboxonline.unleashedinformatics.com/' ; my $sh = Bio::DB::SeqHound->new(); my $seq = $sh->get_Seq_by_acc("CAA28783"); print $seq->display_name, "\n"; chris On Feb 5, 2008, at 2:23 PM, Susan J. Miller wrote: > bioperl-l-request at lists.open-bio.org wrote: >> >> Message: 2 >> Date: Thu, 31 Jan 2008 10:34:31 +0100 >> From: Georg Otto >> Subject: Re: [Bioperl-l] Bio::DB::GenBank and large number of >> requests >> To: bioperl-l at bioperl.org >> Message-ID: >> Content-Type: text/plain; charset=us-ascii >> Hi, >> I succeeded with a similar task using the seqhound database. I had a >> list of > 200,000 gid numbers, but I guess it can work in a similar >> fashion using accession numbers. > > Hi Georg, > > How recently have you used the SeqHound database? We installed it > from CPAN but when we try to run the following test script this > error occurs: > > MSG: HTTP::Request error: 500 Can't connect to > seqhound.blueprint.org:80 (Bad hostname 'seqhound.blueprint.org') > > Script: > #!/usr/local/bin/perl > use warnings; > use Bio::SeqIO; > use Bio::DB::SeqHound; > > my $sh = Bio::DB::SeqHound->new(); > my $seq = $sh->get_Seq_by_acc("CAA28783"); > print $seq->display_name, "\n"; > > > Do you know if SeqHound has moved? Is there a way to comfigure it > so that it works? > > Thanks, > -susan > > Susan J. Miller > Manager, Scientific Data Analysis > Biotechnology Computing Facility > Arizona Research Laboratories > (520) 626-2597 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Tue Feb 5 17:59:48 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 5 Feb 2008 16:59:48 -0600 Subject: [Bioperl-l] SeqHound In-Reply-To: <47A8E3BF.7000308@email.arizona.edu> References: <47A8C5C0.7040401@email.arizona.edu> <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> <47A8E3BF.7000308@email.arizona.edu> Message-ID: <025C4E5C-CD77-442F-AEB1-ACC265B36017@uiuc.edu> On Feb 5, 2008, at 4:31 PM, Susan J. Miller wrote: > Chris Fields wrote: >> The URL has changed. I'll fix this in bioperl-live. >> You can fix this in your script directly for now (though I hate >> globals): >> use Bio::DB::SeqHound; >> $Bio::DB::SeqHound::HOSTBASE = 'http://dogboxonline.unleashedinformatics.com/' >> ; > > Thanks Chris, that helps a little bit, but I'm still not having much > luck with the SeqHound DB. The CPAN SeqHound.pm documentation for > the get_Stream_by_Query method says: > ... No problem. It was an easy fix. ... > I get the error: > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Id list has been truncated even after maxids requested > STACK: Error::throw > STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/ > Root/Root.pm:359 > STACK: Bio::DB::Query::WebQuery::_fetch_ids /usr/lib/perl5/site_perl/ > 5.8.8/Bio/DB/Query/WebQuery.pm:236 > STACK: Bio::DB::Query::WebQuery::ids /usr/lib/perl5/site_perl/5.8.8/ > Bio/DB/Query/WebQuery.pm:200 > STACK: Bio::DB::SeqHound::get_Stream_by_query /usr/lib/perl5/ > site_perl/5.8.8/Bio/DB/SeqHound.pm:314 > STACK: SeqHoundQuery.pl:21 > > There are only 5013 sequences that match this query so it seems odd > that the Id list is too long...or am I using SeqHound improperly? > > (My reason for trying SeqHound is that I want to set up a monthly > cron job to download nucest fasta sequences for drosphila > melanogaster, and I've tried NCBI E-Utilities and the script > generated by the NCBI ebot and in both cases some of the 570828 > records get dropped, even after running repeated attempts.) > > > Thanks, > -susan The URL is likely way too long (a common problem when using a GET as opposed to a POST with LWP). NCBI's efetch has the same problem, which is why using epost is a good idea (except it only takes GI's!). You will have to loop through the IDs in bunches of 250-500 max to get what you want. Don't know if there is a way to post to SeqHound but it might be worth investigating at some point. I also see they have a SOAP interface up. chris From sjmiller at email.arizona.edu Tue Feb 5 17:31:27 2008 From: sjmiller at email.arizona.edu (Susan J. Miller) Date: Tue, 05 Feb 2008 15:31:27 -0700 Subject: [Bioperl-l] SeqHound In-Reply-To: <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> References: <47A8C5C0.7040401@email.arizona.edu> <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> Message-ID: <47A8E3BF.7000308@email.arizona.edu> Chris Fields wrote: > The URL has changed. I'll fix this in bioperl-live. > > You can fix this in your script directly for now (though I hate globals): > > use Bio::DB::SeqHound; > > $Bio::DB::SeqHound::HOSTBASE = > 'http://dogboxonline.unleashedinformatics.com/'; > Thanks Chris, that helps a little bit, but I'm still not having much luck with the SeqHound DB. The CPAN SeqHound.pm documentation for the get_Stream_by_Query method says: Title : get_Stream_by_query Usage : $seq = $db->get_Stream_by_query($query); Function: Retrieves Seq objects from Entrez 'en masse', rather than one at a time. For large numbers of sequences, this is far superior than get_Stream_by_[id/acc](). Example : $query_string = 'Candida maltosa 26S ribosomal RNA gene'; However, when I try: $query_string = 'drosophila simulans[orgn]'; $query = Bio::DB::Query::GenBank->new(-db=>'nucest', -query=>$query_string); $stream = $sh->get_Stream_by_query($query); I get the error: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Id list has been truncated even after maxids requested STACK: Error::throw STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359 STACK: Bio::DB::Query::WebQuery::_fetch_ids /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Query/WebQuery.pm:236 STACK: Bio::DB::Query::WebQuery::ids /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Query/WebQuery.pm:200 STACK: Bio::DB::SeqHound::get_Stream_by_query /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqHound.pm:314 STACK: SeqHoundQuery.pl:21 There are only 5013 sequences that match this query so it seems odd that the Id list is too long...or am I using SeqHound improperly? (My reason for trying SeqHound is that I want to set up a monthly cron job to download nucest fasta sequences for drosphila melanogaster, and I've tried NCBI E-Utilities and the script generated by the NCBI ebot and in both cases some of the 570828 records get dropped, even after running repeated attempts.) Thanks, -susan Susan J. Miller Manager, Scientific Data Analysis Biotechnology Computing Facility Arizona Research Laboratories (520) 626-2597 From lincoln.stein at gmail.com Tue Feb 5 18:43:06 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 5 Feb 2008 18:43:06 -0500 Subject: [Bioperl-l] ActiveState Perl problems Message-ID: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> Hi Scott, Bioperl folk, I'm afraid that the ActiveState ppm install of BioPerl no longer works. Using the current ActiveState (perl version 5.10), I added the Bribes, Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates repositories. However, when I synched up, all but the Bribes reps showed up empty in the ppm tool. In addition, there's nothing in the release candidate rep any longer. I used to use this to get at Bioperl 1.5. Perhaps the architecture needs to be changed? Lincoln -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From cjfields at uiuc.edu Tue Feb 5 19:13:29 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 5 Feb 2008 18:13:29 -0600 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> Message-ID: I'll try changing out package.xml on portal. The one in RC appears to be blank now (which explains why you can't use that one). chris On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: > Hi Scott, Bioperl folk, > > I'm afraid that the ActiveState ppm install of BioPerl no longer > works. > Using the current ActiveState (perl version 5.10), I added the Bribes, > Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates > repositories. However, when I synched up, all but the Bribes reps > showed up > empty in the ppm tool. > > In addition, there's nothing in the release candidate rep any > longer. I used > to use this to get at Bioperl 1.5. > > Perhaps the architecture needs to be changed? > > Lincoln > > > > -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > (516) 367-8380 (voice) > (516) 367-8389 (fax) > FOR URGENT MESSAGES & SCHEDULING, > PLEASE CONTACT MY ASSISTANT, > SANDRA MICHELSEN, AT michelse at cshl.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From golharam at umdnj.edu Tue Feb 5 18:15:43 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Tue, 05 Feb 2008 18:15:43 -0500 Subject: [Bioperl-l] Bio::SeqIO object for GenBank XML format? Message-ID: <47A8EE1F.7050100@umdnj.edu> Is there a SeqIO module for the XML format for GenBank records? The "http://www.bioperl.org/wiki/HOWTO:SeqIO" page doesn't show one listed. From Kevin.M.Brown at asu.edu Tue Feb 5 19:25:58 2008 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Tue, 5 Feb 2008 17:25:58 -0700 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> Message-ID: <1A4207F8295607498283FE9E93B775B4045AA97F@EX02.asurite.ad.asu.edu> Well, Kobes seems to have two different ppm repos. One for 8xx builds of activestate perl and one for 10xx builds. So, Bioperl probably needs to be rebuilt for 5.10 to get it to show in the 5.10 repos. I just opened up Activestate perl 5.8 and I see 1.5.2_100 listed in it from the Regular Release site. > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Lincoln Stein > Sent: Tuesday, February 05, 2008 4:43 PM > To: Scott Cain > Cc: bioperl-l > Subject: [Bioperl-l] ActiveState Perl problems > > Hi Scott, Bioperl folk, > > I'm afraid that the ActiveState ppm install of BioPerl no > longer works. > Using the current ActiveState (perl version 5.10), I added the Bribes, > Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates > repositories. However, when I synched up, all but the Bribes > reps showed up > empty in the ppm tool. > > In addition, there's nothing in the release candidate rep any > longer. I used > to use this to get at Bioperl 1.5. > > Perhaps the architecture needs to be changed? > > Lincoln > > > > -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > (516) 367-8380 (voice) > (516) 367-8389 (fax) > FOR URGENT MESSAGES & SCHEDULING, > PLEASE CONTACT MY ASSISTANT, > SANDRA MICHELSEN, AT michelse at cshl.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From jason at bioperl.org Tue Feb 5 19:45:35 2008 From: jason at bioperl.org (Jason Stajich) Date: Tue, 5 Feb 2008 16:45:35 -0800 Subject: [Bioperl-l] Bio::SeqIO object for GenBank XML format? In-Reply-To: <47A8EE1F.7050100@umdnj.edu> References: <47A8EE1F.7050100@umdnj.edu> Message-ID: <67216BC0-8F2F-432C-B94F-C9A92640E01A@bioperl.org> Then there probably isn't - the codebase Bo/SeqIO directory would tell you otherwise I guess. Does anyone use the format and want to write one? On Feb 5, 2008, at 3:15 PM, Ryan Golhar wrote: > Is there a SeqIO module for the XML format for GenBank records? > The "http://www.bioperl.org/wiki/HOWTO:SeqIO" page doesn't show one > listed. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bosborne11 at verizon.net Tue Feb 5 18:52:57 2008 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 05 Feb 2008 18:52:57 -0500 Subject: [Bioperl-l] SeqHound In-Reply-To: <47A8E3BF.7000308@email.arizona.edu> References: <47A8C5C0.7040401@email.arizona.edu> <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> <47A8E3BF.7000308@email.arizona.edu> Message-ID: <4D3A27D3-D535-4F34-8A7F-966F30B51F86@verizon.net> Susan, It sounds like you could use rsync though perhaps there's some detail that I missed. A typical command would look something like this: rsync -av ftp.ncbi.nlm.nih.gov::blast/db/FASTA/ /local/data/FASTA/ Brian O. On Feb 5, 2008, at 5:31 PM, Susan J. Miller wrote: > (My reason for trying SeqHound is that I want to set up a monthly > cron job to download nucest fasta sequences for drosphila > melanogaster, and I've tried NCBI E-Utilities and the script > generated by the NCBI ebot and in both cases some of the 570828 > records get dropped, even after running repeated attempts.) From barry.moore at genetics.utah.edu Tue Feb 5 20:09:56 2008 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Tue, 5 Feb 2008 18:09:56 -0700 Subject: [Bioperl-l] SeqHound In-Reply-To: <47A8E3BF.7000308@email.arizona.edu> References: <47A8C5C0.7040401@email.arizona.edu> <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> <47A8E3BF.7000308@email.arizona.edu> Message-ID: Susan, I'm joining this discussion late so my apologies if I'm missing the original point. If you're trying to routinely download thousands of sequences from GenBank or SeqHound you probably want to be using ftp to download the flat files and query/parse locally. If you're trying to stay on top of the latest Drosophila ESTs, then how about setting up a nightly cron job to download the incremental updates from NCBIs ftp (ftp://ftp.ncbi.nih.gov/genbank/daily-nc) and parse that for Drosophila EST sequences. The EST division is huge, but I would think nightly incrementals should be manageable. Barry On Feb 5, 2008, at 3:31 PM, Susan J. Miller wrote: > Chris Fields wrote: >> The URL has changed. I'll fix this in bioperl-live. >> >> You can fix this in your script directly for now (though I hate >> globals): >> >> use Bio::DB::SeqHound; >> >> $Bio::DB::SeqHound::HOSTBASE = >> 'http://dogboxonline.unleashedinformatics.com/'; >> > > Thanks Chris, that helps a little bit, but I'm still not having much > luck with the SeqHound DB. The CPAN SeqHound.pm documentation for the > get_Stream_by_Query method says: > > Title : get_Stream_by_query > Usage : $seq = $db->get_Stream_by_query($query); > Function: Retrieves Seq objects from Entrez 'en masse', rather than > one at a time. For large numbers of sequences, this is far superior > than get_Stream_by_[id/acc](). > Example : $query_string = 'Candida maltosa 26S ribosomal RNA gene'; > > However, when I try: > > $query_string = 'drosophila simulans[orgn]'; > $query = Bio::DB::Query::GenBank->new(-db=>'nucest', > -query=>$query_string); > $stream = $sh->get_Stream_by_query($query); > > I get the error: > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Id list has been truncated even after maxids requested > STACK: Error::throw > STACK: Bio::Root::Root::throw > /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359 > STACK: Bio::DB::Query::WebQuery::_fetch_ids > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Query/WebQuery.pm:236 > STACK: Bio::DB::Query::WebQuery::ids > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Query/WebQuery.pm:200 > STACK: Bio::DB::SeqHound::get_Stream_by_query > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqHound.pm:314 > STACK: SeqHoundQuery.pl:21 > > There are only 5013 sequences that match this query so it seems odd > that > the Id list is too long...or am I using SeqHound improperly? > > (My reason for trying SeqHound is that I want to set up a monthly cron > job to download nucest fasta sequences for drosphila melanogaster, and > I've tried NCBI E-Utilities and the script generated by the NCBI ebot > and in both cases some of the 570828 records get dropped, even after > running repeated attempts.) > > > Thanks, > -susan > > Susan J. Miller > Manager, Scientific Data Analysis > Biotechnology Computing Facility > Arizona Research Laboratories > (520) 626-2597 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at uiuc.edu Tue Feb 5 20:19:16 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 5 Feb 2008 19:19:16 -0600 Subject: [Bioperl-l] Bio::SeqIO object for GenBank XML format? In-Reply-To: <67216BC0-8F2F-432C-B94F-C9A92640E01A@bioperl.org> References: <47A8EE1F.7050100@umdnj.edu> <67216BC0-8F2F-432C-B94F-C9A92640E01A@bioperl.org> Message-ID: <9F54378C-9905-4E90-88B9-F539B1E933DF@uiuc.edu> Could probably base it off of the BSML parser. Might be better to write up a general INSDC XML parser, which GenBank/EMBL/DDBJ all use now: http://www.insdc.org/page.php?page=documents&sid=fa24a7d177ab7a687e87a85db6822c01 chris On Feb 5, 2008, at 6:45 PM, Jason Stajich wrote: > Then there probably isn't - the codebase Bo/SeqIO directory would > tell you otherwise I guess. > Does anyone use the format and want to write one? > > On Feb 5, 2008, at 3:15 PM, Ryan Golhar wrote: > >> Is there a SeqIO module for the XML format for GenBank records? >> The "http://www.bioperl.org/wiki/HOWTO:SeqIO" page doesn't show one >> listed. >> >> _______________________________________________ >> 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 Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Tue Feb 5 20:32:52 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 5 Feb 2008 19:32:52 -0600 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <1A4207F8295607498283FE9E93B775B4045AA97F@EX02.asurite.ad.asu.edu> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> <1A4207F8295607498283FE9E93B775B4045AA97F@EX02.asurite.ad.asu.edu> Message-ID: <3BFD59BB-152C-4D43-B8E7-96DC293D8C34@uiuc.edu> Kobes keeps two separate repos because there are several binary-only modules (DBD::mysql, GD, etc) which are incompatible with older major perl releases (5.6, 5.8, 5.10). If the modules are pure perl then there shouldn't be a problem. Saying that, there is one issue which tanks Bio::SeqIO::entrezgene parsing (which mistakenly made pseudohashes) which Stefan and I fixed recently; that'll tank in perl 5.10. chris On Feb 5, 2008, at 6:25 PM, Kevin Brown wrote: > Well, Kobes seems to have two different ppm repos. One for 8xx builds > of activestate perl and one for 10xx builds. So, Bioperl probably > needs > to be rebuilt for 5.10 to get it to show in the 5.10 repos. I just > opened up Activestate perl 5.8 and I see 1.5.2_100 listed in it from > the > Regular Release site. > >> -----Original Message----- >> From: bioperl-l-bounces at lists.open-bio.org >> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of >> Lincoln Stein >> Sent: Tuesday, February 05, 2008 4:43 PM >> To: Scott Cain >> Cc: bioperl-l >> Subject: [Bioperl-l] ActiveState Perl problems >> >> Hi Scott, Bioperl folk, >> >> I'm afraid that the ActiveState ppm install of BioPerl no >> longer works. >> Using the current ActiveState (perl version 5.10), I added the >> Bribes, >> Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates >> repositories. However, when I synched up, all but the Bribes >> reps showed up >> empty in the ppm tool. >> >> In addition, there's nothing in the release candidate rep any >> longer. I used >> to use this to get at Bioperl 1.5. >> >> Perhaps the architecture needs to be changed? >> >> Lincoln >> >> >> >> -- >> Lincoln D. Stein >> Cold Spring Harbor Laboratory >> 1 Bungtown Road >> Cold Spring Harbor, NY 11724 >> (516) 367-8380 (voice) >> (516) 367-8389 (fax) >> FOR URGENT MESSAGES & SCHEDULING, >> PLEASE CONTACT MY ASSISTANT, >> SANDRA MICHELSEN, AT michelse at cshl.edu >> _______________________________________________ >> 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 Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From golharam at umdnj.edu Tue Feb 5 19:54:24 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Tue, 05 Feb 2008 19:54:24 -0500 Subject: [Bioperl-l] Bio::SeqIO object for GenBank XML format? In-Reply-To: <67216BC0-8F2F-432C-B94F-C9A92640E01A@bioperl.org> References: <47A8EE1F.7050100@umdnj.edu> <67216BC0-8F2F-432C-B94F-C9A92640E01A@bioperl.org> Message-ID: <47A90540.9060002@umdnj.edu> If no one else has already built one, then I'd be happy to based on the genbank and chaosxml/tigrxml modules. Ryan Jason Stajich wrote: > Then there probably isn't - the codebase Bo/SeqIO directory would tell > you otherwise I guess. > Does anyone use the format and want to write one? > > On Feb 5, 2008, at 3:15 PM, Ryan Golhar wrote: > >> Is there a SeqIO module for the XML format for GenBank records? The >> "http://www.bioperl.org/wiki/HOWTO:SeqIO" page doesn't show one listed. >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > From cjfields at uiuc.edu Tue Feb 5 22:06:06 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 5 Feb 2008 21:06:06 -0600 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> Message-ID: <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> According to this page you can remove the tags and it will assume the files are for any OS: http://aspn.activestate.com/ASPN/docs/ActivePerl/5.10/lib/ActivePerl/PPM/PPD.html#ppd_xml_format I have moved the old package.xml to package.bak and replaced it with one w/o those tags; I can now pick it up on Mac OS X using ActiveState perl 5.10: ppm> search * Downloading bioperl.org packlist...not modified 1: Bio-ASN1-EntrezGene v1.09 2: Bundle-BioPerl-Core v1.5.2_100 3: Bundle-BioPerl-Db v1.5.2_100 4: Bundle-BioPerl-Network v1.5.2_100 5: Bundle-BioPerl-Run v1.5.2_100 6: Class-AutoClass v1.01 7: GD-SVG v0.25 8: Graph v0.80 9: SVG-Graph v0.01 10: bioperl v1.5.2_100 11: bioperl-db v1.5.2_100 12: bioperl-network v1.5.2_100 13: bioperl-run v1.5.2_100 I'll add ARCHITECTURE versioning tags back when we know it's working (maybe tomorrow, when I can get on to WinXP to test it). chris On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: > Hi Scott, Bioperl folk, > > I'm afraid that the ActiveState ppm install of BioPerl no longer > works. > Using the current ActiveState (perl version 5.10), I added the Bribes, > Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates > repositories. However, when I synched up, all but the Bribes reps > showed up > empty in the ppm tool. > > In addition, there's nothing in the release candidate rep any > longer. I used > to use this to get at Bioperl 1.5. > > Perhaps the architecture needs to be changed? > > Lincoln > > > > -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > (516) 367-8380 (voice) > (516) 367-8389 (fax) > FOR URGENT MESSAGES & SCHEDULING, > PLEASE CONTACT MY ASSISTANT, > SANDRA MICHELSEN, AT michelse at cshl.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From lincoln.stein at gmail.com Tue Feb 5 23:25:27 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 5 Feb 2008 23:25:27 -0500 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> Message-ID: <6dce9a0b0802052025y1243b7den4d19ed4dd1d71ff9@mail.gmail.com> Wow, nice fast work! Thanks all. Lincoln On Feb 5, 2008 10:06 PM, Chris Fields wrote: > According to this page you can remove the tags and it > will assume the files are for any OS: > > > http://aspn.activestate.com/ASPN/docs/ActivePerl/5.10/lib/ActivePerl/PPM/PPD.html#ppd_xml_format > > I have moved the old package.xml to package.bak and replaced it with > one w/o those tags; I can now pick it up on Mac OS X using ActiveState > perl 5.10: > > ppm> search * > Downloading bioperl.org packlist...not modified > 1: Bio-ASN1-EntrezGene v1.09 > 2: Bundle-BioPerl-Core v1.5.2_100 > 3: Bundle-BioPerl-Db v1.5.2_100 > 4: Bundle-BioPerl-Network v1.5.2_100 > 5: Bundle-BioPerl-Run v1.5.2_100 > 6: Class-AutoClass v1.01 > 7: GD-SVG v0.25 > 8: Graph v0.80 > 9: SVG-Graph v0.01 > 10: bioperl v1.5.2_100 > 11: bioperl-db v1.5.2_100 > 12: bioperl-network v1.5.2_100 > 13: bioperl-run v1.5.2_100 > > I'll add ARCHITECTURE versioning tags back when we know it's working > (maybe tomorrow, when I can get on to WinXP to test it). > > chris > > On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: > > > Hi Scott, Bioperl folk, > > > > I'm afraid that the ActiveState ppm install of BioPerl no longer > > works. > > Using the current ActiveState (perl version 5.10), I added the Bribes, > > Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates > > repositories. However, when I synched up, all but the Bribes reps > > showed up > > empty in the ppm tool. > > > > In addition, there's nothing in the release candidate rep any > > longer. I used > > to use this to get at Bioperl 1.5. > > > > Perhaps the architecture needs to be changed? > > > > Lincoln > > > > > > > > -- > > Lincoln D. Stein > > Cold Spring Harbor Laboratory > > 1 Bungtown Road > > Cold Spring Harbor, NY 11724 > > (516) 367-8380 (voice) > > (516) 367-8389 (fax) > > FOR URGENT MESSAGES & SCHEDULING, > > PLEASE CONTACT MY ASSISTANT, > > SANDRA MICHELSEN, AT michelse at cshl.edu > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From bioinfo21 at gmail.com Wed Feb 6 02:04:37 2008 From: bioinfo21 at gmail.com (Priya) Date: Wed, 6 Feb 2008 12:34:37 +0530 Subject: [Bioperl-l] Bioperl Message-ID: <98af6e260802052304y66add58fi65e289cb4b9069f7@mail.gmail.com> Hi all I am new to Bioperl. I have installed Bioperl in Linux. I am trying to use one of the sample programs in bioperl. I couldnt figure out where to set the http proxy authentication. I tried to follow the manual for installation. Still I am not getting it right . Let me know how to set the proxy authentication and where exactly it should be set. I tried to set env variables for http in .bashrc. Still its not working. Help me out. Thanks in advance. Regards Priya.. From lincoln.stein at gmail.com Wed Feb 6 10:03:31 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Wed, 6 Feb 2008 10:03:31 -0500 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> Message-ID: <6dce9a0b0802060703j231704acta813715265f1fab5@mail.gmail.com> Sadly, bioperl still won't install under ActiveState 5.10 because it can't find a repository with the SOAP::Lite prerequisite. Lincoln On Feb 5, 2008 10:06 PM, Chris Fields wrote: > According to this page you can remove the tags and it > will assume the files are for any OS: > > > http://aspn.activestate.com/ASPN/docs/ActivePerl/5.10/lib/ActivePerl/PPM/PPD.html#ppd_xml_format > > I have moved the old package.xml to package.bak and replaced it with > one w/o those tags; I can now pick it up on Mac OS X using ActiveState > perl 5.10: > > ppm> search * > Downloading bioperl.org packlist...not modified > 1: Bio-ASN1-EntrezGene v1.09 > 2: Bundle-BioPerl-Core v1.5.2_100 > 3: Bundle-BioPerl-Db v1.5.2_100 > 4: Bundle-BioPerl-Network v1.5.2_100 > 5: Bundle-BioPerl-Run v1.5.2_100 > 6: Class-AutoClass v1.01 > 7: GD-SVG v0.25 > 8: Graph v0.80 > 9: SVG-Graph v0.01 > 10: bioperl v1.5.2_100 > 11: bioperl-db v1.5.2_100 > 12: bioperl-network v1.5.2_100 > 13: bioperl-run v1.5.2_100 > > I'll add ARCHITECTURE versioning tags back when we know it's working > (maybe tomorrow, when I can get on to WinXP to test it). > > chris > > On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: > > > Hi Scott, Bioperl folk, > > > > I'm afraid that the ActiveState ppm install of BioPerl no longer > > works. > > Using the current ActiveState (perl version 5.10), I added the Bribes, > > Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates > > repositories. However, when I synched up, all but the Bribes reps > > showed up > > empty in the ppm tool. > > > > In addition, there's nothing in the release candidate rep any > > longer. I used > > to use this to get at Bioperl 1.5. > > > > Perhaps the architecture needs to be changed? > > > > Lincoln > > > > > > > > -- > > Lincoln D. Stein > > Cold Spring Harbor Laboratory > > 1 Bungtown Road > > Cold Spring Harbor, NY 11724 > > (516) 367-8380 (voice) > > (516) 367-8389 (fax) > > FOR URGENT MESSAGES & SCHEDULING, > > PLEASE CONTACT MY ASSISTANT, > > SANDRA MICHELSEN, AT michelse at cshl.edu > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From cjfields at uiuc.edu Wed Feb 6 10:55:00 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 6 Feb 2008 09:55:00 -0600 Subject: [Bioperl-l] BOSC 2008? Message-ID: <1182EAB9-7A75-498F-B91B-C14771DFD607@uiuc.edu> Anyone have information on the where/when for BOSC 2008? chris From n.haigh at sheffield.ac.uk Wed Feb 6 11:36:19 2008 From: n.haigh at sheffield.ac.uk (Nathan S Haigh) Date: Wed, 06 Feb 2008 16:36:19 +0000 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <6dce9a0b0802060703j231704acta813715265f1fab5@mail.gmail.com> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> <6dce9a0b0802060703j231704acta813715265f1fab5@mail.gmail.com> Message-ID: <47A9E203.3080008@sheffield.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Last time I was playing with Windows PPM packages, I seem to remember having to build some packages for inclusion in the BioPerl repo so that all dependencies were satisfied. Unfortunately, I don't have time to do this myself, but it's a work around if someone has time to do it? Alternatively, contact one of the other repo's and see if they can do something about it as it will/should be available for at least an older version of ActivePerl. Sorry I can't be more help. Nath Lincoln Stein wrote: > Sadly, bioperl still won't install under ActiveState 5.10 because it can't > find a repository with the SOAP::Lite prerequisite. > > Lincoln > > On Feb 5, 2008 10:06 PM, Chris Fields wrote: > >> According to this page you can remove the tags and it >> will assume the files are for any OS: >> >> >> http://aspn.activestate.com/ASPN/docs/ActivePerl/5.10/lib/ActivePerl/PPM/PPD.html#ppd_xml_format >> >> I have moved the old package.xml to package.bak and replaced it with >> one w/o those tags; I can now pick it up on Mac OS X using ActiveState >> perl 5.10: >> >> ppm> search * >> Downloading bioperl.org packlist...not modified >> 1: Bio-ASN1-EntrezGene v1.09 >> 2: Bundle-BioPerl-Core v1.5.2_100 >> 3: Bundle-BioPerl-Db v1.5.2_100 >> 4: Bundle-BioPerl-Network v1.5.2_100 >> 5: Bundle-BioPerl-Run v1.5.2_100 >> 6: Class-AutoClass v1.01 >> 7: GD-SVG v0.25 >> 8: Graph v0.80 >> 9: SVG-Graph v0.01 >> 10: bioperl v1.5.2_100 >> 11: bioperl-db v1.5.2_100 >> 12: bioperl-network v1.5.2_100 >> 13: bioperl-run v1.5.2_100 >> >> I'll add ARCHITECTURE versioning tags back when we know it's working >> (maybe tomorrow, when I can get on to WinXP to test it). >> >> chris >> >> On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: >> >>> Hi Scott, Bioperl folk, >>> >>> I'm afraid that the ActiveState ppm install of BioPerl no longer >>> works. >>> Using the current ActiveState (perl version 5.10), I added the Bribes, >>> Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates >>> repositories. However, when I synched up, all but the Bribes reps >>> showed up >>> empty in the ppm tool. >>> >>> In addition, there's nothing in the release candidate rep any >>> longer. I used >>> to use this to get at Bioperl 1.5. >>> >>> Perhaps the architecture needs to be changed? >>> >>> Lincoln >>> >>> >>> >>> -- >>> Lincoln D. Stein >>> Cold Spring Harbor Laboratory >>> 1 Bungtown Road >>> Cold Spring Harbor, NY 11724 >>> (516) 367-8380 (voice) >>> (516) 367-8389 (fax) >>> FOR URGENT MESSAGES & SCHEDULING, >>> PLEASE CONTACT MY ASSISTANT, >>> SANDRA MICHELSEN, AT michelse at cshl.edu >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> >> > > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHqeID9gTv6QYzVL4RAsyqAJ0XkCJgdKu6SHzci4XGww4OofRBzgCfQqCL MxylCxJflKjtscupJ5cRHKk= =Brpe -----END PGP SIGNATURE----- From cjfields at uiuc.edu Wed Feb 6 12:09:40 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 6 Feb 2008 11:09:40 -0600 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <47A9E203.3080008@sheffield.ac.uk> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> <6dce9a0b0802060703j231704acta813715265f1fab5@mail.gmail.com> <47A9E203.3080008@sheffield.ac.uk> Message-ID: <0E379930-B25F-42F5-8706-B39C64D6D2EB@uiuc.edu> SOAP::Lite is pretty complicated; I'm not sure if it is pure perl either (which makes it problematic for WinXP). I'll do some checking around to see if there is a perl 5.10 build for Windows. I'm toying around with the idea of setting up a nightly PPM archives of the bioperl distributions in their own directory, along with nightly tar balls. Just need to get time to work on it! chris On Feb 6, 2008, at 10:36 AM, Nathan S Haigh wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Last time I was playing with Windows PPM packages, I seem to > remember having to build some packages for inclusion in the BioPerl > repo so that all > dependencies were satisfied. Unfortunately, I don't have time to do > this myself, but it's a work around if someone has time to do it? > Alternatively, > contact one of the other repo's and see if they can do something > about it as it will/should be available for at least an older > version of ActivePerl. > > Sorry I can't be more help. > Nath > > > Lincoln Stein wrote: >> Sadly, bioperl still won't install under ActiveState 5.10 because >> it can't >> find a repository with the SOAP::Lite prerequisite. >> >> Lincoln >> >> On Feb 5, 2008 10:06 PM, Chris Fields wrote: >> >>> According to this page you can remove the tags and it >>> will assume the files are for any OS: >>> >>> >>> http://aspn.activestate.com/ASPN/docs/ActivePerl/5.10/lib/ActivePerl/PPM/PPD.html#ppd_xml_format >>> >>> I have moved the old package.xml to package.bak and replaced it with >>> one w/o those tags; I can now pick it up on Mac OS X using >>> ActiveState >>> perl 5.10: >>> >>> ppm> search * >>> Downloading bioperl.org packlist...not modified >>> 1: Bio-ASN1-EntrezGene v1.09 >>> 2: Bundle-BioPerl-Core v1.5.2_100 >>> 3: Bundle-BioPerl-Db v1.5.2_100 >>> 4: Bundle-BioPerl-Network v1.5.2_100 >>> 5: Bundle-BioPerl-Run v1.5.2_100 >>> 6: Class-AutoClass v1.01 >>> 7: GD-SVG v0.25 >>> 8: Graph v0.80 >>> 9: SVG-Graph v0.01 >>> 10: bioperl v1.5.2_100 >>> 11: bioperl-db v1.5.2_100 >>> 12: bioperl-network v1.5.2_100 >>> 13: bioperl-run v1.5.2_100 >>> >>> I'll add ARCHITECTURE versioning tags back when we know it's working >>> (maybe tomorrow, when I can get on to WinXP to test it). >>> >>> chris >>> >>> On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: >>> >>>> Hi Scott, Bioperl folk, >>>> >>>> I'm afraid that the ActiveState ppm install of BioPerl no longer >>>> works. >>>> Using the current ActiveState (perl version 5.10), I added the >>>> Bribes, >>>> Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates >>>> repositories. However, when I synched up, all but the Bribes reps >>>> showed up >>>> empty in the ppm tool. >>>> >>>> In addition, there's nothing in the release candidate rep any >>>> longer. I used >>>> to use this to get at Bioperl 1.5. >>>> >>>> Perhaps the architecture needs to be changed? >>>> >>>> Lincoln >>>> >>>> >>>> >>>> -- >>>> Lincoln D. Stein >>>> Cold Spring Harbor Laboratory >>>> 1 Bungtown Road >>>> Cold Spring Harbor, NY 11724 >>>> (516) 367-8380 (voice) >>>> (516) 367-8389 (fax) >>>> FOR URGENT MESSAGES & SCHEDULING, >>>> PLEASE CONTACT MY ASSISTANT, >>>> SANDRA MICHELSEN, AT michelse at cshl.edu >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> Christopher Fields >>> Postdoctoral Researcher >>> Lab of Dr. Robert Switzer >>> Dept of Biochemistry >>> University of Illinois Urbana-Champaign >>> >>> >>> >>> >> >> > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.6 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFHqeID9gTv6QYzVL4RAsyqAJ0XkCJgdKu6SHzci4XGww4OofRBzgCfQqCL > MxylCxJflKjtscupJ5cRHKk= > =Brpe > -----END PGP SIGNATURE----- Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Feb 6 12:54:16 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 6 Feb 2008 11:54:16 -0600 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <47A9E203.3080008@sheffield.ac.uk> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> <6dce9a0b0802060703j231704acta813715265f1fab5@mail.gmail.com> <47A9E203.3080008@sheffield.ac.uk> Message-ID: <48143927-C57B-4525-9025-A6FDC5A49070@uiuc.edu> Just an update: I have installed ActivePerl 5.10 on my WinXP box and added the following repos to PPM4 (in the following order, just in case it matters): Kobes: http://cpan.uwinnipeg.ca/PPMPackages/10xx/ Bribes: http://www.bribes.org/perl/ppm BioPerl: http://bioperl.org/DIST Note that the above Kobes repo is 5.10-specific. SOAP::Lite is in both Kobes and Bribes for perl 5.10. I then ran into issues with XML::SAX::ExpatXS and XML::SAX::Writer (the former is a binary-only, so likely failed with the ActiveState autobuild process; the latter should work though, so it might be worth hosting a version in BioPerl). I removed both dependencies from package.xml on the server and everything appears to install fine now using PPM4. I'll see if Randy Kobes can get an XML::SAX::ExpatXS version up. It is only required for 1.5.2; bioperl-live no longer requires it (just XML::SAX). chris On Feb 6, 2008, at 10:36 AM, Nathan S Haigh wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Last time I was playing with Windows PPM packages, I seem to > remember having to build some packages for inclusion in the BioPerl > repo so that all > dependencies were satisfied. Unfortunately, I don't have time to do > this myself, but it's a work around if someone has time to do it? > Alternatively, > contact one of the other repo's and see if they can do something > about it as it will/should be available for at least an older > version of ActivePerl. > > Sorry I can't be more help. > Nath > > > Lincoln Stein wrote: >> Sadly, bioperl still won't install under ActiveState 5.10 because >> it can't >> find a repository with the SOAP::Lite prerequisite. >> >> Lincoln >> >> On Feb 5, 2008 10:06 PM, Chris Fields wrote: >> >>> According to this page you can remove the tags and it >>> will assume the files are for any OS: >>> >>> >>> http://aspn.activestate.com/ASPN/docs/ActivePerl/5.10/lib/ActivePerl/PPM/PPD.html#ppd_xml_format >>> >>> I have moved the old package.xml to package.bak and replaced it with >>> one w/o those tags; I can now pick it up on Mac OS X using >>> ActiveState >>> perl 5.10: >>> >>> ppm> search * >>> Downloading bioperl.org packlist...not modified >>> 1: Bio-ASN1-EntrezGene v1.09 >>> 2: Bundle-BioPerl-Core v1.5.2_100 >>> 3: Bundle-BioPerl-Db v1.5.2_100 >>> 4: Bundle-BioPerl-Network v1.5.2_100 >>> 5: Bundle-BioPerl-Run v1.5.2_100 >>> 6: Class-AutoClass v1.01 >>> 7: GD-SVG v0.25 >>> 8: Graph v0.80 >>> 9: SVG-Graph v0.01 >>> 10: bioperl v1.5.2_100 >>> 11: bioperl-db v1.5.2_100 >>> 12: bioperl-network v1.5.2_100 >>> 13: bioperl-run v1.5.2_100 >>> >>> I'll add ARCHITECTURE versioning tags back when we know it's working >>> (maybe tomorrow, when I can get on to WinXP to test it). >>> >>> chris >>> >>> On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: >>> >>>> Hi Scott, Bioperl folk, >>>> >>>> I'm afraid that the ActiveState ppm install of BioPerl no longer >>>> works. >>>> Using the current ActiveState (perl version 5.10), I added the >>>> Bribes, >>>> Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates >>>> repositories. However, when I synched up, all but the Bribes reps >>>> showed up >>>> empty in the ppm tool. >>>> >>>> In addition, there's nothing in the release candidate rep any >>>> longer. I used >>>> to use this to get at Bioperl 1.5. >>>> >>>> Perhaps the architecture needs to be changed? >>>> >>>> Lincoln >>>> >>>> >>>> >>>> -- >>>> Lincoln D. Stein >>>> Cold Spring Harbor Laboratory >>>> 1 Bungtown Road >>>> Cold Spring Harbor, NY 11724 >>>> (516) 367-8380 (voice) >>>> (516) 367-8389 (fax) >>>> FOR URGENT MESSAGES & SCHEDULING, >>>> PLEASE CONTACT MY ASSISTANT, >>>> SANDRA MICHELSEN, AT michelse at cshl.edu >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> Christopher Fields >>> Postdoctoral Researcher >>> Lab of Dr. Robert Switzer >>> Dept of Biochemistry >>> University of Illinois Urbana-Champaign >>> >>> >>> >>> >> >> > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.6 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFHqeID9gTv6QYzVL4RAsyqAJ0XkCJgdKu6SHzci4XGww4OofRBzgCfQqCL > MxylCxJflKjtscupJ5cRHKk= > =Brpe > -----END PGP SIGNATURE----- > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From sjmiller at email.arizona.edu Wed Feb 6 15:57:35 2008 From: sjmiller at email.arizona.edu (Susan J. Miller) Date: Wed, 06 Feb 2008 13:57:35 -0700 Subject: [Bioperl-l] SeqHound In-Reply-To: References: <47A8C5C0.7040401@email.arizona.edu> <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> <47A8E3BF.7000308@email.arizona.edu> Message-ID: <47AA1F3F.9000404@email.arizona.edu> Barry Moore wrote: > Susan, > > I'm joining this discussion late so my apologies if I'm missing the > original point. If you're trying to routinely download thousands of > sequences from GenBank or SeqHound you probably want to be using ftp to > download the flat files and query/parse locally. If you're trying to > stay on top of the latest Drosophila ESTs, then how about setting up a > nightly cron job to download the incremental updates from NCBIs ftp > (ftp://ftp.ncbi.nih.gov/genbank/daily-nc) and parse that for Drosophila > EST sequences. The EST division is huge, but I would think nightly > incrementals should be manageable. Hi Barry, I'll try your suggestion. I guess my interpretation of the documentation for SeqHound was erroneous. (Who knows what 'large numbers of sequences' means?) I tried using SeqHound's get_Stream_by_id method to fetch 10000 sequences, 500 at a time, and got a timeout error. -- Regards, -susan Susan J. Miller Manager, Scientific Data Analysis Biotechnology Computing Facility Arizona Research Laboratories (520) 626-2597 From David.Messina at sbc.su.se Wed Feb 6 16:17:46 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 6 Feb 2008 22:17:46 +0100 Subject: [Bioperl-l] BOSC 2008? In-Reply-To: <1182EAB9-7A75-498F-B91B-C14771DFD607@uiuc.edu> References: <1182EAB9-7A75-498F-B91B-C14771DFD607@uiuc.edu> Message-ID: <628aabb70802061317n2f0d1103w9367346166bf8c3f@mail.gmail.com> Hey Chris, Isn't it usually in conjunction with ISMB (which is Toronto 7/19-23 this year)? From cjfields at uiuc.edu Wed Feb 6 16:22:20 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 6 Feb 2008 15:22:20 -0600 Subject: [Bioperl-l] BOSC 2008? In-Reply-To: <628aabb70802061317n2f0d1103w9367346166bf8c3f@mail.gmail.com> References: <1182EAB9-7A75-498F-B91B-C14771DFD607@uiuc.edu> <628aabb70802061317n2f0d1103w9367346166bf8c3f@mail.gmail.com> Message-ID: <9C6A22B1-9E84-4F17-8459-CBBDCB2110D4@uiuc.edu> Yep. I found this out earlier from Darin London. Just trying to plan for it ahead of time! chris On Feb 6, 2008, at 3:17 PM, Dave Messina wrote: > Hey Chris, > > Isn't it usually in conjunction with ISMB (which is Toronto 7/19-23 > this year)? > > Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Feb 6 16:48:45 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 6 Feb 2008 15:48:45 -0600 Subject: [Bioperl-l] SeqHound In-Reply-To: <47AA1F3F.9000404@email.arizona.edu> References: <47A8C5C0.7040401@email.arizona.edu> <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> <47A8E3BF.7000308@email.arizona.edu> <47AA1F3F.9000404@email.arizona.edu> Message-ID: <78824D84-B8B7-4A5C-BD81-7224F26D32E9@uiuc.edu> On Feb 6, 2008, at 2:57 PM, Susan J. Miller wrote: > Barry Moore wrote: >> Susan, >> I'm joining this discussion late so my apologies if I'm missing the >> original point. If you're trying to routinely download thousands >> of sequences from GenBank or SeqHound you probably want to be using >> ftp to download the flat files and query/parse locally. If you're >> trying to stay on top of the latest Drosophila ESTs, then how about >> setting up a nightly cron job to download the incremental updates >> from NCBIs ftp (ftp://ftp.ncbi.nih.gov/genbank/daily-nc) and parse >> that for Drosophila EST sequences. The EST division is huge, but I >> would think nightly incrementals should be manageable. > > > Hi Barry, > > I'll try your suggestion. I guess my interpretation of the > documentation for SeqHound was erroneous. (Who knows what 'large > numbers of sequences' means?) I tried using SeqHound's > get_Stream_by_id method to fetch 10000 sequences, 500 at a time, and > got a timeout error. > > > -- > Regards, > -susan Barry's and Brian's suggestions make more sense. You could also possibly automate a Entrez query to limit retrievals to a period of time instead of munging through the last releases; it all depends on how many sequences you need to parse through. The SeqHound timeout may be set up on their end to prevent a single server from spamming them with tons of requests. NCBI is a bit more tolerant but can be brittle with busy server traffic. chris From barry.moore at genetics.utah.edu Wed Feb 6 16:50:53 2008 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Wed, 6 Feb 2008 14:50:53 -0700 Subject: [Bioperl-l] Fwd: SeqHound References: <6CA6C310-E23C-47ED-9206-7F914BCA689E@genetics.utah.edu> Message-ID: <7167DD26-92F7-4D44-B111-E6CAA30BFB1E@genetics.utah.edu> Susan- Yeah, I used them several years ago, and it seemed like quite a good project at the time. I see that it has recently moved to a new location with a start up company, and I couldn't make heads or tails of their new sight. I wonder if the SeqHound side of their work hasn't suffered - perhaps only temporarily - from their recent move from academia to the brave new world of .com start-up. B On Feb 6, 2008, at 1:57 PM, Susan J. Miller wrote: > Barry Moore wrote: >> Susan, >> >> I'm joining this discussion late so my apologies if I'm missing the >> original point. If you're trying to routinely download thousands of >> sequences from GenBank or SeqHound you probably want to be using >> ftp to >> download the flat files and query/parse locally. If you're trying to >> stay on top of the latest Drosophila ESTs, then how about setting >> up a >> nightly cron job to download the incremental updates from NCBIs ftp >> (ftp://ftp.ncbi.nih.gov/genbank/daily-nc) and parse that for >> Drosophila >> EST sequences. The EST division is huge, but I would think nightly >> incrementals should be manageable. > > > Hi Barry, > > I'll try your suggestion. I guess my interpretation of the > documentation for SeqHound was erroneous. (Who knows what 'large > numbers of sequences' means?) I tried using SeqHound's > get_Stream_by_id > method to fetch 10000 sequences, 500 at a time, and got a timeout > error. > > > -- > Regards, > -susan > > Susan J. Miller > Manager, Scientific Data Analysis > Biotechnology Computing Facility > Arizona Research Laboratories > (520) 626-2597 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From oliverpelz at googlemail.com Thu Feb 7 12:24:38 2008 From: oliverpelz at googlemail.com (Oliver Pelz) Date: Thu, 7 Feb 2008 18:24:38 +0100 Subject: [Bioperl-l] Found dead links in PDoc and a little improvement Message-ID: Hello everybody, I am a beginner in bioperl and currently working heavily with the PDoc's. In this doc here: http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Variation/IO/flat.html the two links to the EBI in the description field are dead. I have looked to find other information but there is nothing available about this pseudo embl format. Has someone the old descriptions and can edit/paste them in this documentation. Another thing would help beginners. At the Bio::SeqIO documentation there are those examples for world fastest ... converter. It would be cool to add a $out->close() to those examples because I was very frustrated in the beginning when the outfiles were empty after the script had finished. Thanks for reading Oliver From bosborne11 at verizon.net Thu Feb 7 13:41:48 2008 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 07 Feb 2008 13:41:48 -0500 Subject: [Bioperl-l] Found dead links in PDoc and a little improvement In-Reply-To: References: Message-ID: Oliver, Removed those dead links, thank you for that. The reason there's no close() in most code examples is that Perl programmers don't usually use this function. The filehandle is closed automatically when open() is called again or when the Perl script finishes. Brian O. On Feb 7, 2008, at 12:24 PM, Oliver Pelz wrote: > Hello everybody, > I am a beginner in bioperl and currently working heavily with the > PDoc's. > > In this doc here: > http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Variation/IO/flat.html > > the two links to the EBI in the description field are dead. I have > looked to > find other information > but there is nothing available about this pseudo embl format. > Has someone the old descriptions and can edit/paste them in this > documentation. > > Another thing would help beginners. > At the Bio::SeqIO documentation there are those examples for world > fastest > ... converter. > It would be cool to add a $out->close() to those examples because I > was very > frustrated in the > beginning when the outfiles were empty after the script had finished. > > Thanks for reading > > Oliver > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From golharam at umdnj.edu Thu Feb 7 16:24:16 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 07 Feb 2008 16:24:16 -0500 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser Message-ID: <47AB7700.8030801@umdnj.edu> Is there a SeqIO parser module for GenBank ASN.1 format? I thought it would have been genbank or entrezgene, but neither of them work. From cjfields at uiuc.edu Thu Feb 7 16:48:25 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 7 Feb 2008 15:48:25 -0600 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <47AB7700.8030801@umdnj.edu> References: <47AB7700.8030801@umdnj.edu> Message-ID: No. The only ASN.1 parser is entrezgene. You could probably try building one using the same ASN.1 parser that SeqIO::entrezgene uses (Bio::ASN1::EntrezGene); it includes a parser for sequences: http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm chris On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: > Is there a SeqIO parser module for GenBank ASN.1 format? I thought > it would have been genbank or entrezgene, but neither of them work. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jason at bioperl.org Thu Feb 7 17:46:41 2008 From: jason at bioperl.org (Jason Stajich) Date: Thu, 7 Feb 2008 14:46:41 -0800 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: References: <47AB7700.8030801@umdnj.edu> Message-ID: <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> ugh - why parse ASN.1? NCBI provides converter application in the ncbi toolkit to many formats : genbank, XML, etc. On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: > No. The only ASN.1 parser is entrezgene. You could probably try > building one using the same ASN.1 parser that SeqIO::entrezgene > uses (Bio::ASN1::EntrezGene); it includes a parser for sequences: > > http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ > ASN1/Sequence.pm > > chris > > On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: > >> Is there a SeqIO parser module for GenBank ASN.1 format? I >> thought it would have been genbank or entrezgene, but neither of >> them work. >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From golharam at umdnj.edu Thu Feb 7 18:00:33 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 07 Feb 2008 18:00:33 -0500 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> Message-ID: <47AB8D91.9080201@umdnj.edu> That I can use from Perl? Such as???? I need to retrieve Gene Ontology information (classification and GO id) from the Entrez Gene record. I thought it would be easiest using BioPerl to do this. BioPerl only has an ASN.1 parser, entrezgene. When I use this to load the Gene record, I'm using: my $io = Bio::SeqIO->new(-file => ' "entrezgene" ); my $seq_obj = $io->next_seq; Something is not working with the second line. I get an error: "Use of uninitialized value in string eq at /home/golharam/bioperl/bioperl-1.5.1//Bio/SeqIO/entrezgene.pm line 244" It sort of makes sense because, well, the Entrez Gene record doesn't have a sequence...it has information about a gene. I figure I must be doing something wrong but I haven't seen anything in BioPerl about parsing entrez gene records any other way. Ryan Jason Stajich wrote: > ugh - why parse ASN.1? NCBI provides converter application in the ncbi > toolkit to many formats : genbank, XML, etc. > On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: > >> No. The only ASN.1 parser is entrezgene. You could probably try >> building one using the same ASN.1 parser that SeqIO::entrezgene uses >> (Bio::ASN1::EntrezGene); it includes a parser for sequences: >> >> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm >> >> >> chris >> >> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >> >>> Is there a SeqIO parser module for GenBank ASN.1 format? I thought >>> it would have been genbank or entrezgene, but neither of them work. >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > From luciap at sas.upenn.edu Thu Feb 7 17:37:46 2008 From: luciap at sas.upenn.edu (Lucia Peixoto) Date: Thu, 07 Feb 2008 17:37:46 -0500 Subject: [Bioperl-l] How to add branch labels for PAML codeml branch models Message-ID: <1202423866.47ab883ab02a3@webmail.sas.upenn.edu> Just a small question in order to label the branches to use model 2 of PAML branch models can I use add_tag_value of Bio::Tree Node? or there's some other way to do it with bioperl? thanks Lucia Peixoto Department of Biology,SAS University of Pennsylvania From cjfields at uiuc.edu Thu Feb 7 18:39:11 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 7 Feb 2008 17:39:11 -0600 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <47AB8E92.4000307@umdnj.edu> References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8E92.4000307@umdnj.edu> Message-ID: Bio::SeqIO::entrezgene should do this. Any dbxrefs (including GO IDs) should be stored in the annotation collection, but I'm not sure how it is parsed; you'll have to test it out. I agree with Jason; ASN.1 isn't a very friendly format. Don't know why NCBI sticks with it, but I'm sure they have their reasons (I think this may have been discussed before on the list). chris On Feb 7, 2008, at 5:04 PM, Ryan Golhar wrote: > Let me re-phrase then - I want to parse an entry such as this: > > http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 > > to retrieve the text of the Gene Ontology entries and the associated > GO IDs for those entries. Is this possible with BioPerl? If so, > how can I do this with BioPerl? > > Ryan > > > > Jason Stajich wrote: >> ugh - why parse ASN.1? NCBI provides converter application in the >> ncbi toolkit to many formats : genbank, XML, etc. >> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: >>> No. The only ASN.1 parser is entrezgene. You could probably try >>> building one using the same ASN.1 parser that SeqIO::entrezgene >>> uses (Bio::ASN1::EntrezGene); it includes a parser for sequences: >>> >>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm >>> >>> chris >>> >>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >>> >>>> Is there a SeqIO parser module for GenBank ASN.1 format? I >>>> thought it would have been genbank or entrezgene, but neither of >>>> them work. >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> Christopher Fields >>> Postdoctoral Researcher >>> Lab of Dr. Robert Switzer >>> Dept of Biochemistry >>> University of Illinois Urbana-Champaign >>> >>> >>> >>> _______________________________________________ >>> 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 > Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From golharam at umdnj.edu Thu Feb 7 18:04:50 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 07 Feb 2008 18:04:50 -0500 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> Message-ID: <47AB8E92.4000307@umdnj.edu> Let me re-phrase then - I want to parse an entry such as this: http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 to retrieve the text of the Gene Ontology entries and the associated GO IDs for those entries. Is this possible with BioPerl? If so, how can I do this with BioPerl? Ryan Jason Stajich wrote: > ugh - why parse ASN.1? NCBI provides converter application in the ncbi > toolkit to many formats : genbank, XML, etc. > On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: > >> No. The only ASN.1 parser is entrezgene. You could probably try >> building one using the same ASN.1 parser that SeqIO::entrezgene uses >> (Bio::ASN1::EntrezGene); it includes a parser for sequences: >> >> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm >> >> >> chris >> >> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >> >>> Is there a SeqIO parser module for GenBank ASN.1 format? I thought >>> it would have been genbank or entrezgene, but neither of them work. >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> >> _______________________________________________ >> 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 golharam at umdnj.edu Thu Feb 7 18:09:06 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 07 Feb 2008 18:09:06 -0500 Subject: [Bioperl-l] BioPipe links don't work Message-ID: <47AB8F92.2030006@umdnj.edu> The links to BioPipe on the HOWTO page do not work. They all lead to http://www.sedoparking.com/biopipe.org From barry.moore at genetics.utah.edu Thu Feb 7 19:31:53 2008 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Thu, 7 Feb 2008 17:31:53 -0700 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <47AB8E92.4000307@umdnj.edu> References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8E92.4000307@umdnj.edu> Message-ID: Ryan, I you have a list of NCBI Gene IDs then you can grab the flatfile gene2go from NCBIs ftp site ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2go.gz. That will give you tax_id, gene_id, go_id, evidence code, qualifier, category etc. From there you can get the description from the GO OBO file http://www.geneontology.org/ontology/ gene_ontology_edit.obo. If all you need is the description then the file is pretty easy to parse on the fly, but if you need to traverse the graphs or if you want an already written parser then add go-perl http://search.cpan.org/~cmungall/go-perl/go-perl.pod Barry On Feb 7, 2008, at 4:04 PM, Ryan Golhar wrote: > Let me re-phrase then - I want to parse an entry such as this: > > http://www.ncbi.nlm.nih.gov/sites/entrez? > db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 > > to retrieve the text of the Gene Ontology entries and the > associated GO > IDs for those entries. Is this possible with BioPerl? If so, how > can I > do this with BioPerl? > > Ryan > > > > Jason Stajich wrote: >> ugh - why parse ASN.1? NCBI provides converter application in the >> ncbi >> toolkit to many formats : genbank, XML, etc. >> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: >> >>> No. The only ASN.1 parser is entrezgene. You could probably try >>> building one using the same ASN.1 parser that SeqIO::entrezgene uses >>> (Bio::ASN1::EntrezGene); it includes a parser for sequences: >>> >>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/ >>> Bio/ASN1/Sequence.pm >>> >>> >>> chris >>> >>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >>> >>>> Is there a SeqIO parser module for GenBank ASN.1 format? I thought >>>> it would have been genbank or entrezgene, but neither of them work. >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> Christopher Fields >>> Postdoctoral Researcher >>> Lab of Dr. Robert Switzer >>> Dept of Biochemistry >>> University of Illinois Urbana-Champaign >>> >>> >>> >>> _______________________________________________ >>> 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 golharam at umdnj.edu Thu Feb 7 19:46:21 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 07 Feb 2008 19:46:21 -0500 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8E92.4000307@umdnj.edu> Message-ID: <47ABA65D.1000705@umdnj.edu> Thank Barry. I did try using go-perl but it is slow when processing queries. I didn't know about ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz. I think that is exactly what I'm looking for. Ryan Barry Moore wrote: > Ryan, > > I you have a list of NCBI Gene IDs then you can grab the flatfile > gene2go from NCBIs ftp site > ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz. That will give you > tax_id, gene_id, go_id, evidence code, qualifier, category etc. From > there you can get the description from the GO OBO file > http://www.geneontology.org/ontology/gene_ontology_edit.obo. If all you > need is the description then the file is pretty easy to parse on the > fly, but if you need to traverse the graphs or if you want an already > written parser then add go-perl > http://search.cpan.org/~cmungall/go-perl/go-perl.pod > > Barry > > > > On Feb 7, 2008, at 4:04 PM, Ryan Golhar wrote: > >> Let me re-phrase then - I want to parse an entry such as this: >> >> http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 >> >> >> to retrieve the text of the Gene Ontology entries and the associated GO >> IDs for those entries. Is this possible with BioPerl? If so, how can I >> do this with BioPerl? >> >> Ryan >> >> >> >> Jason Stajich wrote: >>> ugh - why parse ASN.1? NCBI provides converter application in the ncbi >>> toolkit to many formats : genbank, XML, etc. >>> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: >>> >>>> No. The only ASN.1 parser is entrezgene. You could probably try >>>> building one using the same ASN.1 parser that SeqIO::entrezgene uses >>>> (Bio::ASN1::EntrezGene); it includes a parser for sequences: >>>> >>>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm >>>> >>>> >>>> >>>> chris >>>> >>>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >>>> >>>>> Is there a SeqIO parser module for GenBank ASN.1 format? I thought >>>>> it would have been genbank or entrezgene, but neither of them work. >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> Christopher Fields >>>> Postdoctoral Researcher >>>> Lab of Dr. Robert Switzer >>>> Dept of Biochemistry >>>> University of Illinois Urbana-Champaign >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 golharam at umdnj.edu Thu Feb 7 18:59:52 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 07 Feb 2008 18:59:52 -0500 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8E92.4000307@umdnj.edu> Message-ID: <47AB9B78.5090907@umdnj.edu> That's what I thought too. However, I'm getting errors with a parser. I found Bio::ASN1::EntrezGene online and am using that module outside of Bioperl as it works well for what I'm doing. I've already changed my code and don't want to deal with tracking down the errors I had with BioPerl (I've already spend enough time on this) but they were easy enough to reproduce. Ryan Chris Fields wrote: > Bio::SeqIO::entrezgene should do this. Any dbxrefs (including GO IDs) > should be stored in the annotation collection, but I'm not sure how it > is parsed; you'll have to test it out. > > I agree with Jason; ASN.1 isn't a very friendly format. Don't know why > NCBI sticks with it, but I'm sure they have their reasons (I think this > may have been discussed before on the list). > > chris > > On Feb 7, 2008, at 5:04 PM, Ryan Golhar wrote: > >> Let me re-phrase then - I want to parse an entry such as this: >> >> http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 >> >> >> to retrieve the text of the Gene Ontology entries and the associated >> GO IDs for those entries. Is this possible with BioPerl? If so, how >> can I do this with BioPerl? >> >> Ryan >> >> >> >> Jason Stajich wrote: >>> ugh - why parse ASN.1? NCBI provides converter application in the >>> ncbi toolkit to many formats : genbank, XML, etc. >>> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: >>>> No. The only ASN.1 parser is entrezgene. You could probably try >>>> building one using the same ASN.1 parser that SeqIO::entrezgene uses >>>> (Bio::ASN1::EntrezGene); it includes a parser for sequences: >>>> >>>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm >>>> >>>> >>>> chris >>>> >>>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >>>> >>>>> Is there a SeqIO parser module for GenBank ASN.1 format? I thought >>>>> it would have been genbank or entrezgene, but neither of them work. >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> Christopher Fields >>>> Postdoctoral Researcher >>>> Lab of Dr. Robert Switzer >>>> Dept of Biochemistry >>>> University of Illinois Urbana-Champaign >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >> > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > > From cjfields at uiuc.edu Thu Feb 7 20:32:18 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 7 Feb 2008 19:32:18 -0600 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <47AB9B78.5090907@umdnj.edu> References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8E92.4000307@umdnj.edu> <47AB9B78.5090907@umdnj.edu> Message-ID: <1001C6BB-24D5-4BB8-B135-0E9D2952B49A@uiuc.edu> It's possible that has been fixed in bioperl-live. However, just in case, if you are getting errors could you file a bug report along with the relevant code demonstrating it? chris On Feb 7, 2008, at 5:59 PM, Ryan Golhar wrote: > That's what I thought too. However, I'm getting errors with a parser. > > I found Bio::ASN1::EntrezGene online and am using that module > outside of Bioperl as it works well for what I'm doing. > > I've already changed my code and don't want to deal with tracking > down the errors I had with BioPerl (I've already spend enough time > on this) but they were easy enough to reproduce. > > Ryan > > > Chris Fields wrote: >> Bio::SeqIO::entrezgene should do this. Any dbxrefs (including GO >> IDs) should be stored in the annotation collection, but I'm not >> sure how it is parsed; you'll have to test it out. >> I agree with Jason; ASN.1 isn't a very friendly format. Don't know >> why NCBI sticks with it, but I'm sure they have their reasons (I >> think this may have been discussed before on the list). >> chris >> On Feb 7, 2008, at 5:04 PM, Ryan Golhar wrote: >>> Let me re-phrase then - I want to parse an entry such as this: >>> >>> http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 >>> >>> to retrieve the text of the Gene Ontology entries and the >>> associated GO IDs for those entries. Is this possible with >>> BioPerl? If so, how can I do this with BioPerl? >>> >>> Ryan >>> >>> >>> >>> Jason Stajich wrote: >>>> ugh - why parse ASN.1? NCBI provides converter application in the >>>> ncbi toolkit to many formats : genbank, XML, etc. >>>> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: >>>>> No. The only ASN.1 parser is entrezgene. You could probably >>>>> try building one using the same ASN.1 parser that >>>>> SeqIO::entrezgene uses (Bio::ASN1::EntrezGene); it includes a >>>>> parser for sequences: >>>>> >>>>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm >>>>> >>>>> chris >>>>> >>>>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >>>>> >>>>>> Is there a SeqIO parser module for GenBank ASN.1 format? I >>>>>> thought it would have been genbank or entrezgene, but neither >>>>>> of them work. >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> Christopher Fields >>>>> Postdoctoral Researcher >>>>> Lab of Dr. Robert Switzer >>>>> Dept of Biochemistry >>>>> University of Illinois Urbana-Champaign >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jason at bioperl.org Thu Feb 7 20:52:39 2008 From: jason at bioperl.org (Jason Stajich) Date: Thu, 7 Feb 2008 17:52:39 -0800 Subject: [Bioperl-l] How to add branch labels for PAML codeml branch models In-Reply-To: <1202423866.47ab883ab02a3@webmail.sas.upenn.edu> References: <1202423866.47ab883ab02a3@webmail.sas.upenn.edu> Message-ID: It will work if you just change the node's ID to be something like: 'ID #1' (for tips) and for the internal nodes just set the id to ("#1"), etc... I added some code to demonstrate this one the wiki: http://bioperl.org/wiki/HOWTO:PAML#Setting_up_Branch-specific_labels The format is nonstandard so you have to hack the output some to get what you want, hence the extra part that requires you strip out the " since they are required for escaping space characters. -jason On Feb 7, 2008, at 2:37 PM, Lucia Peixoto wrote: > Just a small question > in order to label the branches to use model 2 of PAML branch models > can I use add_tag_value of Bio::Tree Node? > or there's some other way to do it with bioperl? > > thanks > > Lucia Peixoto > Department of Biology,SAS > University of Pennsylvania > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjm at fruitfly.org Thu Feb 7 21:14:20 2008 From: cjm at fruitfly.org (Chris Mungall) Date: Thu, 7 Feb 2008 18:14:20 -0800 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8E92.4000307@umdnj.edu> Message-ID: Just to add to Barry's suggestions: You can query the database directly: http://www.berkeleybop.org/goose You can also use the go-db-perl API and point it at the mysql port of one of the mirrors; see http://www.geneontology.org/GO.database.shtml On Feb 7, 2008, at 4:31 PM, Barry Moore wrote: > Ryan, > > I you have a list of NCBI Gene IDs then you can grab the flatfile > gene2go from NCBIs ftp site ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ > gene2go.gz. That will give you tax_id, gene_id, go_id, evidence > code, qualifier, category etc. From there you can get the > description from the GO OBO file http://www.geneontology.org/ > ontology/gene_ontology_edit.obo. If all you need is the > description then the file is pretty easy to parse on the fly, but > if you need to traverse the graphs or if you want an already > written parser then add go-perl http://search.cpan.org/~cmungall/go- > perl/go-perl.pod > > Barry > > > > On Feb 7, 2008, at 4:04 PM, Ryan Golhar wrote: > >> Let me re-phrase then - I want to parse an entry such as this: >> >> http://www.ncbi.nlm.nih.gov/sites/entrez? >> db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 >> >> to retrieve the text of the Gene Ontology entries and the >> associated GO >> IDs for those entries. Is this possible with BioPerl? If so, how >> can I >> do this with BioPerl? >> >> Ryan >> >> >> >> Jason Stajich wrote: >>> ugh - why parse ASN.1? NCBI provides converter application in the >>> ncbi >>> toolkit to many formats : genbank, XML, etc. >>> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: >>> >>>> No. The only ASN.1 parser is entrezgene. You could probably try >>>> building one using the same ASN.1 parser that SeqIO::entrezgene >>>> uses >>>> (Bio::ASN1::EntrezGene); it includes a parser for sequences: >>>> >>>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/ >>>> Bio/ASN1/Sequence.pm >>>> >>>> >>>> chris >>>> >>>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >>>> >>>>> Is there a SeqIO parser module for GenBank ASN.1 format? I >>>>> thought >>>>> it would have been genbank or entrezgene, but neither of them >>>>> work. >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> Christopher Fields >>>> Postdoctoral Researcher >>>> Lab of Dr. Robert Switzer >>>> Dept of Biochemistry >>>> University of Illinois Urbana-Champaign >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 hlapp at gmx.net Thu Feb 7 21:45:48 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 7 Feb 2008 21:45:48 -0500 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <47AB8D91.9080201@umdnj.edu> References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8D91.9080201@umdnj.edu> Message-ID: On Feb 7, 2008, at 6:00 PM, Ryan Golhar wrote: > Something is not working with the second line. I get an error: > > "Use of uninitialized value in string eq at > /home/golharam/bioperl/bioperl-1.5.1//Bio/SeqIO/ > entrezgene.pm line 244" This isn't an error, is it - it's a warning, no? -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Thu Feb 7 22:24:45 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 7 Feb 2008 21:24:45 -0600 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8D91.9080201@umdnj.edu> Message-ID: I agree. I also noticed Ryan's running bioperl 1.5.1. Probably worth trying the latest code from Subversion. chris On Feb 7, 2008, at 8:45 PM, Hilmar Lapp wrote: > > On Feb 7, 2008, at 6:00 PM, Ryan Golhar wrote: > >> Something is not working with the second line. I get an error: >> >> "Use of uninitialized value in string eq at >> /home/golharam/bioperl/bioperl-1.5.1//Bio/SeqIO/ >> entrezgene.pm line 244" > > > This isn't an error, is it - it's a warning, no? > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From David.Messina at sbc.su.se Fri Feb 8 04:00:05 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Fri, 8 Feb 2008 10:00:05 +0100 Subject: [Bioperl-l] BioPipe links don't work In-Reply-To: <47AB8F92.2030006@umdnj.edu> References: <47AB8F92.2030006@umdnj.edu> Message-ID: <628aabb70802080100g43c02f0btdc8c8065c576ff3d@mail.gmail.com> BioPipe, as far as I can tell, is dead, and indeed the HOWTO is no longer active. Therefore I've removed the BioPipe entry entirely. If anyone would prefer it stay, please let me know and I'll revert the change and update the links to point to the GMOD "BioPipe is no longer supported" page. Dave From luciap at sas.upenn.edu Fri Feb 8 10:53:36 2008 From: luciap at sas.upenn.edu (Lucia Peixoto) Date: Fri, 08 Feb 2008 10:53:36 -0500 Subject: [Bioperl-l] How to add branch labels for PAML codeml branch models In-Reply-To: References: <1202423866.47ab883ab02a3@webmail.sas.upenn.edu> Message-ID: <1202486016.47ac7b003b860@webmail.sas.upenn.edu> Hi as I have my trees right now the bootstrap support ends up as the node ID so I guess I have to assign node ID to bootstrap first and then change? Lucia Quoting Jason Stajich : > It will work if you just change the node's ID to be something like: > 'ID #1' (for tips) and for the internal nodes just set the id to > ("#1"), etc... > > I added some code to demonstrate this one the wiki: > http://bioperl.org/wiki/HOWTO:PAML#Setting_up_Branch-specific_labels > > The format is nonstandard so you have to hack the output some to get > what you want, hence the extra part that requires you strip out the " > since they are required for escaping space characters. > > -jason > On Feb 7, 2008, at 2:37 PM, Lucia Peixoto wrote: > > > Just a small question > > in order to label the branches to use model 2 of PAML branch models > > can I use add_tag_value of Bio::Tree Node? > > or there's some other way to do it with bioperl? > > > > thanks > > > > Lucia Peixoto > > Department of Biology,SAS > > University of Pennsylvania > > _______________________________________________ > > 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 > Lucia Peixoto Department of Biology,SAS University of Pennsylvania From jason at bioperl.org Fri Feb 8 13:18:59 2008 From: jason at bioperl.org (Jason Stajich) Date: Fri, 8 Feb 2008 10:18:59 -0800 Subject: [Bioperl-l] How to add branch labels for PAML codeml branch models In-Reply-To: <1202486016.47ac7b003b860@webmail.sas.upenn.edu> References: <1202423866.47ab883ab02a3@webmail.sas.upenn.edu> <1202486016.47ac7b003b860@webmail.sas.upenn.edu> Message-ID: <793E2862-7D2F-4936-93E3-960BD6D74EB3@bioperl.org> http://bioperl.org/wiki/HOWTO:Trees#Reading_and_Writing_Trees Remember that in newick format bootstrap and internal node ids are effectively the same thing - that we store in them separate slots in bioperl is that fact that other formats can separate out this data but there is no standard in newick format. In sometime cases formats do accept the node labels that look like NODEID[BOOTSTRAP] for internal nodes (and BioPerl parses those out nicely) but most programs don't recognize that. On parsing, unless you tell Bioperl that the internal IDs are bootstrap values it is going to store that data as an ID. You will want to clear the bootstraps anyways to write PAML trees anyways. -jason On Feb 8, 2008, at 7:53 AM, Lucia Peixoto wrote: > Hi > as I have my trees right now the bootstrap support ends up as the > node ID > so I guess I have to assign node ID to bootstrap first and then > change? > > > Lucia > > Quoting Jason Stajich : > >> It will work if you just change the node's ID to be something like: >> 'ID #1' (for tips) and for the internal nodes just set the id to >> ("#1"), etc... >> >> I added some code to demonstrate this one the wiki: >> http://bioperl.org/wiki/HOWTO:PAML#Setting_up_Branch- >> specific_labels >> >> The format is nonstandard so you have to hack the output some to get >> what you want, hence the extra part that requires you strip out the " >> since they are required for escaping space characters. >> >> -jason >> On Feb 7, 2008, at 2:37 PM, Lucia Peixoto wrote: >> >>> Just a small question >>> in order to label the branches to use model 2 of PAML branch models >>> can I use add_tag_value of Bio::Tree Node? >>> or there's some other way to do it with bioperl? >>> >>> thanks >>> >>> Lucia Peixoto >>> Department of Biology,SAS >>> University of Pennsylvania >>> _______________________________________________ >>> 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 >> > > > Lucia Peixoto > Department of Biology,SAS > University of Pennsylvania From golharam at umdnj.edu Fri Feb 8 21:01:45 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 08 Feb 2008 21:01:45 -0500 Subject: [Bioperl-l] error in build.pl of bioperl-live Message-ID: <47AD0989.1050904@umdnj.edu> I just obtained the latest build of bioperl from svn. When I run 'perl Build.pl', I get an error "Use of uninitialized value in concatenation (.) or string at Build.PL line 184.". Here's the output I see (The error is at the end): [golharam at hydrogen bioperl-live]$ perl Build.PL Checking prerequisites... Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] * Optional prerequisite Ace is not installed (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF:: Adaptor::ace) * Optional prerequisite Algorithm::Munkres is not installed (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) * Optional prerequisite Math::Random is not installed (wanted for Random Phylogenetic Networks, used by Bio::PhyloNetwork::RandomFactory) * Optional prerequisite GraphViz is not installed (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz) * Class::AutoClass (0.091) is installed, but we prefer to have 1 (wanted for creating objects, used by Bio::Graph::SimpleGraph, Bio::Graph::SimpleGraph::Traversal and Bio::Graph::ProteinGraph) * Optional prerequisite Array::Compare is not installed (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Checking features: Network..................enabled BioDBSeqFeature_mysql....enabled BioDBGFF.................enabled BioDBSeqFeature_BDB......enabled Do you want to run the BioDBGFF or BioDBSeqFeature_mysql live database tests? y/ n [n] n - will not run the BioDBGFF live database tests Use of uninitialized value in concatenation (.) or string at Build.PL line 184. Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] From golharam at umdnj.edu Fri Feb 8 21:08:30 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 08 Feb 2008 21:08:30 -0500 Subject: [Bioperl-l] error in build.pl of bioperl-live In-Reply-To: <47AD0989.1050904@umdnj.edu> References: <47AD0989.1050904@umdnj.edu> Message-ID: <47AD0B1E.3050200@umdnj.edu> In addition, if I continue past the error and run './Build test', I get a bunch of errors like this: BEGIN failed--compilation aborted at t/lib/BioperlTest.pm line 109. Compilation failed in require at t/Allele.t line 9. BEGIN failed--compilation aborted at t/Allele.t line 9. t/Allele.......................... Dubious, test returned 255 (wstat 65280, 0xff00) No subtests run All the tests fail. The last few lines read: Files=257, Tests=0, 19 wallclock secs ( 0.77 usr 0.51 sys + 12.18 cusr 1.75 csys = 15.21 CPU) Result: FAIL Failed 255/257 test programs. 0/0 subtests failed. Am I missing something? This can't be related to the missing prereqs as all the tests are failing. Ryan Golhar wrote: > I just obtained the latest build of bioperl from svn. When I run 'perl > Build.pl', I get an error "Use of uninitialized value in concatenation > (.) or string at Build.PL line 184.". Here's the output I see (The > error is at the end): > > [golharam at hydrogen bioperl-live]$ perl Build.PL > Checking prerequisites... > Install [a]ll optional external modules, [n]one, or choose > [i]nteractively? [n] > * Optional prerequisite Ace is not installed > (wanted for access of ACeDB database, used by Bio::DB::Ace and > Bio::DB::GFF:: > Adaptor::ace) > * Optional prerequisite Algorithm::Munkres is not installed > (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) > * Optional prerequisite Math::Random is not installed > (wanted for Random Phylogenetic Networks, used by > Bio::PhyloNetwork::RandomFactory) > * Optional prerequisite GraphViz is not installed > (wanted for Phylogenetic Network Visulization, used by > Bio::PhyloNetwork::GraphViz) > * Class::AutoClass (0.091) is installed, but we prefer to have 1 > (wanted for creating objects, used by Bio::Graph::SimpleGraph, > Bio::Graph::SimpleGraph::Traversal and Bio::Graph::ProteinGraph) > * Optional prerequisite Array::Compare is not installed > (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) > > ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the > versions > of the modules indicated above before proceeding with this installation > > Checking features: > Network..................enabled > BioDBSeqFeature_mysql....enabled > BioDBGFF.................enabled > BioDBSeqFeature_BDB......enabled > > Do you want to run the BioDBGFF or BioDBSeqFeature_mysql live database > tests? y/ > n [n] n > - will not run the BioDBGFF live database tests > > Use of uninitialized value in concatenation (.) or string at Build.PL > line 184. > Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? > [a] > From hlapp at gmx.net Fri Feb 8 22:33:55 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 8 Feb 2008 22:33:55 -0500 Subject: [Bioperl-l] error in build.pl of bioperl-live In-Reply-To: <47AD0989.1050904@umdnj.edu> References: <47AD0989.1050904@umdnj.edu> Message-ID: Hi Ryan, On Feb 8, 2008, at 9:01 PM, Ryan Golhar wrote: > I get an error "Use of uninitialized value in concatenation (.) or > string at Build.PL line 184.". do keep in mind that this kind of message is almost never an error. It's simply a warning that you wouldn't even see w/o -w. All that it means is that a scalar with an undefined value is being evaluated to a string (which results, by default, in an empty string). Is the build failing or halting at this point for you? That said, it's indeed a good to point those out, as someone either should have initialized a scalar when it wasn't, or that someone was expecting the scalar to always have a value, and so the absence of it may indicate an unexpected condition resulting from an error elsewhere. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From golharam at umdnj.edu Fri Feb 8 22:58:02 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 08 Feb 2008 22:58:02 -0500 Subject: [Bioperl-l] error in build.pl of bioperl-live In-Reply-To: References: <47AD0989.1050904@umdnj.edu> Message-ID: <47AD24CA.2050102@umdnj.edu> Hi Hilmar, The script doesn't halt, but the tests do fail. I sent another message with the errors I am seeing. I do not know if they are related to this or not. Ryan Hilmar Lapp wrote: > Hi Ryan, > > On Feb 8, 2008, at 9:01 PM, Ryan Golhar wrote: > >> I get an error "Use of uninitialized value in concatenation (.) or >> string at Build.PL line 184.". > > > do keep in mind that this kind of message is almost never an error. It's > simply a warning that you wouldn't even see w/o -w. All that it means is > that a scalar with an undefined value is being evaluated to a string > (which results, by default, in an empty string). > > Is the build failing or halting at this point for you? > > That said, it's indeed a good to point those out, as someone either > should have initialized a scalar when it wasn't, or that someone was > expecting the scalar to always have a value, and so the absence of it > may indicate an unexpected condition resulting from an error elsewhere. > > -hilmar From hlapp at gmx.net Fri Feb 8 23:07:31 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 8 Feb 2008 23:07:31 -0500 Subject: [Bioperl-l] error in build.pl of bioperl-live In-Reply-To: <47AD24CA.2050102@umdnj.edu> References: <47AD0989.1050904@umdnj.edu> <47AD24CA.2050102@umdnj.edu> Message-ID: On Feb 8, 2008, at 10:58 PM, Ryan Golhar wrote: > The script doesn't halt, but the tests do fail. I sent another > message with the errors I am seeing. I do not know if they are > related to this or not. Yep I saw that. They might be related if, for example, the issue is related to not finding BioPerl? Can you run one test in verbose mode? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Fri Feb 8 23:47:08 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 8 Feb 2008 22:47:08 -0600 Subject: [Bioperl-l] error in build.pl of bioperl-live In-Reply-To: <47AD24CA.2050102@umdnj.edu> References: <47AD0989.1050904@umdnj.edu> <47AD24CA.2050102@umdnj.edu> Message-ID: Ryan, I don't see either the 'Use of initialized' error or the massive failed test issue using Mac OS X (perl 5.8). I get a different set of warnings using perl 5.10 related to Data::Dumper but not this (and everything runs fine). It might be of help to know what perl version, OS, etc. you are using. It also might be worth upgrading Module::Build and Test::Harness as well (though the Build.PL script should catch that and warn you). chris On Feb 8, 2008, at 9:58 PM, Ryan Golhar wrote: > Hi Hilmar, > > The script doesn't halt, but the tests do fail. I sent another > message with the errors I am seeing. I do not know if they are > related to this or not. > > Ryan > > > Hilmar Lapp wrote: >> Hi Ryan, >> On Feb 8, 2008, at 9:01 PM, Ryan Golhar wrote: >>> I get an error "Use of uninitialized value in concatenation (.) or >>> string at Build.PL line 184.". >> do keep in mind that this kind of message is almost never an error. >> It's simply a warning that you wouldn't even see w/o -w. All that >> it means is that a scalar with an undefined value is being >> evaluated to a string (which results, by default, in an empty >> string). >> Is the build failing or halting at this point for you? >> That said, it's indeed a good to point those out, as someone either >> should have initialized a scalar when it wasn't, or that someone >> was expecting the scalar to always have a value, and so the absence >> of it may indicate an unexpected condition resulting from an error >> elsewhere. >> -hilmar > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Fri Feb 8 23:49:14 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 8 Feb 2008 22:49:14 -0600 Subject: [Bioperl-l] error in build.pl of bioperl-live In-Reply-To: References: <47AD0989.1050904@umdnj.edu> <47AD24CA.2050102@umdnj.edu> Message-ID: <35C30475-6CC6-470E-B40B-DF13E65FC8A3@uiuc.edu> On Feb 8, 2008, at 10:07 PM, Hilmar Lapp wrote: > > On Feb 8, 2008, at 10:58 PM, Ryan Golhar wrote: > >> The script doesn't halt, but the tests do fail. I sent another >> message with the errors I am seeing. I do not know if they are >> related to this or not. > > > Yep I saw that. They might be related if, for example, the issue is > related to not finding BioPerl? > > Can you run one test in verbose mode? > > -hilmar To add to that, 'perl -I. t/SearchIO.t' should also still work for most (but not all). chris From heikki at sanbi.ac.za Tue Feb 12 03:25:32 2008 From: heikki at sanbi.ac.za (Heikki Lehvaslaiho) Date: Tue, 12 Feb 2008 10:25:32 +0200 Subject: [Bioperl-l] BioHackathon 2008 Message-ID: <200802121025.32797.heikki@sanbi.ac.za> Hi all, BioHackathon 2008 is happening right now in Tokyo, Japan. See http://hackathon.dbcls.jp/ The focus is on web services but some direct work on Bio* projects is getting done, too. See page: http://hackathon.dbcls.jp/wiki/OpenBio* for ideas thrown in the air. I just had a look how well the most common sequence file formats survive reading from a flat file into BioPerl objects and writing back into the same format: http://hackathon.dbcls.jp/wiki/BioPerlRoundTripFirstPass -Heikki -- ______ _/ _/_____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za _/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho _/ _/ _/ SANBI, South African National Bioinformatics Institute _/ _/ _/ University of Western Cape, South Africa _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 ___ _/_/_/_/_/________________________________________________________ From lenski at mdc-berlin.de Tue Feb 12 04:54:25 2008 From: lenski at mdc-berlin.de (Ulf Lenski) Date: Tue, 12 Feb 2008 10:54:25 +0100 Subject: [Bioperl-l] fetch protein-na-complexes from pdb Message-ID: <47B16CD1.2060307@mdc-berlin.de> is there a bioperl modul for fetching protein-na-complexes from the pdb? and can i distinguish ss-dna from dna chains without parsing the pdb files and go through the coordinates (calculate distances etc...)? tx - ulf. -------------- next part -------------- A non-text attachment was scrubbed... Name: lenski.vcf Type: text/x-vcard Size: 216 bytes Desc: not available URL: From bernd.web at gmail.com Tue Feb 12 07:45:51 2008 From: bernd.web at gmail.com (Bernd Web) Date: Tue, 12 Feb 2008 13:45:51 +0100 Subject: [Bioperl-l] fetch protein-na-complexes from pdb In-Reply-To: <47B16CD1.2060307@mdc-berlin.de> References: <47B16CD1.2060307@mdc-berlin.de> Message-ID: <716af09c0802120445n6d477c7dj5de7819408eb2c48@mail.gmail.com> Hi Ulf, At rcsb.org you can get a list of PDB IDs for Protein/NA complexes and even download the entries there. See http://www.rcsb.org/pdb/statistics/holdings.do Also see "webdownload" on the RCSB site. Alternatively, you could fetch the files one by one (e.g. with wget). The file "ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_entry_type.txt" contains the entry type of all PDB entries (i.e.: prot/nuc/prot-nuc and diffraction/NMR). Regards, Bernd 2008/2/12 Ulf Lenski : > is there a bioperl modul for fetching protein-na-complexes from the pdb? > and can i distinguish ss-dna from dna chains without parsing the pdb > files and go through the coordinates (calculate distances etc...)? > > tx - ulf. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From lenski at mdc-berlin.de Tue Feb 12 08:43:51 2008 From: lenski at mdc-berlin.de (Ulf Lenski) Date: Tue, 12 Feb 2008 14:43:51 +0100 Subject: [Bioperl-l] fetch protein-na-complexes from pdb In-Reply-To: <716af09c0802120445n6d477c7dj5de7819408eb2c48@mail.gmail.com> References: <47B16CD1.2060307@mdc-berlin.de> <716af09c0802120445n6d477c7dj5de7819408eb2c48@mail.gmail.com> Message-ID: <47B1A297.7030406@mdc-berlin.de> hi bernd, thanks a lot - that helps me for my first question. but how can I distinguish the nuc chains? How I can find out the type of a single chain? ss-rna ss-dna ds-rna ds-dna regards, ulf. Bernd Web schrieb: > Hi Ulf, > > At rcsb.org you can get a list of PDB IDs for Protein/NA complexes and > even download the entries there. See > http://www.rcsb.org/pdb/statistics/holdings.do > Also see "webdownload" on the RCSB site. > > Alternatively, you could fetch the files one by one (e.g. with wget). > The file "ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_entry_type.txt" > contains the entry type of all PDB entries (i.e.: prot/nuc/prot-nuc > and diffraction/NMR). > > Regards, > Bernd > > > 2008/2/12 Ulf Lenski : > >> is there a bioperl modul for fetching protein-na-complexes from the pdb? >> and can i distinguish ss-dna from dna chains without parsing the pdb >> files and go through the coordinates (calculate distances etc...)? >> >> tx - ulf. >> >> _______________________________________________ >> 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 > > -------------- next part -------------- A non-text attachment was scrubbed... Name: lenski.vcf Type: text/x-vcard Size: 216 bytes Desc: not available URL: From cjfields at uiuc.edu Tue Feb 12 12:02:13 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 12 Feb 2008 11:02:13 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release Message-ID: Now that SVN migration is complete and a BioSQL 1.0 release is imminent (congrats Hilmar and Heikki), I would like to get a new bioperl core release out the door soon, preferably by the next BOSC meeting, end of summer by the latest. One major issue that all the core devs have right now is time, or a serious lack thereof. I, for instance, will be moving into a new research position in the next few months or so. I'm assuming Jason, Hilmar, Heikki, Sendu, and the other core developers are facing similar time constraints. In that light, we need to decide whether we are planning a new 1.5 release, or if we want to start a new stable (1.6) release. With the latter, we need to define very specifically what needs to be accomplished for that release, and it needs to be realistic with the timeframe above in mind. I would also like to extend the invitation for anyone who wishes to help to join in. For my vote, I would like to release a new stable 1.6; 1.5.x has been around for too long and the end goals were never really defined clearly (something we need to keep in mind for the next dev release). I also vote for separating out experimental/untested/undocumented/ unmaintained modules into a separate 'bioperl-dev' release (the 'here be dragons' of bioperl). I believe it would help the core release cycle tremendously. Issues raised in the past just off the top of my head (add more as needed): * perl 5.10 compliance (appears to mostly work now) * outstanding bugs (core only) * GFF/GFF3 compliance * BioSQL 1.0 compliance (impending) * POD and test coverage * smoke tests for bioperl-live/db/etc. * smaller, more focused core (less dependencies) * separating out experimental or poorly maintained modules into a separate 'bioperl-dev' distribution * bioperl-db issues with Bio::Species changes * module maintenance * sequence format roundtripping (i.e. genbank, embl, swissetc) * additional sequence parsers (insdcxml, etc) * enhancement requests in bugzilla (Albert?) chris From hangsyin at gmail.com Tue Feb 12 11:50:33 2008 From: hangsyin at gmail.com (Hang) Date: Tue, 12 Feb 2008 08:50:33 -0800 (PST) Subject: [Bioperl-l] BLAT in memory Message-ID: <15435321.post@talk.nabble.com> Dear all, I wonder whether it is a way that allows me to BLAT sequences and retrieve the result without writing to a file. Thank you! Best, Hang -- View this message in context: http://www.nabble.com/BLAT-in-memory-tp15435321p15435321.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From jason at bioperl.org Tue Feb 12 12:49:56 2008 From: jason at bioperl.org (Jason Stajich) Date: Tue, 12 Feb 2008 09:49:56 -0800 Subject: [Bioperl-l] BLAT in memory In-Reply-To: <15435321.post@talk.nabble.com> References: <15435321.post@talk.nabble.com> Message-ID: <63C04F95-2EFB-433B-91F8-7907829E18CB@bioperl.org> Specify 'stdout' as the filename. -jason On Feb 12, 2008, at 8:50 AM, Hang wrote: > > Dear all, > > I wonder whether it is a way that allows me to BLAT sequences and > retrieve > the result without writing to a file. Thank you! > > Best, > Hang > -- > View this message in context: http://www.nabble.com/BLAT-in-memory- > tp15435321p15435321.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 bix at sendu.me.uk Tue Feb 12 13:10:52 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 12 Feb 2008 18:10:52 +0000 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: Message-ID: <47B1E12C.9010708@sendu.me.uk> Chris Fields wrote: > * perl 5.10 compliance (appears to mostly work now) > * outstanding bugs (core only) > * POD and test coverage I'm fine with everything you said, but I'll just say that, at a minimum, the above is what needs to be done. Someone needs to step up and organise that 3rd point, since it will require a lot of work. As I've already done work on the test suite, if no one else expresses an interest I might look into it myself. > Now that SVN migration is complete Speaking of which, is there a way a file (like, oh, I don't know, bioperl-live/trunk/t/lib/BioperlTest.pm) can exist just once in SVN but be seen in other locations (like bioperl-run/trunk/t/lib/BioperlTest.pm)? Such that a commit to the version in bioperl-run also affects the version in bioperl-live? Or is there some appropriate other way to organise where cross-repository files are kept and dealt with? From cjfields at uiuc.edu Tue Feb 12 13:51:57 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 12 Feb 2008 12:51:57 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <47B1E12C.9010708@sendu.me.uk> References: <47B1E12C.9010708@sendu.me.uk> Message-ID: <9424A11E-7541-442C-B53E-C791A2D8C6FB@uiuc.edu> On Feb 12, 2008, at 12:10 PM, Sendu Bala wrote: > Chris Fields wrote: >> * perl 5.10 compliance (appears to mostly work now) >> * outstanding bugs (core only) >> * POD and test coverage > > I'm fine with everything you said, but I'll just say that, at a > minimum, the above is what needs to be done. I think we should also try to get bioperl-db up to speed for the BioSQL 1.0 release (at least Bio::Species-related issues). > Someone needs to step up and organise that 3rd point, since it will > require a lot of work. As I've already done work on the test suite, > if no one else expresses an interest I might look into it myself. Jason and I discussed it off list (along with Nathan Haigh). We also brought up the idea of smoke tests, which should pinpoint how stable bioperl-live distributions are. Having those set up would pinpoint modules we think need to stay in core or should go into a separate 'dev/extras' distribution. We could test smoke/coverage/POD on those as well. >> Now that SVN migration is complete > > Speaking of which, is there a way a file (like, oh, I don't know, > bioperl-live/trunk/t/lib/BioperlTest.pm) can exist just once in SVN > but be seen in other locations (like bioperl-run/trunk/t/lib/ > BioperlTest.pm)? Such that a commit to the version in bioperl-run > also affects the version in bioperl-live? Or is there some > appropriate other way to organise where cross-repository files are > kept and dealt with? Maybe using external definitions, though I haven't messed with it personally. http://svnbook.red-bean.com/en/1.4/svn.advanced.externals.html One of the outstanding issues on SVN migration is the use of aliases for a checkout ('bioperl-all'); that would probably require setting svn:externals in some way. chris From hlapp at gmx.net Tue Feb 12 18:24:31 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 13 Feb 2008 08:24:31 +0900 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <47B1E12C.9010708@sendu.me.uk> References: <47B1E12C.9010708@sendu.me.uk> Message-ID: On Feb 13, 2008, at 3:10 AM, Sendu Bala wrote: > Speaking of which, is there a way a file (like, oh, I don't know, > bioperl-live/trunk/t/lib/BioperlTest.pm) can exist just once in SVN > but be seen in other locations (like bioperl-run/trunk/t/lib/ > BioperlTest.pm)? svn supposedly supports symlinks (though I haven't tested that myself yet), and since bioperl-live and bioperl-run are under the same svn root (aren't they?) you could make a symbolic link. The downside of this is that if someone only checks out bioperl-run the link would presumably be dangling. Though maybe not, not sure how super-smart svn is in this regard. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Tue Feb 12 21:10:23 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 13 Feb 2008 11:10:23 +0900 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <9424A11E-7541-442C-B53E-C791A2D8C6FB@uiuc.edu> References: <47B1E12C.9010708@sendu.me.uk> <9424A11E-7541-442C-B53E-C791A2D8C6FB@uiuc.edu> Message-ID: <66FBC084-74E4-458D-9F46-FCAD124AB8DE@gmx.net> On Feb 13, 2008, at 3:51 AM, Chris Fields wrote: > I think we should also try to get bioperl-db up to speed for the > BioSQL 1.0 release (at least Bio::Species-related issues). I agree. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From n.haigh at sheffield.ac.uk Wed Feb 13 03:46:02 2008 From: n.haigh at sheffield.ac.uk (Nathan S Haigh) Date: Wed, 13 Feb 2008 08:46:02 +0000 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <9424A11E-7541-442C-B53E-C791A2D8C6FB@uiuc.edu> References: <47B1E12C.9010708@sendu.me.uk> <9424A11E-7541-442C-B53E-C791A2D8C6FB@uiuc.edu> Message-ID: <47B2AE4A.3040509@sheffield.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Chris Fields wrote: > On Feb 12, 2008, at 12:10 PM, Sendu Bala wrote: > >> Chris Fields wrote: >>> * perl 5.10 compliance (appears to mostly work now) >>> * outstanding bugs (core only) >>> * POD and test coverage >> >> I'm fine with everything you said, but I'll just say that, at a >> minimum, the above is what needs to be done. > > I think we should also try to get bioperl-db up to speed for the BioSQL > 1.0 release (at least Bio::Species-related issues). > >> Someone needs to step up and organise that 3rd point, since it will >> require a lot of work. As I've already done work on the test suite, if >> no one else expresses an interest I might look into it myself. > > Jason and I discussed it off list (along with Nathan Haigh). We also > brought up the idea of smoke tests, which should pinpoint how stable > bioperl-live distributions are. Having those set up would pinpoint > modules we think need to stay in core or should go into a separate > 'dev/extras' distribution. We could test smoke/coverage/POD on those as > well. > I've moved away from Perl coding over the past 6-12 months but try to keep an eye on the BioPerl mailing list and chip in when I can. The last time the Devel::Cover module came up, it was lacking the ability to sort the coverage report table by each of the coverage metrics - which was a problem for us as we have so many modules and it was time consuming to find those with poor coverage. However, this feature were implemented in Devel::Cover 0.62, so it makes things slightly easier/neater. I'm not sure if the problem of failing tests still mess up the completion of the coverage report or not. >>> Now that SVN migration is complete >> >> Speaking of which, is there a way a file (like, oh, I don't know, >> bioperl-live/trunk/t/lib/BioperlTest.pm) can exist just once in SVN >> but be seen in other locations (like >> bioperl-run/trunk/t/lib/BioperlTest.pm)? Such that a commit to the >> version in bioperl-run also affects the version in bioperl-live? Or is >> there some appropriate other way to organise where cross-repository >> files are kept and dealt with? > See the subversion FAQs: http://subversion.tigris.org/faq.html#symlinks > Maybe using external definitions, though I haven't messed with it > personally. > > http://svnbook.red-bean.com/en/1.4/svn.advanced.externals.html > > One of the outstanding issues on SVN migration is the use of aliases for > a checkout ('bioperl-all'); that would probably require setting > svn:externals in some way. > > chris -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHsq5K9gTv6QYzVL4RAuJWAKCM/eEEXL5LqTsG/fGAmGIM6+dW9QCfe/6w T2a/dKg6d8HHXNXrOnSbdcs= =T8pz -----END PGP SIGNATURE----- From David.Messina at sbc.su.se Wed Feb 13 06:06:58 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 13 Feb 2008 12:06:58 +0100 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: Message-ID: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> I agree with Chris that the next BioPerl release should be 1.6. Shunting abandoned, experimental, and less-developed code to "bioperl-dev" would be extremely beneficial. As Chris stated, not only does it reduce the number of modules needing full test coverage, but the most important core modules are the ones most likely to have good test coverage already. And it would make BioPerl easier to grok for newcomers, too, which is always nice. I've made a first go at dividing the current bioperl core along these lines here: http://www.bioperl.org/wiki/Proposed_1.6_core_modules It's a very rough cut, so those with more familiarity with the bioperl corpus, please go in and rearrange as you see fit. Dave From n.haigh at sheffield.ac.uk Wed Feb 13 07:07:16 2008 From: n.haigh at sheffield.ac.uk (Nathan S Haigh) Date: Wed, 13 Feb 2008 12:07:16 +0000 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> Message-ID: <47B2DD74.5020503@sheffield.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I remember a conversion about how/if to split bioperl modules up in the past. If I remember rightly, there was talk of splitting all modules up and then creating a CPAN bundle for the core modules. I don't know if this make the admin really complex, but this allows people to install just those modules they require rather than the whole bioperl-core. For example, if I write a script or a module that wants to make use of BioPerl's SeqIO abilities, the end user has to download and install a load of modules that he/she may never use. Instead, it would be nicer to simply install SeqIO and it's dependecies. If I want to install all the BioPerl core, I can install a CPAN bundle. Just a thought. Nath Dave Messina wrote: > I agree with Chris that the next BioPerl release should be 1.6. > > Shunting abandoned, experimental, and less-developed code to "bioperl-dev" > would be extremely beneficial. As Chris stated, not only does it reduce the > number of modules needing full test coverage, but the most important core > modules are the ones most likely to have good test coverage already. And it > would make BioPerl easier to grok for newcomers, too, which is always nice. > > I've made a first go at dividing the current bioperl core along these lines > here: > http://www.bioperl.org/wiki/Proposed_1.6_core_modules > > It's a very rough cut, so those with more familiarity with the bioperl > corpus, please go in and rearrange as you see fit. > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHst109gTv6QYzVL4RAvmAAKCmJa5X0dvyPiQ6lADQ0BBk/tu3OQCg1cNC ZZVlnTSKc6dcCbYJ5JgUGjA= =bvUu -----END PGP SIGNATURE----- From bosborne11 at verizon.net Wed Feb 13 10:08:36 2008 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 13 Feb 2008 10:08:36 -0500 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> Message-ID: Dave, A few of those modules are supposed to be removed in 1.6, according to the notes in the DEPRECATED file. I've marked them. Brian O. On Feb 13, 2008, at 6:06 AM, Dave Messina wrote: > I've made a first go at dividing the current bioperl core along > these lines > here: > http://www.bioperl.org/wiki/Proposed_1.6_core_modules From cjfields at uiuc.edu Wed Feb 13 11:58:03 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 13 Feb 2008 10:58:03 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> Message-ID: I've added/modified the page as well; moved Bio::FeatureIO and Bio::SeqFeature::Annotated over to the bioperl-dev for now, along with Bio::Assembly and Bio::Restriction. We'll have to test out removing those modules to see what blows up. chris On Feb 13, 2008, at 9:08 AM, Brian Osborne wrote: > Dave, > > A few of those modules are supposed to be removed in 1.6, according > to the notes in the DEPRECATED file. I've marked them. > > Brian O. > > > On Feb 13, 2008, at 6:06 AM, Dave Messina wrote: > >> I've made a first go at dividing the current bioperl core along >> these lines >> here: >> http://www.bioperl.org/wiki/Proposed_1.6_core_modules > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Feb 13 14:11:34 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 13 Feb 2008 13:11:34 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> Message-ID: <8C98F03E-0424-4383-A08C-F227745DBEF6@uiuc.edu> On Feb 13, 2008, at 12:32 PM, Brian Osborne wrote: > Chris, > > You should be careful about the names of these packages. For > example, Bio::Biblio and Bio::Restriction are not "in development" > as the term bioperl-dev implies. They're tried and true. And there > may be sets of modules that are experimental in "bioperl-dev", of > course. Is it possible to have 2 packages, "dev" and "tools"? Or > something along those lines? > > Calling things by the wrong names leads to confusion, witness the > Bioperl newcomers who would install an antiquated version 1.4 > because it was labelled 'stable'. > > BIO I agree the name 'dev' is misleading. 'tools' or 'extras' sounds better, maybe using 'dev' for experimental implementations, such as Jason's SeqFeature::Slim or my SeqIO driver/handler modules. The problem with the two namespaces you mention is lack of maintenance and documentation, though I agree they're stable (so maybe in those cases maintenance isn't an issue). We do need to clean up documentation issues with those classes as well as many more (mine included); POD/test coverage will help out there. chris From bosborne11 at verizon.net Wed Feb 13 13:32:46 2008 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 13 Feb 2008 13:32:46 -0500 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> Message-ID: <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> Chris, You should be careful about the names of these packages. For example, Bio::Biblio and Bio::Restriction are not "in development" as the term bioperl-dev implies. They're tried and true. And there may be sets of modules that are experimental in "bioperl-dev", of course. Is it possible to have 2 packages, "dev" and "tools"? Or something along those lines? Calling things by the wrong names leads to confusion, witness the Bioperl newcomers who would install an antiquated version 1.4 because it was labelled 'stable'. BIO On Feb 13, 2008, at 11:58 AM, Chris Fields wrote: > I've added/modified the page as well; moved Bio::FeatureIO and > Bio::SeqFeature::Annotated over to the bioperl-dev for now, along > with Bio::Assembly and Bio::Restriction. We'll have to test out > removing those modules to see what blows up. From David.Messina at sbc.su.se Wed Feb 13 14:55:26 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 13 Feb 2008 20:55:26 +0100 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> Message-ID: <628aabb70802131155q73674b72qad547c55c5443e2d@mail.gmail.com> Great, thanks guys. From bix at sendu.me.uk Wed Feb 13 15:19:01 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 13 Feb 2008 20:19:01 +0000 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> Message-ID: <47B350B5.3060501@sendu.me.uk> Brian Osborne wrote: > You should be careful about the names of these packages. For example, > Bio::Biblio and Bio::Restriction are not "in development" as the term > bioperl-dev implies. They're tried and true. And there may be sets of > modules that are experimental in "bioperl-dev", of course. Is it > possible to have 2 packages, "dev" and "tools"? Or something along those > lines? > > Calling things by the wrong names leads to confusion, witness the > Bioperl newcomers who would install an antiquated version 1.4 because it > was labelled 'stable'. On the topic of confusion, I think 'bioperl-tools' is a very bad choice since we have Bio::Tools. Why would Bio::Microarray (for example) be in there? (And then we have Bio::Microarray::Tools ...) Can all of the non Bio::Tools modules currently in the bioperl-tools section of the wiki page be annotated as to why they're there and not in core? Then maybe we can come up with a better name to categorize them all under. Perhaps we could also annotate the things in core to justify why they should be in core? Is anyone good at creating maps so we can easily see what Bioperl modules are most used (by other Bioperl modules)? Or is the split intended to be 'core' == "anything and everything that was in 1.4", '????' == "everything else"? In which case, what's a good name for "modules created after 1.4"? 'crust'? ;) From cjfields at uiuc.edu Wed Feb 13 16:05:16 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 13 Feb 2008 15:05:16 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <47B350B5.3060501@sendu.me.uk> References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> <47B350B5.3060501@sendu.me.uk> Message-ID: <477CF001-FF35-4A08-A360-C9FA2031E353@uiuc.edu> On Feb 13, 2008, at 2:19 PM, Sendu Bala wrote: > Brian Osborne wrote: >> You should be careful about the names of these packages. For >> example, Bio::Biblio and Bio::Restriction are not "in development" >> as the term bioperl-dev implies. They're tried and true. And there >> may be sets of modules that are experimental in "bioperl-dev", of >> course. Is it possible to have 2 packages, "dev" and "tools"? Or >> something along those lines? >> Calling things by the wrong names leads to confusion, witness the >> Bioperl newcomers who would install an antiquated version 1.4 >> because it was labelled 'stable'. > > On the topic of confusion, I think 'bioperl-tools' is a very bad > choice since we have Bio::Tools. Why would Bio::Microarray (for > example) be in there? (And then we have Bio::Microarray::Tools ...) > > Can all of the non Bio::Tools modules currently in the bioperl-tools > section of the wiki page be annotated as to why they're there and > not in core? Then maybe we can come up with a better name to > categorize them all under. > > Perhaps we could also annotate the things in core to justify why > they should be in core? Is anyone good at creating maps so we can > easily see what Bioperl modules are most used (by other Bioperl > modules)? Frankly, it will be hard for a handful of people (Dave, Brian, and I) to justify the existence for every bioperl module or it's placement in bioperl-?, but at least we have a start on it. The page is open for editing by anyone (Dave, Brian, and I have already added quite a bit). There is also a discussion page to add to, which is a good place for proposals and to sketch out ideas. I think we should take some time on this to stew over the options available, maybe a month or two, and set some deadline for starting up. > Or is the split intended to be 'core' == "anything and everything > that was in 1.4", '????' == "everything else"? In which case, what's > a good name for "modules created after 1.4"? 'crust'? ;) I personally take the extreme view of having a very tight core with just the basic sequence, feature, alignment, and annotation classes (just for maintenance sake); everything else just uses those base classes anyway, so I don't necessarily consider them core. I don't think paring down to that level is feasible for a 1.6 release, but moving some of the unmaintained cruft out into a separate installation would be a good start. chris From pengchy at yahoo.com.cn Wed Feb 13 20:26:21 2008 From: pengchy at yahoo.com.cn (Åô³Ì) Date: 14 Feb 2008 01:26:21 -0000 Subject: Åô³ÌÑûÇëÄú¼ÓÈëÈô±ÈÁÚ Message-ID: <20080214012621.30230.qmail@zorpia.com> Hi bioperl! Your friend ???? from ????, just invited you to online photo albums and journals at Zorpia.com. So what is Zorpia? It is an online community that allows you to upload unlimited amount of photos, write journals and make friends. We also have a variety of skins in store for you so that you can customize your homepage freely. Join now for free! Please click the following link to join Zorpia: http://cn.signup.zorpia.com/signup?invitation_key=200802c0d8af2b64f8ef03d6417e4ab4&referral=pengchy This message was delivered with the ????'s initiation. If you wish to discontinue receiving invitations from us, please click the following link: http://cn.signup.zorpia.com/email/optout/bioperl-l at lists.open-bio.org From hangsyin at gmail.com Wed Feb 13 22:10:54 2008 From: hangsyin at gmail.com (Hang) Date: Wed, 13 Feb 2008 19:10:54 -0800 (PST) Subject: [Bioperl-l] Re trieve ID tag in GFF3 Message-ID: <15473188.post@talk.nabble.com> Dear All, I wonder what method I should call to retrieve values of ID tags in GFF3 format. For example, a GFF3 entry in the database is like this: 4 FlyBase gene 24068 25621 . + . ID=FBgn0040037;Name=ABC;Ontology_term=... I'd like to retrieve the scalar value 'FBgn0040037' to compare with another value. Please complete the code below: use Bio::DB::SeqFeature::Store; my $db = Bio::DB::SeqFeature::Store->new(-adaptor => 'DBI::mysql', -dsn => 'dbi:mysql:XXX_gff', -user => 'XXX', -pass => 'XXX')|| die "Database open failed"; ??? Thanks alot! Hang -- View this message in context: http://www.nabble.com/Retrieve-ID-tag-in-GFF3-tp15473188p15473188.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From cjfields at uiuc.edu Thu Feb 14 15:36:27 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 14 Feb 2008 14:36:27 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <47B350B5.3060501@sendu.me.uk> References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> <47B350B5.3060501@sendu.me.uk> Message-ID: <3C0A6ADA-AABC-4D7A-B858-CEB8E87AFDDE@uiuc.edu> On Feb 13, 2008, at 2:19 PM, Sendu Bala wrote: > Brian Osborne wrote: >> You should be careful about the names of these packages. For >> example, Bio::Biblio and Bio::Restriction are not "in development" >> as the term bioperl-dev implies. They're tried and true. And there >> may be sets of modules that are experimental in "bioperl-dev", of >> course. Is it possible to have 2 packages, "dev" and "tools"? Or >> something along those lines? >> Calling things by the wrong names leads to confusion, witness the >> Bioperl newcomers who would install an antiquated version 1.4 >> because it was labelled 'stable'. > > On the topic of confusion, I think 'bioperl-tools' is a very bad > choice since we have Bio::Tools. Why would Bio::Microarray (for > example) be in there? (And then we have Bio::Microarray::Tools ...) > > Can all of the non Bio::Tools modules currently in the bioperl-tools > section of the wiki page be annotated as to why they're there and > not in core? Then maybe we can come up with a better name to > categorize them all under. > > Perhaps we could also annotate the things in core to justify why > they should be in core? Is anyone good at creating maps so we can > easily see what Bioperl modules are most used (by other Bioperl > modules)? > > > Or is the split intended to be 'core' == "anything and everything > that was in 1.4", '????' == "everything else"? In which case, what's > a good name for "modules created after 1.4"? 'crust'? ;) I added a modified proposal to the Talk page for the Release: http://www.bioperl.org/wiki/Talk:Proposed_1.6_core_modules I'm pretty flexible on any of that; it's a proposal only and I think some of it may be wrongheaded, but hey, I'm willing to take a few rotten tomatoes. The key issue is we should try to work out what we mean by 'core' or the core library. I have a rather extreme view of it as being the bare essentials without external, non-perl core dependencies (only SeqI/PrimarySeqI, AlignI, AnnotationI, SeqFeatureI and required modules for those classes) but I'm sure others would lump in parsers, DB functionality, etc. I basically suggest placing those (and any stable but potentially non-core code) in a 'bioperl-main', with any unstable or untested code going into a 'bioperl-unstable'. In essence, bioperl-main would require core and resemble a stable release; bioperl-unstable would require bioperl-main (and core) and resemble a dev release. Not sure how versioning would go or if this is a viable option at all, but it's worth discussing. chris From aaron.j.mackey at gsk.com Fri Feb 15 13:06:58 2008 From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com) Date: Fri, 15 Feb 2008 13:06:58 -0500 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <47B350B5.3060501@sendu.me.uk> Message-ID: > Or is the split intended to be 'core' == "anything and everything that > was in 1.4", '????' == "everything else"? In which case, what's a good > name for "modules created after 1.4"? 'crust'? ;) Nah, "icing". a module "use" map might be very useful to help identify "core" vs. other layers of mantle/crust/icing. http://www.perlmonks.org/?node_id=87329 http://search.cpan.org/src/NEILB/pmusage-1.2/ Some more serious alternatives to "bioperl-dev" and "-tools" might be: "-accessory" or "-optional" or "-other" or "-addons", etc. -Aaron From lincoln.stein at gmail.com Fri Feb 15 15:17:31 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Fri, 15 Feb 2008 15:17:31 -0500 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: Message-ID: <6dce9a0b0802151217t59e41ccq2bcb10c68b8aede1@mail.gmail.com> > * perl 5.10 compliance (appears to mostly work now) > * GFF/GFF3 compliance I've been doing a lot of work on this recently. I think it's much improved. No problems with 5.10 for the modules that I use frequently. Lincoln > > * BioSQL 1.0 compliance (impending) > * POD and test coverage > * smoke tests for bioperl-live/db/etc. > * smaller, more focused core (less dependencies) > * separating out experimental or poorly maintained modules into a > separate 'bioperl-dev' distribution > * bioperl-db issues with Bio::Species changes > * module maintenance > * sequence format roundtripping (i.e. genbank, embl, swissetc) > * additional sequence parsers (insdcxml, etc) > * enhancement requests in bugzilla (Albert?) > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From cjfields at uiuc.edu Fri Feb 15 16:43:42 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 15 Feb 2008 15:43:42 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <6dce9a0b0802151217t59e41ccq2bcb10c68b8aede1@mail.gmail.com> References: <6dce9a0b0802151217t59e41ccq2bcb10c68b8aede1@mail.gmail.com> Message-ID: On Feb 15, 2008, at 2:17 PM, Lincoln Stein wrote: >> * perl 5.10 compliance (appears to mostly work now) >> * GFF/GFF3 compliance > > > I've been doing a lot of work on this recently. I think it's much > improved. > No problems with 5.10 for the modules that I use frequently. > > Lincoln I think bioperl works now for perl 5.10. The only significant issue we ran into were problems with Bio::SeqIO::entrezgene. The parser looped and created a pseudohash under some conditions, which threw all sorts of errors with 5.8. Stefan and I fixed that one in Subversion. There were some odd Data::Dumper-related messages popping up with 'perl Build.PL' using perl 5.10; not sure what's going on there, but it appears harmless: Encountered CODE ref, using dummy placeholder at /opt/perl/lib/5.10.0/ darwin-2level/Data/Dumper.pm line 190. chris From cjfields at uiuc.edu Fri Feb 15 16:49:33 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 15 Feb 2008 15:49:33 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: Message-ID: On Feb 15, 2008, at 12:06 PM, aaron.j.mackey at gsk.com wrote: >> Or is the split intended to be 'core' == "anything and everything >> that >> was in 1.4", '????' == "everything else"? In which case, what's a >> good >> name for "modules created after 1.4"? 'crust'? ;) > > Nah, "icing". > > a module "use" map might be very useful to help identify "core" vs. > other > layers of mantle/crust/icing. > > http://www.perlmonks.org/?node_id=87329 > http://search.cpan.org/src/NEILB/pmusage-1.2/ > > Some more serious alternatives to "bioperl-dev" and "-tools" might be: > "-accessory" or "-optional" or "-other" or "-addons", etc. > > -Aaron 'bioperl-extras' (Ricky Gervais fan myself) chris From hlapp at gmx.net Fri Feb 15 17:14:10 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 16 Feb 2008 07:14:10 +0900 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: Message-ID: <82E17B18-32D9-4858-9245-EEF9D143DA11@gmx.net> On Feb 16, 2008, at 6:49 AM, Chris Fields wrote: >> >> Some more serious alternatives to "bioperl-dev" and "-tools" might >> be: >> "-accessory" or "-optional" or "-other" or "-addons", etc. >> >> -Aaron > > 'bioperl-extras' (Ricky Gervais fan myself) > Actually I like bioperl-opt - sounds somehow reminiscent of the /opt directory we all know (often containing the best things :) -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Sun Feb 17 09:07:20 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 17 Feb 2008 08:07:20 -0600 Subject: [Bioperl-l] [Bioperl-guts-l] [14510] bioperl-live/trunk/Bio/SeqIO/swiss.pm: GN line output now follows the new format. In-Reply-To: <200802171000.m1HA0oGq003135@dev.open-bio.org> References: <200802171000.m1HA0oGq003135@dev.open-bio.org> Message-ID: Heikki, See bug 1825: http://bugzilla.open-bio.org/show_bug.cgi?id=1825 Hilmar's final comments about restructuring Bio::Annotation::StructuredValue using Data::Stag should work. chris On Feb 17, 2008, at 4:00 AM, Heikki Lehvaslaiho wrote: > Revision: 14510 > Author: heikki > Date: 2008-02-17 05:00:50 -0500 (Sun, 17 Feb 2008) > > Log Message: > ----------- > GN line output now follows the new format. BioPerl would need new > objects to store all infomation so for now only the official name > (Name=) and synonym categories are kept. ORFNames and > OrderedLocusNames are treated as synonyms. > > Modified Paths: > -------------- > bioperl-live/trunk/Bio/SeqIO/swiss.pm > > Modified: bioperl-live/trunk/Bio/SeqIO/swiss.pm > =================================================================== > --- bioperl-live/trunk/Bio/SeqIO/swiss.pm 2008-02-17 09:48:07 UTC > (rev 14509) > +++ bioperl-live/trunk/Bio/SeqIO/swiss.pm 2008-02-17 10:00:50 UTC > (rev 14510) > @@ -494,16 +494,13 @@ > #Definition lines > $self->_write_line_swissprot_regex("DE ","DE ",$seq- > >desc(),"\\s\+\|\$",$LINE_LENGTH); > > - #Gene name > - if ((my @genes = $seq->annotation- > >get_Annotations('gene_name') ) ) { > - $self->_print("GN ", > - join(' OR ', > - map { > - $_->isa("Bio::Annotation::StructuredValue") ? > - $_->value(-joins => [" AND ", " OR "]) : > - $_->value(); > - } @genes), > - ".\n"); > + #Gene name; print out new format but only two categories: Name > and Synonyms > + if ( my @genes = $seq->annotation- > >get_Annotations('gene_name') ) { > + my @gene_names = map { $_->get_all_values} @genes; > + my $gn_string = 'Name='. shift(@gene_names). ';'; > + $gn_string .= ' Synonyms='. join(', ', @gene_names). ";" if > scalar @gene_names; > + $self->_write_line_swissprot_regex("GN ","GN ", > $gn_string,"\\s\+\|\$",$LINE_LENGTH); > + > } > > # Organism lines > @@ -1267,7 +1264,6 @@ > } > > my $subl = $length - (length $pre1) -1 ; > - my @lines; > > my $first_line = 1; > while($line =~ m/(.{1,$subl})($regex)/g) { > > > _______________________________________________ > Bioperl-guts-l mailing list > Bioperl-guts-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From heikki at sanbi.ac.za Mon Feb 18 03:12:11 2008 From: heikki at sanbi.ac.za (Heikki Lehvaslaiho) Date: Mon, 18 Feb 2008 10:12:11 +0200 Subject: [Bioperl-l] [Bioperl-guts-l] [14510] bioperl-live/trunk/Bio/SeqIO/swiss.pm: GN line output now follows the new format. In-Reply-To: References: <200802171000.m1HA0oGq003135@dev.open-bio.org> Message-ID: <200802181012.11295.heikki@sanbi.ac.za> Thanks for pointing this out to me. Looks like I've solved the first level: "Problem #1 is to have all the value tokens available from the created object, regardless of their tags." Anybody want to go on to the next level and code in the complete representation of the GN line? -Heikki On Sunday 17 February 2008 16:07:20 Chris Fields wrote: > Heikki, > > See bug 1825: > > http://bugzilla.open-bio.org/show_bug.cgi?id=1825 > > Hilmar's final comments about restructuring > Bio::Annotation::StructuredValue using Data::Stag should work. > > chris > > On Feb 17, 2008, at 4:00 AM, Heikki Lehvaslaiho wrote: > > Revision: 14510 > > Author: heikki > > Date: 2008-02-17 05:00:50 -0500 (Sun, 17 Feb 2008) > > > > Log Message: > > ----------- > > GN line output now follows the new format. BioPerl would need new > > objects to store all infomation so for now only the official name > > (Name=) and synonym categories are kept. ORFNames and > > OrderedLocusNames are treated as synonyms. > > > > Modified Paths: > > -------------- > > bioperl-live/trunk/Bio/SeqIO/swiss.pm > > > > Modified: bioperl-live/trunk/Bio/SeqIO/swiss.pm > > =================================================================== > > --- bioperl-live/trunk/Bio/SeqIO/swiss.pm 2008-02-17 09:48:07 UTC > > (rev 14509) > > +++ bioperl-live/trunk/Bio/SeqIO/swiss.pm 2008-02-17 10:00:50 UTC > > (rev 14510) > > @@ -494,16 +494,13 @@ > > #Definition lines > > $self->_write_line_swissprot_regex("DE ","DE ",$seq- > > > > >desc(),"\\s\+\|\$",$LINE_LENGTH); > > > > - #Gene name > > - if ((my @genes = $seq->annotation- > > > > >get_Annotations('gene_name') ) ) { > > > > - $self->_print("GN ", > > - join(' OR ', > > - map { > > - $_->isa("Bio::Annotation::StructuredValue") ? > > - $_->value(-joins => [" AND ", " OR "]) : > > - $_->value(); > > - } @genes), > > - ".\n"); > > + #Gene name; print out new format but only two categories: Name > > and Synonyms > > + if ( my @genes = $seq->annotation- > > > > >get_Annotations('gene_name') ) { > > > > + my @gene_names = map { $_->get_all_values} @genes; > > + my $gn_string = 'Name='. shift(@gene_names). ';'; > > + $gn_string .= ' Synonyms='. join(', ', @gene_names). ";" if > > scalar @gene_names; > > + $self->_write_line_swissprot_regex("GN ","GN ", > > $gn_string,"\\s\+\|\$",$LINE_LENGTH); > > + > > } > > > > # Organism lines > > @@ -1267,7 +1264,6 @@ > > } > > > > my $subl = $length - (length $pre1) -1 ; > > - my @lines; > > > > my $first_line = 1; > > while($line =~ m/(.{1,$subl})($regex)/g) { > > > > > > _______________________________________________ > > Bioperl-guts-l mailing list > > Bioperl-guts-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za _/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho _/ _/ _/ SANBI, South African National Bioinformatics Institute _/ _/ _/ University of Western Cape, South Africa _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 ___ _/_/_/_/_/________________________________________________________ From cjfields at uiuc.edu Mon Feb 18 13:56:32 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 18 Feb 2008 12:56:32 -0600 Subject: [Bioperl-l] [Bioperl-guts-l] [14510] bioperl-live/trunk/Bio/SeqIO/swiss.pm: GN line output now follows the new format. In-Reply-To: <200802181012.11295.heikki@sanbi.ac.za> References: <200802171000.m1HA0oGq003135@dev.open-bio.org> <200802181012.11295.heikki@sanbi.ac.za> Message-ID: <670A1145-D1A6-4245-A621-750E0F4FFB6E@uiuc.edu> I may try working on the next. I had indicated that I would do this in the past, just never got around to it; time is the enemy of us all. chris On Feb 18, 2008, at 2:12 AM, Heikki Lehvaslaiho wrote: > Thanks for pointing this out to me. Looks like I've solved the first > level: > > "Problem #1 is to have all the value tokens > available from the created object, regardless of their tags." > > Anybody want to go on to the next level and code in the complete > representation of the GN line? > > -Heikki > > > On Sunday 17 February 2008 16:07:20 Chris Fields wrote: >> Heikki, >> >> See bug 1825: >> >> http://bugzilla.open-bio.org/show_bug.cgi?id=1825 >> >> Hilmar's final comments about restructuring >> Bio::Annotation::StructuredValue using Data::Stag should work. >> >> chris >> >> On Feb 17, 2008, at 4:00 AM, Heikki Lehvaslaiho wrote: >>> Revision: 14510 >>> Author: heikki >>> Date: 2008-02-17 05:00:50 -0500 (Sun, 17 Feb 2008) >>> >>> Log Message: >>> ----------- >>> GN line output now follows the new format. BioPerl would need new >>> objects to store all infomation so for now only the official name >>> (Name=) and synonym categories are kept. ORFNames and >>> OrderedLocusNames are treated as synonyms. >>> >>> Modified Paths: >>> -------------- >>> bioperl-live/trunk/Bio/SeqIO/swiss.pm >>> >>> Modified: bioperl-live/trunk/Bio/SeqIO/swiss.pm >>> =================================================================== >>> --- bioperl-live/trunk/Bio/SeqIO/swiss.pm 2008-02-17 09:48:07 UTC >>> (rev 14509) >>> +++ bioperl-live/trunk/Bio/SeqIO/swiss.pm 2008-02-17 10:00:50 UTC >>> (rev 14510) >>> @@ -494,16 +494,13 @@ >>> #Definition lines >>> $self->_write_line_swissprot_regex("DE ","DE ",$seq- >>> >>>> desc(),"\\s\+\|\$",$LINE_LENGTH); >>> >>> - #Gene name >>> - if ((my @genes = $seq->annotation- >>> >>>> get_Annotations('gene_name') ) ) { >>> >>> - $self->_print("GN ", >>> - join(' OR ', >>> - map { >>> - $_->isa("Bio::Annotation::StructuredValue") ? >>> - $_->value(-joins => [" AND ", " OR "]) : >>> - $_->value(); >>> - } @genes), >>> - ".\n"); >>> + #Gene name; print out new format but only two categories: Name >>> and Synonyms >>> + if ( my @genes = $seq->annotation- >>> >>>> get_Annotations('gene_name') ) { >>> >>> + my @gene_names = map { $_->get_all_values} @genes; >>> + my $gn_string = 'Name='. shift(@gene_names). ';'; >>> + $gn_string .= ' Synonyms='. join(', ', @gene_names). ";" if >>> scalar @gene_names; >>> + $self->_write_line_swissprot_regex("GN ","GN ", >>> $gn_string,"\\s\+\|\$",$LINE_LENGTH); >>> + >>> } >>> >>> # Organism lines >>> @@ -1267,7 +1264,6 @@ >>> } >>> >>> my $subl = $length - (length $pre1) -1 ; >>> - my @lines; >>> >>> my $first_line = 1; >>> while($line =~ m/(.{1,$subl})($regex)/g) { >>> >>> >>> _______________________________________________ >>> Bioperl-guts-l mailing list >>> Bioperl-guts-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l >> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > -- > ______ _/ _/_____________________________________________________ > _/ _/ > _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za > _/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho > _/ _/ _/ SANBI, South African National Bioinformatics Institute > _/ _/ _/ University of Western Cape, South Africa > _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 > ___ _/_/_/_/_/________________________________________________________ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From hlapp at gmx.net Mon Feb 18 17:14:33 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 18 Feb 2008 17:14:33 -0500 Subject: [Bioperl-l] BOSC 2008? In-Reply-To: <9C6A22B1-9E84-4F17-8459-CBBDCB2110D4@uiuc.edu> References: <1182EAB9-7A75-498F-B91B-C14771DFD607@uiuc.edu> <628aabb70802061317n2f0d1103w9367346166bf8c3f@mail.gmail.com> <9C6A22B1-9E84-4F17-8459-CBBDCB2110D4@uiuc.edu> Message-ID: As an aside, I've posted the (so far "unofficial") update on the news.open-bio.org blog. -hilmar On Feb 6, 2008, at 4:22 PM, Chris Fields wrote: > Yep. I found this out earlier from Darin London. Just trying to > plan for it ahead of time! > > chris > > On Feb 6, 2008, at 3:17 PM, Dave Messina wrote: > >> Hey Chris, >> >> Isn't it usually in conjunction with ISMB (which is Toronto >> 7/19-23 this year)? >> >> > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From johan.nilsson at sh.se Tue Feb 19 09:42:52 2008 From: johan.nilsson at sh.se (Johan Nilsson) Date: Tue, 19 Feb 2008 15:42:52 +0100 Subject: [Bioperl-l] Dumping a MSA from BLAST results Message-ID: <47BAEAEC.5080203@sh.se> Hello, I have a question regarding the conversion from a Blast search result (PSI-blast using blastpgp, to be more exact) to a multiple sequence alignment file. I'm running the Bio::Tools::Run::StandAloneBlast and I retrieve the HSPs from the resulting Bio::Search::Hit::HitI objects. I have no problems obtaining each HSP alignment using $hit->get_aln. However, rather than dumping many local alignments, I would like to write a single result file where the HSPs are interleaved. I guess this shouldn't be too hard, but nevertheless I haven't found out how to do this in a simple way. Any suggestions would be highly appreciated! Best Regards /Johan Nilsson From jason at bioperl.org Tue Feb 19 11:17:32 2008 From: jason at bioperl.org (Jason Stajich) Date: Tue, 19 Feb 2008 08:17:32 -0800 Subject: [Bioperl-l] Dumping a MSA from BLAST results In-Reply-To: <47BAEAEC.5080203@sh.se> References: <47BAEAEC.5080203@sh.se> Message-ID: <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> All the individual pairwise alignments won't necessarily be an alignment of the same region and the gap insertions can be different in each instance of the query sequence that is participating in the pairwise alns so it won't fit into an MSA. It makes more sense to extract the aligned part of the hit sequences identified and a subsequence of the query which is the min and max region aligned. Run this through a MSA program. -jason On Feb 19, 2008, at 6:42 AM, Johan Nilsson wrote: > Hello, > > I have a question regarding the conversion from a Blast search > result (PSI-blast using blastpgp, to be more exact) to a multiple > sequence alignment file. I'm running the > Bio::Tools::Run::StandAloneBlast and I retrieve the HSPs from the > resulting Bio::Search::Hit::HitI objects. I have no problems > obtaining each HSP alignment using $hit->get_aln. However, rather > than dumping many local alignments, I would like to write a single > result file where the HSPs are interleaved. > > I guess this shouldn't be too hard, but nevertheless I haven't > found out how to do this in a simple way. Any suggestions would be > highly appreciated! > > Best Regards > /Johan Nilsson > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at uiuc.edu Tue Feb 19 12:18:34 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 19 Feb 2008 11:18:34 -0600 Subject: [Bioperl-l] Dumping a MSA from BLAST results In-Reply-To: <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> Message-ID: One could use an alternative blastall output format (like -m1 to -m6), which give various anchored alignments. None of these are parsed via bioperl as far as I know; might be worth getting something up and running if there is enough interest in it. chris PS. Here's example output using 'blastall -p blastp -i test2.faa -d CP000560.faa -m6', which is query-anchored, flat, blunt ends: BLASTP 2.2.16 [Mar-25-2007] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= gi|1373160|gb|AAB57770.1| PyrR (173 letters) Database: CP000560.faa 3693 sequences; 1,147,568 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gb|ABS73893.1| PyrR [Bacillus amyloliquefaciens FZB42] 322 1e-89 gb|ABS75590.1| ComFC [Bacillus amyloliquefaciens FZB42] 37 6e-04 gb|ABS72500.1| Prs [Bacillus amyloliquefaciens FZB42] 28 0.22 gb|ABS72703.1| YcdA [Bacillus amyloliquefaciens FZB42] 27 0.49 gb|ABS74832.1| Apt [Bacillus amyloliquefaciens FZB42] 26 1.1 gb|ABS75734.1| Upp [Bacillus amyloliquefaciens FZB42] 26 1.4 gb|ABS74081.1| NrdE [Bacillus amyloliquefaciens FZB42] 25 1.9 gb|ABS76054.1| RocD [Bacillus amyloliquefaciens FZB42] 24 4.1 gb|ABS74744.1| Gpr [Bacillus amyloliquefaciens FZB42] 24 5.4 gb|ABS74336.1| UvrX [Bacillus amyloliquefaciens FZB42] 23 7.1 gb|ABS74825.1| YrvM [Bacillus amyloliquefaciens FZB42] 23 9.2 gb|ABS72555.1| RpoB [Bacillus amyloliquefaciens FZB42] 23 9.2 1_0 1 MNQKAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKR--- LAER---- 53 ABS73893 1 MNQKAVILDEQAIRRALTRIAHEMIERNKGMNDCILVGIKTRGIYLAKR--- LAER---- 53 ABS75590 116 ------------------------------- NTHTLIPIPLSGERLAERGFNQSEL---- 140 ABS72500 164 ----------------------------KDLKDIVIVSPDHGGVTRARK--- LADR---- 188 ABS72703 55 ----------------------------------------------ALK--- VTVT---- 61 ABS74832 ------------------------------------------------------------ ABS75734 ------------------------------------------------------------ ABS74081 ------------------------------------------------------------ ABS74081 502 -----------------------------------------RSAELAKE--- KGET---- 513 ABS76054 305 ------VLEEEGLAERSLQLGRYFKEELEKIDNPIIKDVRGRGLFIGVE--- LTEAARPY 355 ABS74744 43 -------------------------ERDKG-------GIKVRTVDITKE--- GAEL---- 63 ABS74336 ------------------------------------------------------------ ABS74825 ------------------------------------------------------------ ABS72555 ------------------------------------------------------------ 1_0 54 IEQIEGNPVTVGEIDITLYRDDLSKKTSNDEPLVKGADIP-V--DITD--- QKVILVDDV 107 ABS73893 54 IEQIEGNPVTVGEIDITLYRDDLTKKTSNEEPLVKGADIP-A--DITD--- QKVIVVDDV 107 ABS75590 141 LASLLGMPVISPLIRLNNEKQSKKSKTDRLSAEKKFSAAE-N--SATG--- MNVILIDDI 194 ABS72500 189 LKA----PIAI---------IDKRRPRPNE---VEVMNIV-G--NVEG--- KTAILIDDI 226 ABS72703 62 VKNTGKDPLTVKSSDFSLYQDD--AKTAK-----------------TD--- KEDLMQSGT 99 ABS74832 112 --------------------------------------------------- QRVLITDDL 120 ABS75734 100 ---------------VGLYRDPETLK-----PVEYYVKLP-S--DVEE--- REFIVVDPM 133 ABS74081 386 -----------------LQASQVSAYTDYDEEDEIGLDIS-C--NLGS--- LNILNVMKH 422 ABS74081 514 FEHYEGSTYATGEYFNKYIEKEFSPAYEKIAALFEGMHIP-TIEDWKE--- LKAFVAENG 569 ABS76054 356 CEKLKGEGLLCKETHDTVIR---------------------------------------- 375 ABS74744 64 SGKKQGRYVTIEAQGVREHDSDMQEKVT-------------------------------- 91 ABS74336 109 ----------------------------------KTIDLP-T-- NITMDIYRYCLILFDK 131 ABS74825 199 ------------------- REDVRKEVGNDEAKIRKAQMP-------------------- 219 ABS72555 1090 -----GAAYTLQEI-LTVKSDDVVGRVKTYEAIVKGDNVPEP--GVPE--- SFKVLIKEL 1138 1_0 108 LYTGRTVRAGMDALVDVGRPSSIQLAVLVDRGHRELPIRADYIGKNIPTSKSEKVMVQLD 167 ABS73893 108 LYTGRTVRAAMDALVDVGRPSSIQLAVLVDRGHRELPIRADYIGKNIPTSKAEKVMVQLS 167 ABS75590 195 YTTGATLHQAAEVLLTAGKASSVSSFTLI------------------------------- 223 ABS72500 227 IDTAGTITLAANALVENG------------------------------------------ 244 ABS72703 100 LHAGKTVTGNLYFTADEGK----------------------------------------- 118 ABS74832 121 LATGGTIEATIKLVEELG------------------------------------------ 138 ABS75734 134 LATGGSAVEAINSL---------------------------------------------- 147 ABS74081 423 KSIERTVKLATDSLTHVSETTDIRNAPAVRRANKAM------------------------ 458 ABS74081 570 MY---------------------------------------------------------- 571 ABS76054 374 ------------------------------------------------------------ 375 ABS74744 90 ------------------------------------------------------------ 91 ABS74336 132 FYTGKTVRS--------------------------------------------------- 140 ABS74825 218 ------------------------------------------------------------ 219 ABS72555 1139 ------ QSLGMDVKILSGDEEEIEMRDLED------------------------------ 1162 1_0 168 EVDQND 173 ABS73893 168 EVDQTD 173 ABS75590 222 ------ 223 ABS72500 243 ------ 244 ABS72703 117 ------ 118 ABS74832 137 ------ 138 ABS75734 146 ------ 147 ABS74081 457 ------ 458 ABS74081 570 ------ 571 ABS76054 374 ------ 375 ABS74744 90 ------ 91 ABS74336 139 ------ 140 ABS74825 218 ------ 219 ABS72555 1161 ------ 1162 On Feb 19, 2008, at 10:17 AM, Jason Stajich wrote: > All the individual pairwise alignments won't necessarily be an > alignment of the same region and the gap insertions can be different > in each instance of the query sequence that is participating in the > pairwise alns so it won't fit into an MSA. > > It makes more sense to extract the aligned part of the hit sequences > identified and a subsequence of the query which is the min and max > region aligned. Run this through a MSA program. > > -jason > On Feb 19, 2008, at 6:42 AM, Johan Nilsson wrote: > >> Hello, >> >> I have a question regarding the conversion from a Blast search >> result (PSI-blast using blastpgp, to be more exact) to a multiple >> sequence alignment file. I'm running the >> Bio::Tools::Run::StandAloneBlast and I retrieve the HSPs from the >> resulting Bio::Search::Hit::HitI objects. I have no problems >> obtaining each HSP alignment using $hit->get_aln. However, rather >> than dumping many local alignments, I would like to write a single >> result file where the HSPs are interleaved. >> >> I guess this shouldn't be too hard, but nevertheless I haven't >> found out how to do this in a simple way. Any suggestions would be >> highly appreciated! >> >> Best Regards >> /Johan Nilsson >> _______________________________________________ >> 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 Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From hangsyin at gmail.com Tue Feb 19 19:20:18 2008 From: hangsyin at gmail.com (Hang) Date: Tue, 19 Feb 2008 16:20:18 -0800 (PST) Subject: [Bioperl-l] Bio::SeqIO fastq Message-ID: <15579570.post@talk.nabble.com> Hi, I'd like to read and write fastq entry. I don't know what is wrong with the following code: use Bio::SeqIO; my $in = Bio::SeqIO->new(-format => "fastq", -file => "test.fq"); while( my $seq = $in->next_seq ) { my $qual = $seq->qual; print $qual; } my test.fq file: @test AAAAA +test IIIII I got "Can't locate method 'qual' via package "AAAAA", perhaps you forgot to load "AAAAA?" at line XX ". Thanks Hang -- View this message in context: http://www.nabble.com/Bio%3A%3ASeqIO-fastq-tp15579570p15579570.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From heikki at sanbi.ac.za Wed Feb 20 15:12:40 2008 From: heikki at sanbi.ac.za (Heikki Lehvaslaiho) Date: Wed, 20 Feb 2008 22:12:40 +0200 Subject: [Bioperl-l] Bio::SeqIO fastq In-Reply-To: <15579570.post@talk.nabble.com> References: <15579570.post@talk.nabble.com> Message-ID: <200802202212.40772.heikki@sanbi.ac.za> Hang, It works for me. The last statement should be print "@$qual", "\n"; to print out readable values. Maybe you have an old version of BioPerl? Try: perl -MBio::Perl -le 'print Bio::Perl->VERSION;' I recommend installing the latest from CVS/SVN. -Heikki On Wednesday 20 February 2008 02:20:18 Hang wrote: > Hi, > > I'd like to read and write fastq entry. I don't know what is wrong with the > following code: > > use Bio::SeqIO; > my $in = Bio::SeqIO->new(-format => "fastq", > -file => "test.fq"); > while( my $seq = $in->next_seq ) { > my $qual = $seq->qual; > print $qual; > } > > my test.fq file: > @test > AAAAA > +test > IIIII > > I got "Can't locate method 'qual' via package "AAAAA", perhaps you forgot > to load "AAAAA?" at line XX ". > > Thanks > Hang -- ______ _/ _/_____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za _/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho _/ _/ _/ SANBI, South African National Bioinformatics Institute _/ _/ _/ University of Western Cape, South Africa _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 ___ _/_/_/_/_/________________________________________________________ From j.s.soares at gmail.com Wed Feb 20 18:04:35 2008 From: j.s.soares at gmail.com (Djodja) Date: Wed, 20 Feb 2008 15:04:35 -0800 (PST) Subject: [Bioperl-l] Bio::SeqIO fastq In-Reply-To: <200802202212.40772.heikki@sanbi.ac.za> References: <15579570.post@talk.nabble.com> <200802202212.40772.heikki@sanbi.ac.za> Message-ID: <15601113.post@talk.nabble.com> Hang, It works fine for me as well. My Bioperl version is: djodja at djodja-desktop:~$ perl -MBio::Perl -le 'print Bio::Perl->VERSION;' 1.005002102 djodja at djodja-desktop:~$ Maybe that is the problem. All the best, Djodja -- View this message in context: http://www.nabble.com/Bio%3A%3ASeqIO-fastq-tp15579570p15601113.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From shameer at ncbs.res.in Wed Feb 20 04:35:43 2008 From: shameer at ncbs.res.in (K. Shameer) Date: Wed, 20 Feb 2008 15:05:43 +0530 (IST) Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> Message-ID: <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> Dear All, Is there any module available in Bioperl that can be used to perform clustering of Gene Ontology terms from a set of Gene IDs and its respective Flybase GO annotations. These Gene IDs where hits from a high-throughput experiment. We would like to find the GO-Term enriched areas to get better biological insight irrespective of the experimental parameters. I am extremely sorry if this is off-topic : Can you please point me towards any paper/libraries that had used Gene Ontology based clustering ? Many thanks in advance, -- K. Shameer Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group National Centre for Biological Sciences (TIFR) GKVK Campus, Bangalore - 65, Karnataka - India T - 91-080-23666001 EXT - 6251 W - http://www.ncbs.res.in From sdavis2 at mail.nih.gov Thu Feb 21 06:54:47 2008 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Thu, 21 Feb 2008 06:54:47 -0500 Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> Message-ID: <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> On Wed, Feb 20, 2008 at 4:35 AM, K. Shameer wrote: > Dear All, > > Is there any module available in Bioperl that can be used to perform > clustering of Gene Ontology terms from a set of Gene IDs and its > respective Flybase GO annotations. These Gene IDs where hits from a > high-throughput experiment. We would like to find the GO-Term enriched > areas to get better biological insight irrespective of the experimental > parameters. > > I am extremely sorry if this is off-topic : > Can you please point me towards any paper/libraries that had used Gene > Ontology based clustering ? I'm not sure what you mean by GO clustering. However, there are a number of packages that will look for enriched GO terms given a set of Gene IDs. If you are looking for programmatic support for custom pipelines, you can look at R/Bioconductor. Here is a website that will look for GO enrichment and takes Flybase IDs as the gene identifier: http://niaid.abcc.ncifcrf.gov/home.jsp Sean From thiago.venancio at gmail.com Thu Feb 21 07:00:10 2008 From: thiago.venancio at gmail.com (Thiago M. Venancio) Date: Thu, 21 Feb 2008 09:00:10 -0300 Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> Message-ID: <44255ea80802210400u6e5242fdpae4c724621395f05@mail.gmail.com> Hi, This is off topic, but here we go. For enrichment analysis, I use Ontologizer: http://www.charite.de/ch/medgen/ontologizer/ But I am also not sure what do you mean by clustering. Best. T On Thu, Feb 21, 2008 at 8:54 AM, Sean Davis wrote: > On Wed, Feb 20, 2008 at 4:35 AM, K. Shameer wrote: > > Dear All, > > > > Is there any module available in Bioperl that can be used to perform > > clustering of Gene Ontology terms from a set of Gene IDs and its > > respective Flybase GO annotations. These Gene IDs where hits from a > > high-throughput experiment. We would like to find the GO-Term enriched > > areas to get better biological insight irrespective of the experimental > > parameters. > > > > I am extremely sorry if this is off-topic : > > Can you please point me towards any paper/libraries that had used Gene > > Ontology based clustering ? > > I'm not sure what you mean by GO clustering. However, there are a > number of packages that will look for enriched GO terms given a set of > Gene IDs. If you are looking for programmatic support for custom > pipelines, you can look at R/Bioconductor. > > Here is a website that will look for GO enrichment and takes Flybase > IDs as the gene identifier: > > http://niaid.abcc.ncifcrf.gov/home.jsp > > Sean > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- "At the center of your being you have the answer; You know who you are and you know what you want." Lao Tzu ======================== Thiago Motta Venancio, M.Sc., PhD Laboratory of Bioinformatics University of Sao Paulo ======================== From shameer at ncbs.res.in Thu Feb 21 07:29:01 2008 From: shameer at ncbs.res.in (K. Shameer) Date: Thu, 21 Feb 2008 17:59:01 +0530 (IST) Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> Message-ID: <60630.192.168.1.1.1203596941.squirrel@mail.ncbs.res.in> Dear All, Thanks for your reply. > I'm not sure what you mean by GO clustering. However, there are a > number of packages that will look for enriched GO terms given a set of > Gene IDs. In simple terms I have a list of genes, irrespective of any experimental value I need to cluster them based on their GO-Terms using the Di Acyclic Graph data structure of the Gene ontology databases. I found an interesting package from CPAN : GO::TermFinder . http://search.cpan.org/dist/GO-TermFinder/ I am not sure if this is a part of Bioperl :). I have tried with few examples it is working fine but I got few wrong results. If this is not part of Bioperl project, I may need to write to the authors. > If you are looking for programmatic support for custom > pipelines, you can look at R/Bioconductor. Thanks a lot !! I have seen a couple of R packages related to GO. But, I honestly wanted to do it in Perl :) !!! > > Here is a website that will look for GO enrichment and takes Flybase > IDs as the gene identifier: > http://niaid.abcc.ncifcrf.gov/home.jsp Thanks for the link. But I am specifically for something stand alone due to huge volume of my dataset. Cheers, Shameer NCBS - TIFR From golharam at umdnj.edu Thu Feb 21 07:26:58 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 21 Feb 2008 07:26:58 -0500 Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <44255ea80802210400u6e5242fdpae4c724621395f05@mail.gmail.com> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> <44255ea80802210400u6e5242fdpae4c724621395f05@mail.gmail.com> Message-ID: <47BD6E12.3000808@umdnj.edu> ArrayTrack is a good tool to do this, available from the FDA. It has some nice output and performs some statistical analysis for you. I'm using it now to cluster GO terms. Thiago M. Venancio wrote: > Hi, > This is off topic, but here we go. > For enrichment analysis, I use Ontologizer: > > http://www.charite.de/ch/medgen/ontologizer/ > > But I am also not sure what do you mean by clustering. > > Best. > > T > > On Thu, Feb 21, 2008 at 8:54 AM, Sean Davis wrote: > >> On Wed, Feb 20, 2008 at 4:35 AM, K. Shameer wrote: >>> Dear All, >>> >>> Is there any module available in Bioperl that can be used to perform >>> clustering of Gene Ontology terms from a set of Gene IDs and its >>> respective Flybase GO annotations. These Gene IDs where hits from a >>> high-throughput experiment. We would like to find the GO-Term enriched >>> areas to get better biological insight irrespective of the experimental >>> parameters. >>> >>> I am extremely sorry if this is off-topic : >>> Can you please point me towards any paper/libraries that had used Gene >>> Ontology based clustering ? >> I'm not sure what you mean by GO clustering. However, there are a >> number of packages that will look for enriched GO terms given a set of >> Gene IDs. If you are looking for programmatic support for custom >> pipelines, you can look at R/Bioconductor. >> >> Here is a website that will look for GO enrichment and takes Flybase >> IDs as the gene identifier: >> >> http://niaid.abcc.ncifcrf.gov/home.jsp >> >> Sean >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > From cjfields at uiuc.edu Thu Feb 21 09:21:14 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 21 Feb 2008 08:21:14 -0600 Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <60630.192.168.1.1.1203596941.squirrel@mail.ncbs.res.in> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> <60630.192.168.1.1.1203596941.squirrel@mail.ncbs.res.in> Message-ID: <96A3AC13-1963-4802-8ADA-77D00B393823@uiuc.edu> On Feb 21, 2008, at 6:29 AM, K. Shameer wrote: > Dear All, > > Thanks for your reply. > >> I'm not sure what you mean by GO clustering. However, there are a >> number of packages that will look for enriched GO terms given a set >> of >> Gene IDs. > > In simple terms I have a list of genes, irrespective of any > experimental > value I need to cluster them based on their GO-Terms using the Di > Acyclic > Graph data structure of the Gene ontology databases. > > I found an interesting package from CPAN : GO::TermFinder . > http://search.cpan.org/dist/GO-TermFinder/ > > I am not sure if this is a part of Bioperl :). I have tried with few > examples it is working fine but I got few wrong results. If this is > not > part of Bioperl project, I may need to write to the authors. It's not part of BioPerl, so you should contact the author. >> If you are looking for programmatic support for custom >> pipelines, you can look at R/Bioconductor. > > Thanks a lot !! I have seen a couple of R packages related to GO. > But, I > honestly wanted to do it in Perl :) !!! >> BioPerl's ontology classes are all in Bio::Ontology and Bio::OntologyIO. I would also recommend looking at Chris Mungall's go- perl: http://search.cpan.org/~cmungall/go-perl-0.08/go-perl.pod >> Here is a website that will look for GO enrichment and takes Flybase >> IDs as the gene identifier: >> http://niaid.abcc.ncifcrf.gov/home.jsp > > Thanks for the link. But I am specifically for something stand alone > due > to huge volume of my dataset. > > Cheers, > Shameer > NCBS - TIFR It's always faster to do it locally, I agree, as long as the tools are available to do so. chris From donald.jackson at bms.com Thu Feb 21 09:01:51 2008 From: donald.jackson at bms.com (Donald Jackson (Genomics)) Date: Thu, 21 Feb 2008 09:01:51 -0500 Subject: [Bioperl-l] qury In-Reply-To: <4e5ea6f60802191727x1980d2c8p4783300b4223cd5f@mail.gmail.com> References: <4e5ea6f60802191727x1980d2c8p4783300b4223cd5f@mail.gmail.com> Message-ID: <47BD844F.4070801@bms.com> Hi Somil, I get the same error from my test script. It will be a few days before I can troubleshoot and upload the fix to CVS; I'll let you know when I've posted the fix. Don Jackson Somil Dutt wrote: >Hello > >I used the SiRNA tool which is written below > > >use Bio::Tools::SiRNA; > >* > my $sirna_designer = Bio::Tools::SiRNA->new( -target => $bio_seq, > -rules => 'saigo' > ); > my @pairs = $sirna_designer->design; > > foreach $pair (@pairs) { > my $sense_oligo_sequence = $pair->sense->seq; > my $antisense_oligo_sequence = $pair->antisense->seq; > > # print out results > print join ("\t", $pair->start, $pair->end, $pair->rank, > $sense_oligo_sequence, $antisense_oligo_sequence), "\n";* > } > > >But the following problem > >------------- EXCEPTION Bio::Root::BadParameter ------------- >MSG: Target must be passed as a Bio::Seq object >STACK Bio::Tools::SiRNA::target C:/Perl/site/lib/Bio/Tools/SiRNA.pm:220 >STACK Bio::Tools::SiRNA::new C:/Perl/site/lib/Bio/Tools/SiRNA.pm:198 >STACK toplevel start.pl:32 > >I dont understand why this error is coming. > >Regards > > From shameer at ncbs.res.in Thu Feb 21 14:12:16 2008 From: shameer at ncbs.res.in (K. Shameer) Date: Fri, 22 Feb 2008 00:42:16 +0530 (IST) Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <96A3AC13-1963-4802-8ADA-77D00B393823@uiuc.edu> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> <60630.192.168.1.1.1203596941.squirrel@mail.ncbs.res.in> <96A3AC13-1963-4802-8ADA-77D00B393823@uiuc.edu> Message-ID: <39220.192.168.1.1.1203621136.squirrel@mail.ncbs.res.in> >> I am not sure if this is a part of Bioperl :). I have tried with few >> examples it is working fine but I got few wrong results. If this is >> not part of Bioperl project, I may need to write to the authors. > > It's not part of BioPerl, so you should contact the author. Thanks Chris, Is there any specific way to check installed bioperl modules ? > > BioPerl's ontology classes are all in Bio::Ontology and > Bio::OntologyIO. I would also recommend looking at Chris Mungall's go- > perl: > > http://search.cpan.org/~cmungall/go-perl-0.08/go-perl.pod Thanks for the information. > It's always faster to do it locally, I agree, as long as the tools are > available to do so. :) K. Shameer NCBS - TIFR From cjfields at uiuc.edu Thu Feb 21 23:37:54 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 21 Feb 2008 22:37:54 -0600 Subject: [Bioperl-l] Bio::Graphics and perl 5.10 Message-ID: <25A5CCCB-CE0F-4E12-8C31-451775C7FB4E@uiuc.edu> I'm getting a single failed test for Bio::Graphics in bioperl-live which appears to be perl 5.10-specific and is related to Bio::Graphics::FeatureFile: t/BioGraphics...... 1..35 ok 1 - use Bio::Graphics::FeatureFile; ok 2 - use Bio::Graphics::Panel; ok 3 not ok 4 # Failed test at t/BioGraphics.t line 49. # got: '7' # expected: '5' ok 5 ok 6 ok 7 ok 8 ... It appears to be coming from render() passing two extra tracks under perl 5.10 over what is passed in perl 5.8. If anyone is running perl 5.10, can they test this out? chris From cjfields at uiuc.edu Fri Feb 22 11:28:01 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 22 Feb 2008 10:28:01 -0600 Subject: [Bioperl-l] Bio::Graphics and perl 5.10 In-Reply-To: <25A5CCCB-CE0F-4E12-8C31-451775C7FB4E@uiuc.edu> References: <25A5CCCB-CE0F-4E12-8C31-451775C7FB4E@uiuc.edu> Message-ID: <116A7145-55FD-4254-AA94-1D1AAD8D7853@uiuc.edu> (cc'ing to gbrowse list as this pertains somewhat...) Just added a bioperl bug report for this along with the png file output from perl 5.8 and perl 5.10: http://bugzilla.open-bio.org/show_bug.cgi?id=2457 Lincoln's recent commits to Bio::Graphics::FeatureFile didn't fix the issue. However, it is now pinpointing the problem for both perl 5.8 and perl 5.10 (same warning for both, with only perl 5.10 failing): 1..35 ok 1 - use Bio::Graphics::FeatureFile; ok 2 - use Bio::Graphics::Panel; ok 3 Cosmid EST FGENESH SwissProt P-element / yk53c10.3 yk53c10.5 at Bio/ Graphics/FeatureFile.pm line 285. not ok 4 # Failed test at t/BioGraphics.t line 49. # got: '7' # expected: '5' ok 5 ok 6 ok 7 ok 8 ... chris On Feb 21, 2008, at 10:37 PM, Chris Fields wrote: > I'm getting a single failed test for Bio::Graphics in bioperl-live > which appears to be perl 5.10-specific and is related to > Bio::Graphics::FeatureFile: > > t/BioGraphics...... > 1..35 > ok 1 - use Bio::Graphics::FeatureFile; > ok 2 - use Bio::Graphics::Panel; > ok 3 > not ok 4 > > # Failed test at t/BioGraphics.t line 49. > # got: '7' > # expected: '5' > ok 5 > ok 6 > ok 7 > ok 8 > ... > > It appears to be coming from render() passing two extra tracks under > perl 5.10 over what is passed in perl 5.8. If anyone is running > perl 5.10, can they test this out? > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From heikki at sanbi.ac.za Mon Feb 25 01:18:33 2008 From: heikki at sanbi.ac.za (Heikki Lehvaslaiho) Date: Mon, 25 Feb 2008 08:18:33 +0200 Subject: [Bioperl-l] GN line parsing from Uniprot/Swiss-Prot Message-ID: <200802250818.33345.heikki@sanbi.ac.za> There has been an longstanding problem with GN (gene name) line parsing in SwissProt format. It has solved in a way that deals with all the complexity in that line but unfortunately is not backward compatible. You have to upgrade your scripts if you use bioperl-live. This documentation is now part of Bio::SeqIO::swiss.pm: =head2 GN (Gene name) line management details A Uniprot/Swiss-Prot entry holds information on one protein sequence. If that sequence is identical across genes and species, they are all merged into one entry. This creates complex needs for several annotation fields in swiss-prot format. The latest syntax for GN line is described in the user manual: http://www.expasy.ch/sprot/userman.html#GN_line Each of the possibly multiple genes in an entry can have Name, Synonyms (only if there is a name), OrderedLocusNames (names from genomic sequences) and ORFNames (temporary or cosmid names). "Name" here really means "symbol". This complexity is now dealth with the following way: Each gene is an Bio::Annotation::Collection object that is accessed like all other annotations. The tag name is 'gene_name': my @genes = $seq->annotation->get_Annotations('gene_name'); Note that if you are not interested in the complexity of multiple genes, you can easily just take the first value: my ($gene) = $seq->annotation->get_Annotations('gene_name'); None of the four categories for gene_names are obligatory, so you have to test returned objects for existence before using them: my ($name) = $gene->get_Annotations('name'); if ($name) { print "The official gene symbol is: ". $name->value. "\n"; } The can be only one name, so $name is a Bio::Annotation::SimpleValue object. In other categories (tags: synonyms, orderedlocusnames, orfnames; all lower case) there can be more than one value, so they are stored in Bio::Annotation::StructuredValue objects. There can be only one object with a given tag within a given gene. All values for that category are stored in an ordered list within the StructureValue object. e.g: if ( my ($synonyms) = $gene->get_Annotations('synonyms') ) { print "Synonyms: ". join(', ', $synonyms->get_all_values). "\n"; } Since Uniprot/Swiss-Prot format have been around for quite some time, the parser is also able to read in the older GN line syntax where genes are separated by AND and various symbols by OR. The first symbol is taken to be the name and the remaining ones are stored as synonyms. Thanks for Chris Fields for helping out, Enjoy, -Heikki -- ______ _/ _/_____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za _/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho _/ _/ _/ SANBI, South African National Bioinformatics Institute _/ _/ _/ University of Western Cape, South Africa _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 ___ _/_/_/_/_/________________________________________________________ From hangsyin at gmail.com Thu Feb 21 16:14:05 2008 From: hangsyin at gmail.com (Hang) Date: Thu, 21 Feb 2008 13:14:05 -0800 (PST) Subject: [Bioperl-l] Bio::SeqIO fastq In-Reply-To: <15601113.post@talk.nabble.com> References: <15579570.post@talk.nabble.com> <200802202212.40772.heikki@sanbi.ac.za> <15601113.post@talk.nabble.com> Message-ID: <15618960.post@talk.nabble.com> Heikki and Djodja, Many thanks for you guys' help! That code is working right now. Hang Djodja wrote: > > Hang, > > It works fine for me as well. > > My Bioperl version is: > > djodja at djodja-desktop:~$ perl -MBio::Perl -le 'print Bio::Perl->VERSION;' > > 1.005002102 > > djodja at djodja-desktop:~$ > > Maybe that is the problem. > > All the best, > > Djodja > > > -- View this message in context: http://www.nabble.com/Bio%3A%3ASeqIO-fastq-tp15579570p15618960.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From sheila.zuniga at sistemasgenomicos.com Mon Feb 25 10:48:18 2008 From: sheila.zuniga at sistemasgenomicos.com (=?iso-8859-1?Q?Sheila_Zu=F1iga_Trejos?=) Date: Mon, 25 Feb 2008 16:48:18 +0100 Subject: [Bioperl-l] bioperl installation problems with CPAN Message-ID: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Dear Sir, I'm trying to install Bioperl using CPAN but it seems impossible. I get several error messages when running cpan > install Bundle::CPAN. Please find attached a file containing these error messages. Any idea of what is happening? Thanks very much for your help, Sheila -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: error.txt URL: From rchu at coh.org Mon Feb 25 16:33:10 2008 From: rchu at coh.org (Roy) Date: Mon, 25 Feb 2008 21:33:10 +0000 (UTC) Subject: [Bioperl-l] SeqIO and large GenBank files Message-ID: Hi everyone, I want to parse some of the .gbk RefSeq files from ncbi, more specifically, ref_chr*.gbk. My script seems to open the sequence stream okay, but when I try to get the next sequence in the stream, my script spits out a lot of warnings of subroutine redefinitions. Is this file incompatible with SeqIO genbank reader? Any insight is appreciated, thanks. Roy test file: ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_01 ===start_code=== #!/usr/bin/perl -w use strict; use warnings; use Bio::Perl; use Bio::SeqIO; my $USAGE = "usage: $0 \n\n"; unless (@ARGV) { print $USAGE; exit; } my $stream = Bio::SeqIO->new(-file => $ARGV[0], -format => "genbank"); my $seq_obj = $stream->next_seq; exit; ===end_code=== ===start warnings=== Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 80, line 36. Subroutine start redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 102, line 36. Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 128, line 36. Subroutine length redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 165, line 36. Subroutine location_type redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 256, line 36. Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 303, line 36. Subroutine trunc redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 334, line 36. Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 91, line 49. Subroutine each_Location redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 123, line 49. Subroutine sub_Location redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 152, line 49. Subroutine add_sub_Location redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 221, line 49. Subroutine splittype redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 245, line 49. Subroutine is_single_sequence redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 273, line 49. Subroutine guide_strand redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 298, line 49. Subroutine strand redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 326, line 49. Subroutine flip_strand redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 367, line 49. Subroutine start redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 388, line 49. Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 407, line 49. Subroutine min_start redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 426, line 49. Subroutine max_start redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 448, line 49. Subroutine start_pos_type redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 471, line 49. Subroutine min_end redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 492, line 49. Subroutine max_end redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 515, line 49. Subroutine end_pos_type redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 539, line 49. Subroutine seq_id redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 565, line 49. Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 611, line 49. Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 134, line 747. Subroutine location_type redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 161, line 747. Subroutine start redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 223, line 747. Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 250, line 747. Subroutine min_start redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 277, line 747. Subroutine max_start redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 296, line 747. Subroutine start_pos_type redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 316, line 747. Subroutine min_end redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 346, line 747. Subroutine max_end redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 365, line 747. Subroutine end_pos_type redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 385, line 747. Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 456, line 747. Subroutine _fuzzypointdecode redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 557, line 747. ==end warnings== From cjfields at uiuc.edu Mon Feb 25 17:17:49 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 25 Feb 2008 16:17:49 -0600 Subject: [Bioperl-l] SeqIO and large GenBank files In-Reply-To: References: Message-ID: <4F9A56D3-1EAE-4916-A2F6-E10DB4CE3C18@uiuc.edu> The perl executable is overly paranoid on Windows for some reason when the '-w' flag is set on the shebang line ('#!/usr/bin/perl -w'); it doesn't like method overloading for some reason. Remove it and the warnings should go away (note: you should still leave 'use strict' and 'use warnings'). chris On Feb 25, 2008, at 3:33 PM, Roy wrote: > Hi everyone, > > I want to parse some of the .gbk RefSeq files from ncbi, more > specifically, > ref_chr*.gbk. My script seems to open the sequence stream okay, but > when I try > to get the next sequence in the stream, my script spits out a lot of > warnings of > subroutine redefinitions. Is this file incompatible with SeqIO > genbank reader? > Any insight is appreciated, thanks. > > Roy > > test file: > > ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_01 > > ===start_code=== > #!/usr/bin/perl -w > use strict; > use warnings; > use Bio::Perl; > use Bio::SeqIO; > my $USAGE = "usage: $0 \n\n"; > unless (@ARGV) { > print $USAGE; > exit; > } > my $stream = Bio::SeqIO->new(-file => $ARGV[0], -format => "genbank"); > my $seq_obj = $stream->next_seq; > exit; > ===end_code=== > > ===start warnings=== > Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Simple.pm > line 80, > line 36. > Subroutine start redefined at C:/Perl/site/lib/Bio\Location > \Simple.pm line 102, > line 36. > Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Simple.pm > line 128, > line 36. > Subroutine length redefined at C:/Perl/site/lib/Bio\Location > \Simple.pm line 165, > line 36. > Subroutine location_type redefined at C:/Perl/site/lib/Bio\Location > \Simple.pm > line 256, line 36. > Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location > \Simple.pm line > 303, line 36. > Subroutine trunc redefined at C:/Perl/site/lib/Bio\Location > \Simple.pm line 334, > line 36. > Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Split.pm > line 91, > line 49. > Subroutine each_Location redefined at C:/Perl/site/lib/Bio\Location > \Split.pm > line 123, line 49. > Subroutine sub_Location redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 152, line 49. > Subroutine add_sub_Location redefined at C:/Perl/site/lib/Bio > \Location\Split.pm > line 221, line 49. > Subroutine splittype redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 245, line 49. > Subroutine is_single_sequence redefined at > C:/Perl/site/lib/Bio\Location\Split.pm line 273, line 49. > Subroutine guide_strand redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 298, line 49. > Subroutine strand redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line 326, > line 49. > Subroutine flip_strand redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 367, line 49. > Subroutine start redefined at C:/Perl/site/lib/Bio\Location\Split.pm > line 388, > line 49. > Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Split.pm > line 407, > line 49. > Subroutine min_start redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 426, line 49. > Subroutine max_start redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 448, line 49. > Subroutine start_pos_type redefined at C:/Perl/site/lib/Bio\Location > \Split.pm > line 471, line 49. > Subroutine min_end redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line 492, > line 49. > Subroutine max_end redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line 515, > line 49. > Subroutine end_pos_type redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 539, line 49. > Subroutine seq_id redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line 565, > line 49. > Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 611, line 49. > Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm > line 134, > line 747. > Subroutine location_type redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm > line 161, line 747. > Subroutine start redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm > line 223, > line 747. > Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm > line 250, > line 747. > Subroutine min_start redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm line > 277, line 747. > Subroutine max_start redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm line > 296, line 747. > Subroutine start_pos_type redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm > line 316, line 747. > Subroutine min_end redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm line 346, > line 747. > Subroutine max_end redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm line 365, > line 747. > Subroutine end_pos_type redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm line > 385, line 747. > Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm line > 456, line 747. > Subroutine _fuzzypointdecode redefined at C:/Perl/site/lib/Bio > \Location\Fuzzy.pm > line 557, line 747. > ==end warnings== > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From Russell.Smithies at agresearch.co.nz Mon Feb 25 17:12:39 2008 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 26 Feb 2008 11:12:39 +1300 Subject: [Bioperl-l] Bio::Assembly::IO problems In-Reply-To: <000001c877c5$d8dc2d70$7000000a@sistemas.local> References: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Message-ID: Is the Bio::Assembly::IO stuff working? I want to parse some .ace files but keep getting errors: [smithiesr at impala ace_phrap]$ perl 454_read_ace.pl Can't call method "get_consensus_sequence" on an undefined value at /usr/lib/perl5/site_perl/5.8.8/Bio/Assembly/IO/ace.pm line 169, line 20. My code is: #!perl -w use Bio::Assembly::IO; use Data::Dumper; my $in = "454Contigs.ace"; $io = new Bio::Assembly::IO(-file=>$in,-format=>"ace"); $ass = $io->next_assembly; print Dumper $ass; exit; any ideas? Thanx, Russell Smithies Bioinformatics Software Developer T +64 3 489 9085 E? russell.smithies at agresearch.co.nz Invermay? Research Centre Puddle Alley, Mosgiel, New Zealand T? +64 3 489 3809?? F? +64 3 489 9174? www.agresearch.co.nz ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From cjfields at uiuc.edu Mon Feb 25 18:01:42 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 25 Feb 2008 17:01:42 -0600 Subject: [Bioperl-l] Bio::Assembly::IO problems In-Reply-To: References: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Message-ID: <5827D6E2-B798-4001-84DB-8C38586D3CF2@uiuc.edu> Russell, Using the test data from the bioperl installation appears to work, but I wouldn't be surprised if this is a bug. Can you file this as a bug along with some test data? http://bugzilla.open-bio.org/ chris On Feb 25, 2008, at 4:12 PM, Smithies, Russell wrote: > Is the Bio::Assembly::IO stuff working? > I want to parse some .ace files but keep getting errors: > > [smithiesr at impala ace_phrap]$ perl 454_read_ace.pl > Can't call method "get_consensus_sequence" on an undefined value > at /usr/lib/perl5/site_perl/5.8.8/Bio/Assembly/IO/ace.pm line 169, > line 20. > > My code is: > > #!perl -w > > use Bio::Assembly::IO; > use Data::Dumper; > > my $in = "454Contigs.ace"; > > $io = new Bio::Assembly::IO(-file=>$in,-format=>"ace"); > $ass = $io->next_assembly; > > print Dumper $ass; > exit; > > any ideas? > > Thanx, > > Russell Smithies > > Bioinformatics Software 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 > > > = > ====================================================================== > 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 Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From rchu at coh.org Mon Feb 25 18:21:26 2008 From: rchu at coh.org (Roy) Date: Mon, 25 Feb 2008 23:21:26 +0000 (UTC) Subject: [Bioperl-l] SeqIO and large GenBank files References: <4F9A56D3-1EAE-4916-A2F6-E10DB4CE3C18@uiuc.edu> Message-ID: Chris Fields uiuc.edu> writes: > > The perl executable is overly paranoid on Windows for some reason when > the '-w' flag is set on the shebang line ('#!/usr/bin/perl -w'); it > doesn't like method overloading for some reason. Remove it and the > warnings should go away (note: you should still leave 'use strict' and > 'use warnings'). > > chris Thanks Chris. Your suggestion worked. I was concerned that there may be some other error because it was taking an ungodly amount of time to process, but that resolved the problems. -Roy From Russell.Smithies at agresearch.co.nz Mon Feb 25 18:23:06 2008 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 26 Feb 2008 12:23:06 +1300 Subject: [Bioperl-l] Bio::Assembly::IO problems - FIXED! In-Reply-To: References: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Message-ID: I solved the problem :-) The contig lines in our .ace files have a lower-case 'c' in the contig name instead of upper-case so weren't being found by this regex in ace.pm line 142: (/^CO Contig(\d+) (\d+) (\d+) (\d+) (\w+)/) && do { # New contig found! e.g: CO contig00001 711 12 6 U instead of: CO Contig00001 711 12 6 U Our contigs were generated with Newbler version 1.1.01.20. so might be something to watch out for in future. Russell Smithies Bioinformatics Software Developer T +64 3 489 9085 E? russell.smithies at agresearch.co.nz Invermay? Research Centre Puddle Alley, Mosgiel, New Zealand T? +64 3 489 3809?? F? +64 3 489 9174? www.agresearch.co.nz > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open- > bio.org] On Behalf Of Smithies, Russell > Sent: Tuesday, 26 February 2008 11:13 a.m. > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] Bio::Assembly::IO problems > > Is the Bio::Assembly::IO stuff working? > I want to parse some .ace files but keep getting errors: > > [smithiesr at impala ace_phrap]$ perl 454_read_ace.pl > Can't call method "get_consensus_sequence" on an undefined value at > /usr/lib/perl5/site_perl/5.8.8/Bio/Assembly/IO/ace.pm line 169, line 20. > > My code is: > > #!perl -w > > use Bio::Assembly::IO; > use Data::Dumper; > > my $in = "454Contigs.ace"; > > $io = new Bio::Assembly::IO(-file=>$in,-format=>"ace"); > $ass = $io->next_assembly; > > print Dumper $ass; > exit; > > any ideas? > > Thanx, > > Russell Smithies > > Bioinformatics Software 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 > > > ============================================================= > ========== > 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 ======================================================================= 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 David.Messina at sbc.su.se Mon Feb 25 18:46:44 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 26 Feb 2008 00:46:44 +0100 Subject: [Bioperl-l] bioperl installation problems with CPAN In-Reply-To: <000001c877c5$d8dc2d70$7000000a@sistemas.local> References: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Message-ID: <628aabb70802251546i3f43212eo705e762bf34ec27a@mail.gmail.com> Hi Sheila, It looks like your cpan configuration has gotten messed up. It's giving invalid parameters to the make command: make: *** No hay ninguna regla para construir el objetivo `dual'. Alto. /usr/bin/make dual processor system -- NOT OK Go to the command line on your system. Enter the cpan shell: % cpan Type the following: cpan> o conf makepl_arg "" cpan> o conf commit That should reset the arguments that cpan adds to the make command. If that doesn't fix your problem, reset everything by typing cpan> o conf defaults cpan> o conf commit and see if that does it. Dave From schaffer at scripps.edu Mon Feb 25 20:04:50 2008 From: schaffer at scripps.edu (Lana Schaffer) Date: Mon, 25 Feb 2008 17:04:50 -0800 Subject: [Bioperl-l] statistics Message-ID: <8F897BD2B0EB714CB79B96D84911B30209E543@EXCHV1.lj.ad.scripps.edu> Hi, I want to know if Bioperl does t-tests and how to do it? Also, I need to get a chi-squared statistic. Thanks, Lana Schaffer Biostatistics/Informatics The Scripps Research Institute DNA Array Core Facility La Jolla, CA 92037 (858) 784-2263 (858) 784-2994 schaffer at scripps.edu From sdavis2 at mail.nih.gov Mon Feb 25 21:45:00 2008 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Mon, 25 Feb 2008 21:45:00 -0500 Subject: [Bioperl-l] statistics In-Reply-To: <8F897BD2B0EB714CB79B96D84911B30209E543@EXCHV1.lj.ad.scripps.edu> References: <8F897BD2B0EB714CB79B96D84911B30209E543@EXCHV1.lj.ad.scripps.edu> Message-ID: <264855a00802251845p25130950q5dbdc4228dbb2b93@mail.gmail.com> On Mon, Feb 25, 2008 at 8:04 PM, Lana Schaffer wrote: > Hi, > I want to know if Bioperl does t-tests and how to do it? > Also, I need to get a chi-squared statistic. Hi, Lana. I don't think bioperl offers this functionality. However, a quick search of cpan (http://search.cpan.org) turns up: http://search.cpan.org/~yunfang/Statistics-TTest-1.1.0/TTest.pm http://search.cpan.org/~dcantrell/Statistics-ChiSquare-0.5/lib/Statistics/ChiSquare.pm That said, I know you are an R user. I generally stick to R for any numerics. If you need both a parsing/data munging language and statistics, consider python, where the rpy package allows you access R from python and even does data conversion, etc. Sean From florent.angly at gmail.com Tue Feb 26 00:37:20 2008 From: florent.angly at gmail.com (Florent Angly) Date: Mon, 25 Feb 2008 21:37:20 -0800 Subject: [Bioperl-l] Bio::Assembly::IO problems - FIXED! In-Reply-To: References: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Message-ID: <47C3A590.4070204@gmail.com> As far as I know, there really isn't a specification of the ACE file format, that would rule if it is legal to have the kind of contig name (non capitalized), other that its original implementation in Phrap. According to the spirit of the ACE file format, my guess is that any contig name should be allowed. For example, on this webpage http://www.cbcb.umd.edu/research/contig_representation.shtml, the contig name is just a number. So please Russel file this as a bug so that the developers can keep track of this bug, Regards, Florent Smithies, Russell wrote: > I solved the problem :-) > The contig lines in our .ace files have a lower-case 'c' in the contig name instead of upper-case so weren't being found by this regex in ace.pm line 142: > (/^CO Contig(\d+) (\d+) (\d+) (\d+) (\w+)/) && do { # New contig found! > > e.g: > CO contig00001 711 12 6 U > instead of: > CO Contig00001 711 12 6 U > > Our contigs were generated with Newbler version 1.1.01.20. so might be something to watch out for in future. > > > Russell Smithies > > Bioinformatics Software Developer > T +64 3 489 9085 > E russell.smithies at agresearch.co.nz > > Invermay Research Centre > Puddle Alley, > Mosgiel, > New Zealand > T +64 3 489 3809 > F +64 3 489 9174 > www.agresearch.co.nz > > > > > > > > > >> -----Original Message----- >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open- >> bio.org] On Behalf Of Smithies, Russell >> Sent: Tuesday, 26 February 2008 11:13 a.m. >> To: bioperl-l at lists.open-bio.org >> Subject: [Bioperl-l] Bio::Assembly::IO problems >> >> Is the Bio::Assembly::IO stuff working? >> I want to parse some .ace files but keep getting errors: >> >> [smithiesr at impala ace_phrap]$ perl 454_read_ace.pl >> Can't call method "get_consensus_sequence" on an undefined value at >> /usr/lib/perl5/site_perl/5.8.8/Bio/Assembly/IO/ace.pm line 169, line 20. >> >> My code is: >> >> #!perl -w >> >> use Bio::Assembly::IO; >> use Data::Dumper; >> >> my $in = "454Contigs.ace"; >> >> $io = new Bio::Assembly::IO(-file=>$in,-format=>"ace"); >> $ass = $io->next_assembly; >> >> print Dumper $ass; >> exit; >> >> any ideas? >> >> Thanx, >> >> Russell Smithies >> >> Bioinformatics Software 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 >> >> >> ============================================================= >> ========== >> 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 >> > ======================================================================= > 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 David.Messina at sbc.su.se Tue Feb 26 05:47:36 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 26 Feb 2008 11:47:36 +0100 Subject: [Bioperl-l] bioperl installation problems with CPAN In-Reply-To: <000701c87857$15dd6d60$7000000a@sistemas.local> References: <628aabb70802251546i3f43212eo705e762bf34ec27a@mail.gmail.com> <000701c87857$15dd6d60$7000000a@sistemas.local> Message-ID: <628aabb70802260247h2d063d4ah489318aad66c4e6a@mail.gmail.com> Hi Sheila, Please be sure to keep bioperl-l on the Cc so that everyone can follow along the discussion. I don't think this is a BioPerl-specific problem. Can you successfully install other modules from CPAN? Could you type "o conf" in cpan and paste the results into your reply to this message? Dave On 2/26/08, Sheila Zu?iga Trejos wrote: > > Hi Dave, > I've tried the two options and in both cases I got the same error message. > I even restart the server both times in case it could make any difference > but nothing changed. > First attempt: > > Type: cpan> o conf makepl_arg "" > Return: makepl_arg > Type: cpan> o conf commit > Return: commit: wrote /etc/perl/CPAN/Config.pm > Type: cpan> install Bundle::CPAN > Return: error message attached (same as before) > > Second attempt: > > Type: cpan> o conf defaults > (did not return anything) > Type: cpan> o conf commit > Return: commit: wrote /etc/perl/CPAN/Config.pm > Type: cpan> install Bundle::CPAN > Return: error message attached (same as before) > > I installed Bioperl in Debian Sarge before and I never had any problem with CPAN but with Debian Etch...Well, I hope you have other ideas. > > Thanks very much for your help. > > Sheila > > ------------------------------ > *De:* dave at davemessina.com [mailto:dave at davemessina.com] *En nombre de *Dave > Messina > *Enviado el:* martes, 26 de febrero de 2008 0:47 > *Para:* Sheila Zu?iga Trejos > *CC:* bioperl-l at bioperl.org > *Asunto:* Re: [Bioperl-l] bioperl installation problems with CPAN > > Hi Sheila, > > It looks like your cpan configuration has gotten messed up. It's giving > invalid parameters to the make command: > > make: *** No hay ninguna regla para construir el objetivo `dual'. Alto. > > /usr/bin/make dual processor system -- NOT OK > > > > Go to the command line on your system. Enter the cpan shell: > > % cpan > > Type the following: > > cpan> o conf makepl_arg "" > cpan> o conf commit > > > That should reset the arguments that cpan adds to the make command. If > that doesn't fix your problem, reset everything by typing > > cpan> o conf defaults > cpan> o conf commit > > and see if that does it. > > > Dave > > > From David.Messina at sbc.su.se Tue Feb 26 06:43:35 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 26 Feb 2008 12:43:35 +0100 Subject: [Bioperl-l] bioperl installation problems with CPAN In-Reply-To: <001001c87868$4e11cb20$7000000a@sistemas.local> References: <628aabb70802260247h2d063d4ah489318aad66c4e6a@mail.gmail.com> <001001c87868$4e11cb20$7000000a@sistemas.local> Message-ID: <628aabb70802260343n43b216a2q580827e26266c8b6@mail.gmail.com> The following two lines show the problem: > make_arg dual processor system > make_install_arg to always uninstall potentially conflicting files > The configuration parameters are key-value pairs. So here the parameter "make_arg" is set to the value "dual processor system". "dual processor system" is not a valid command-line argument for the make program, so that's why cpan can't install BioPerl (or anything else, I would suspect). Type the following in cpan: cpan> o conf make_arg "" cpan> o conf make_install_arg "" cpan> o conf commit Then type cpan> o conf and verify that those two parameters have indeed been changed successfully. If so, then try installing BioPerl again. I think it should work, but let me know if not. Dave From sheila.zuniga at sistemasgenomicos.com Tue Feb 26 06:11:09 2008 From: sheila.zuniga at sistemasgenomicos.com (=?iso-8859-1?Q?Sheila_Zu=F1iga_Trejos?=) Date: Tue, 26 Feb 2008 12:11:09 +0100 Subject: [Bioperl-l] bioperl installation problems with CPAN In-Reply-To: <628aabb70802260247h2d063d4ah489318aad66c4e6a@mail.gmail.com> Message-ID: <001001c87868$4e11cb20$7000000a@sistemas.local> Hi Dave, Thanks for your quick reply. Here is the output: cpan> o conf CPAN::Config options from /etc/perl/CPAN/Config.pm: commit Commit changes to disk defaults Reload defaults from disk init Interactive setting of all options build_cache 10 build_dir /root/.cpan/build cache_metadata 1 cpan_home /root/.cpan cpan_version_check 1 dontload_hash ftp /usr/bin/ftp ftp_proxy getcwd cwd gpg /usr/bin/gpg gzip /bin/gzip histfile /root/.cpan/histfile histsize 100 http_proxy inactivity_timeout 0 index_expire 1 inhibit_startup_message 0 keep_source_where /root/.cpan/sources lynx make /usr/bin/make make_arg dual processor system make_install_arg to always uninstall potentially conflicting files makepl_arg ncftpget /usr/bin/ncftpget no_proxy pager /usr/bin/less prefer_installer MB prerequisites_policy ask scan_cache atstart shell /bin/bash tar /bin/tar term_is_latin 1 unzip /usr/bin/unzip urllist ftp://ftp.rediris.es/mirror/CPAN/ wget /usr/bin/wget Sheila _____ De: dave at davemessina.com [mailto:dave at davemessina.com] En nombre de Dave Messina Enviado el: martes, 26 de febrero de 2008 11:48 Para: Sheila Zu?iga Trejos CC: bioperl-l at bioperl.org Asunto: Re: [Bioperl-l] bioperl installation problems with CPAN Hi Sheila, Please be sure to keep bioperl-l on the Cc so that everyone can follow along the discussion. I don't think this is a BioPerl-specific problem. Can you successfully install other modules from CPAN? Could you type "o conf" in cpan and paste the results into your reply to this message? Dave On 2/26/08, Sheila Zu?iga Trejos wrote: Hi Dave, I've tried the two options and in both cases I got the same error message. I even restart the server both times in case it could make any difference but nothing changed. First attempt: Type: cpan> o conf makepl_arg "" Return: makepl_arg Type: cpan> o conf commit Return: commit: wrote /etc/perl/CPAN/Config.pm Type: cpan> install Bundle::CPAN Return: error message attached (same as before) Second attempt: Type: cpan> o conf defaults (did not return anything) Type: cpan> o conf commit Return: commit: wrote /etc/perl/CPAN/Config.pm Type: cpan> install Bundle::CPAN Return: error message attached (same as before) I installed Bioperl in Debian Sarge before and I never had any problem with CPAN but with Debian Etch... Well, I hope you have other ideas. Thanks very much for your help. Sheila _____ De: dave at davemessina.com [mailto:dave at davemessina.com] En nombre de Dave Messina Enviado el: martes, 26 de febrero de 2008 0:47 Para: Sheila Zu?iga Trejos CC: bioperl-l at bioperl.org Asunto: Re: [Bioperl-l] bioperl installation problems with CPAN Hi Sheila, It looks like your cpan configuration has gotten messed up. It's giving invalid parameters to the make command: make: *** No hay ninguna regla para construir el objetivo `dual'. Alto. /usr/bin/make dual processor system -- NOT OK Go to the command line on your system. Enter the cpan shell: % cpan Type the following: cpan> o conf makepl_arg "" cpan> o conf commit That should reset the arguments that cpan adds to the make command. If that doesn't fix your problem, reset everything by typing cpan> o conf defaults cpan> o conf commit and see if that does it. Dave From sheila.zuniga at sistemasgenomicos.com Tue Feb 26 06:54:53 2008 From: sheila.zuniga at sistemasgenomicos.com (=?iso-8859-1?Q?Sheila_Zu=F1iga_Trejos?=) Date: Tue, 26 Feb 2008 12:54:53 +0100 Subject: [Bioperl-l] bioperl installation problems with CPAN In-Reply-To: <628aabb70802260343n43b216a2q580827e26266c8b6@mail.gmail.com> Message-ID: <001801c8786e$6a04bc10$7000000a@sistemas.local> Hi Dave, You're right! It works! Thanks very much for your help. Sheila _____ De: dave at davemessina.com [mailto:dave at davemessina.com] En nombre de Dave Messina Enviado el: martes, 26 de febrero de 2008 12:44 Para: Sheila Zu?iga Trejos CC: bioperl-l at bioperl.org Asunto: Re: [Bioperl-l] bioperl installation problems with CPAN The following two lines show the problem: make_arg dual processor system make_install_arg to always uninstall potentially conflicting files The configuration parameters are key-value pairs. So here the parameter "make_arg" is set to the value "dual processor system". "dual processor system" is not a valid command-line argument for the make program, so that's why cpan can't install BioPerl (or anything else, I would suspect). Type the following in cpan: cpan> o conf make_arg "" cpan> o conf make_install_arg "" cpan> o conf commit Then type cpan> o conf and verify that those two parameters have indeed been changed successfully. If so, then try installing BioPerl again. I think it should work, but let me know if not. Dave From bix at sendu.me.uk Mon Feb 25 17:35:18 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 25 Feb 2008 22:35:18 +0000 Subject: [Bioperl-l] bioperl installation problems with CPAN In-Reply-To: <000001c877c5$d8dc2d70$7000000a@sistemas.local> References: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Message-ID: <47C342A6.7090009@sendu.me.uk> Sheila Zu?iga Trejos wrote: > Dear Sir, > I'm trying to install Bioperl using CPAN but it seems impossible. I get > several error messages when running cpan > install Bundle::CPAN. Please find > attached a file containing these error messages. > Any idea of what is happening? Looks like you've given one of the CPAN options (when you first ran CPAN it asked a bunch of questions) a dodgy value: 'dual processor system'. The easiest thing to do would be to delete your .cpan directory and start over, making sure to answer all the questions carefully and correctly. From bix at sendu.me.uk Tue Feb 26 05:34:04 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 26 Feb 2008 10:34:04 +0000 Subject: [Bioperl-l] statistics In-Reply-To: <264855a00802251845p25130950q5dbdc4228dbb2b93@mail.gmail.com> References: <8F897BD2B0EB714CB79B96D84911B30209E543@EXCHV1.lj.ad.scripps.edu> <264855a00802251845p25130950q5dbdc4228dbb2b93@mail.gmail.com> Message-ID: <47C3EB1C.2000407@sendu.me.uk> Sean Davis wrote: > On Mon, Feb 25, 2008 at 8:04 PM, Lana Schaffer wrote: >> Hi, >> I want to know if Bioperl does t-tests and how to do it? >> Also, I need to get a chi-squared statistic. > > Hi, Lana. I don't think bioperl offers this functionality. However, > a quick search of cpan (http://search.cpan.org) turns up: > > http://search.cpan.org/~yunfang/Statistics-TTest-1.1.0/TTest.pm > http://search.cpan.org/~dcantrell/Statistics-ChiSquare-0.5/lib/Statistics/ChiSquare.pm > > That said, I know you are an R user. I generally stick to R for any > numerics. If you need both a parsing/data munging language and > statistics, consider python, where the rpy package allows you access R > from python and even does data conversion, etc. There's also an R interface for perl: http://www.omegahat.org/RSPerl/ From johnsonm at gmail.com Tue Feb 26 19:47:02 2008 From: johnsonm at gmail.com (Mark Johnson) Date: Tue, 26 Feb 2008 18:47:02 -0600 Subject: [Bioperl-l] Bio::Tools::Run::Fgenesh anyone? Message-ID: We've got fgenesh/fgenesh+ installed locally and I'm going to need Bio::Tools::Run::Fgenesh for a nematode annotation pipeline. Does Bio::Tools::Fgenesh still need unit tests as well? Throw 'em in genpred.t with everything else? From jay at jays.net Thu Feb 28 15:25:29 2008 From: jay at jays.net (Jay Hannah) Date: Thu, 28 Feb 2008 14:25:29 -0600 Subject: [Bioperl-l] helpdesk@open-bio.org ... User unknown References: <200802281949.m1SJnIeD000744@ferret.jays.net> Message-ID: <78E7CE4E-9633-4015-B37C-A097D7F5B411@jays.net> Did I remember that address incorrectly? I'd look it up, but... :) j Begin forwarded message: > From: Mail Delivery Subsystem > Date: February 28, 2008 1:49:18 PM CST > To: > Subject: Returned mail: see transcript for details > > The original message was received at Thu, 28 Feb 2008 13:10:05 -0600 > from host-137-197-64-194.unmc.edu [137.197.64.194] > > ----- The following addresses had permanent fatal errors ----- > > (reason: 550 5.1.1 ... User unknown) > > ----- Transcript of session follows ----- > ... while talking to open-bio.org.: >>>> DATA > <<< 550 5.1.1 ... User unknown > 550 5.1.1 ... User unknown > <<< 503 5.0.0 Need RCPT (recipient) > Reporting-MTA: dns; ferret.jays.net > Arrival-Date: Thu, 28 Feb 2008 13:10:05 -0600 > > Final-Recipient: RFC822; helpdesk at open-bio.org > Action: failed > Status: 5.1.1 > Remote-MTA: DNS; open-bio.org > Diagnostic-Code: SMTP; 550 5.1.1 ... User > unknown > Last-Attempt-Date: Thu, 28 Feb 2008 13:49:18 -0600 > > From: Jay Hannah > Date: February 28, 2008 1:09:57 PM CST > To: helpdesk at open-bio.org > Subject: Websites are down? > > > Is this the right email address to report this to? > > I can't reach: > > http://bioperl.org > http://open-bio.org > > Thanks, > > j > > > > From David.Messina at sbc.su.se Thu Feb 28 16:56:46 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Thu, 28 Feb 2008 22:56:46 +0100 Subject: [Bioperl-l] helpdesk@open-bio.org ... User unknown In-Reply-To: <78E7CE4E-9633-4015-B37C-A097D7F5B411@jays.net> References: <200802281949.m1SJnIeD000744@ferret.jays.net> <78E7CE4E-9633-4015-B37C-A097D7F5B411@jays.net> Message-ID: <628aabb70802281356w693787e0r19aa80b56079182d@mail.gmail.com> Close. :) support at helpdesk.open-bio.org > I can't reach: > > > > http://bioperl.org > > http://open-bio.org Both work for me at the moment, by the way. Perhaps 'twas transient? Dave From cjfields at uiuc.edu Fri Feb 1 14:03:36 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 1 Feb 2008 13:03:36 -0600 Subject: [Bioperl-l] Odd issue with HSP::seq_inds() Message-ID: Apologies ahead of time for the longish post! While working on a recent bug (http://bugzilla.open-bio.org/show_bug.cgi?id=2436 ) I found a pretty significant bug. It appears that seq_inds() is giving some bad return values tied specifically to reports where either or both query or hit are translated. I'll file a full bug report but I felt it might be worth bringing up here to discuss specifically what values should be expected when these reports are parsed (all three nucleotide positions or only the first for each nonmatching translated position, etc). I used the following script to track the total HSPs as well as those where seq_inds() returns positions within the HSP bounds for query and hit: ------------------------------------------- use Bio::SearchIO; use Test::More qw(no_plan); my $file = shift || die; my $io = Bio::SearchIO->new(-format => 'blast', -file => $file); my ($hsp_co, $correctq, $correcth) = (0,0,0); while (my $res = $io->next_result) { while (my $hit = $res->next_hit) { while (my $hsp = $hit->next_hsp) { $hsp_co++; my ($qs, $qe, $hs, $he) = ($hsp->start('query'),$hsp- >end('query'), $hsp->start('hit'),$hsp- >end('hit')); my @pos = $hsp->seq_inds('query','nomatch'); my @pos2 = grep {$_ >= $qs && $_ <= $qe} @pos; # should always be true if (scalar(@pos2) == scalar(@pos)) { $correctq++; } @pos = $hsp->seq_inds('hit','nomatch'); @pos2 = grep {$_ >= $hs && $_ <= $he} @pos; # should always be true if (scalar(@pos2) == scalar(@pos)) { $correcth++; } } } } is($correctq, $hsp_co, 'Query seq_inds() positions fall within HSP bounds'); is($correcth, $hsp_co, 'Subject seq_inds() positions fall within HSP bounds'); ------------------------------------------- Here are the results for the following BLAST report types (culled from test reports used in SearchIO.t): BLASTN : both pass TBLASTN : query passes, subject fails BLASTX : query fails, subject passes TBLASTX : both fail When looking at the failed query seq_inds() data for the first HSP in the TBLASTX report used in SearchIO.t (HUMBETGLOA.tblastx), I get these positions for the query: 355 364 365 367 368 370 371 373 374 375 and for the hit: 1941 1942 1943 1945 1946 1948 1949 1951 1952 1961 This is the actual first HSP for that report: ------------------------------------------- >gb|AE000479.1|AE000479 Escherichia coli K-12 MG1655 section 369 of 400 of the complete genome Length = 10934 Score = 33.6 bits (67), Expect = 0.13 Identities = 11/26 (42%), Positives = 16/26 (61%) Frame = +1 / -2 Query: 1057 SAYWSIFPPLGCWWSTLGPRGSLSPL 1134 +A W++FPP+G W L + SPL Sbjct: 5893 AAVWALFPPVGSQWGCLASQWRTSPL 5816 ------------------------------------------- It looks like it has something to do with the positions getting divided by 3 but not converted back to correspond to the nucleotide position. When fixing this (and as mentioned above), do we want to only report the first nucleotide position where the mismatch occurs, or report the three positions corresponding to that codon region? Any thoughts? chris From tthmok at gmail.com Sun Feb 3 16:54:49 2008 From: tthmok at gmail.com (Terrance Mok) Date: Sun, 3 Feb 2008 14:54:49 -0700 Subject: [Bioperl-l] Problems Installing Bioperl 1.5.2 - Windows Message-ID: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> Hi I've been trying to install bioperl on a fresh install of ActivePerl on Windows. Following the installation guide using the GUI Perl Package Manager, I add the 4 locations and all of them list 0 packages except for "Bribes http://www.Bribes.org/perl/ppm ". Then when searching for bioperl (with all package view), nothing shows up since no packages are found for all the other locations I added. I've also had problems installing on Ubuntu (helping a friend), when using CPAN and following exactly the guide on the bioperl installation it will not work. When doing the install command in CPAN, install S/SE/SENDU/bioperl- 1.5.2_102.tar.gz she gets an error that "/home/username/.cpan/build/bioperl-1.5.2_102: No such file or directory at Makefile.PL line 25." From anjan.purkayastha at gmail.com Sun Feb 3 12:10:49 2008 From: anjan.purkayastha at gmail.com (ANJAN PURKAYASTHA) Date: Sun, 3 Feb 2008 12:10:49 -0500 Subject: [Bioperl-l] sequence object question Message-ID: hi, here is the problem i'm facing. i parse a genbank file with the statement: my $gb_stream = Bio::SeqIO->new( -file => 'gb_test_file', -format => 'GenBank'); while (my $seq_obj= $gb_stream->next_seq){ ..... } presumably $seq_obj is a Bio::Seq::RichSeq object. now, when I try: my $feat_obj($seq_obj->getSeqFeatures){ ..... } i get an error message: Can't locate object method "getSeqFeatures" via package "Bio::Seq::RichSeq" at gb_file_reader.pl line 11. on reading docs I find that Bio::Seq::RichSeq does not have a getSeqFeatures method. but, RIchSeq is a child of the Seq class, which HAS a getSeqFeatures method (i presume this method is also inherited by the RichSeq class). so, why am i getting an error message and how do i go about getting the features within each genbank file? appreciate any pointers. TIA. anjan -- ANJAN PURKAYASTHA, PhD. Senior Computational Biologist ========================== 1101 King Street, Suite 310, Alexandria, VA 22314. 703.518.8040 (office) 703.740.6939 (mobile) email: anjan at vbi.vt.edu; anjan.purkayastha at gmail.com http://www.vbi.vt.edu ========================== From jason at bioperl.org Sun Feb 3 18:51:21 2008 From: jason at bioperl.org (Jason Stajich) Date: Sun, 3 Feb 2008 15:51:21 -0800 Subject: [Bioperl-l] sequence object question In-Reply-To: References: Message-ID: <212091BA-2942-4A95-9329-AB76D8F102A5@bioperl.org> It is 'get_SeqFeatures' http://doc.bioperl.org/bioperl-live/Bio/FeatureHolderI.html#POD1 Deobfuscator: http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio %3A%3ASeq&sort_order=by+method&search_string=Bio%3A%3ASeq http://bioperl.org/cgi-bin/deob_detail.cgi? method=Bio::Seq::get_SeqFeatures HOWTO: http://bioperl.org/wiki/HOWTO:Feature-Annotation On Feb 3, 2008, at 9:10 AM, ANJAN PURKAYASTHA wrote: > hi, > here is the problem i'm facing. > > i parse a genbank file with the statement: > my $gb_stream = Bio::SeqIO->new( -file => 'gb_test_file', -format => > 'GenBank'); > while (my $seq_obj= $gb_stream->next_seq){ > ..... > > } > > presumably $seq_obj is a Bio::Seq::RichSeq object. > > now, when I try: > my $feat_obj($seq_obj->getSeqFeatures){ > ..... > } > i get an error message: Can't locate object method "getSeqFeatures" > via > package "Bio::Seq::RichSeq" at gb_file_reader.pl line 11. > > > on reading docs I find that Bio::Seq::RichSeq does not have a > getSeqFeatures > method. > but, RIchSeq is a child of the Seq class, which HAS a > getSeqFeatures method > (i presume this method is also inherited by the RichSeq class). > > so, why am i getting an error message and how do i go about getting > the > features within each genbank file? > > appreciate any pointers. > > TIA. > > anjan > > -- > ANJAN PURKAYASTHA, PhD. > Senior Computational Biologist > ========================== > > 1101 King Street, Suite 310, > Alexandria, VA 22314. > 703.518.8040 (office) > 703.740.6939 (mobile) > > email: > anjan at vbi.vt.edu; > anjan.purkayastha at gmail.com > > http://www.vbi.vt.edu > > ========================== > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From anjan.purkayastha at gmail.com Sun Feb 3 23:00:33 2008 From: anjan.purkayastha at gmail.com (ANJAN PURKAYASTHA) Date: Sun, 3 Feb 2008 23:00:33 -0500 Subject: [Bioperl-l] sequence object question In-Reply-To: <212091BA-2942-4A95-9329-AB76D8F102A5@bioperl.org> References: <212091BA-2942-4A95-9329-AB76D8F102A5@bioperl.org> Message-ID: Thanks a lot! On Feb 3, 2008 6:51 PM, Jason Stajich wrote: > It is 'get_SeqFeatures' > http://doc.bioperl.org/bioperl-live/Bio/FeatureHolderI.html#POD1 > > Deobfuscator: > http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio > %3A%3ASeq&sort_order=by+method&search_string=Bio%3A%3ASeq > http://bioperl.org/cgi-bin/deob_detail.cgi? > method=Bio::Seq::get_SeqFeatures > > HOWTO: > http://bioperl.org/wiki/HOWTO:Feature-Annotation > > > On Feb 3, 2008, at 9:10 AM, ANJAN PURKAYASTHA wrote: > > > hi, > > here is the problem i'm facing. > > > > i parse a genbank file with the statement: > > my $gb_stream = Bio::SeqIO->new( -file => 'gb_test_file', -format => > > 'GenBank'); > > while (my $seq_obj= $gb_stream->next_seq){ > > ..... > > > > } > > > > presumably $seq_obj is a Bio::Seq::RichSeq object. > > > > now, when I try: > > my $feat_obj($seq_obj->getSeqFeatures){ > > ..... > > } > > i get an error message: Can't locate object method "getSeqFeatures" > > via > > package "Bio::Seq::RichSeq" at gb_file_reader.pl line 11. > > > > > > on reading docs I find that Bio::Seq::RichSeq does not have a > > getSeqFeatures > > method. > > but, RIchSeq is a child of the Seq class, which HAS a > > getSeqFeatures method > > (i presume this method is also inherited by the RichSeq class). > > > > so, why am i getting an error message and how do i go about getting > > the > > features within each genbank file? > > > > appreciate any pointers. > > > > TIA. > > > > anjan > > > > -- > > ANJAN PURKAYASTHA, PhD. > > Senior Computational Biologist > > ========================== > > > > 1101 King Street, Suite 310, > > Alexandria, VA 22314. > > 703.518.8040 (office) > > 703.740.6939 (mobile) > > > > email: > > anjan at vbi.vt.edu; > > anjan.purkayastha at gmail.com > > > > http://www.vbi.vt.edu > > > > ========================== > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- ANJAN PURKAYASTHA, PhD. Senior Computational Biologist ========================== 1101 King Street, Suite 310, Alexandria, VA 22314. 703.518.8040 (office) 703.740.6939 (mobile) email: anjan at vbi.vt.edu; anjan.purkayastha at gmail.com http://www.vbi.vt.edu ========================== From bix at sendu.me.uk Mon Feb 4 03:45:31 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 04 Feb 2008 08:45:31 +0000 Subject: [Bioperl-l] Problems Installing Bioperl 1.5.2 - Windows In-Reply-To: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> References: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> Message-ID: <47A6D0AB.7050702@sendu.me.uk> Terrance Mok wrote: > Hi I've been trying to install bioperl on a fresh install of ActivePerl on > Windows. > Following the installation guide using the GUI Perl Package Manager, I add > the 4 locations and all of them list 0 packages except for "Bribes > http://www.Bribes.org/perl/ppm ". > Then when searching for bioperl (with all package view), nothing shows up > since no packages are found for all the other locations I added. Hopefully someone else will chime in, but perhaps there's something wrong with the server? Can anyone else confirm? > I've also had problems installing on Ubuntu (helping a friend), when using > CPAN and following exactly the guide on the bioperl installation it will not > work. When doing the install command in CPAN, install S/SE/SENDU/bioperl- > 1.5.2_102.tar.gz she gets an error that > "/home/username/.cpan/build/bioperl-1.5.2_102: No such file or directory at > Makefile.PL line 25." Hard to figure out what might be wrong without complete details. Can she install anything else via CPAN? Has she run out of disc space? From darren.obbard at ed.ac.uk Mon Feb 4 03:56:06 2008 From: darren.obbard at ed.ac.uk (Darren Obbard) Date: Mon, 04 Feb 2008 08:56:06 +0000 Subject: [Bioperl-l] Problems Installing Bioperl 1.5.2 - Windows In-Reply-To: <47A6D0AB.7050702@sendu.me.uk> References: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> <47A6D0AB.7050702@sendu.me.uk> Message-ID: <47A6D326.40103@ed.ac.uk> Hi, > Terrance Mok wrote: >> Then when searching for bioperl (with all package view), nothing >> shows up >> since no packages are found for all the other locations I added. > Hopefully someone else will chime in, but perhaps there's something > wrong with the server? Can anyone else confirm? Just to note that I too have had the same problem. From ca. 2 weeks ago I could see no packages on the recommended bioperl repository. I just assumed I was doing something wrong, and thought I'd wait until my need became urgent. -- Darren Obbard University of Edinburgh, UK From darren.obbard at ed.ac.uk Mon Feb 4 06:07:23 2008 From: darren.obbard at ed.ac.uk (Darren Obbard) Date: Mon, 04 Feb 2008 11:07:23 +0000 Subject: [Bioperl-l] Problems Installing Bioperl 1.5.2 - Windows In-Reply-To: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> References: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> Message-ID: <47A6F1EB.8060806@ed.ac.uk> Hi again, Having just looked, it seems fine on this machine (XP proffessional, sp2). The problem I was (and am) having are on a clean install of Vista (ultimate). Perhaps this is a vista/activestate issue? What versions of windows/activeperl are people having problems with? From cjfields at uiuc.edu Mon Feb 4 12:53:08 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 4 Feb 2008 11:53:08 -0600 Subject: [Bioperl-l] Problems Installing Bioperl 1.5.2 - Windows In-Reply-To: <47A6D0AB.7050702@sendu.me.uk> References: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> <47A6D0AB.7050702@sendu.me.uk> Message-ID: <8863D982-5CEF-4E0E-8840-FC8850D96F06@uiuc.edu> On Feb 4, 2008, at 2:45 AM, Sendu Bala wrote: > Terrance Mok wrote: >> Hi I've been trying to install bioperl on a fresh install of >> ActivePerl on >> Windows. >> Following the installation guide using the GUI Perl Package >> Manager, I add >> the 4 locations and all of them list 0 packages except for "Bribes >> http://www.Bribes.org/perl/ppm ". >> Then when searching for bioperl (with all package view), nothing >> shows up >> since no packages are found for all the other locations I added. > > Hopefully someone else will chime in, but perhaps there's something > wrong with the server? Can anyone else confirm? I haven't used ActivePerl in a while personally since switching to OS X (even when using perl 5.10). Terrance, did you follow the ActivePerl instructions or our installation instructions? Also, we don't guarantee that it will work with AtcivePerl's 5.10 port but it's worth a try; if not downgrade to the latest 5.8 build. >> I've also had problems installing on Ubuntu (helping a friend), >> when using >> CPAN and following exactly the guide on the bioperl installation it >> will not >> work. When doing the install command in CPAN, install S/SE/SENDU/ >> bioperl- >> 1.5.2_102.tar.gz she gets an error that >> "/home/username/.cpan/build/bioperl-1.5.2_102: No such file or >> directory at >> Makefile.PL line 25." > > Hard to figure out what might be wrong without complete details. Can > she install anything else via CPAN? Has she run out of disc space? Haven't seen that before but it works for me using cpan and perl 5.8 and perl 5.10. chris From jay at jays.net Mon Feb 4 14:42:17 2008 From: jay at jays.net (Jay Hannah) Date: Mon, 04 Feb 2008 13:42:17 -0600 Subject: [Bioperl-l] SVN server trouble? Message-ID: <47A76A99.2080307@jays.net> I'm getting this error trying to check out trunk, from 2 different servers on 2 different networks: $ svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk bioperl-live svn: Can't find a temporary directory: Error string not specified yet Is this an SVN server problem of some sort, or is it just me somehow? ( Oh, and come hang out with us: irc.freenode.net #bioperl ) Thanks, Jay Hannah http://clab.ist.unomaha.edu/CLAB/index.php/User:Jhannah From David.Messina at sbc.su.se Mon Feb 4 16:35:42 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Mon, 4 Feb 2008 22:35:42 +0100 Subject: [Bioperl-l] SVN server trouble? In-Reply-To: <47A76A99.2080307@jays.net> References: <47A76A99.2080307@jays.net> Message-ID: <628aabb70802041335o300dca9dha7b75d4e0037ef54@mail.gmail.com> Not just you, Jay. I'm getting the same error trying to 'svn update' on a previously-checked-out working copy. Dave From cjfields at uiuc.edu Mon Feb 4 16:48:00 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 4 Feb 2008 15:48:00 -0600 Subject: [Bioperl-l] SVN server trouble? In-Reply-To: <628aabb70802041335o300dca9dha7b75d4e0037ef54@mail.gmail.com> References: <47A76A99.2080307@jays.net> <628aabb70802041335o300dca9dha7b75d4e0037ef54@mail.gmail.com> Message-ID: I went ahead and reported it to support. It's an odd issue, but a checkout works from dev (for those with dev accounts), so it has to be something wonky on code.open-bio.org. chris On Feb 4, 2008, at 3:35 PM, Dave Messina wrote: > Not just you, Jay. I'm getting the same error trying to 'svn update' > on a > previously-checked-out working copy. > Dave From jason at bioperl.org Mon Feb 4 17:11:14 2008 From: jason at bioperl.org (Jason Stajich) Date: Mon, 4 Feb 2008 14:11:14 -0800 Subject: [Bioperl-l] SVN server trouble? In-Reply-To: References: <47A76A99.2080307@jays.net> <628aabb70802041335o300dca9dha7b75d4e0037ef54@mail.gmail.com> Message-ID: ChrisD says that something with is eating up free space on the host so /tmp is full causing the problem(s). Will report in when it's been fixed and we can figure out whether the SVNweb runaway svn diffs are creating the glut of big files. -jason On Feb 4, 2008, at 1:48 PM, Chris Fields wrote: > I went ahead and reported it to support. It's an odd issue, but a > checkout works from dev (for those with dev accounts), so it has to > be something wonky on code.open-bio.org. > > chris > > On Feb 4, 2008, at 3:35 PM, Dave Messina wrote: > >> Not just you, Jay. I'm getting the same error trying to 'svn >> update' on a >> previously-checked-out working copy. >> Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From luisecarracedo at hotmail.com Tue Feb 5 12:59:33 2008 From: luisecarracedo at hotmail.com (luis esteban) Date: Tue, 5 Feb 2008 19:59:33 +0200 Subject: [Bioperl-l] Eland report Message-ID: Hi to everibody!! Is there anybody working in any project tryng to convert Blat or Blast reports in Eland reports. Any Idea, any sugestions would be apreciated. Thanks a Lot Luis Esteban PhD _________________________________________________________________ ?Aburrido? Ingres? ya y divertite como nunca en MSN Juegos. http://juegos.ar.msn.com/ From jason at bioperl.org Tue Feb 5 14:22:14 2008 From: jason at bioperl.org (Jason Stajich) Date: Tue, 5 Feb 2008 11:22:14 -0800 Subject: [Bioperl-l] Eland report In-Reply-To: References: Message-ID: You mean print out eland reports from a BLAST/BLAT/table report? I really hope eland report doesn't become the standard though... -jason On Feb 5, 2008, at 9:59 AM, luis esteban wrote: > > Hi to everibody!! > Is there anybody working in any project tryng to convert Blat or > Blast reports in Eland reports. > Any Idea, any sugestions would be apreciated. > Thanks a Lot > Luis Esteban PhD > _________________________________________________________________ > ?Aburrido? Ingres? ya y divertite como nunca en MSN Juegos. > http://juegos.ar.msn.com/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From sjmiller at email.arizona.edu Tue Feb 5 15:23:28 2008 From: sjmiller at email.arizona.edu (Susan J. Miller) Date: Tue, 05 Feb 2008 13:23:28 -0700 Subject: [Bioperl-l] Bioperl-l Digest, Vol 57, Issue 10 In-Reply-To: References: Message-ID: <47A8C5C0.7040401@email.arizona.edu> bioperl-l-request at lists.open-bio.org wrote: > > Message: 2 > Date: Thu, 31 Jan 2008 10:34:31 +0100 > From: Georg Otto > Subject: Re: [Bioperl-l] Bio::DB::GenBank and large number of requests > To: bioperl-l at bioperl.org > Message-ID: > Content-Type: text/plain; charset=us-ascii > > Hi, > > I succeeded with a similar task using the seqhound database. I had a > list of > 200,000 gid numbers, but I guess it can work in a similar > fashion using accession numbers. Hi Georg, How recently have you used the SeqHound database? We installed it from CPAN but when we try to run the following test script this error occurs: MSG: HTTP::Request error: 500 Can't connect to seqhound.blueprint.org:80 (Bad hostname 'seqhound.blueprint.org') Script: #!/usr/local/bin/perl use warnings; use Bio::SeqIO; use Bio::DB::SeqHound; my $sh = Bio::DB::SeqHound->new(); my $seq = $sh->get_Seq_by_acc("CAA28783"); print $seq->display_name, "\n"; Do you know if SeqHound has moved? Is there a way to comfigure it so that it works? Thanks, -susan Susan J. Miller Manager, Scientific Data Analysis Biotechnology Computing Facility Arizona Research Laboratories (520) 626-2597 From cjfields at uiuc.edu Tue Feb 5 16:38:31 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 5 Feb 2008 15:38:31 -0600 Subject: [Bioperl-l] SeqHound In-Reply-To: <47A8C5C0.7040401@email.arizona.edu> References: <47A8C5C0.7040401@email.arizona.edu> Message-ID: <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> The URL has changed. I'll fix this in bioperl-live. You can fix this in your script directly for now (though I hate globals): use Bio::DB::SeqHound; $Bio::DB::SeqHound::HOSTBASE = 'http://dogboxonline.unleashedinformatics.com/' ; my $sh = Bio::DB::SeqHound->new(); my $seq = $sh->get_Seq_by_acc("CAA28783"); print $seq->display_name, "\n"; chris On Feb 5, 2008, at 2:23 PM, Susan J. Miller wrote: > bioperl-l-request at lists.open-bio.org wrote: >> >> Message: 2 >> Date: Thu, 31 Jan 2008 10:34:31 +0100 >> From: Georg Otto >> Subject: Re: [Bioperl-l] Bio::DB::GenBank and large number of >> requests >> To: bioperl-l at bioperl.org >> Message-ID: >> Content-Type: text/plain; charset=us-ascii >> Hi, >> I succeeded with a similar task using the seqhound database. I had a >> list of > 200,000 gid numbers, but I guess it can work in a similar >> fashion using accession numbers. > > Hi Georg, > > How recently have you used the SeqHound database? We installed it > from CPAN but when we try to run the following test script this > error occurs: > > MSG: HTTP::Request error: 500 Can't connect to > seqhound.blueprint.org:80 (Bad hostname 'seqhound.blueprint.org') > > Script: > #!/usr/local/bin/perl > use warnings; > use Bio::SeqIO; > use Bio::DB::SeqHound; > > my $sh = Bio::DB::SeqHound->new(); > my $seq = $sh->get_Seq_by_acc("CAA28783"); > print $seq->display_name, "\n"; > > > Do you know if SeqHound has moved? Is there a way to comfigure it > so that it works? > > Thanks, > -susan > > Susan J. Miller > Manager, Scientific Data Analysis > Biotechnology Computing Facility > Arizona Research Laboratories > (520) 626-2597 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Tue Feb 5 17:59:48 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 5 Feb 2008 16:59:48 -0600 Subject: [Bioperl-l] SeqHound In-Reply-To: <47A8E3BF.7000308@email.arizona.edu> References: <47A8C5C0.7040401@email.arizona.edu> <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> <47A8E3BF.7000308@email.arizona.edu> Message-ID: <025C4E5C-CD77-442F-AEB1-ACC265B36017@uiuc.edu> On Feb 5, 2008, at 4:31 PM, Susan J. Miller wrote: > Chris Fields wrote: >> The URL has changed. I'll fix this in bioperl-live. >> You can fix this in your script directly for now (though I hate >> globals): >> use Bio::DB::SeqHound; >> $Bio::DB::SeqHound::HOSTBASE = 'http://dogboxonline.unleashedinformatics.com/' >> ; > > Thanks Chris, that helps a little bit, but I'm still not having much > luck with the SeqHound DB. The CPAN SeqHound.pm documentation for > the get_Stream_by_Query method says: > ... No problem. It was an easy fix. ... > I get the error: > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Id list has been truncated even after maxids requested > STACK: Error::throw > STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/ > Root/Root.pm:359 > STACK: Bio::DB::Query::WebQuery::_fetch_ids /usr/lib/perl5/site_perl/ > 5.8.8/Bio/DB/Query/WebQuery.pm:236 > STACK: Bio::DB::Query::WebQuery::ids /usr/lib/perl5/site_perl/5.8.8/ > Bio/DB/Query/WebQuery.pm:200 > STACK: Bio::DB::SeqHound::get_Stream_by_query /usr/lib/perl5/ > site_perl/5.8.8/Bio/DB/SeqHound.pm:314 > STACK: SeqHoundQuery.pl:21 > > There are only 5013 sequences that match this query so it seems odd > that the Id list is too long...or am I using SeqHound improperly? > > (My reason for trying SeqHound is that I want to set up a monthly > cron job to download nucest fasta sequences for drosphila > melanogaster, and I've tried NCBI E-Utilities and the script > generated by the NCBI ebot and in both cases some of the 570828 > records get dropped, even after running repeated attempts.) > > > Thanks, > -susan The URL is likely way too long (a common problem when using a GET as opposed to a POST with LWP). NCBI's efetch has the same problem, which is why using epost is a good idea (except it only takes GI's!). You will have to loop through the IDs in bunches of 250-500 max to get what you want. Don't know if there is a way to post to SeqHound but it might be worth investigating at some point. I also see they have a SOAP interface up. chris From sjmiller at email.arizona.edu Tue Feb 5 17:31:27 2008 From: sjmiller at email.arizona.edu (Susan J. Miller) Date: Tue, 05 Feb 2008 15:31:27 -0700 Subject: [Bioperl-l] SeqHound In-Reply-To: <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> References: <47A8C5C0.7040401@email.arizona.edu> <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> Message-ID: <47A8E3BF.7000308@email.arizona.edu> Chris Fields wrote: > The URL has changed. I'll fix this in bioperl-live. > > You can fix this in your script directly for now (though I hate globals): > > use Bio::DB::SeqHound; > > $Bio::DB::SeqHound::HOSTBASE = > 'http://dogboxonline.unleashedinformatics.com/'; > Thanks Chris, that helps a little bit, but I'm still not having much luck with the SeqHound DB. The CPAN SeqHound.pm documentation for the get_Stream_by_Query method says: Title : get_Stream_by_query Usage : $seq = $db->get_Stream_by_query($query); Function: Retrieves Seq objects from Entrez 'en masse', rather than one at a time. For large numbers of sequences, this is far superior than get_Stream_by_[id/acc](). Example : $query_string = 'Candida maltosa 26S ribosomal RNA gene'; However, when I try: $query_string = 'drosophila simulans[orgn]'; $query = Bio::DB::Query::GenBank->new(-db=>'nucest', -query=>$query_string); $stream = $sh->get_Stream_by_query($query); I get the error: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Id list has been truncated even after maxids requested STACK: Error::throw STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359 STACK: Bio::DB::Query::WebQuery::_fetch_ids /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Query/WebQuery.pm:236 STACK: Bio::DB::Query::WebQuery::ids /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Query/WebQuery.pm:200 STACK: Bio::DB::SeqHound::get_Stream_by_query /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqHound.pm:314 STACK: SeqHoundQuery.pl:21 There are only 5013 sequences that match this query so it seems odd that the Id list is too long...or am I using SeqHound improperly? (My reason for trying SeqHound is that I want to set up a monthly cron job to download nucest fasta sequences for drosphila melanogaster, and I've tried NCBI E-Utilities and the script generated by the NCBI ebot and in both cases some of the 570828 records get dropped, even after running repeated attempts.) Thanks, -susan Susan J. Miller Manager, Scientific Data Analysis Biotechnology Computing Facility Arizona Research Laboratories (520) 626-2597 From lincoln.stein at gmail.com Tue Feb 5 18:43:06 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 5 Feb 2008 18:43:06 -0500 Subject: [Bioperl-l] ActiveState Perl problems Message-ID: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> Hi Scott, Bioperl folk, I'm afraid that the ActiveState ppm install of BioPerl no longer works. Using the current ActiveState (perl version 5.10), I added the Bribes, Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates repositories. However, when I synched up, all but the Bribes reps showed up empty in the ppm tool. In addition, there's nothing in the release candidate rep any longer. I used to use this to get at Bioperl 1.5. Perhaps the architecture needs to be changed? Lincoln -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From cjfields at uiuc.edu Tue Feb 5 19:13:29 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 5 Feb 2008 18:13:29 -0600 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> Message-ID: I'll try changing out package.xml on portal. The one in RC appears to be blank now (which explains why you can't use that one). chris On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: > Hi Scott, Bioperl folk, > > I'm afraid that the ActiveState ppm install of BioPerl no longer > works. > Using the current ActiveState (perl version 5.10), I added the Bribes, > Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates > repositories. However, when I synched up, all but the Bribes reps > showed up > empty in the ppm tool. > > In addition, there's nothing in the release candidate rep any > longer. I used > to use this to get at Bioperl 1.5. > > Perhaps the architecture needs to be changed? > > Lincoln > > > > -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > (516) 367-8380 (voice) > (516) 367-8389 (fax) > FOR URGENT MESSAGES & SCHEDULING, > PLEASE CONTACT MY ASSISTANT, > SANDRA MICHELSEN, AT michelse at cshl.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From golharam at umdnj.edu Tue Feb 5 18:15:43 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Tue, 05 Feb 2008 18:15:43 -0500 Subject: [Bioperl-l] Bio::SeqIO object for GenBank XML format? Message-ID: <47A8EE1F.7050100@umdnj.edu> Is there a SeqIO module for the XML format for GenBank records? The "http://www.bioperl.org/wiki/HOWTO:SeqIO" page doesn't show one listed. From Kevin.M.Brown at asu.edu Tue Feb 5 19:25:58 2008 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Tue, 5 Feb 2008 17:25:58 -0700 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> Message-ID: <1A4207F8295607498283FE9E93B775B4045AA97F@EX02.asurite.ad.asu.edu> Well, Kobes seems to have two different ppm repos. One for 8xx builds of activestate perl and one for 10xx builds. So, Bioperl probably needs to be rebuilt for 5.10 to get it to show in the 5.10 repos. I just opened up Activestate perl 5.8 and I see 1.5.2_100 listed in it from the Regular Release site. > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Lincoln Stein > Sent: Tuesday, February 05, 2008 4:43 PM > To: Scott Cain > Cc: bioperl-l > Subject: [Bioperl-l] ActiveState Perl problems > > Hi Scott, Bioperl folk, > > I'm afraid that the ActiveState ppm install of BioPerl no > longer works. > Using the current ActiveState (perl version 5.10), I added the Bribes, > Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates > repositories. However, when I synched up, all but the Bribes > reps showed up > empty in the ppm tool. > > In addition, there's nothing in the release candidate rep any > longer. I used > to use this to get at Bioperl 1.5. > > Perhaps the architecture needs to be changed? > > Lincoln > > > > -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > (516) 367-8380 (voice) > (516) 367-8389 (fax) > FOR URGENT MESSAGES & SCHEDULING, > PLEASE CONTACT MY ASSISTANT, > SANDRA MICHELSEN, AT michelse at cshl.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From jason at bioperl.org Tue Feb 5 19:45:35 2008 From: jason at bioperl.org (Jason Stajich) Date: Tue, 5 Feb 2008 16:45:35 -0800 Subject: [Bioperl-l] Bio::SeqIO object for GenBank XML format? In-Reply-To: <47A8EE1F.7050100@umdnj.edu> References: <47A8EE1F.7050100@umdnj.edu> Message-ID: <67216BC0-8F2F-432C-B94F-C9A92640E01A@bioperl.org> Then there probably isn't - the codebase Bo/SeqIO directory would tell you otherwise I guess. Does anyone use the format and want to write one? On Feb 5, 2008, at 3:15 PM, Ryan Golhar wrote: > Is there a SeqIO module for the XML format for GenBank records? > The "http://www.bioperl.org/wiki/HOWTO:SeqIO" page doesn't show one > listed. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bosborne11 at verizon.net Tue Feb 5 18:52:57 2008 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 05 Feb 2008 18:52:57 -0500 Subject: [Bioperl-l] SeqHound In-Reply-To: <47A8E3BF.7000308@email.arizona.edu> References: <47A8C5C0.7040401@email.arizona.edu> <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> <47A8E3BF.7000308@email.arizona.edu> Message-ID: <4D3A27D3-D535-4F34-8A7F-966F30B51F86@verizon.net> Susan, It sounds like you could use rsync though perhaps there's some detail that I missed. A typical command would look something like this: rsync -av ftp.ncbi.nlm.nih.gov::blast/db/FASTA/ /local/data/FASTA/ Brian O. On Feb 5, 2008, at 5:31 PM, Susan J. Miller wrote: > (My reason for trying SeqHound is that I want to set up a monthly > cron job to download nucest fasta sequences for drosphila > melanogaster, and I've tried NCBI E-Utilities and the script > generated by the NCBI ebot and in both cases some of the 570828 > records get dropped, even after running repeated attempts.) From barry.moore at genetics.utah.edu Tue Feb 5 20:09:56 2008 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Tue, 5 Feb 2008 18:09:56 -0700 Subject: [Bioperl-l] SeqHound In-Reply-To: <47A8E3BF.7000308@email.arizona.edu> References: <47A8C5C0.7040401@email.arizona.edu> <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> <47A8E3BF.7000308@email.arizona.edu> Message-ID: Susan, I'm joining this discussion late so my apologies if I'm missing the original point. If you're trying to routinely download thousands of sequences from GenBank or SeqHound you probably want to be using ftp to download the flat files and query/parse locally. If you're trying to stay on top of the latest Drosophila ESTs, then how about setting up a nightly cron job to download the incremental updates from NCBIs ftp (ftp://ftp.ncbi.nih.gov/genbank/daily-nc) and parse that for Drosophila EST sequences. The EST division is huge, but I would think nightly incrementals should be manageable. Barry On Feb 5, 2008, at 3:31 PM, Susan J. Miller wrote: > Chris Fields wrote: >> The URL has changed. I'll fix this in bioperl-live. >> >> You can fix this in your script directly for now (though I hate >> globals): >> >> use Bio::DB::SeqHound; >> >> $Bio::DB::SeqHound::HOSTBASE = >> 'http://dogboxonline.unleashedinformatics.com/'; >> > > Thanks Chris, that helps a little bit, but I'm still not having much > luck with the SeqHound DB. The CPAN SeqHound.pm documentation for the > get_Stream_by_Query method says: > > Title : get_Stream_by_query > Usage : $seq = $db->get_Stream_by_query($query); > Function: Retrieves Seq objects from Entrez 'en masse', rather than > one at a time. For large numbers of sequences, this is far superior > than get_Stream_by_[id/acc](). > Example : $query_string = 'Candida maltosa 26S ribosomal RNA gene'; > > However, when I try: > > $query_string = 'drosophila simulans[orgn]'; > $query = Bio::DB::Query::GenBank->new(-db=>'nucest', > -query=>$query_string); > $stream = $sh->get_Stream_by_query($query); > > I get the error: > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Id list has been truncated even after maxids requested > STACK: Error::throw > STACK: Bio::Root::Root::throw > /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359 > STACK: Bio::DB::Query::WebQuery::_fetch_ids > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Query/WebQuery.pm:236 > STACK: Bio::DB::Query::WebQuery::ids > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Query/WebQuery.pm:200 > STACK: Bio::DB::SeqHound::get_Stream_by_query > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqHound.pm:314 > STACK: SeqHoundQuery.pl:21 > > There are only 5013 sequences that match this query so it seems odd > that > the Id list is too long...or am I using SeqHound improperly? > > (My reason for trying SeqHound is that I want to set up a monthly cron > job to download nucest fasta sequences for drosphila melanogaster, and > I've tried NCBI E-Utilities and the script generated by the NCBI ebot > and in both cases some of the 570828 records get dropped, even after > running repeated attempts.) > > > Thanks, > -susan > > Susan J. Miller > Manager, Scientific Data Analysis > Biotechnology Computing Facility > Arizona Research Laboratories > (520) 626-2597 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at uiuc.edu Tue Feb 5 20:19:16 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 5 Feb 2008 19:19:16 -0600 Subject: [Bioperl-l] Bio::SeqIO object for GenBank XML format? In-Reply-To: <67216BC0-8F2F-432C-B94F-C9A92640E01A@bioperl.org> References: <47A8EE1F.7050100@umdnj.edu> <67216BC0-8F2F-432C-B94F-C9A92640E01A@bioperl.org> Message-ID: <9F54378C-9905-4E90-88B9-F539B1E933DF@uiuc.edu> Could probably base it off of the BSML parser. Might be better to write up a general INSDC XML parser, which GenBank/EMBL/DDBJ all use now: http://www.insdc.org/page.php?page=documents&sid=fa24a7d177ab7a687e87a85db6822c01 chris On Feb 5, 2008, at 6:45 PM, Jason Stajich wrote: > Then there probably isn't - the codebase Bo/SeqIO directory would > tell you otherwise I guess. > Does anyone use the format and want to write one? > > On Feb 5, 2008, at 3:15 PM, Ryan Golhar wrote: > >> Is there a SeqIO module for the XML format for GenBank records? >> The "http://www.bioperl.org/wiki/HOWTO:SeqIO" page doesn't show one >> listed. >> >> _______________________________________________ >> 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 Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Tue Feb 5 20:32:52 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 5 Feb 2008 19:32:52 -0600 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <1A4207F8295607498283FE9E93B775B4045AA97F@EX02.asurite.ad.asu.edu> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> <1A4207F8295607498283FE9E93B775B4045AA97F@EX02.asurite.ad.asu.edu> Message-ID: <3BFD59BB-152C-4D43-B8E7-96DC293D8C34@uiuc.edu> Kobes keeps two separate repos because there are several binary-only modules (DBD::mysql, GD, etc) which are incompatible with older major perl releases (5.6, 5.8, 5.10). If the modules are pure perl then there shouldn't be a problem. Saying that, there is one issue which tanks Bio::SeqIO::entrezgene parsing (which mistakenly made pseudohashes) which Stefan and I fixed recently; that'll tank in perl 5.10. chris On Feb 5, 2008, at 6:25 PM, Kevin Brown wrote: > Well, Kobes seems to have two different ppm repos. One for 8xx builds > of activestate perl and one for 10xx builds. So, Bioperl probably > needs > to be rebuilt for 5.10 to get it to show in the 5.10 repos. I just > opened up Activestate perl 5.8 and I see 1.5.2_100 listed in it from > the > Regular Release site. > >> -----Original Message----- >> From: bioperl-l-bounces at lists.open-bio.org >> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of >> Lincoln Stein >> Sent: Tuesday, February 05, 2008 4:43 PM >> To: Scott Cain >> Cc: bioperl-l >> Subject: [Bioperl-l] ActiveState Perl problems >> >> Hi Scott, Bioperl folk, >> >> I'm afraid that the ActiveState ppm install of BioPerl no >> longer works. >> Using the current ActiveState (perl version 5.10), I added the >> Bribes, >> Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates >> repositories. However, when I synched up, all but the Bribes >> reps showed up >> empty in the ppm tool. >> >> In addition, there's nothing in the release candidate rep any >> longer. I used >> to use this to get at Bioperl 1.5. >> >> Perhaps the architecture needs to be changed? >> >> Lincoln >> >> >> >> -- >> Lincoln D. Stein >> Cold Spring Harbor Laboratory >> 1 Bungtown Road >> Cold Spring Harbor, NY 11724 >> (516) 367-8380 (voice) >> (516) 367-8389 (fax) >> FOR URGENT MESSAGES & SCHEDULING, >> PLEASE CONTACT MY ASSISTANT, >> SANDRA MICHELSEN, AT michelse at cshl.edu >> _______________________________________________ >> 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 Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From golharam at umdnj.edu Tue Feb 5 19:54:24 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Tue, 05 Feb 2008 19:54:24 -0500 Subject: [Bioperl-l] Bio::SeqIO object for GenBank XML format? In-Reply-To: <67216BC0-8F2F-432C-B94F-C9A92640E01A@bioperl.org> References: <47A8EE1F.7050100@umdnj.edu> <67216BC0-8F2F-432C-B94F-C9A92640E01A@bioperl.org> Message-ID: <47A90540.9060002@umdnj.edu> If no one else has already built one, then I'd be happy to based on the genbank and chaosxml/tigrxml modules. Ryan Jason Stajich wrote: > Then there probably isn't - the codebase Bo/SeqIO directory would tell > you otherwise I guess. > Does anyone use the format and want to write one? > > On Feb 5, 2008, at 3:15 PM, Ryan Golhar wrote: > >> Is there a SeqIO module for the XML format for GenBank records? The >> "http://www.bioperl.org/wiki/HOWTO:SeqIO" page doesn't show one listed. >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > From cjfields at uiuc.edu Tue Feb 5 22:06:06 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 5 Feb 2008 21:06:06 -0600 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> Message-ID: <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> According to this page you can remove the tags and it will assume the files are for any OS: http://aspn.activestate.com/ASPN/docs/ActivePerl/5.10/lib/ActivePerl/PPM/PPD.html#ppd_xml_format I have moved the old package.xml to package.bak and replaced it with one w/o those tags; I can now pick it up on Mac OS X using ActiveState perl 5.10: ppm> search * Downloading bioperl.org packlist...not modified 1: Bio-ASN1-EntrezGene v1.09 2: Bundle-BioPerl-Core v1.5.2_100 3: Bundle-BioPerl-Db v1.5.2_100 4: Bundle-BioPerl-Network v1.5.2_100 5: Bundle-BioPerl-Run v1.5.2_100 6: Class-AutoClass v1.01 7: GD-SVG v0.25 8: Graph v0.80 9: SVG-Graph v0.01 10: bioperl v1.5.2_100 11: bioperl-db v1.5.2_100 12: bioperl-network v1.5.2_100 13: bioperl-run v1.5.2_100 I'll add ARCHITECTURE versioning tags back when we know it's working (maybe tomorrow, when I can get on to WinXP to test it). chris On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: > Hi Scott, Bioperl folk, > > I'm afraid that the ActiveState ppm install of BioPerl no longer > works. > Using the current ActiveState (perl version 5.10), I added the Bribes, > Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates > repositories. However, when I synched up, all but the Bribes reps > showed up > empty in the ppm tool. > > In addition, there's nothing in the release candidate rep any > longer. I used > to use this to get at Bioperl 1.5. > > Perhaps the architecture needs to be changed? > > Lincoln > > > > -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > (516) 367-8380 (voice) > (516) 367-8389 (fax) > FOR URGENT MESSAGES & SCHEDULING, > PLEASE CONTACT MY ASSISTANT, > SANDRA MICHELSEN, AT michelse at cshl.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From lincoln.stein at gmail.com Tue Feb 5 23:25:27 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 5 Feb 2008 23:25:27 -0500 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> Message-ID: <6dce9a0b0802052025y1243b7den4d19ed4dd1d71ff9@mail.gmail.com> Wow, nice fast work! Thanks all. Lincoln On Feb 5, 2008 10:06 PM, Chris Fields wrote: > According to this page you can remove the tags and it > will assume the files are for any OS: > > > http://aspn.activestate.com/ASPN/docs/ActivePerl/5.10/lib/ActivePerl/PPM/PPD.html#ppd_xml_format > > I have moved the old package.xml to package.bak and replaced it with > one w/o those tags; I can now pick it up on Mac OS X using ActiveState > perl 5.10: > > ppm> search * > Downloading bioperl.org packlist...not modified > 1: Bio-ASN1-EntrezGene v1.09 > 2: Bundle-BioPerl-Core v1.5.2_100 > 3: Bundle-BioPerl-Db v1.5.2_100 > 4: Bundle-BioPerl-Network v1.5.2_100 > 5: Bundle-BioPerl-Run v1.5.2_100 > 6: Class-AutoClass v1.01 > 7: GD-SVG v0.25 > 8: Graph v0.80 > 9: SVG-Graph v0.01 > 10: bioperl v1.5.2_100 > 11: bioperl-db v1.5.2_100 > 12: bioperl-network v1.5.2_100 > 13: bioperl-run v1.5.2_100 > > I'll add ARCHITECTURE versioning tags back when we know it's working > (maybe tomorrow, when I can get on to WinXP to test it). > > chris > > On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: > > > Hi Scott, Bioperl folk, > > > > I'm afraid that the ActiveState ppm install of BioPerl no longer > > works. > > Using the current ActiveState (perl version 5.10), I added the Bribes, > > Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates > > repositories. However, when I synched up, all but the Bribes reps > > showed up > > empty in the ppm tool. > > > > In addition, there's nothing in the release candidate rep any > > longer. I used > > to use this to get at Bioperl 1.5. > > > > Perhaps the architecture needs to be changed? > > > > Lincoln > > > > > > > > -- > > Lincoln D. Stein > > Cold Spring Harbor Laboratory > > 1 Bungtown Road > > Cold Spring Harbor, NY 11724 > > (516) 367-8380 (voice) > > (516) 367-8389 (fax) > > FOR URGENT MESSAGES & SCHEDULING, > > PLEASE CONTACT MY ASSISTANT, > > SANDRA MICHELSEN, AT michelse at cshl.edu > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From bioinfo21 at gmail.com Wed Feb 6 02:04:37 2008 From: bioinfo21 at gmail.com (Priya) Date: Wed, 6 Feb 2008 12:34:37 +0530 Subject: [Bioperl-l] Bioperl Message-ID: <98af6e260802052304y66add58fi65e289cb4b9069f7@mail.gmail.com> Hi all I am new to Bioperl. I have installed Bioperl in Linux. I am trying to use one of the sample programs in bioperl. I couldnt figure out where to set the http proxy authentication. I tried to follow the manual for installation. Still I am not getting it right . Let me know how to set the proxy authentication and where exactly it should be set. I tried to set env variables for http in .bashrc. Still its not working. Help me out. Thanks in advance. Regards Priya.. From lincoln.stein at gmail.com Wed Feb 6 10:03:31 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Wed, 6 Feb 2008 10:03:31 -0500 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> Message-ID: <6dce9a0b0802060703j231704acta813715265f1fab5@mail.gmail.com> Sadly, bioperl still won't install under ActiveState 5.10 because it can't find a repository with the SOAP::Lite prerequisite. Lincoln On Feb 5, 2008 10:06 PM, Chris Fields wrote: > According to this page you can remove the tags and it > will assume the files are for any OS: > > > http://aspn.activestate.com/ASPN/docs/ActivePerl/5.10/lib/ActivePerl/PPM/PPD.html#ppd_xml_format > > I have moved the old package.xml to package.bak and replaced it with > one w/o those tags; I can now pick it up on Mac OS X using ActiveState > perl 5.10: > > ppm> search * > Downloading bioperl.org packlist...not modified > 1: Bio-ASN1-EntrezGene v1.09 > 2: Bundle-BioPerl-Core v1.5.2_100 > 3: Bundle-BioPerl-Db v1.5.2_100 > 4: Bundle-BioPerl-Network v1.5.2_100 > 5: Bundle-BioPerl-Run v1.5.2_100 > 6: Class-AutoClass v1.01 > 7: GD-SVG v0.25 > 8: Graph v0.80 > 9: SVG-Graph v0.01 > 10: bioperl v1.5.2_100 > 11: bioperl-db v1.5.2_100 > 12: bioperl-network v1.5.2_100 > 13: bioperl-run v1.5.2_100 > > I'll add ARCHITECTURE versioning tags back when we know it's working > (maybe tomorrow, when I can get on to WinXP to test it). > > chris > > On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: > > > Hi Scott, Bioperl folk, > > > > I'm afraid that the ActiveState ppm install of BioPerl no longer > > works. > > Using the current ActiveState (perl version 5.10), I added the Bribes, > > Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates > > repositories. However, when I synched up, all but the Bribes reps > > showed up > > empty in the ppm tool. > > > > In addition, there's nothing in the release candidate rep any > > longer. I used > > to use this to get at Bioperl 1.5. > > > > Perhaps the architecture needs to be changed? > > > > Lincoln > > > > > > > > -- > > Lincoln D. Stein > > Cold Spring Harbor Laboratory > > 1 Bungtown Road > > Cold Spring Harbor, NY 11724 > > (516) 367-8380 (voice) > > (516) 367-8389 (fax) > > FOR URGENT MESSAGES & SCHEDULING, > > PLEASE CONTACT MY ASSISTANT, > > SANDRA MICHELSEN, AT michelse at cshl.edu > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From cjfields at uiuc.edu Wed Feb 6 10:55:00 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 6 Feb 2008 09:55:00 -0600 Subject: [Bioperl-l] BOSC 2008? Message-ID: <1182EAB9-7A75-498F-B91B-C14771DFD607@uiuc.edu> Anyone have information on the where/when for BOSC 2008? chris From n.haigh at sheffield.ac.uk Wed Feb 6 11:36:19 2008 From: n.haigh at sheffield.ac.uk (Nathan S Haigh) Date: Wed, 06 Feb 2008 16:36:19 +0000 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <6dce9a0b0802060703j231704acta813715265f1fab5@mail.gmail.com> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> <6dce9a0b0802060703j231704acta813715265f1fab5@mail.gmail.com> Message-ID: <47A9E203.3080008@sheffield.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Last time I was playing with Windows PPM packages, I seem to remember having to build some packages for inclusion in the BioPerl repo so that all dependencies were satisfied. Unfortunately, I don't have time to do this myself, but it's a work around if someone has time to do it? Alternatively, contact one of the other repo's and see if they can do something about it as it will/should be available for at least an older version of ActivePerl. Sorry I can't be more help. Nath Lincoln Stein wrote: > Sadly, bioperl still won't install under ActiveState 5.10 because it can't > find a repository with the SOAP::Lite prerequisite. > > Lincoln > > On Feb 5, 2008 10:06 PM, Chris Fields wrote: > >> According to this page you can remove the tags and it >> will assume the files are for any OS: >> >> >> http://aspn.activestate.com/ASPN/docs/ActivePerl/5.10/lib/ActivePerl/PPM/PPD.html#ppd_xml_format >> >> I have moved the old package.xml to package.bak and replaced it with >> one w/o those tags; I can now pick it up on Mac OS X using ActiveState >> perl 5.10: >> >> ppm> search * >> Downloading bioperl.org packlist...not modified >> 1: Bio-ASN1-EntrezGene v1.09 >> 2: Bundle-BioPerl-Core v1.5.2_100 >> 3: Bundle-BioPerl-Db v1.5.2_100 >> 4: Bundle-BioPerl-Network v1.5.2_100 >> 5: Bundle-BioPerl-Run v1.5.2_100 >> 6: Class-AutoClass v1.01 >> 7: GD-SVG v0.25 >> 8: Graph v0.80 >> 9: SVG-Graph v0.01 >> 10: bioperl v1.5.2_100 >> 11: bioperl-db v1.5.2_100 >> 12: bioperl-network v1.5.2_100 >> 13: bioperl-run v1.5.2_100 >> >> I'll add ARCHITECTURE versioning tags back when we know it's working >> (maybe tomorrow, when I can get on to WinXP to test it). >> >> chris >> >> On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: >> >>> Hi Scott, Bioperl folk, >>> >>> I'm afraid that the ActiveState ppm install of BioPerl no longer >>> works. >>> Using the current ActiveState (perl version 5.10), I added the Bribes, >>> Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates >>> repositories. However, when I synched up, all but the Bribes reps >>> showed up >>> empty in the ppm tool. >>> >>> In addition, there's nothing in the release candidate rep any >>> longer. I used >>> to use this to get at Bioperl 1.5. >>> >>> Perhaps the architecture needs to be changed? >>> >>> Lincoln >>> >>> >>> >>> -- >>> Lincoln D. Stein >>> Cold Spring Harbor Laboratory >>> 1 Bungtown Road >>> Cold Spring Harbor, NY 11724 >>> (516) 367-8380 (voice) >>> (516) 367-8389 (fax) >>> FOR URGENT MESSAGES & SCHEDULING, >>> PLEASE CONTACT MY ASSISTANT, >>> SANDRA MICHELSEN, AT michelse at cshl.edu >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> >> > > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHqeID9gTv6QYzVL4RAsyqAJ0XkCJgdKu6SHzci4XGww4OofRBzgCfQqCL MxylCxJflKjtscupJ5cRHKk= =Brpe -----END PGP SIGNATURE----- From cjfields at uiuc.edu Wed Feb 6 12:09:40 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 6 Feb 2008 11:09:40 -0600 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <47A9E203.3080008@sheffield.ac.uk> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> <6dce9a0b0802060703j231704acta813715265f1fab5@mail.gmail.com> <47A9E203.3080008@sheffield.ac.uk> Message-ID: <0E379930-B25F-42F5-8706-B39C64D6D2EB@uiuc.edu> SOAP::Lite is pretty complicated; I'm not sure if it is pure perl either (which makes it problematic for WinXP). I'll do some checking around to see if there is a perl 5.10 build for Windows. I'm toying around with the idea of setting up a nightly PPM archives of the bioperl distributions in their own directory, along with nightly tar balls. Just need to get time to work on it! chris On Feb 6, 2008, at 10:36 AM, Nathan S Haigh wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Last time I was playing with Windows PPM packages, I seem to > remember having to build some packages for inclusion in the BioPerl > repo so that all > dependencies were satisfied. Unfortunately, I don't have time to do > this myself, but it's a work around if someone has time to do it? > Alternatively, > contact one of the other repo's and see if they can do something > about it as it will/should be available for at least an older > version of ActivePerl. > > Sorry I can't be more help. > Nath > > > Lincoln Stein wrote: >> Sadly, bioperl still won't install under ActiveState 5.10 because >> it can't >> find a repository with the SOAP::Lite prerequisite. >> >> Lincoln >> >> On Feb 5, 2008 10:06 PM, Chris Fields wrote: >> >>> According to this page you can remove the tags and it >>> will assume the files are for any OS: >>> >>> >>> http://aspn.activestate.com/ASPN/docs/ActivePerl/5.10/lib/ActivePerl/PPM/PPD.html#ppd_xml_format >>> >>> I have moved the old package.xml to package.bak and replaced it with >>> one w/o those tags; I can now pick it up on Mac OS X using >>> ActiveState >>> perl 5.10: >>> >>> ppm> search * >>> Downloading bioperl.org packlist...not modified >>> 1: Bio-ASN1-EntrezGene v1.09 >>> 2: Bundle-BioPerl-Core v1.5.2_100 >>> 3: Bundle-BioPerl-Db v1.5.2_100 >>> 4: Bundle-BioPerl-Network v1.5.2_100 >>> 5: Bundle-BioPerl-Run v1.5.2_100 >>> 6: Class-AutoClass v1.01 >>> 7: GD-SVG v0.25 >>> 8: Graph v0.80 >>> 9: SVG-Graph v0.01 >>> 10: bioperl v1.5.2_100 >>> 11: bioperl-db v1.5.2_100 >>> 12: bioperl-network v1.5.2_100 >>> 13: bioperl-run v1.5.2_100 >>> >>> I'll add ARCHITECTURE versioning tags back when we know it's working >>> (maybe tomorrow, when I can get on to WinXP to test it). >>> >>> chris >>> >>> On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: >>> >>>> Hi Scott, Bioperl folk, >>>> >>>> I'm afraid that the ActiveState ppm install of BioPerl no longer >>>> works. >>>> Using the current ActiveState (perl version 5.10), I added the >>>> Bribes, >>>> Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates >>>> repositories. However, when I synched up, all but the Bribes reps >>>> showed up >>>> empty in the ppm tool. >>>> >>>> In addition, there's nothing in the release candidate rep any >>>> longer. I used >>>> to use this to get at Bioperl 1.5. >>>> >>>> Perhaps the architecture needs to be changed? >>>> >>>> Lincoln >>>> >>>> >>>> >>>> -- >>>> Lincoln D. Stein >>>> Cold Spring Harbor Laboratory >>>> 1 Bungtown Road >>>> Cold Spring Harbor, NY 11724 >>>> (516) 367-8380 (voice) >>>> (516) 367-8389 (fax) >>>> FOR URGENT MESSAGES & SCHEDULING, >>>> PLEASE CONTACT MY ASSISTANT, >>>> SANDRA MICHELSEN, AT michelse at cshl.edu >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> Christopher Fields >>> Postdoctoral Researcher >>> Lab of Dr. Robert Switzer >>> Dept of Biochemistry >>> University of Illinois Urbana-Champaign >>> >>> >>> >>> >> >> > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.6 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFHqeID9gTv6QYzVL4RAsyqAJ0XkCJgdKu6SHzci4XGww4OofRBzgCfQqCL > MxylCxJflKjtscupJ5cRHKk= > =Brpe > -----END PGP SIGNATURE----- Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Feb 6 12:54:16 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 6 Feb 2008 11:54:16 -0600 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <47A9E203.3080008@sheffield.ac.uk> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> <6dce9a0b0802060703j231704acta813715265f1fab5@mail.gmail.com> <47A9E203.3080008@sheffield.ac.uk> Message-ID: <48143927-C57B-4525-9025-A6FDC5A49070@uiuc.edu> Just an update: I have installed ActivePerl 5.10 on my WinXP box and added the following repos to PPM4 (in the following order, just in case it matters): Kobes: http://cpan.uwinnipeg.ca/PPMPackages/10xx/ Bribes: http://www.bribes.org/perl/ppm BioPerl: http://bioperl.org/DIST Note that the above Kobes repo is 5.10-specific. SOAP::Lite is in both Kobes and Bribes for perl 5.10. I then ran into issues with XML::SAX::ExpatXS and XML::SAX::Writer (the former is a binary-only, so likely failed with the ActiveState autobuild process; the latter should work though, so it might be worth hosting a version in BioPerl). I removed both dependencies from package.xml on the server and everything appears to install fine now using PPM4. I'll see if Randy Kobes can get an XML::SAX::ExpatXS version up. It is only required for 1.5.2; bioperl-live no longer requires it (just XML::SAX). chris On Feb 6, 2008, at 10:36 AM, Nathan S Haigh wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Last time I was playing with Windows PPM packages, I seem to > remember having to build some packages for inclusion in the BioPerl > repo so that all > dependencies were satisfied. Unfortunately, I don't have time to do > this myself, but it's a work around if someone has time to do it? > Alternatively, > contact one of the other repo's and see if they can do something > about it as it will/should be available for at least an older > version of ActivePerl. > > Sorry I can't be more help. > Nath > > > Lincoln Stein wrote: >> Sadly, bioperl still won't install under ActiveState 5.10 because >> it can't >> find a repository with the SOAP::Lite prerequisite. >> >> Lincoln >> >> On Feb 5, 2008 10:06 PM, Chris Fields wrote: >> >>> According to this page you can remove the tags and it >>> will assume the files are for any OS: >>> >>> >>> http://aspn.activestate.com/ASPN/docs/ActivePerl/5.10/lib/ActivePerl/PPM/PPD.html#ppd_xml_format >>> >>> I have moved the old package.xml to package.bak and replaced it with >>> one w/o those tags; I can now pick it up on Mac OS X using >>> ActiveState >>> perl 5.10: >>> >>> ppm> search * >>> Downloading bioperl.org packlist...not modified >>> 1: Bio-ASN1-EntrezGene v1.09 >>> 2: Bundle-BioPerl-Core v1.5.2_100 >>> 3: Bundle-BioPerl-Db v1.5.2_100 >>> 4: Bundle-BioPerl-Network v1.5.2_100 >>> 5: Bundle-BioPerl-Run v1.5.2_100 >>> 6: Class-AutoClass v1.01 >>> 7: GD-SVG v0.25 >>> 8: Graph v0.80 >>> 9: SVG-Graph v0.01 >>> 10: bioperl v1.5.2_100 >>> 11: bioperl-db v1.5.2_100 >>> 12: bioperl-network v1.5.2_100 >>> 13: bioperl-run v1.5.2_100 >>> >>> I'll add ARCHITECTURE versioning tags back when we know it's working >>> (maybe tomorrow, when I can get on to WinXP to test it). >>> >>> chris >>> >>> On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: >>> >>>> Hi Scott, Bioperl folk, >>>> >>>> I'm afraid that the ActiveState ppm install of BioPerl no longer >>>> works. >>>> Using the current ActiveState (perl version 5.10), I added the >>>> Bribes, >>>> Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates >>>> repositories. However, when I synched up, all but the Bribes reps >>>> showed up >>>> empty in the ppm tool. >>>> >>>> In addition, there's nothing in the release candidate rep any >>>> longer. I used >>>> to use this to get at Bioperl 1.5. >>>> >>>> Perhaps the architecture needs to be changed? >>>> >>>> Lincoln >>>> >>>> >>>> >>>> -- >>>> Lincoln D. Stein >>>> Cold Spring Harbor Laboratory >>>> 1 Bungtown Road >>>> Cold Spring Harbor, NY 11724 >>>> (516) 367-8380 (voice) >>>> (516) 367-8389 (fax) >>>> FOR URGENT MESSAGES & SCHEDULING, >>>> PLEASE CONTACT MY ASSISTANT, >>>> SANDRA MICHELSEN, AT michelse at cshl.edu >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> Christopher Fields >>> Postdoctoral Researcher >>> Lab of Dr. Robert Switzer >>> Dept of Biochemistry >>> University of Illinois Urbana-Champaign >>> >>> >>> >>> >> >> > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.6 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFHqeID9gTv6QYzVL4RAsyqAJ0XkCJgdKu6SHzci4XGww4OofRBzgCfQqCL > MxylCxJflKjtscupJ5cRHKk= > =Brpe > -----END PGP SIGNATURE----- > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From sjmiller at email.arizona.edu Wed Feb 6 15:57:35 2008 From: sjmiller at email.arizona.edu (Susan J. Miller) Date: Wed, 06 Feb 2008 13:57:35 -0700 Subject: [Bioperl-l] SeqHound In-Reply-To: References: <47A8C5C0.7040401@email.arizona.edu> <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> <47A8E3BF.7000308@email.arizona.edu> Message-ID: <47AA1F3F.9000404@email.arizona.edu> Barry Moore wrote: > Susan, > > I'm joining this discussion late so my apologies if I'm missing the > original point. If you're trying to routinely download thousands of > sequences from GenBank or SeqHound you probably want to be using ftp to > download the flat files and query/parse locally. If you're trying to > stay on top of the latest Drosophila ESTs, then how about setting up a > nightly cron job to download the incremental updates from NCBIs ftp > (ftp://ftp.ncbi.nih.gov/genbank/daily-nc) and parse that for Drosophila > EST sequences. The EST division is huge, but I would think nightly > incrementals should be manageable. Hi Barry, I'll try your suggestion. I guess my interpretation of the documentation for SeqHound was erroneous. (Who knows what 'large numbers of sequences' means?) I tried using SeqHound's get_Stream_by_id method to fetch 10000 sequences, 500 at a time, and got a timeout error. -- Regards, -susan Susan J. Miller Manager, Scientific Data Analysis Biotechnology Computing Facility Arizona Research Laboratories (520) 626-2597 From David.Messina at sbc.su.se Wed Feb 6 16:17:46 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 6 Feb 2008 22:17:46 +0100 Subject: [Bioperl-l] BOSC 2008? In-Reply-To: <1182EAB9-7A75-498F-B91B-C14771DFD607@uiuc.edu> References: <1182EAB9-7A75-498F-B91B-C14771DFD607@uiuc.edu> Message-ID: <628aabb70802061317n2f0d1103w9367346166bf8c3f@mail.gmail.com> Hey Chris, Isn't it usually in conjunction with ISMB (which is Toronto 7/19-23 this year)? From cjfields at uiuc.edu Wed Feb 6 16:22:20 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 6 Feb 2008 15:22:20 -0600 Subject: [Bioperl-l] BOSC 2008? In-Reply-To: <628aabb70802061317n2f0d1103w9367346166bf8c3f@mail.gmail.com> References: <1182EAB9-7A75-498F-B91B-C14771DFD607@uiuc.edu> <628aabb70802061317n2f0d1103w9367346166bf8c3f@mail.gmail.com> Message-ID: <9C6A22B1-9E84-4F17-8459-CBBDCB2110D4@uiuc.edu> Yep. I found this out earlier from Darin London. Just trying to plan for it ahead of time! chris On Feb 6, 2008, at 3:17 PM, Dave Messina wrote: > Hey Chris, > > Isn't it usually in conjunction with ISMB (which is Toronto 7/19-23 > this year)? > > Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Feb 6 16:48:45 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 6 Feb 2008 15:48:45 -0600 Subject: [Bioperl-l] SeqHound In-Reply-To: <47AA1F3F.9000404@email.arizona.edu> References: <47A8C5C0.7040401@email.arizona.edu> <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> <47A8E3BF.7000308@email.arizona.edu> <47AA1F3F.9000404@email.arizona.edu> Message-ID: <78824D84-B8B7-4A5C-BD81-7224F26D32E9@uiuc.edu> On Feb 6, 2008, at 2:57 PM, Susan J. Miller wrote: > Barry Moore wrote: >> Susan, >> I'm joining this discussion late so my apologies if I'm missing the >> original point. If you're trying to routinely download thousands >> of sequences from GenBank or SeqHound you probably want to be using >> ftp to download the flat files and query/parse locally. If you're >> trying to stay on top of the latest Drosophila ESTs, then how about >> setting up a nightly cron job to download the incremental updates >> from NCBIs ftp (ftp://ftp.ncbi.nih.gov/genbank/daily-nc) and parse >> that for Drosophila EST sequences. The EST division is huge, but I >> would think nightly incrementals should be manageable. > > > Hi Barry, > > I'll try your suggestion. I guess my interpretation of the > documentation for SeqHound was erroneous. (Who knows what 'large > numbers of sequences' means?) I tried using SeqHound's > get_Stream_by_id method to fetch 10000 sequences, 500 at a time, and > got a timeout error. > > > -- > Regards, > -susan Barry's and Brian's suggestions make more sense. You could also possibly automate a Entrez query to limit retrievals to a period of time instead of munging through the last releases; it all depends on how many sequences you need to parse through. The SeqHound timeout may be set up on their end to prevent a single server from spamming them with tons of requests. NCBI is a bit more tolerant but can be brittle with busy server traffic. chris From barry.moore at genetics.utah.edu Wed Feb 6 16:50:53 2008 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Wed, 6 Feb 2008 14:50:53 -0700 Subject: [Bioperl-l] Fwd: SeqHound References: <6CA6C310-E23C-47ED-9206-7F914BCA689E@genetics.utah.edu> Message-ID: <7167DD26-92F7-4D44-B111-E6CAA30BFB1E@genetics.utah.edu> Susan- Yeah, I used them several years ago, and it seemed like quite a good project at the time. I see that it has recently moved to a new location with a start up company, and I couldn't make heads or tails of their new sight. I wonder if the SeqHound side of their work hasn't suffered - perhaps only temporarily - from their recent move from academia to the brave new world of .com start-up. B On Feb 6, 2008, at 1:57 PM, Susan J. Miller wrote: > Barry Moore wrote: >> Susan, >> >> I'm joining this discussion late so my apologies if I'm missing the >> original point. If you're trying to routinely download thousands of >> sequences from GenBank or SeqHound you probably want to be using >> ftp to >> download the flat files and query/parse locally. If you're trying to >> stay on top of the latest Drosophila ESTs, then how about setting >> up a >> nightly cron job to download the incremental updates from NCBIs ftp >> (ftp://ftp.ncbi.nih.gov/genbank/daily-nc) and parse that for >> Drosophila >> EST sequences. The EST division is huge, but I would think nightly >> incrementals should be manageable. > > > Hi Barry, > > I'll try your suggestion. I guess my interpretation of the > documentation for SeqHound was erroneous. (Who knows what 'large > numbers of sequences' means?) I tried using SeqHound's > get_Stream_by_id > method to fetch 10000 sequences, 500 at a time, and got a timeout > error. > > > -- > Regards, > -susan > > Susan J. Miller > Manager, Scientific Data Analysis > Biotechnology Computing Facility > Arizona Research Laboratories > (520) 626-2597 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From oliverpelz at googlemail.com Thu Feb 7 12:24:38 2008 From: oliverpelz at googlemail.com (Oliver Pelz) Date: Thu, 7 Feb 2008 18:24:38 +0100 Subject: [Bioperl-l] Found dead links in PDoc and a little improvement Message-ID: Hello everybody, I am a beginner in bioperl and currently working heavily with the PDoc's. In this doc here: http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Variation/IO/flat.html the two links to the EBI in the description field are dead. I have looked to find other information but there is nothing available about this pseudo embl format. Has someone the old descriptions and can edit/paste them in this documentation. Another thing would help beginners. At the Bio::SeqIO documentation there are those examples for world fastest ... converter. It would be cool to add a $out->close() to those examples because I was very frustrated in the beginning when the outfiles were empty after the script had finished. Thanks for reading Oliver From bosborne11 at verizon.net Thu Feb 7 13:41:48 2008 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 07 Feb 2008 13:41:48 -0500 Subject: [Bioperl-l] Found dead links in PDoc and a little improvement In-Reply-To: References: Message-ID: Oliver, Removed those dead links, thank you for that. The reason there's no close() in most code examples is that Perl programmers don't usually use this function. The filehandle is closed automatically when open() is called again or when the Perl script finishes. Brian O. On Feb 7, 2008, at 12:24 PM, Oliver Pelz wrote: > Hello everybody, > I am a beginner in bioperl and currently working heavily with the > PDoc's. > > In this doc here: > http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Variation/IO/flat.html > > the two links to the EBI in the description field are dead. I have > looked to > find other information > but there is nothing available about this pseudo embl format. > Has someone the old descriptions and can edit/paste them in this > documentation. > > Another thing would help beginners. > At the Bio::SeqIO documentation there are those examples for world > fastest > ... converter. > It would be cool to add a $out->close() to those examples because I > was very > frustrated in the > beginning when the outfiles were empty after the script had finished. > > Thanks for reading > > Oliver > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From golharam at umdnj.edu Thu Feb 7 16:24:16 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 07 Feb 2008 16:24:16 -0500 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser Message-ID: <47AB7700.8030801@umdnj.edu> Is there a SeqIO parser module for GenBank ASN.1 format? I thought it would have been genbank or entrezgene, but neither of them work. From cjfields at uiuc.edu Thu Feb 7 16:48:25 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 7 Feb 2008 15:48:25 -0600 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <47AB7700.8030801@umdnj.edu> References: <47AB7700.8030801@umdnj.edu> Message-ID: No. The only ASN.1 parser is entrezgene. You could probably try building one using the same ASN.1 parser that SeqIO::entrezgene uses (Bio::ASN1::EntrezGene); it includes a parser for sequences: http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm chris On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: > Is there a SeqIO parser module for GenBank ASN.1 format? I thought > it would have been genbank or entrezgene, but neither of them work. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jason at bioperl.org Thu Feb 7 17:46:41 2008 From: jason at bioperl.org (Jason Stajich) Date: Thu, 7 Feb 2008 14:46:41 -0800 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: References: <47AB7700.8030801@umdnj.edu> Message-ID: <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> ugh - why parse ASN.1? NCBI provides converter application in the ncbi toolkit to many formats : genbank, XML, etc. On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: > No. The only ASN.1 parser is entrezgene. You could probably try > building one using the same ASN.1 parser that SeqIO::entrezgene > uses (Bio::ASN1::EntrezGene); it includes a parser for sequences: > > http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ > ASN1/Sequence.pm > > chris > > On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: > >> Is there a SeqIO parser module for GenBank ASN.1 format? I >> thought it would have been genbank or entrezgene, but neither of >> them work. >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From golharam at umdnj.edu Thu Feb 7 18:00:33 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 07 Feb 2008 18:00:33 -0500 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> Message-ID: <47AB8D91.9080201@umdnj.edu> That I can use from Perl? Such as???? I need to retrieve Gene Ontology information (classification and GO id) from the Entrez Gene record. I thought it would be easiest using BioPerl to do this. BioPerl only has an ASN.1 parser, entrezgene. When I use this to load the Gene record, I'm using: my $io = Bio::SeqIO->new(-file => ' "entrezgene" ); my $seq_obj = $io->next_seq; Something is not working with the second line. I get an error: "Use of uninitialized value in string eq at /home/golharam/bioperl/bioperl-1.5.1//Bio/SeqIO/entrezgene.pm line 244" It sort of makes sense because, well, the Entrez Gene record doesn't have a sequence...it has information about a gene. I figure I must be doing something wrong but I haven't seen anything in BioPerl about parsing entrez gene records any other way. Ryan Jason Stajich wrote: > ugh - why parse ASN.1? NCBI provides converter application in the ncbi > toolkit to many formats : genbank, XML, etc. > On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: > >> No. The only ASN.1 parser is entrezgene. You could probably try >> building one using the same ASN.1 parser that SeqIO::entrezgene uses >> (Bio::ASN1::EntrezGene); it includes a parser for sequences: >> >> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm >> >> >> chris >> >> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >> >>> Is there a SeqIO parser module for GenBank ASN.1 format? I thought >>> it would have been genbank or entrezgene, but neither of them work. >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > From luciap at sas.upenn.edu Thu Feb 7 17:37:46 2008 From: luciap at sas.upenn.edu (Lucia Peixoto) Date: Thu, 07 Feb 2008 17:37:46 -0500 Subject: [Bioperl-l] How to add branch labels for PAML codeml branch models Message-ID: <1202423866.47ab883ab02a3@webmail.sas.upenn.edu> Just a small question in order to label the branches to use model 2 of PAML branch models can I use add_tag_value of Bio::Tree Node? or there's some other way to do it with bioperl? thanks Lucia Peixoto Department of Biology,SAS University of Pennsylvania From cjfields at uiuc.edu Thu Feb 7 18:39:11 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 7 Feb 2008 17:39:11 -0600 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <47AB8E92.4000307@umdnj.edu> References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8E92.4000307@umdnj.edu> Message-ID: Bio::SeqIO::entrezgene should do this. Any dbxrefs (including GO IDs) should be stored in the annotation collection, but I'm not sure how it is parsed; you'll have to test it out. I agree with Jason; ASN.1 isn't a very friendly format. Don't know why NCBI sticks with it, but I'm sure they have their reasons (I think this may have been discussed before on the list). chris On Feb 7, 2008, at 5:04 PM, Ryan Golhar wrote: > Let me re-phrase then - I want to parse an entry such as this: > > http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 > > to retrieve the text of the Gene Ontology entries and the associated > GO IDs for those entries. Is this possible with BioPerl? If so, > how can I do this with BioPerl? > > Ryan > > > > Jason Stajich wrote: >> ugh - why parse ASN.1? NCBI provides converter application in the >> ncbi toolkit to many formats : genbank, XML, etc. >> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: >>> No. The only ASN.1 parser is entrezgene. You could probably try >>> building one using the same ASN.1 parser that SeqIO::entrezgene >>> uses (Bio::ASN1::EntrezGene); it includes a parser for sequences: >>> >>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm >>> >>> chris >>> >>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >>> >>>> Is there a SeqIO parser module for GenBank ASN.1 format? I >>>> thought it would have been genbank or entrezgene, but neither of >>>> them work. >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> Christopher Fields >>> Postdoctoral Researcher >>> Lab of Dr. Robert Switzer >>> Dept of Biochemistry >>> University of Illinois Urbana-Champaign >>> >>> >>> >>> _______________________________________________ >>> 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 > Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From golharam at umdnj.edu Thu Feb 7 18:04:50 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 07 Feb 2008 18:04:50 -0500 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> Message-ID: <47AB8E92.4000307@umdnj.edu> Let me re-phrase then - I want to parse an entry such as this: http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 to retrieve the text of the Gene Ontology entries and the associated GO IDs for those entries. Is this possible with BioPerl? If so, how can I do this with BioPerl? Ryan Jason Stajich wrote: > ugh - why parse ASN.1? NCBI provides converter application in the ncbi > toolkit to many formats : genbank, XML, etc. > On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: > >> No. The only ASN.1 parser is entrezgene. You could probably try >> building one using the same ASN.1 parser that SeqIO::entrezgene uses >> (Bio::ASN1::EntrezGene); it includes a parser for sequences: >> >> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm >> >> >> chris >> >> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >> >>> Is there a SeqIO parser module for GenBank ASN.1 format? I thought >>> it would have been genbank or entrezgene, but neither of them work. >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> >> _______________________________________________ >> 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 golharam at umdnj.edu Thu Feb 7 18:09:06 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 07 Feb 2008 18:09:06 -0500 Subject: [Bioperl-l] BioPipe links don't work Message-ID: <47AB8F92.2030006@umdnj.edu> The links to BioPipe on the HOWTO page do not work. They all lead to http://www.sedoparking.com/biopipe.org From barry.moore at genetics.utah.edu Thu Feb 7 19:31:53 2008 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Thu, 7 Feb 2008 17:31:53 -0700 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <47AB8E92.4000307@umdnj.edu> References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8E92.4000307@umdnj.edu> Message-ID: Ryan, I you have a list of NCBI Gene IDs then you can grab the flatfile gene2go from NCBIs ftp site ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2go.gz. That will give you tax_id, gene_id, go_id, evidence code, qualifier, category etc. From there you can get the description from the GO OBO file http://www.geneontology.org/ontology/ gene_ontology_edit.obo. If all you need is the description then the file is pretty easy to parse on the fly, but if you need to traverse the graphs or if you want an already written parser then add go-perl http://search.cpan.org/~cmungall/go-perl/go-perl.pod Barry On Feb 7, 2008, at 4:04 PM, Ryan Golhar wrote: > Let me re-phrase then - I want to parse an entry such as this: > > http://www.ncbi.nlm.nih.gov/sites/entrez? > db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 > > to retrieve the text of the Gene Ontology entries and the > associated GO > IDs for those entries. Is this possible with BioPerl? If so, how > can I > do this with BioPerl? > > Ryan > > > > Jason Stajich wrote: >> ugh - why parse ASN.1? NCBI provides converter application in the >> ncbi >> toolkit to many formats : genbank, XML, etc. >> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: >> >>> No. The only ASN.1 parser is entrezgene. You could probably try >>> building one using the same ASN.1 parser that SeqIO::entrezgene uses >>> (Bio::ASN1::EntrezGene); it includes a parser for sequences: >>> >>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/ >>> Bio/ASN1/Sequence.pm >>> >>> >>> chris >>> >>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >>> >>>> Is there a SeqIO parser module for GenBank ASN.1 format? I thought >>>> it would have been genbank or entrezgene, but neither of them work. >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> Christopher Fields >>> Postdoctoral Researcher >>> Lab of Dr. Robert Switzer >>> Dept of Biochemistry >>> University of Illinois Urbana-Champaign >>> >>> >>> >>> _______________________________________________ >>> 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 golharam at umdnj.edu Thu Feb 7 19:46:21 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 07 Feb 2008 19:46:21 -0500 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8E92.4000307@umdnj.edu> Message-ID: <47ABA65D.1000705@umdnj.edu> Thank Barry. I did try using go-perl but it is slow when processing queries. I didn't know about ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz. I think that is exactly what I'm looking for. Ryan Barry Moore wrote: > Ryan, > > I you have a list of NCBI Gene IDs then you can grab the flatfile > gene2go from NCBIs ftp site > ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz. That will give you > tax_id, gene_id, go_id, evidence code, qualifier, category etc. From > there you can get the description from the GO OBO file > http://www.geneontology.org/ontology/gene_ontology_edit.obo. If all you > need is the description then the file is pretty easy to parse on the > fly, but if you need to traverse the graphs or if you want an already > written parser then add go-perl > http://search.cpan.org/~cmungall/go-perl/go-perl.pod > > Barry > > > > On Feb 7, 2008, at 4:04 PM, Ryan Golhar wrote: > >> Let me re-phrase then - I want to parse an entry such as this: >> >> http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 >> >> >> to retrieve the text of the Gene Ontology entries and the associated GO >> IDs for those entries. Is this possible with BioPerl? If so, how can I >> do this with BioPerl? >> >> Ryan >> >> >> >> Jason Stajich wrote: >>> ugh - why parse ASN.1? NCBI provides converter application in the ncbi >>> toolkit to many formats : genbank, XML, etc. >>> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: >>> >>>> No. The only ASN.1 parser is entrezgene. You could probably try >>>> building one using the same ASN.1 parser that SeqIO::entrezgene uses >>>> (Bio::ASN1::EntrezGene); it includes a parser for sequences: >>>> >>>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm >>>> >>>> >>>> >>>> chris >>>> >>>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >>>> >>>>> Is there a SeqIO parser module for GenBank ASN.1 format? I thought >>>>> it would have been genbank or entrezgene, but neither of them work. >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> Christopher Fields >>>> Postdoctoral Researcher >>>> Lab of Dr. Robert Switzer >>>> Dept of Biochemistry >>>> University of Illinois Urbana-Champaign >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 golharam at umdnj.edu Thu Feb 7 18:59:52 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 07 Feb 2008 18:59:52 -0500 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8E92.4000307@umdnj.edu> Message-ID: <47AB9B78.5090907@umdnj.edu> That's what I thought too. However, I'm getting errors with a parser. I found Bio::ASN1::EntrezGene online and am using that module outside of Bioperl as it works well for what I'm doing. I've already changed my code and don't want to deal with tracking down the errors I had with BioPerl (I've already spend enough time on this) but they were easy enough to reproduce. Ryan Chris Fields wrote: > Bio::SeqIO::entrezgene should do this. Any dbxrefs (including GO IDs) > should be stored in the annotation collection, but I'm not sure how it > is parsed; you'll have to test it out. > > I agree with Jason; ASN.1 isn't a very friendly format. Don't know why > NCBI sticks with it, but I'm sure they have their reasons (I think this > may have been discussed before on the list). > > chris > > On Feb 7, 2008, at 5:04 PM, Ryan Golhar wrote: > >> Let me re-phrase then - I want to parse an entry such as this: >> >> http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 >> >> >> to retrieve the text of the Gene Ontology entries and the associated >> GO IDs for those entries. Is this possible with BioPerl? If so, how >> can I do this with BioPerl? >> >> Ryan >> >> >> >> Jason Stajich wrote: >>> ugh - why parse ASN.1? NCBI provides converter application in the >>> ncbi toolkit to many formats : genbank, XML, etc. >>> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: >>>> No. The only ASN.1 parser is entrezgene. You could probably try >>>> building one using the same ASN.1 parser that SeqIO::entrezgene uses >>>> (Bio::ASN1::EntrezGene); it includes a parser for sequences: >>>> >>>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm >>>> >>>> >>>> chris >>>> >>>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >>>> >>>>> Is there a SeqIO parser module for GenBank ASN.1 format? I thought >>>>> it would have been genbank or entrezgene, but neither of them work. >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> Christopher Fields >>>> Postdoctoral Researcher >>>> Lab of Dr. Robert Switzer >>>> Dept of Biochemistry >>>> University of Illinois Urbana-Champaign >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >> > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > > From cjfields at uiuc.edu Thu Feb 7 20:32:18 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 7 Feb 2008 19:32:18 -0600 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <47AB9B78.5090907@umdnj.edu> References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8E92.4000307@umdnj.edu> <47AB9B78.5090907@umdnj.edu> Message-ID: <1001C6BB-24D5-4BB8-B135-0E9D2952B49A@uiuc.edu> It's possible that has been fixed in bioperl-live. However, just in case, if you are getting errors could you file a bug report along with the relevant code demonstrating it? chris On Feb 7, 2008, at 5:59 PM, Ryan Golhar wrote: > That's what I thought too. However, I'm getting errors with a parser. > > I found Bio::ASN1::EntrezGene online and am using that module > outside of Bioperl as it works well for what I'm doing. > > I've already changed my code and don't want to deal with tracking > down the errors I had with BioPerl (I've already spend enough time > on this) but they were easy enough to reproduce. > > Ryan > > > Chris Fields wrote: >> Bio::SeqIO::entrezgene should do this. Any dbxrefs (including GO >> IDs) should be stored in the annotation collection, but I'm not >> sure how it is parsed; you'll have to test it out. >> I agree with Jason; ASN.1 isn't a very friendly format. Don't know >> why NCBI sticks with it, but I'm sure they have their reasons (I >> think this may have been discussed before on the list). >> chris >> On Feb 7, 2008, at 5:04 PM, Ryan Golhar wrote: >>> Let me re-phrase then - I want to parse an entry such as this: >>> >>> http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 >>> >>> to retrieve the text of the Gene Ontology entries and the >>> associated GO IDs for those entries. Is this possible with >>> BioPerl? If so, how can I do this with BioPerl? >>> >>> Ryan >>> >>> >>> >>> Jason Stajich wrote: >>>> ugh - why parse ASN.1? NCBI provides converter application in the >>>> ncbi toolkit to many formats : genbank, XML, etc. >>>> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: >>>>> No. The only ASN.1 parser is entrezgene. You could probably >>>>> try building one using the same ASN.1 parser that >>>>> SeqIO::entrezgene uses (Bio::ASN1::EntrezGene); it includes a >>>>> parser for sequences: >>>>> >>>>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm >>>>> >>>>> chris >>>>> >>>>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >>>>> >>>>>> Is there a SeqIO parser module for GenBank ASN.1 format? I >>>>>> thought it would have been genbank or entrezgene, but neither >>>>>> of them work. >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> Christopher Fields >>>>> Postdoctoral Researcher >>>>> Lab of Dr. Robert Switzer >>>>> Dept of Biochemistry >>>>> University of Illinois Urbana-Champaign >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jason at bioperl.org Thu Feb 7 20:52:39 2008 From: jason at bioperl.org (Jason Stajich) Date: Thu, 7 Feb 2008 17:52:39 -0800 Subject: [Bioperl-l] How to add branch labels for PAML codeml branch models In-Reply-To: <1202423866.47ab883ab02a3@webmail.sas.upenn.edu> References: <1202423866.47ab883ab02a3@webmail.sas.upenn.edu> Message-ID: It will work if you just change the node's ID to be something like: 'ID #1' (for tips) and for the internal nodes just set the id to ("#1"), etc... I added some code to demonstrate this one the wiki: http://bioperl.org/wiki/HOWTO:PAML#Setting_up_Branch-specific_labels The format is nonstandard so you have to hack the output some to get what you want, hence the extra part that requires you strip out the " since they are required for escaping space characters. -jason On Feb 7, 2008, at 2:37 PM, Lucia Peixoto wrote: > Just a small question > in order to label the branches to use model 2 of PAML branch models > can I use add_tag_value of Bio::Tree Node? > or there's some other way to do it with bioperl? > > thanks > > Lucia Peixoto > Department of Biology,SAS > University of Pennsylvania > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjm at fruitfly.org Thu Feb 7 21:14:20 2008 From: cjm at fruitfly.org (Chris Mungall) Date: Thu, 7 Feb 2008 18:14:20 -0800 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8E92.4000307@umdnj.edu> Message-ID: Just to add to Barry's suggestions: You can query the database directly: http://www.berkeleybop.org/goose You can also use the go-db-perl API and point it at the mysql port of one of the mirrors; see http://www.geneontology.org/GO.database.shtml On Feb 7, 2008, at 4:31 PM, Barry Moore wrote: > Ryan, > > I you have a list of NCBI Gene IDs then you can grab the flatfile > gene2go from NCBIs ftp site ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ > gene2go.gz. That will give you tax_id, gene_id, go_id, evidence > code, qualifier, category etc. From there you can get the > description from the GO OBO file http://www.geneontology.org/ > ontology/gene_ontology_edit.obo. If all you need is the > description then the file is pretty easy to parse on the fly, but > if you need to traverse the graphs or if you want an already > written parser then add go-perl http://search.cpan.org/~cmungall/go- > perl/go-perl.pod > > Barry > > > > On Feb 7, 2008, at 4:04 PM, Ryan Golhar wrote: > >> Let me re-phrase then - I want to parse an entry such as this: >> >> http://www.ncbi.nlm.nih.gov/sites/entrez? >> db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 >> >> to retrieve the text of the Gene Ontology entries and the >> associated GO >> IDs for those entries. Is this possible with BioPerl? If so, how >> can I >> do this with BioPerl? >> >> Ryan >> >> >> >> Jason Stajich wrote: >>> ugh - why parse ASN.1? NCBI provides converter application in the >>> ncbi >>> toolkit to many formats : genbank, XML, etc. >>> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: >>> >>>> No. The only ASN.1 parser is entrezgene. You could probably try >>>> building one using the same ASN.1 parser that SeqIO::entrezgene >>>> uses >>>> (Bio::ASN1::EntrezGene); it includes a parser for sequences: >>>> >>>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/ >>>> Bio/ASN1/Sequence.pm >>>> >>>> >>>> chris >>>> >>>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >>>> >>>>> Is there a SeqIO parser module for GenBank ASN.1 format? I >>>>> thought >>>>> it would have been genbank or entrezgene, but neither of them >>>>> work. >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> Christopher Fields >>>> Postdoctoral Researcher >>>> Lab of Dr. Robert Switzer >>>> Dept of Biochemistry >>>> University of Illinois Urbana-Champaign >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 hlapp at gmx.net Thu Feb 7 21:45:48 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 7 Feb 2008 21:45:48 -0500 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <47AB8D91.9080201@umdnj.edu> References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8D91.9080201@umdnj.edu> Message-ID: On Feb 7, 2008, at 6:00 PM, Ryan Golhar wrote: > Something is not working with the second line. I get an error: > > "Use of uninitialized value in string eq at > /home/golharam/bioperl/bioperl-1.5.1//Bio/SeqIO/ > entrezgene.pm line 244" This isn't an error, is it - it's a warning, no? -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Thu Feb 7 22:24:45 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 7 Feb 2008 21:24:45 -0600 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8D91.9080201@umdnj.edu> Message-ID: I agree. I also noticed Ryan's running bioperl 1.5.1. Probably worth trying the latest code from Subversion. chris On Feb 7, 2008, at 8:45 PM, Hilmar Lapp wrote: > > On Feb 7, 2008, at 6:00 PM, Ryan Golhar wrote: > >> Something is not working with the second line. I get an error: >> >> "Use of uninitialized value in string eq at >> /home/golharam/bioperl/bioperl-1.5.1//Bio/SeqIO/ >> entrezgene.pm line 244" > > > This isn't an error, is it - it's a warning, no? > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From David.Messina at sbc.su.se Fri Feb 8 04:00:05 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Fri, 8 Feb 2008 10:00:05 +0100 Subject: [Bioperl-l] BioPipe links don't work In-Reply-To: <47AB8F92.2030006@umdnj.edu> References: <47AB8F92.2030006@umdnj.edu> Message-ID: <628aabb70802080100g43c02f0btdc8c8065c576ff3d@mail.gmail.com> BioPipe, as far as I can tell, is dead, and indeed the HOWTO is no longer active. Therefore I've removed the BioPipe entry entirely. If anyone would prefer it stay, please let me know and I'll revert the change and update the links to point to the GMOD "BioPipe is no longer supported" page. Dave From luciap at sas.upenn.edu Fri Feb 8 10:53:36 2008 From: luciap at sas.upenn.edu (Lucia Peixoto) Date: Fri, 08 Feb 2008 10:53:36 -0500 Subject: [Bioperl-l] How to add branch labels for PAML codeml branch models In-Reply-To: References: <1202423866.47ab883ab02a3@webmail.sas.upenn.edu> Message-ID: <1202486016.47ac7b003b860@webmail.sas.upenn.edu> Hi as I have my trees right now the bootstrap support ends up as the node ID so I guess I have to assign node ID to bootstrap first and then change? Lucia Quoting Jason Stajich : > It will work if you just change the node's ID to be something like: > 'ID #1' (for tips) and for the internal nodes just set the id to > ("#1"), etc... > > I added some code to demonstrate this one the wiki: > http://bioperl.org/wiki/HOWTO:PAML#Setting_up_Branch-specific_labels > > The format is nonstandard so you have to hack the output some to get > what you want, hence the extra part that requires you strip out the " > since they are required for escaping space characters. > > -jason > On Feb 7, 2008, at 2:37 PM, Lucia Peixoto wrote: > > > Just a small question > > in order to label the branches to use model 2 of PAML branch models > > can I use add_tag_value of Bio::Tree Node? > > or there's some other way to do it with bioperl? > > > > thanks > > > > Lucia Peixoto > > Department of Biology,SAS > > University of Pennsylvania > > _______________________________________________ > > 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 > Lucia Peixoto Department of Biology,SAS University of Pennsylvania From jason at bioperl.org Fri Feb 8 13:18:59 2008 From: jason at bioperl.org (Jason Stajich) Date: Fri, 8 Feb 2008 10:18:59 -0800 Subject: [Bioperl-l] How to add branch labels for PAML codeml branch models In-Reply-To: <1202486016.47ac7b003b860@webmail.sas.upenn.edu> References: <1202423866.47ab883ab02a3@webmail.sas.upenn.edu> <1202486016.47ac7b003b860@webmail.sas.upenn.edu> Message-ID: <793E2862-7D2F-4936-93E3-960BD6D74EB3@bioperl.org> http://bioperl.org/wiki/HOWTO:Trees#Reading_and_Writing_Trees Remember that in newick format bootstrap and internal node ids are effectively the same thing - that we store in them separate slots in bioperl is that fact that other formats can separate out this data but there is no standard in newick format. In sometime cases formats do accept the node labels that look like NODEID[BOOTSTRAP] for internal nodes (and BioPerl parses those out nicely) but most programs don't recognize that. On parsing, unless you tell Bioperl that the internal IDs are bootstrap values it is going to store that data as an ID. You will want to clear the bootstraps anyways to write PAML trees anyways. -jason On Feb 8, 2008, at 7:53 AM, Lucia Peixoto wrote: > Hi > as I have my trees right now the bootstrap support ends up as the > node ID > so I guess I have to assign node ID to bootstrap first and then > change? > > > Lucia > > Quoting Jason Stajich : > >> It will work if you just change the node's ID to be something like: >> 'ID #1' (for tips) and for the internal nodes just set the id to >> ("#1"), etc... >> >> I added some code to demonstrate this one the wiki: >> http://bioperl.org/wiki/HOWTO:PAML#Setting_up_Branch- >> specific_labels >> >> The format is nonstandard so you have to hack the output some to get >> what you want, hence the extra part that requires you strip out the " >> since they are required for escaping space characters. >> >> -jason >> On Feb 7, 2008, at 2:37 PM, Lucia Peixoto wrote: >> >>> Just a small question >>> in order to label the branches to use model 2 of PAML branch models >>> can I use add_tag_value of Bio::Tree Node? >>> or there's some other way to do it with bioperl? >>> >>> thanks >>> >>> Lucia Peixoto >>> Department of Biology,SAS >>> University of Pennsylvania >>> _______________________________________________ >>> 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 >> > > > Lucia Peixoto > Department of Biology,SAS > University of Pennsylvania From golharam at umdnj.edu Fri Feb 8 21:01:45 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 08 Feb 2008 21:01:45 -0500 Subject: [Bioperl-l] error in build.pl of bioperl-live Message-ID: <47AD0989.1050904@umdnj.edu> I just obtained the latest build of bioperl from svn. When I run 'perl Build.pl', I get an error "Use of uninitialized value in concatenation (.) or string at Build.PL line 184.". Here's the output I see (The error is at the end): [golharam at hydrogen bioperl-live]$ perl Build.PL Checking prerequisites... Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] * Optional prerequisite Ace is not installed (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF:: Adaptor::ace) * Optional prerequisite Algorithm::Munkres is not installed (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) * Optional prerequisite Math::Random is not installed (wanted for Random Phylogenetic Networks, used by Bio::PhyloNetwork::RandomFactory) * Optional prerequisite GraphViz is not installed (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz) * Class::AutoClass (0.091) is installed, but we prefer to have 1 (wanted for creating objects, used by Bio::Graph::SimpleGraph, Bio::Graph::SimpleGraph::Traversal and Bio::Graph::ProteinGraph) * Optional prerequisite Array::Compare is not installed (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Checking features: Network..................enabled BioDBSeqFeature_mysql....enabled BioDBGFF.................enabled BioDBSeqFeature_BDB......enabled Do you want to run the BioDBGFF or BioDBSeqFeature_mysql live database tests? y/ n [n] n - will not run the BioDBGFF live database tests Use of uninitialized value in concatenation (.) or string at Build.PL line 184. Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] From golharam at umdnj.edu Fri Feb 8 21:08:30 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 08 Feb 2008 21:08:30 -0500 Subject: [Bioperl-l] error in build.pl of bioperl-live In-Reply-To: <47AD0989.1050904@umdnj.edu> References: <47AD0989.1050904@umdnj.edu> Message-ID: <47AD0B1E.3050200@umdnj.edu> In addition, if I continue past the error and run './Build test', I get a bunch of errors like this: BEGIN failed--compilation aborted at t/lib/BioperlTest.pm line 109. Compilation failed in require at t/Allele.t line 9. BEGIN failed--compilation aborted at t/Allele.t line 9. t/Allele.......................... Dubious, test returned 255 (wstat 65280, 0xff00) No subtests run All the tests fail. The last few lines read: Files=257, Tests=0, 19 wallclock secs ( 0.77 usr 0.51 sys + 12.18 cusr 1.75 csys = 15.21 CPU) Result: FAIL Failed 255/257 test programs. 0/0 subtests failed. Am I missing something? This can't be related to the missing prereqs as all the tests are failing. Ryan Golhar wrote: > I just obtained the latest build of bioperl from svn. When I run 'perl > Build.pl', I get an error "Use of uninitialized value in concatenation > (.) or string at Build.PL line 184.". Here's the output I see (The > error is at the end): > > [golharam at hydrogen bioperl-live]$ perl Build.PL > Checking prerequisites... > Install [a]ll optional external modules, [n]one, or choose > [i]nteractively? [n] > * Optional prerequisite Ace is not installed > (wanted for access of ACeDB database, used by Bio::DB::Ace and > Bio::DB::GFF:: > Adaptor::ace) > * Optional prerequisite Algorithm::Munkres is not installed > (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) > * Optional prerequisite Math::Random is not installed > (wanted for Random Phylogenetic Networks, used by > Bio::PhyloNetwork::RandomFactory) > * Optional prerequisite GraphViz is not installed > (wanted for Phylogenetic Network Visulization, used by > Bio::PhyloNetwork::GraphViz) > * Class::AutoClass (0.091) is installed, but we prefer to have 1 > (wanted for creating objects, used by Bio::Graph::SimpleGraph, > Bio::Graph::SimpleGraph::Traversal and Bio::Graph::ProteinGraph) > * Optional prerequisite Array::Compare is not installed > (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) > > ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the > versions > of the modules indicated above before proceeding with this installation > > Checking features: > Network..................enabled > BioDBSeqFeature_mysql....enabled > BioDBGFF.................enabled > BioDBSeqFeature_BDB......enabled > > Do you want to run the BioDBGFF or BioDBSeqFeature_mysql live database > tests? y/ > n [n] n > - will not run the BioDBGFF live database tests > > Use of uninitialized value in concatenation (.) or string at Build.PL > line 184. > Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? > [a] > From hlapp at gmx.net Fri Feb 8 22:33:55 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 8 Feb 2008 22:33:55 -0500 Subject: [Bioperl-l] error in build.pl of bioperl-live In-Reply-To: <47AD0989.1050904@umdnj.edu> References: <47AD0989.1050904@umdnj.edu> Message-ID: Hi Ryan, On Feb 8, 2008, at 9:01 PM, Ryan Golhar wrote: > I get an error "Use of uninitialized value in concatenation (.) or > string at Build.PL line 184.". do keep in mind that this kind of message is almost never an error. It's simply a warning that you wouldn't even see w/o -w. All that it means is that a scalar with an undefined value is being evaluated to a string (which results, by default, in an empty string). Is the build failing or halting at this point for you? That said, it's indeed a good to point those out, as someone either should have initialized a scalar when it wasn't, or that someone was expecting the scalar to always have a value, and so the absence of it may indicate an unexpected condition resulting from an error elsewhere. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From golharam at umdnj.edu Fri Feb 8 22:58:02 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 08 Feb 2008 22:58:02 -0500 Subject: [Bioperl-l] error in build.pl of bioperl-live In-Reply-To: References: <47AD0989.1050904@umdnj.edu> Message-ID: <47AD24CA.2050102@umdnj.edu> Hi Hilmar, The script doesn't halt, but the tests do fail. I sent another message with the errors I am seeing. I do not know if they are related to this or not. Ryan Hilmar Lapp wrote: > Hi Ryan, > > On Feb 8, 2008, at 9:01 PM, Ryan Golhar wrote: > >> I get an error "Use of uninitialized value in concatenation (.) or >> string at Build.PL line 184.". > > > do keep in mind that this kind of message is almost never an error. It's > simply a warning that you wouldn't even see w/o -w. All that it means is > that a scalar with an undefined value is being evaluated to a string > (which results, by default, in an empty string). > > Is the build failing or halting at this point for you? > > That said, it's indeed a good to point those out, as someone either > should have initialized a scalar when it wasn't, or that someone was > expecting the scalar to always have a value, and so the absence of it > may indicate an unexpected condition resulting from an error elsewhere. > > -hilmar From hlapp at gmx.net Fri Feb 8 23:07:31 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 8 Feb 2008 23:07:31 -0500 Subject: [Bioperl-l] error in build.pl of bioperl-live In-Reply-To: <47AD24CA.2050102@umdnj.edu> References: <47AD0989.1050904@umdnj.edu> <47AD24CA.2050102@umdnj.edu> Message-ID: On Feb 8, 2008, at 10:58 PM, Ryan Golhar wrote: > The script doesn't halt, but the tests do fail. I sent another > message with the errors I am seeing. I do not know if they are > related to this or not. Yep I saw that. They might be related if, for example, the issue is related to not finding BioPerl? Can you run one test in verbose mode? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Fri Feb 8 23:47:08 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 8 Feb 2008 22:47:08 -0600 Subject: [Bioperl-l] error in build.pl of bioperl-live In-Reply-To: <47AD24CA.2050102@umdnj.edu> References: <47AD0989.1050904@umdnj.edu> <47AD24CA.2050102@umdnj.edu> Message-ID: Ryan, I don't see either the 'Use of initialized' error or the massive failed test issue using Mac OS X (perl 5.8). I get a different set of warnings using perl 5.10 related to Data::Dumper but not this (and everything runs fine). It might be of help to know what perl version, OS, etc. you are using. It also might be worth upgrading Module::Build and Test::Harness as well (though the Build.PL script should catch that and warn you). chris On Feb 8, 2008, at 9:58 PM, Ryan Golhar wrote: > Hi Hilmar, > > The script doesn't halt, but the tests do fail. I sent another > message with the errors I am seeing. I do not know if they are > related to this or not. > > Ryan > > > Hilmar Lapp wrote: >> Hi Ryan, >> On Feb 8, 2008, at 9:01 PM, Ryan Golhar wrote: >>> I get an error "Use of uninitialized value in concatenation (.) or >>> string at Build.PL line 184.". >> do keep in mind that this kind of message is almost never an error. >> It's simply a warning that you wouldn't even see w/o -w. All that >> it means is that a scalar with an undefined value is being >> evaluated to a string (which results, by default, in an empty >> string). >> Is the build failing or halting at this point for you? >> That said, it's indeed a good to point those out, as someone either >> should have initialized a scalar when it wasn't, or that someone >> was expecting the scalar to always have a value, and so the absence >> of it may indicate an unexpected condition resulting from an error >> elsewhere. >> -hilmar > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Fri Feb 8 23:49:14 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 8 Feb 2008 22:49:14 -0600 Subject: [Bioperl-l] error in build.pl of bioperl-live In-Reply-To: References: <47AD0989.1050904@umdnj.edu> <47AD24CA.2050102@umdnj.edu> Message-ID: <35C30475-6CC6-470E-B40B-DF13E65FC8A3@uiuc.edu> On Feb 8, 2008, at 10:07 PM, Hilmar Lapp wrote: > > On Feb 8, 2008, at 10:58 PM, Ryan Golhar wrote: > >> The script doesn't halt, but the tests do fail. I sent another >> message with the errors I am seeing. I do not know if they are >> related to this or not. > > > Yep I saw that. They might be related if, for example, the issue is > related to not finding BioPerl? > > Can you run one test in verbose mode? > > -hilmar To add to that, 'perl -I. t/SearchIO.t' should also still work for most (but not all). chris From heikki at sanbi.ac.za Tue Feb 12 03:25:32 2008 From: heikki at sanbi.ac.za (Heikki Lehvaslaiho) Date: Tue, 12 Feb 2008 10:25:32 +0200 Subject: [Bioperl-l] BioHackathon 2008 Message-ID: <200802121025.32797.heikki@sanbi.ac.za> Hi all, BioHackathon 2008 is happening right now in Tokyo, Japan. See http://hackathon.dbcls.jp/ The focus is on web services but some direct work on Bio* projects is getting done, too. See page: http://hackathon.dbcls.jp/wiki/OpenBio* for ideas thrown in the air. I just had a look how well the most common sequence file formats survive reading from a flat file into BioPerl objects and writing back into the same format: http://hackathon.dbcls.jp/wiki/BioPerlRoundTripFirstPass -Heikki -- ______ _/ _/_____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za _/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho _/ _/ _/ SANBI, South African National Bioinformatics Institute _/ _/ _/ University of Western Cape, South Africa _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 ___ _/_/_/_/_/________________________________________________________ From lenski at mdc-berlin.de Tue Feb 12 04:54:25 2008 From: lenski at mdc-berlin.de (Ulf Lenski) Date: Tue, 12 Feb 2008 10:54:25 +0100 Subject: [Bioperl-l] fetch protein-na-complexes from pdb Message-ID: <47B16CD1.2060307@mdc-berlin.de> is there a bioperl modul for fetching protein-na-complexes from the pdb? and can i distinguish ss-dna from dna chains without parsing the pdb files and go through the coordinates (calculate distances etc...)? tx - ulf. -------------- next part -------------- A non-text attachment was scrubbed... Name: lenski.vcf Type: text/x-vcard Size: 216 bytes Desc: not available URL: From bernd.web at gmail.com Tue Feb 12 07:45:51 2008 From: bernd.web at gmail.com (Bernd Web) Date: Tue, 12 Feb 2008 13:45:51 +0100 Subject: [Bioperl-l] fetch protein-na-complexes from pdb In-Reply-To: <47B16CD1.2060307@mdc-berlin.de> References: <47B16CD1.2060307@mdc-berlin.de> Message-ID: <716af09c0802120445n6d477c7dj5de7819408eb2c48@mail.gmail.com> Hi Ulf, At rcsb.org you can get a list of PDB IDs for Protein/NA complexes and even download the entries there. See http://www.rcsb.org/pdb/statistics/holdings.do Also see "webdownload" on the RCSB site. Alternatively, you could fetch the files one by one (e.g. with wget). The file "ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_entry_type.txt" contains the entry type of all PDB entries (i.e.: prot/nuc/prot-nuc and diffraction/NMR). Regards, Bernd 2008/2/12 Ulf Lenski : > is there a bioperl modul for fetching protein-na-complexes from the pdb? > and can i distinguish ss-dna from dna chains without parsing the pdb > files and go through the coordinates (calculate distances etc...)? > > tx - ulf. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From lenski at mdc-berlin.de Tue Feb 12 08:43:51 2008 From: lenski at mdc-berlin.de (Ulf Lenski) Date: Tue, 12 Feb 2008 14:43:51 +0100 Subject: [Bioperl-l] fetch protein-na-complexes from pdb In-Reply-To: <716af09c0802120445n6d477c7dj5de7819408eb2c48@mail.gmail.com> References: <47B16CD1.2060307@mdc-berlin.de> <716af09c0802120445n6d477c7dj5de7819408eb2c48@mail.gmail.com> Message-ID: <47B1A297.7030406@mdc-berlin.de> hi bernd, thanks a lot - that helps me for my first question. but how can I distinguish the nuc chains? How I can find out the type of a single chain? ss-rna ss-dna ds-rna ds-dna regards, ulf. Bernd Web schrieb: > Hi Ulf, > > At rcsb.org you can get a list of PDB IDs for Protein/NA complexes and > even download the entries there. See > http://www.rcsb.org/pdb/statistics/holdings.do > Also see "webdownload" on the RCSB site. > > Alternatively, you could fetch the files one by one (e.g. with wget). > The file "ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_entry_type.txt" > contains the entry type of all PDB entries (i.e.: prot/nuc/prot-nuc > and diffraction/NMR). > > Regards, > Bernd > > > 2008/2/12 Ulf Lenski : > >> is there a bioperl modul for fetching protein-na-complexes from the pdb? >> and can i distinguish ss-dna from dna chains without parsing the pdb >> files and go through the coordinates (calculate distances etc...)? >> >> tx - ulf. >> >> _______________________________________________ >> 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 > > -------------- next part -------------- A non-text attachment was scrubbed... Name: lenski.vcf Type: text/x-vcard Size: 216 bytes Desc: not available URL: From cjfields at uiuc.edu Tue Feb 12 12:02:13 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 12 Feb 2008 11:02:13 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release Message-ID: Now that SVN migration is complete and a BioSQL 1.0 release is imminent (congrats Hilmar and Heikki), I would like to get a new bioperl core release out the door soon, preferably by the next BOSC meeting, end of summer by the latest. One major issue that all the core devs have right now is time, or a serious lack thereof. I, for instance, will be moving into a new research position in the next few months or so. I'm assuming Jason, Hilmar, Heikki, Sendu, and the other core developers are facing similar time constraints. In that light, we need to decide whether we are planning a new 1.5 release, or if we want to start a new stable (1.6) release. With the latter, we need to define very specifically what needs to be accomplished for that release, and it needs to be realistic with the timeframe above in mind. I would also like to extend the invitation for anyone who wishes to help to join in. For my vote, I would like to release a new stable 1.6; 1.5.x has been around for too long and the end goals were never really defined clearly (something we need to keep in mind for the next dev release). I also vote for separating out experimental/untested/undocumented/ unmaintained modules into a separate 'bioperl-dev' release (the 'here be dragons' of bioperl). I believe it would help the core release cycle tremendously. Issues raised in the past just off the top of my head (add more as needed): * perl 5.10 compliance (appears to mostly work now) * outstanding bugs (core only) * GFF/GFF3 compliance * BioSQL 1.0 compliance (impending) * POD and test coverage * smoke tests for bioperl-live/db/etc. * smaller, more focused core (less dependencies) * separating out experimental or poorly maintained modules into a separate 'bioperl-dev' distribution * bioperl-db issues with Bio::Species changes * module maintenance * sequence format roundtripping (i.e. genbank, embl, swissetc) * additional sequence parsers (insdcxml, etc) * enhancement requests in bugzilla (Albert?) chris From hangsyin at gmail.com Tue Feb 12 11:50:33 2008 From: hangsyin at gmail.com (Hang) Date: Tue, 12 Feb 2008 08:50:33 -0800 (PST) Subject: [Bioperl-l] BLAT in memory Message-ID: <15435321.post@talk.nabble.com> Dear all, I wonder whether it is a way that allows me to BLAT sequences and retrieve the result without writing to a file. Thank you! Best, Hang -- View this message in context: http://www.nabble.com/BLAT-in-memory-tp15435321p15435321.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From jason at bioperl.org Tue Feb 12 12:49:56 2008 From: jason at bioperl.org (Jason Stajich) Date: Tue, 12 Feb 2008 09:49:56 -0800 Subject: [Bioperl-l] BLAT in memory In-Reply-To: <15435321.post@talk.nabble.com> References: <15435321.post@talk.nabble.com> Message-ID: <63C04F95-2EFB-433B-91F8-7907829E18CB@bioperl.org> Specify 'stdout' as the filename. -jason On Feb 12, 2008, at 8:50 AM, Hang wrote: > > Dear all, > > I wonder whether it is a way that allows me to BLAT sequences and > retrieve > the result without writing to a file. Thank you! > > Best, > Hang > -- > View this message in context: http://www.nabble.com/BLAT-in-memory- > tp15435321p15435321.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 bix at sendu.me.uk Tue Feb 12 13:10:52 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 12 Feb 2008 18:10:52 +0000 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: Message-ID: <47B1E12C.9010708@sendu.me.uk> Chris Fields wrote: > * perl 5.10 compliance (appears to mostly work now) > * outstanding bugs (core only) > * POD and test coverage I'm fine with everything you said, but I'll just say that, at a minimum, the above is what needs to be done. Someone needs to step up and organise that 3rd point, since it will require a lot of work. As I've already done work on the test suite, if no one else expresses an interest I might look into it myself. > Now that SVN migration is complete Speaking of which, is there a way a file (like, oh, I don't know, bioperl-live/trunk/t/lib/BioperlTest.pm) can exist just once in SVN but be seen in other locations (like bioperl-run/trunk/t/lib/BioperlTest.pm)? Such that a commit to the version in bioperl-run also affects the version in bioperl-live? Or is there some appropriate other way to organise where cross-repository files are kept and dealt with? From cjfields at uiuc.edu Tue Feb 12 13:51:57 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 12 Feb 2008 12:51:57 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <47B1E12C.9010708@sendu.me.uk> References: <47B1E12C.9010708@sendu.me.uk> Message-ID: <9424A11E-7541-442C-B53E-C791A2D8C6FB@uiuc.edu> On Feb 12, 2008, at 12:10 PM, Sendu Bala wrote: > Chris Fields wrote: >> * perl 5.10 compliance (appears to mostly work now) >> * outstanding bugs (core only) >> * POD and test coverage > > I'm fine with everything you said, but I'll just say that, at a > minimum, the above is what needs to be done. I think we should also try to get bioperl-db up to speed for the BioSQL 1.0 release (at least Bio::Species-related issues). > Someone needs to step up and organise that 3rd point, since it will > require a lot of work. As I've already done work on the test suite, > if no one else expresses an interest I might look into it myself. Jason and I discussed it off list (along with Nathan Haigh). We also brought up the idea of smoke tests, which should pinpoint how stable bioperl-live distributions are. Having those set up would pinpoint modules we think need to stay in core or should go into a separate 'dev/extras' distribution. We could test smoke/coverage/POD on those as well. >> Now that SVN migration is complete > > Speaking of which, is there a way a file (like, oh, I don't know, > bioperl-live/trunk/t/lib/BioperlTest.pm) can exist just once in SVN > but be seen in other locations (like bioperl-run/trunk/t/lib/ > BioperlTest.pm)? Such that a commit to the version in bioperl-run > also affects the version in bioperl-live? Or is there some > appropriate other way to organise where cross-repository files are > kept and dealt with? Maybe using external definitions, though I haven't messed with it personally. http://svnbook.red-bean.com/en/1.4/svn.advanced.externals.html One of the outstanding issues on SVN migration is the use of aliases for a checkout ('bioperl-all'); that would probably require setting svn:externals in some way. chris From hlapp at gmx.net Tue Feb 12 18:24:31 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 13 Feb 2008 08:24:31 +0900 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <47B1E12C.9010708@sendu.me.uk> References: <47B1E12C.9010708@sendu.me.uk> Message-ID: On Feb 13, 2008, at 3:10 AM, Sendu Bala wrote: > Speaking of which, is there a way a file (like, oh, I don't know, > bioperl-live/trunk/t/lib/BioperlTest.pm) can exist just once in SVN > but be seen in other locations (like bioperl-run/trunk/t/lib/ > BioperlTest.pm)? svn supposedly supports symlinks (though I haven't tested that myself yet), and since bioperl-live and bioperl-run are under the same svn root (aren't they?) you could make a symbolic link. The downside of this is that if someone only checks out bioperl-run the link would presumably be dangling. Though maybe not, not sure how super-smart svn is in this regard. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Tue Feb 12 21:10:23 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 13 Feb 2008 11:10:23 +0900 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <9424A11E-7541-442C-B53E-C791A2D8C6FB@uiuc.edu> References: <47B1E12C.9010708@sendu.me.uk> <9424A11E-7541-442C-B53E-C791A2D8C6FB@uiuc.edu> Message-ID: <66FBC084-74E4-458D-9F46-FCAD124AB8DE@gmx.net> On Feb 13, 2008, at 3:51 AM, Chris Fields wrote: > I think we should also try to get bioperl-db up to speed for the > BioSQL 1.0 release (at least Bio::Species-related issues). I agree. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From n.haigh at sheffield.ac.uk Wed Feb 13 03:46:02 2008 From: n.haigh at sheffield.ac.uk (Nathan S Haigh) Date: Wed, 13 Feb 2008 08:46:02 +0000 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <9424A11E-7541-442C-B53E-C791A2D8C6FB@uiuc.edu> References: <47B1E12C.9010708@sendu.me.uk> <9424A11E-7541-442C-B53E-C791A2D8C6FB@uiuc.edu> Message-ID: <47B2AE4A.3040509@sheffield.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Chris Fields wrote: > On Feb 12, 2008, at 12:10 PM, Sendu Bala wrote: > >> Chris Fields wrote: >>> * perl 5.10 compliance (appears to mostly work now) >>> * outstanding bugs (core only) >>> * POD and test coverage >> >> I'm fine with everything you said, but I'll just say that, at a >> minimum, the above is what needs to be done. > > I think we should also try to get bioperl-db up to speed for the BioSQL > 1.0 release (at least Bio::Species-related issues). > >> Someone needs to step up and organise that 3rd point, since it will >> require a lot of work. As I've already done work on the test suite, if >> no one else expresses an interest I might look into it myself. > > Jason and I discussed it off list (along with Nathan Haigh). We also > brought up the idea of smoke tests, which should pinpoint how stable > bioperl-live distributions are. Having those set up would pinpoint > modules we think need to stay in core or should go into a separate > 'dev/extras' distribution. We could test smoke/coverage/POD on those as > well. > I've moved away from Perl coding over the past 6-12 months but try to keep an eye on the BioPerl mailing list and chip in when I can. The last time the Devel::Cover module came up, it was lacking the ability to sort the coverage report table by each of the coverage metrics - which was a problem for us as we have so many modules and it was time consuming to find those with poor coverage. However, this feature were implemented in Devel::Cover 0.62, so it makes things slightly easier/neater. I'm not sure if the problem of failing tests still mess up the completion of the coverage report or not. >>> Now that SVN migration is complete >> >> Speaking of which, is there a way a file (like, oh, I don't know, >> bioperl-live/trunk/t/lib/BioperlTest.pm) can exist just once in SVN >> but be seen in other locations (like >> bioperl-run/trunk/t/lib/BioperlTest.pm)? Such that a commit to the >> version in bioperl-run also affects the version in bioperl-live? Or is >> there some appropriate other way to organise where cross-repository >> files are kept and dealt with? > See the subversion FAQs: http://subversion.tigris.org/faq.html#symlinks > Maybe using external definitions, though I haven't messed with it > personally. > > http://svnbook.red-bean.com/en/1.4/svn.advanced.externals.html > > One of the outstanding issues on SVN migration is the use of aliases for > a checkout ('bioperl-all'); that would probably require setting > svn:externals in some way. > > chris -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHsq5K9gTv6QYzVL4RAuJWAKCM/eEEXL5LqTsG/fGAmGIM6+dW9QCfe/6w T2a/dKg6d8HHXNXrOnSbdcs= =T8pz -----END PGP SIGNATURE----- From David.Messina at sbc.su.se Wed Feb 13 06:06:58 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 13 Feb 2008 12:06:58 +0100 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: Message-ID: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> I agree with Chris that the next BioPerl release should be 1.6. Shunting abandoned, experimental, and less-developed code to "bioperl-dev" would be extremely beneficial. As Chris stated, not only does it reduce the number of modules needing full test coverage, but the most important core modules are the ones most likely to have good test coverage already. And it would make BioPerl easier to grok for newcomers, too, which is always nice. I've made a first go at dividing the current bioperl core along these lines here: http://www.bioperl.org/wiki/Proposed_1.6_core_modules It's a very rough cut, so those with more familiarity with the bioperl corpus, please go in and rearrange as you see fit. Dave From n.haigh at sheffield.ac.uk Wed Feb 13 07:07:16 2008 From: n.haigh at sheffield.ac.uk (Nathan S Haigh) Date: Wed, 13 Feb 2008 12:07:16 +0000 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> Message-ID: <47B2DD74.5020503@sheffield.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I remember a conversion about how/if to split bioperl modules up in the past. If I remember rightly, there was talk of splitting all modules up and then creating a CPAN bundle for the core modules. I don't know if this make the admin really complex, but this allows people to install just those modules they require rather than the whole bioperl-core. For example, if I write a script or a module that wants to make use of BioPerl's SeqIO abilities, the end user has to download and install a load of modules that he/she may never use. Instead, it would be nicer to simply install SeqIO and it's dependecies. If I want to install all the BioPerl core, I can install a CPAN bundle. Just a thought. Nath Dave Messina wrote: > I agree with Chris that the next BioPerl release should be 1.6. > > Shunting abandoned, experimental, and less-developed code to "bioperl-dev" > would be extremely beneficial. As Chris stated, not only does it reduce the > number of modules needing full test coverage, but the most important core > modules are the ones most likely to have good test coverage already. And it > would make BioPerl easier to grok for newcomers, too, which is always nice. > > I've made a first go at dividing the current bioperl core along these lines > here: > http://www.bioperl.org/wiki/Proposed_1.6_core_modules > > It's a very rough cut, so those with more familiarity with the bioperl > corpus, please go in and rearrange as you see fit. > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHst109gTv6QYzVL4RAvmAAKCmJa5X0dvyPiQ6lADQ0BBk/tu3OQCg1cNC ZZVlnTSKc6dcCbYJ5JgUGjA= =bvUu -----END PGP SIGNATURE----- From bosborne11 at verizon.net Wed Feb 13 10:08:36 2008 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 13 Feb 2008 10:08:36 -0500 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> Message-ID: Dave, A few of those modules are supposed to be removed in 1.6, according to the notes in the DEPRECATED file. I've marked them. Brian O. On Feb 13, 2008, at 6:06 AM, Dave Messina wrote: > I've made a first go at dividing the current bioperl core along > these lines > here: > http://www.bioperl.org/wiki/Proposed_1.6_core_modules From cjfields at uiuc.edu Wed Feb 13 11:58:03 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 13 Feb 2008 10:58:03 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> Message-ID: I've added/modified the page as well; moved Bio::FeatureIO and Bio::SeqFeature::Annotated over to the bioperl-dev for now, along with Bio::Assembly and Bio::Restriction. We'll have to test out removing those modules to see what blows up. chris On Feb 13, 2008, at 9:08 AM, Brian Osborne wrote: > Dave, > > A few of those modules are supposed to be removed in 1.6, according > to the notes in the DEPRECATED file. I've marked them. > > Brian O. > > > On Feb 13, 2008, at 6:06 AM, Dave Messina wrote: > >> I've made a first go at dividing the current bioperl core along >> these lines >> here: >> http://www.bioperl.org/wiki/Proposed_1.6_core_modules > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Feb 13 14:11:34 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 13 Feb 2008 13:11:34 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> Message-ID: <8C98F03E-0424-4383-A08C-F227745DBEF6@uiuc.edu> On Feb 13, 2008, at 12:32 PM, Brian Osborne wrote: > Chris, > > You should be careful about the names of these packages. For > example, Bio::Biblio and Bio::Restriction are not "in development" > as the term bioperl-dev implies. They're tried and true. And there > may be sets of modules that are experimental in "bioperl-dev", of > course. Is it possible to have 2 packages, "dev" and "tools"? Or > something along those lines? > > Calling things by the wrong names leads to confusion, witness the > Bioperl newcomers who would install an antiquated version 1.4 > because it was labelled 'stable'. > > BIO I agree the name 'dev' is misleading. 'tools' or 'extras' sounds better, maybe using 'dev' for experimental implementations, such as Jason's SeqFeature::Slim or my SeqIO driver/handler modules. The problem with the two namespaces you mention is lack of maintenance and documentation, though I agree they're stable (so maybe in those cases maintenance isn't an issue). We do need to clean up documentation issues with those classes as well as many more (mine included); POD/test coverage will help out there. chris From bosborne11 at verizon.net Wed Feb 13 13:32:46 2008 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 13 Feb 2008 13:32:46 -0500 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> Message-ID: <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> Chris, You should be careful about the names of these packages. For example, Bio::Biblio and Bio::Restriction are not "in development" as the term bioperl-dev implies. They're tried and true. And there may be sets of modules that are experimental in "bioperl-dev", of course. Is it possible to have 2 packages, "dev" and "tools"? Or something along those lines? Calling things by the wrong names leads to confusion, witness the Bioperl newcomers who would install an antiquated version 1.4 because it was labelled 'stable'. BIO On Feb 13, 2008, at 11:58 AM, Chris Fields wrote: > I've added/modified the page as well; moved Bio::FeatureIO and > Bio::SeqFeature::Annotated over to the bioperl-dev for now, along > with Bio::Assembly and Bio::Restriction. We'll have to test out > removing those modules to see what blows up. From David.Messina at sbc.su.se Wed Feb 13 14:55:26 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 13 Feb 2008 20:55:26 +0100 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> Message-ID: <628aabb70802131155q73674b72qad547c55c5443e2d@mail.gmail.com> Great, thanks guys. From bix at sendu.me.uk Wed Feb 13 15:19:01 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 13 Feb 2008 20:19:01 +0000 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> Message-ID: <47B350B5.3060501@sendu.me.uk> Brian Osborne wrote: > You should be careful about the names of these packages. For example, > Bio::Biblio and Bio::Restriction are not "in development" as the term > bioperl-dev implies. They're tried and true. And there may be sets of > modules that are experimental in "bioperl-dev", of course. Is it > possible to have 2 packages, "dev" and "tools"? Or something along those > lines? > > Calling things by the wrong names leads to confusion, witness the > Bioperl newcomers who would install an antiquated version 1.4 because it > was labelled 'stable'. On the topic of confusion, I think 'bioperl-tools' is a very bad choice since we have Bio::Tools. Why would Bio::Microarray (for example) be in there? (And then we have Bio::Microarray::Tools ...) Can all of the non Bio::Tools modules currently in the bioperl-tools section of the wiki page be annotated as to why they're there and not in core? Then maybe we can come up with a better name to categorize them all under. Perhaps we could also annotate the things in core to justify why they should be in core? Is anyone good at creating maps so we can easily see what Bioperl modules are most used (by other Bioperl modules)? Or is the split intended to be 'core' == "anything and everything that was in 1.4", '????' == "everything else"? In which case, what's a good name for "modules created after 1.4"? 'crust'? ;) From cjfields at uiuc.edu Wed Feb 13 16:05:16 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 13 Feb 2008 15:05:16 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <47B350B5.3060501@sendu.me.uk> References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> <47B350B5.3060501@sendu.me.uk> Message-ID: <477CF001-FF35-4A08-A360-C9FA2031E353@uiuc.edu> On Feb 13, 2008, at 2:19 PM, Sendu Bala wrote: > Brian Osborne wrote: >> You should be careful about the names of these packages. For >> example, Bio::Biblio and Bio::Restriction are not "in development" >> as the term bioperl-dev implies. They're tried and true. And there >> may be sets of modules that are experimental in "bioperl-dev", of >> course. Is it possible to have 2 packages, "dev" and "tools"? Or >> something along those lines? >> Calling things by the wrong names leads to confusion, witness the >> Bioperl newcomers who would install an antiquated version 1.4 >> because it was labelled 'stable'. > > On the topic of confusion, I think 'bioperl-tools' is a very bad > choice since we have Bio::Tools. Why would Bio::Microarray (for > example) be in there? (And then we have Bio::Microarray::Tools ...) > > Can all of the non Bio::Tools modules currently in the bioperl-tools > section of the wiki page be annotated as to why they're there and > not in core? Then maybe we can come up with a better name to > categorize them all under. > > Perhaps we could also annotate the things in core to justify why > they should be in core? Is anyone good at creating maps so we can > easily see what Bioperl modules are most used (by other Bioperl > modules)? Frankly, it will be hard for a handful of people (Dave, Brian, and I) to justify the existence for every bioperl module or it's placement in bioperl-?, but at least we have a start on it. The page is open for editing by anyone (Dave, Brian, and I have already added quite a bit). There is also a discussion page to add to, which is a good place for proposals and to sketch out ideas. I think we should take some time on this to stew over the options available, maybe a month or two, and set some deadline for starting up. > Or is the split intended to be 'core' == "anything and everything > that was in 1.4", '????' == "everything else"? In which case, what's > a good name for "modules created after 1.4"? 'crust'? ;) I personally take the extreme view of having a very tight core with just the basic sequence, feature, alignment, and annotation classes (just for maintenance sake); everything else just uses those base classes anyway, so I don't necessarily consider them core. I don't think paring down to that level is feasible for a 1.6 release, but moving some of the unmaintained cruft out into a separate installation would be a good start. chris From pengchy at yahoo.com.cn Wed Feb 13 20:26:21 2008 From: pengchy at yahoo.com.cn (Åô³Ì) Date: 14 Feb 2008 01:26:21 -0000 Subject: Åô³ÌÑûÇëÄú¼ÓÈëÈô±ÈÁÚ Message-ID: <20080214012621.30230.qmail@zorpia.com> Hi bioperl! Your friend ???? from ????, just invited you to online photo albums and journals at Zorpia.com. So what is Zorpia? It is an online community that allows you to upload unlimited amount of photos, write journals and make friends. We also have a variety of skins in store for you so that you can customize your homepage freely. Join now for free! Please click the following link to join Zorpia: http://cn.signup.zorpia.com/signup?invitation_key=200802c0d8af2b64f8ef03d6417e4ab4&referral=pengchy This message was delivered with the ????'s initiation. If you wish to discontinue receiving invitations from us, please click the following link: http://cn.signup.zorpia.com/email/optout/bioperl-l at lists.open-bio.org From hangsyin at gmail.com Wed Feb 13 22:10:54 2008 From: hangsyin at gmail.com (Hang) Date: Wed, 13 Feb 2008 19:10:54 -0800 (PST) Subject: [Bioperl-l] Re trieve ID tag in GFF3 Message-ID: <15473188.post@talk.nabble.com> Dear All, I wonder what method I should call to retrieve values of ID tags in GFF3 format. For example, a GFF3 entry in the database is like this: 4 FlyBase gene 24068 25621 . + . ID=FBgn0040037;Name=ABC;Ontology_term=... I'd like to retrieve the scalar value 'FBgn0040037' to compare with another value. Please complete the code below: use Bio::DB::SeqFeature::Store; my $db = Bio::DB::SeqFeature::Store->new(-adaptor => 'DBI::mysql', -dsn => 'dbi:mysql:XXX_gff', -user => 'XXX', -pass => 'XXX')|| die "Database open failed"; ??? Thanks alot! Hang -- View this message in context: http://www.nabble.com/Retrieve-ID-tag-in-GFF3-tp15473188p15473188.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From cjfields at uiuc.edu Thu Feb 14 15:36:27 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 14 Feb 2008 14:36:27 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <47B350B5.3060501@sendu.me.uk> References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> <47B350B5.3060501@sendu.me.uk> Message-ID: <3C0A6ADA-AABC-4D7A-B858-CEB8E87AFDDE@uiuc.edu> On Feb 13, 2008, at 2:19 PM, Sendu Bala wrote: > Brian Osborne wrote: >> You should be careful about the names of these packages. For >> example, Bio::Biblio and Bio::Restriction are not "in development" >> as the term bioperl-dev implies. They're tried and true. And there >> may be sets of modules that are experimental in "bioperl-dev", of >> course. Is it possible to have 2 packages, "dev" and "tools"? Or >> something along those lines? >> Calling things by the wrong names leads to confusion, witness the >> Bioperl newcomers who would install an antiquated version 1.4 >> because it was labelled 'stable'. > > On the topic of confusion, I think 'bioperl-tools' is a very bad > choice since we have Bio::Tools. Why would Bio::Microarray (for > example) be in there? (And then we have Bio::Microarray::Tools ...) > > Can all of the non Bio::Tools modules currently in the bioperl-tools > section of the wiki page be annotated as to why they're there and > not in core? Then maybe we can come up with a better name to > categorize them all under. > > Perhaps we could also annotate the things in core to justify why > they should be in core? Is anyone good at creating maps so we can > easily see what Bioperl modules are most used (by other Bioperl > modules)? > > > Or is the split intended to be 'core' == "anything and everything > that was in 1.4", '????' == "everything else"? In which case, what's > a good name for "modules created after 1.4"? 'crust'? ;) I added a modified proposal to the Talk page for the Release: http://www.bioperl.org/wiki/Talk:Proposed_1.6_core_modules I'm pretty flexible on any of that; it's a proposal only and I think some of it may be wrongheaded, but hey, I'm willing to take a few rotten tomatoes. The key issue is we should try to work out what we mean by 'core' or the core library. I have a rather extreme view of it as being the bare essentials without external, non-perl core dependencies (only SeqI/PrimarySeqI, AlignI, AnnotationI, SeqFeatureI and required modules for those classes) but I'm sure others would lump in parsers, DB functionality, etc. I basically suggest placing those (and any stable but potentially non-core code) in a 'bioperl-main', with any unstable or untested code going into a 'bioperl-unstable'. In essence, bioperl-main would require core and resemble a stable release; bioperl-unstable would require bioperl-main (and core) and resemble a dev release. Not sure how versioning would go or if this is a viable option at all, but it's worth discussing. chris From aaron.j.mackey at gsk.com Fri Feb 15 13:06:58 2008 From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com) Date: Fri, 15 Feb 2008 13:06:58 -0500 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <47B350B5.3060501@sendu.me.uk> Message-ID: > Or is the split intended to be 'core' == "anything and everything that > was in 1.4", '????' == "everything else"? In which case, what's a good > name for "modules created after 1.4"? 'crust'? ;) Nah, "icing". a module "use" map might be very useful to help identify "core" vs. other layers of mantle/crust/icing. http://www.perlmonks.org/?node_id=87329 http://search.cpan.org/src/NEILB/pmusage-1.2/ Some more serious alternatives to "bioperl-dev" and "-tools" might be: "-accessory" or "-optional" or "-other" or "-addons", etc. -Aaron From lincoln.stein at gmail.com Fri Feb 15 15:17:31 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Fri, 15 Feb 2008 15:17:31 -0500 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: Message-ID: <6dce9a0b0802151217t59e41ccq2bcb10c68b8aede1@mail.gmail.com> > * perl 5.10 compliance (appears to mostly work now) > * GFF/GFF3 compliance I've been doing a lot of work on this recently. I think it's much improved. No problems with 5.10 for the modules that I use frequently. Lincoln > > * BioSQL 1.0 compliance (impending) > * POD and test coverage > * smoke tests for bioperl-live/db/etc. > * smaller, more focused core (less dependencies) > * separating out experimental or poorly maintained modules into a > separate 'bioperl-dev' distribution > * bioperl-db issues with Bio::Species changes > * module maintenance > * sequence format roundtripping (i.e. genbank, embl, swissetc) > * additional sequence parsers (insdcxml, etc) > * enhancement requests in bugzilla (Albert?) > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From cjfields at uiuc.edu Fri Feb 15 16:43:42 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 15 Feb 2008 15:43:42 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <6dce9a0b0802151217t59e41ccq2bcb10c68b8aede1@mail.gmail.com> References: <6dce9a0b0802151217t59e41ccq2bcb10c68b8aede1@mail.gmail.com> Message-ID: On Feb 15, 2008, at 2:17 PM, Lincoln Stein wrote: >> * perl 5.10 compliance (appears to mostly work now) >> * GFF/GFF3 compliance > > > I've been doing a lot of work on this recently. I think it's much > improved. > No problems with 5.10 for the modules that I use frequently. > > Lincoln I think bioperl works now for perl 5.10. The only significant issue we ran into were problems with Bio::SeqIO::entrezgene. The parser looped and created a pseudohash under some conditions, which threw all sorts of errors with 5.8. Stefan and I fixed that one in Subversion. There were some odd Data::Dumper-related messages popping up with 'perl Build.PL' using perl 5.10; not sure what's going on there, but it appears harmless: Encountered CODE ref, using dummy placeholder at /opt/perl/lib/5.10.0/ darwin-2level/Data/Dumper.pm line 190. chris From cjfields at uiuc.edu Fri Feb 15 16:49:33 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 15 Feb 2008 15:49:33 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: Message-ID: On Feb 15, 2008, at 12:06 PM, aaron.j.mackey at gsk.com wrote: >> Or is the split intended to be 'core' == "anything and everything >> that >> was in 1.4", '????' == "everything else"? In which case, what's a >> good >> name for "modules created after 1.4"? 'crust'? ;) > > Nah, "icing". > > a module "use" map might be very useful to help identify "core" vs. > other > layers of mantle/crust/icing. > > http://www.perlmonks.org/?node_id=87329 > http://search.cpan.org/src/NEILB/pmusage-1.2/ > > Some more serious alternatives to "bioperl-dev" and "-tools" might be: > "-accessory" or "-optional" or "-other" or "-addons", etc. > > -Aaron 'bioperl-extras' (Ricky Gervais fan myself) chris From hlapp at gmx.net Fri Feb 15 17:14:10 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 16 Feb 2008 07:14:10 +0900 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: Message-ID: <82E17B18-32D9-4858-9245-EEF9D143DA11@gmx.net> On Feb 16, 2008, at 6:49 AM, Chris Fields wrote: >> >> Some more serious alternatives to "bioperl-dev" and "-tools" might >> be: >> "-accessory" or "-optional" or "-other" or "-addons", etc. >> >> -Aaron > > 'bioperl-extras' (Ricky Gervais fan myself) > Actually I like bioperl-opt - sounds somehow reminiscent of the /opt directory we all know (often containing the best things :) -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Sun Feb 17 09:07:20 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 17 Feb 2008 08:07:20 -0600 Subject: [Bioperl-l] [Bioperl-guts-l] [14510] bioperl-live/trunk/Bio/SeqIO/swiss.pm: GN line output now follows the new format. In-Reply-To: <200802171000.m1HA0oGq003135@dev.open-bio.org> References: <200802171000.m1HA0oGq003135@dev.open-bio.org> Message-ID: Heikki, See bug 1825: http://bugzilla.open-bio.org/show_bug.cgi?id=1825 Hilmar's final comments about restructuring Bio::Annotation::StructuredValue using Data::Stag should work. chris On Feb 17, 2008, at 4:00 AM, Heikki Lehvaslaiho wrote: > Revision: 14510 > Author: heikki > Date: 2008-02-17 05:00:50 -0500 (Sun, 17 Feb 2008) > > Log Message: > ----------- > GN line output now follows the new format. BioPerl would need new > objects to store all infomation so for now only the official name > (Name=) and synonym categories are kept. ORFNames and > OrderedLocusNames are treated as synonyms. > > Modified Paths: > -------------- > bioperl-live/trunk/Bio/SeqIO/swiss.pm > > Modified: bioperl-live/trunk/Bio/SeqIO/swiss.pm > =================================================================== > --- bioperl-live/trunk/Bio/SeqIO/swiss.pm 2008-02-17 09:48:07 UTC > (rev 14509) > +++ bioperl-live/trunk/Bio/SeqIO/swiss.pm 2008-02-17 10:00:50 UTC > (rev 14510) > @@ -494,16 +494,13 @@ > #Definition lines > $self->_write_line_swissprot_regex("DE ","DE ",$seq- > >desc(),"\\s\+\|\$",$LINE_LENGTH); > > - #Gene name > - if ((my @genes = $seq->annotation- > >get_Annotations('gene_name') ) ) { > - $self->_print("GN ", > - join(' OR ', > - map { > - $_->isa("Bio::Annotation::StructuredValue") ? > - $_->value(-joins => [" AND ", " OR "]) : > - $_->value(); > - } @genes), > - ".\n"); > + #Gene name; print out new format but only two categories: Name > and Synonyms > + if ( my @genes = $seq->annotation- > >get_Annotations('gene_name') ) { > + my @gene_names = map { $_->get_all_values} @genes; > + my $gn_string = 'Name='. shift(@gene_names). ';'; > + $gn_string .= ' Synonyms='. join(', ', @gene_names). ";" if > scalar @gene_names; > + $self->_write_line_swissprot_regex("GN ","GN ", > $gn_string,"\\s\+\|\$",$LINE_LENGTH); > + > } > > # Organism lines > @@ -1267,7 +1264,6 @@ > } > > my $subl = $length - (length $pre1) -1 ; > - my @lines; > > my $first_line = 1; > while($line =~ m/(.{1,$subl})($regex)/g) { > > > _______________________________________________ > Bioperl-guts-l mailing list > Bioperl-guts-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From heikki at sanbi.ac.za Mon Feb 18 03:12:11 2008 From: heikki at sanbi.ac.za (Heikki Lehvaslaiho) Date: Mon, 18 Feb 2008 10:12:11 +0200 Subject: [Bioperl-l] [Bioperl-guts-l] [14510] bioperl-live/trunk/Bio/SeqIO/swiss.pm: GN line output now follows the new format. In-Reply-To: References: <200802171000.m1HA0oGq003135@dev.open-bio.org> Message-ID: <200802181012.11295.heikki@sanbi.ac.za> Thanks for pointing this out to me. Looks like I've solved the first level: "Problem #1 is to have all the value tokens available from the created object, regardless of their tags." Anybody want to go on to the next level and code in the complete representation of the GN line? -Heikki On Sunday 17 February 2008 16:07:20 Chris Fields wrote: > Heikki, > > See bug 1825: > > http://bugzilla.open-bio.org/show_bug.cgi?id=1825 > > Hilmar's final comments about restructuring > Bio::Annotation::StructuredValue using Data::Stag should work. > > chris > > On Feb 17, 2008, at 4:00 AM, Heikki Lehvaslaiho wrote: > > Revision: 14510 > > Author: heikki > > Date: 2008-02-17 05:00:50 -0500 (Sun, 17 Feb 2008) > > > > Log Message: > > ----------- > > GN line output now follows the new format. BioPerl would need new > > objects to store all infomation so for now only the official name > > (Name=) and synonym categories are kept. ORFNames and > > OrderedLocusNames are treated as synonyms. > > > > Modified Paths: > > -------------- > > bioperl-live/trunk/Bio/SeqIO/swiss.pm > > > > Modified: bioperl-live/trunk/Bio/SeqIO/swiss.pm > > =================================================================== > > --- bioperl-live/trunk/Bio/SeqIO/swiss.pm 2008-02-17 09:48:07 UTC > > (rev 14509) > > +++ bioperl-live/trunk/Bio/SeqIO/swiss.pm 2008-02-17 10:00:50 UTC > > (rev 14510) > > @@ -494,16 +494,13 @@ > > #Definition lines > > $self->_write_line_swissprot_regex("DE ","DE ",$seq- > > > > >desc(),"\\s\+\|\$",$LINE_LENGTH); > > > > - #Gene name > > - if ((my @genes = $seq->annotation- > > > > >get_Annotations('gene_name') ) ) { > > > > - $self->_print("GN ", > > - join(' OR ', > > - map { > > - $_->isa("Bio::Annotation::StructuredValue") ? > > - $_->value(-joins => [" AND ", " OR "]) : > > - $_->value(); > > - } @genes), > > - ".\n"); > > + #Gene name; print out new format but only two categories: Name > > and Synonyms > > + if ( my @genes = $seq->annotation- > > > > >get_Annotations('gene_name') ) { > > > > + my @gene_names = map { $_->get_all_values} @genes; > > + my $gn_string = 'Name='. shift(@gene_names). ';'; > > + $gn_string .= ' Synonyms='. join(', ', @gene_names). ";" if > > scalar @gene_names; > > + $self->_write_line_swissprot_regex("GN ","GN ", > > $gn_string,"\\s\+\|\$",$LINE_LENGTH); > > + > > } > > > > # Organism lines > > @@ -1267,7 +1264,6 @@ > > } > > > > my $subl = $length - (length $pre1) -1 ; > > - my @lines; > > > > my $first_line = 1; > > while($line =~ m/(.{1,$subl})($regex)/g) { > > > > > > _______________________________________________ > > Bioperl-guts-l mailing list > > Bioperl-guts-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za _/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho _/ _/ _/ SANBI, South African National Bioinformatics Institute _/ _/ _/ University of Western Cape, South Africa _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 ___ _/_/_/_/_/________________________________________________________ From cjfields at uiuc.edu Mon Feb 18 13:56:32 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 18 Feb 2008 12:56:32 -0600 Subject: [Bioperl-l] [Bioperl-guts-l] [14510] bioperl-live/trunk/Bio/SeqIO/swiss.pm: GN line output now follows the new format. In-Reply-To: <200802181012.11295.heikki@sanbi.ac.za> References: <200802171000.m1HA0oGq003135@dev.open-bio.org> <200802181012.11295.heikki@sanbi.ac.za> Message-ID: <670A1145-D1A6-4245-A621-750E0F4FFB6E@uiuc.edu> I may try working on the next. I had indicated that I would do this in the past, just never got around to it; time is the enemy of us all. chris On Feb 18, 2008, at 2:12 AM, Heikki Lehvaslaiho wrote: > Thanks for pointing this out to me. Looks like I've solved the first > level: > > "Problem #1 is to have all the value tokens > available from the created object, regardless of their tags." > > Anybody want to go on to the next level and code in the complete > representation of the GN line? > > -Heikki > > > On Sunday 17 February 2008 16:07:20 Chris Fields wrote: >> Heikki, >> >> See bug 1825: >> >> http://bugzilla.open-bio.org/show_bug.cgi?id=1825 >> >> Hilmar's final comments about restructuring >> Bio::Annotation::StructuredValue using Data::Stag should work. >> >> chris >> >> On Feb 17, 2008, at 4:00 AM, Heikki Lehvaslaiho wrote: >>> Revision: 14510 >>> Author: heikki >>> Date: 2008-02-17 05:00:50 -0500 (Sun, 17 Feb 2008) >>> >>> Log Message: >>> ----------- >>> GN line output now follows the new format. BioPerl would need new >>> objects to store all infomation so for now only the official name >>> (Name=) and synonym categories are kept. ORFNames and >>> OrderedLocusNames are treated as synonyms. >>> >>> Modified Paths: >>> -------------- >>> bioperl-live/trunk/Bio/SeqIO/swiss.pm >>> >>> Modified: bioperl-live/trunk/Bio/SeqIO/swiss.pm >>> =================================================================== >>> --- bioperl-live/trunk/Bio/SeqIO/swiss.pm 2008-02-17 09:48:07 UTC >>> (rev 14509) >>> +++ bioperl-live/trunk/Bio/SeqIO/swiss.pm 2008-02-17 10:00:50 UTC >>> (rev 14510) >>> @@ -494,16 +494,13 @@ >>> #Definition lines >>> $self->_write_line_swissprot_regex("DE ","DE ",$seq- >>> >>>> desc(),"\\s\+\|\$",$LINE_LENGTH); >>> >>> - #Gene name >>> - if ((my @genes = $seq->annotation- >>> >>>> get_Annotations('gene_name') ) ) { >>> >>> - $self->_print("GN ", >>> - join(' OR ', >>> - map { >>> - $_->isa("Bio::Annotation::StructuredValue") ? >>> - $_->value(-joins => [" AND ", " OR "]) : >>> - $_->value(); >>> - } @genes), >>> - ".\n"); >>> + #Gene name; print out new format but only two categories: Name >>> and Synonyms >>> + if ( my @genes = $seq->annotation- >>> >>>> get_Annotations('gene_name') ) { >>> >>> + my @gene_names = map { $_->get_all_values} @genes; >>> + my $gn_string = 'Name='. shift(@gene_names). ';'; >>> + $gn_string .= ' Synonyms='. join(', ', @gene_names). ";" if >>> scalar @gene_names; >>> + $self->_write_line_swissprot_regex("GN ","GN ", >>> $gn_string,"\\s\+\|\$",$LINE_LENGTH); >>> + >>> } >>> >>> # Organism lines >>> @@ -1267,7 +1264,6 @@ >>> } >>> >>> my $subl = $length - (length $pre1) -1 ; >>> - my @lines; >>> >>> my $first_line = 1; >>> while($line =~ m/(.{1,$subl})($regex)/g) { >>> >>> >>> _______________________________________________ >>> Bioperl-guts-l mailing list >>> Bioperl-guts-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l >> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > -- > ______ _/ _/_____________________________________________________ > _/ _/ > _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za > _/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho > _/ _/ _/ SANBI, South African National Bioinformatics Institute > _/ _/ _/ University of Western Cape, South Africa > _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 > ___ _/_/_/_/_/________________________________________________________ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From hlapp at gmx.net Mon Feb 18 17:14:33 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 18 Feb 2008 17:14:33 -0500 Subject: [Bioperl-l] BOSC 2008? In-Reply-To: <9C6A22B1-9E84-4F17-8459-CBBDCB2110D4@uiuc.edu> References: <1182EAB9-7A75-498F-B91B-C14771DFD607@uiuc.edu> <628aabb70802061317n2f0d1103w9367346166bf8c3f@mail.gmail.com> <9C6A22B1-9E84-4F17-8459-CBBDCB2110D4@uiuc.edu> Message-ID: As an aside, I've posted the (so far "unofficial") update on the news.open-bio.org blog. -hilmar On Feb 6, 2008, at 4:22 PM, Chris Fields wrote: > Yep. I found this out earlier from Darin London. Just trying to > plan for it ahead of time! > > chris > > On Feb 6, 2008, at 3:17 PM, Dave Messina wrote: > >> Hey Chris, >> >> Isn't it usually in conjunction with ISMB (which is Toronto >> 7/19-23 this year)? >> >> > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From johan.nilsson at sh.se Tue Feb 19 09:42:52 2008 From: johan.nilsson at sh.se (Johan Nilsson) Date: Tue, 19 Feb 2008 15:42:52 +0100 Subject: [Bioperl-l] Dumping a MSA from BLAST results Message-ID: <47BAEAEC.5080203@sh.se> Hello, I have a question regarding the conversion from a Blast search result (PSI-blast using blastpgp, to be more exact) to a multiple sequence alignment file. I'm running the Bio::Tools::Run::StandAloneBlast and I retrieve the HSPs from the resulting Bio::Search::Hit::HitI objects. I have no problems obtaining each HSP alignment using $hit->get_aln. However, rather than dumping many local alignments, I would like to write a single result file where the HSPs are interleaved. I guess this shouldn't be too hard, but nevertheless I haven't found out how to do this in a simple way. Any suggestions would be highly appreciated! Best Regards /Johan Nilsson From jason at bioperl.org Tue Feb 19 11:17:32 2008 From: jason at bioperl.org (Jason Stajich) Date: Tue, 19 Feb 2008 08:17:32 -0800 Subject: [Bioperl-l] Dumping a MSA from BLAST results In-Reply-To: <47BAEAEC.5080203@sh.se> References: <47BAEAEC.5080203@sh.se> Message-ID: <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> All the individual pairwise alignments won't necessarily be an alignment of the same region and the gap insertions can be different in each instance of the query sequence that is participating in the pairwise alns so it won't fit into an MSA. It makes more sense to extract the aligned part of the hit sequences identified and a subsequence of the query which is the min and max region aligned. Run this through a MSA program. -jason On Feb 19, 2008, at 6:42 AM, Johan Nilsson wrote: > Hello, > > I have a question regarding the conversion from a Blast search > result (PSI-blast using blastpgp, to be more exact) to a multiple > sequence alignment file. I'm running the > Bio::Tools::Run::StandAloneBlast and I retrieve the HSPs from the > resulting Bio::Search::Hit::HitI objects. I have no problems > obtaining each HSP alignment using $hit->get_aln. However, rather > than dumping many local alignments, I would like to write a single > result file where the HSPs are interleaved. > > I guess this shouldn't be too hard, but nevertheless I haven't > found out how to do this in a simple way. Any suggestions would be > highly appreciated! > > Best Regards > /Johan Nilsson > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at uiuc.edu Tue Feb 19 12:18:34 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 19 Feb 2008 11:18:34 -0600 Subject: [Bioperl-l] Dumping a MSA from BLAST results In-Reply-To: <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> Message-ID: One could use an alternative blastall output format (like -m1 to -m6), which give various anchored alignments. None of these are parsed via bioperl as far as I know; might be worth getting something up and running if there is enough interest in it. chris PS. Here's example output using 'blastall -p blastp -i test2.faa -d CP000560.faa -m6', which is query-anchored, flat, blunt ends: BLASTP 2.2.16 [Mar-25-2007] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= gi|1373160|gb|AAB57770.1| PyrR (173 letters) Database: CP000560.faa 3693 sequences; 1,147,568 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gb|ABS73893.1| PyrR [Bacillus amyloliquefaciens FZB42] 322 1e-89 gb|ABS75590.1| ComFC [Bacillus amyloliquefaciens FZB42] 37 6e-04 gb|ABS72500.1| Prs [Bacillus amyloliquefaciens FZB42] 28 0.22 gb|ABS72703.1| YcdA [Bacillus amyloliquefaciens FZB42] 27 0.49 gb|ABS74832.1| Apt [Bacillus amyloliquefaciens FZB42] 26 1.1 gb|ABS75734.1| Upp [Bacillus amyloliquefaciens FZB42] 26 1.4 gb|ABS74081.1| NrdE [Bacillus amyloliquefaciens FZB42] 25 1.9 gb|ABS76054.1| RocD [Bacillus amyloliquefaciens FZB42] 24 4.1 gb|ABS74744.1| Gpr [Bacillus amyloliquefaciens FZB42] 24 5.4 gb|ABS74336.1| UvrX [Bacillus amyloliquefaciens FZB42] 23 7.1 gb|ABS74825.1| YrvM [Bacillus amyloliquefaciens FZB42] 23 9.2 gb|ABS72555.1| RpoB [Bacillus amyloliquefaciens FZB42] 23 9.2 1_0 1 MNQKAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKR--- LAER---- 53 ABS73893 1 MNQKAVILDEQAIRRALTRIAHEMIERNKGMNDCILVGIKTRGIYLAKR--- LAER---- 53 ABS75590 116 ------------------------------- NTHTLIPIPLSGERLAERGFNQSEL---- 140 ABS72500 164 ----------------------------KDLKDIVIVSPDHGGVTRARK--- LADR---- 188 ABS72703 55 ----------------------------------------------ALK--- VTVT---- 61 ABS74832 ------------------------------------------------------------ ABS75734 ------------------------------------------------------------ ABS74081 ------------------------------------------------------------ ABS74081 502 -----------------------------------------RSAELAKE--- KGET---- 513 ABS76054 305 ------VLEEEGLAERSLQLGRYFKEELEKIDNPIIKDVRGRGLFIGVE--- LTEAARPY 355 ABS74744 43 -------------------------ERDKG-------GIKVRTVDITKE--- GAEL---- 63 ABS74336 ------------------------------------------------------------ ABS74825 ------------------------------------------------------------ ABS72555 ------------------------------------------------------------ 1_0 54 IEQIEGNPVTVGEIDITLYRDDLSKKTSNDEPLVKGADIP-V--DITD--- QKVILVDDV 107 ABS73893 54 IEQIEGNPVTVGEIDITLYRDDLTKKTSNEEPLVKGADIP-A--DITD--- QKVIVVDDV 107 ABS75590 141 LASLLGMPVISPLIRLNNEKQSKKSKTDRLSAEKKFSAAE-N--SATG--- MNVILIDDI 194 ABS72500 189 LKA----PIAI---------IDKRRPRPNE---VEVMNIV-G--NVEG--- KTAILIDDI 226 ABS72703 62 VKNTGKDPLTVKSSDFSLYQDD--AKTAK-----------------TD--- KEDLMQSGT 99 ABS74832 112 --------------------------------------------------- QRVLITDDL 120 ABS75734 100 ---------------VGLYRDPETLK-----PVEYYVKLP-S--DVEE--- REFIVVDPM 133 ABS74081 386 -----------------LQASQVSAYTDYDEEDEIGLDIS-C--NLGS--- LNILNVMKH 422 ABS74081 514 FEHYEGSTYATGEYFNKYIEKEFSPAYEKIAALFEGMHIP-TIEDWKE--- LKAFVAENG 569 ABS76054 356 CEKLKGEGLLCKETHDTVIR---------------------------------------- 375 ABS74744 64 SGKKQGRYVTIEAQGVREHDSDMQEKVT-------------------------------- 91 ABS74336 109 ----------------------------------KTIDLP-T-- NITMDIYRYCLILFDK 131 ABS74825 199 ------------------- REDVRKEVGNDEAKIRKAQMP-------------------- 219 ABS72555 1090 -----GAAYTLQEI-LTVKSDDVVGRVKTYEAIVKGDNVPEP--GVPE--- SFKVLIKEL 1138 1_0 108 LYTGRTVRAGMDALVDVGRPSSIQLAVLVDRGHRELPIRADYIGKNIPTSKSEKVMVQLD 167 ABS73893 108 LYTGRTVRAAMDALVDVGRPSSIQLAVLVDRGHRELPIRADYIGKNIPTSKAEKVMVQLS 167 ABS75590 195 YTTGATLHQAAEVLLTAGKASSVSSFTLI------------------------------- 223 ABS72500 227 IDTAGTITLAANALVENG------------------------------------------ 244 ABS72703 100 LHAGKTVTGNLYFTADEGK----------------------------------------- 118 ABS74832 121 LATGGTIEATIKLVEELG------------------------------------------ 138 ABS75734 134 LATGGSAVEAINSL---------------------------------------------- 147 ABS74081 423 KSIERTVKLATDSLTHVSETTDIRNAPAVRRANKAM------------------------ 458 ABS74081 570 MY---------------------------------------------------------- 571 ABS76054 374 ------------------------------------------------------------ 375 ABS74744 90 ------------------------------------------------------------ 91 ABS74336 132 FYTGKTVRS--------------------------------------------------- 140 ABS74825 218 ------------------------------------------------------------ 219 ABS72555 1139 ------ QSLGMDVKILSGDEEEIEMRDLED------------------------------ 1162 1_0 168 EVDQND 173 ABS73893 168 EVDQTD 173 ABS75590 222 ------ 223 ABS72500 243 ------ 244 ABS72703 117 ------ 118 ABS74832 137 ------ 138 ABS75734 146 ------ 147 ABS74081 457 ------ 458 ABS74081 570 ------ 571 ABS76054 374 ------ 375 ABS74744 90 ------ 91 ABS74336 139 ------ 140 ABS74825 218 ------ 219 ABS72555 1161 ------ 1162 On Feb 19, 2008, at 10:17 AM, Jason Stajich wrote: > All the individual pairwise alignments won't necessarily be an > alignment of the same region and the gap insertions can be different > in each instance of the query sequence that is participating in the > pairwise alns so it won't fit into an MSA. > > It makes more sense to extract the aligned part of the hit sequences > identified and a subsequence of the query which is the min and max > region aligned. Run this through a MSA program. > > -jason > On Feb 19, 2008, at 6:42 AM, Johan Nilsson wrote: > >> Hello, >> >> I have a question regarding the conversion from a Blast search >> result (PSI-blast using blastpgp, to be more exact) to a multiple >> sequence alignment file. I'm running the >> Bio::Tools::Run::StandAloneBlast and I retrieve the HSPs from the >> resulting Bio::Search::Hit::HitI objects. I have no problems >> obtaining each HSP alignment using $hit->get_aln. However, rather >> than dumping many local alignments, I would like to write a single >> result file where the HSPs are interleaved. >> >> I guess this shouldn't be too hard, but nevertheless I haven't >> found out how to do this in a simple way. Any suggestions would be >> highly appreciated! >> >> Best Regards >> /Johan Nilsson >> _______________________________________________ >> 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 Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From hangsyin at gmail.com Tue Feb 19 19:20:18 2008 From: hangsyin at gmail.com (Hang) Date: Tue, 19 Feb 2008 16:20:18 -0800 (PST) Subject: [Bioperl-l] Bio::SeqIO fastq Message-ID: <15579570.post@talk.nabble.com> Hi, I'd like to read and write fastq entry. I don't know what is wrong with the following code: use Bio::SeqIO; my $in = Bio::SeqIO->new(-format => "fastq", -file => "test.fq"); while( my $seq = $in->next_seq ) { my $qual = $seq->qual; print $qual; } my test.fq file: @test AAAAA +test IIIII I got "Can't locate method 'qual' via package "AAAAA", perhaps you forgot to load "AAAAA?" at line XX ". Thanks Hang -- View this message in context: http://www.nabble.com/Bio%3A%3ASeqIO-fastq-tp15579570p15579570.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From heikki at sanbi.ac.za Wed Feb 20 15:12:40 2008 From: heikki at sanbi.ac.za (Heikki Lehvaslaiho) Date: Wed, 20 Feb 2008 22:12:40 +0200 Subject: [Bioperl-l] Bio::SeqIO fastq In-Reply-To: <15579570.post@talk.nabble.com> References: <15579570.post@talk.nabble.com> Message-ID: <200802202212.40772.heikki@sanbi.ac.za> Hang, It works for me. The last statement should be print "@$qual", "\n"; to print out readable values. Maybe you have an old version of BioPerl? Try: perl -MBio::Perl -le 'print Bio::Perl->VERSION;' I recommend installing the latest from CVS/SVN. -Heikki On Wednesday 20 February 2008 02:20:18 Hang wrote: > Hi, > > I'd like to read and write fastq entry. I don't know what is wrong with the > following code: > > use Bio::SeqIO; > my $in = Bio::SeqIO->new(-format => "fastq", > -file => "test.fq"); > while( my $seq = $in->next_seq ) { > my $qual = $seq->qual; > print $qual; > } > > my test.fq file: > @test > AAAAA > +test > IIIII > > I got "Can't locate method 'qual' via package "AAAAA", perhaps you forgot > to load "AAAAA?" at line XX ". > > Thanks > Hang -- ______ _/ _/_____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za _/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho _/ _/ _/ SANBI, South African National Bioinformatics Institute _/ _/ _/ University of Western Cape, South Africa _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 ___ _/_/_/_/_/________________________________________________________ From j.s.soares at gmail.com Wed Feb 20 18:04:35 2008 From: j.s.soares at gmail.com (Djodja) Date: Wed, 20 Feb 2008 15:04:35 -0800 (PST) Subject: [Bioperl-l] Bio::SeqIO fastq In-Reply-To: <200802202212.40772.heikki@sanbi.ac.za> References: <15579570.post@talk.nabble.com> <200802202212.40772.heikki@sanbi.ac.za> Message-ID: <15601113.post@talk.nabble.com> Hang, It works fine for me as well. My Bioperl version is: djodja at djodja-desktop:~$ perl -MBio::Perl -le 'print Bio::Perl->VERSION;' 1.005002102 djodja at djodja-desktop:~$ Maybe that is the problem. All the best, Djodja -- View this message in context: http://www.nabble.com/Bio%3A%3ASeqIO-fastq-tp15579570p15601113.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From shameer at ncbs.res.in Wed Feb 20 04:35:43 2008 From: shameer at ncbs.res.in (K. Shameer) Date: Wed, 20 Feb 2008 15:05:43 +0530 (IST) Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> Message-ID: <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> Dear All, Is there any module available in Bioperl that can be used to perform clustering of Gene Ontology terms from a set of Gene IDs and its respective Flybase GO annotations. These Gene IDs where hits from a high-throughput experiment. We would like to find the GO-Term enriched areas to get better biological insight irrespective of the experimental parameters. I am extremely sorry if this is off-topic : Can you please point me towards any paper/libraries that had used Gene Ontology based clustering ? Many thanks in advance, -- K. Shameer Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group National Centre for Biological Sciences (TIFR) GKVK Campus, Bangalore - 65, Karnataka - India T - 91-080-23666001 EXT - 6251 W - http://www.ncbs.res.in From sdavis2 at mail.nih.gov Thu Feb 21 06:54:47 2008 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Thu, 21 Feb 2008 06:54:47 -0500 Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> Message-ID: <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> On Wed, Feb 20, 2008 at 4:35 AM, K. Shameer wrote: > Dear All, > > Is there any module available in Bioperl that can be used to perform > clustering of Gene Ontology terms from a set of Gene IDs and its > respective Flybase GO annotations. These Gene IDs where hits from a > high-throughput experiment. We would like to find the GO-Term enriched > areas to get better biological insight irrespective of the experimental > parameters. > > I am extremely sorry if this is off-topic : > Can you please point me towards any paper/libraries that had used Gene > Ontology based clustering ? I'm not sure what you mean by GO clustering. However, there are a number of packages that will look for enriched GO terms given a set of Gene IDs. If you are looking for programmatic support for custom pipelines, you can look at R/Bioconductor. Here is a website that will look for GO enrichment and takes Flybase IDs as the gene identifier: http://niaid.abcc.ncifcrf.gov/home.jsp Sean From thiago.venancio at gmail.com Thu Feb 21 07:00:10 2008 From: thiago.venancio at gmail.com (Thiago M. Venancio) Date: Thu, 21 Feb 2008 09:00:10 -0300 Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> Message-ID: <44255ea80802210400u6e5242fdpae4c724621395f05@mail.gmail.com> Hi, This is off topic, but here we go. For enrichment analysis, I use Ontologizer: http://www.charite.de/ch/medgen/ontologizer/ But I am also not sure what do you mean by clustering. Best. T On Thu, Feb 21, 2008 at 8:54 AM, Sean Davis wrote: > On Wed, Feb 20, 2008 at 4:35 AM, K. Shameer wrote: > > Dear All, > > > > Is there any module available in Bioperl that can be used to perform > > clustering of Gene Ontology terms from a set of Gene IDs and its > > respective Flybase GO annotations. These Gene IDs where hits from a > > high-throughput experiment. We would like to find the GO-Term enriched > > areas to get better biological insight irrespective of the experimental > > parameters. > > > > I am extremely sorry if this is off-topic : > > Can you please point me towards any paper/libraries that had used Gene > > Ontology based clustering ? > > I'm not sure what you mean by GO clustering. However, there are a > number of packages that will look for enriched GO terms given a set of > Gene IDs. If you are looking for programmatic support for custom > pipelines, you can look at R/Bioconductor. > > Here is a website that will look for GO enrichment and takes Flybase > IDs as the gene identifier: > > http://niaid.abcc.ncifcrf.gov/home.jsp > > Sean > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- "At the center of your being you have the answer; You know who you are and you know what you want." Lao Tzu ======================== Thiago Motta Venancio, M.Sc., PhD Laboratory of Bioinformatics University of Sao Paulo ======================== From shameer at ncbs.res.in Thu Feb 21 07:29:01 2008 From: shameer at ncbs.res.in (K. Shameer) Date: Thu, 21 Feb 2008 17:59:01 +0530 (IST) Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> Message-ID: <60630.192.168.1.1.1203596941.squirrel@mail.ncbs.res.in> Dear All, Thanks for your reply. > I'm not sure what you mean by GO clustering. However, there are a > number of packages that will look for enriched GO terms given a set of > Gene IDs. In simple terms I have a list of genes, irrespective of any experimental value I need to cluster them based on their GO-Terms using the Di Acyclic Graph data structure of the Gene ontology databases. I found an interesting package from CPAN : GO::TermFinder . http://search.cpan.org/dist/GO-TermFinder/ I am not sure if this is a part of Bioperl :). I have tried with few examples it is working fine but I got few wrong results. If this is not part of Bioperl project, I may need to write to the authors. > If you are looking for programmatic support for custom > pipelines, you can look at R/Bioconductor. Thanks a lot !! I have seen a couple of R packages related to GO. But, I honestly wanted to do it in Perl :) !!! > > Here is a website that will look for GO enrichment and takes Flybase > IDs as the gene identifier: > http://niaid.abcc.ncifcrf.gov/home.jsp Thanks for the link. But I am specifically for something stand alone due to huge volume of my dataset. Cheers, Shameer NCBS - TIFR From golharam at umdnj.edu Thu Feb 21 07:26:58 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 21 Feb 2008 07:26:58 -0500 Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <44255ea80802210400u6e5242fdpae4c724621395f05@mail.gmail.com> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> <44255ea80802210400u6e5242fdpae4c724621395f05@mail.gmail.com> Message-ID: <47BD6E12.3000808@umdnj.edu> ArrayTrack is a good tool to do this, available from the FDA. It has some nice output and performs some statistical analysis for you. I'm using it now to cluster GO terms. Thiago M. Venancio wrote: > Hi, > This is off topic, but here we go. > For enrichment analysis, I use Ontologizer: > > http://www.charite.de/ch/medgen/ontologizer/ > > But I am also not sure what do you mean by clustering. > > Best. > > T > > On Thu, Feb 21, 2008 at 8:54 AM, Sean Davis wrote: > >> On Wed, Feb 20, 2008 at 4:35 AM, K. Shameer wrote: >>> Dear All, >>> >>> Is there any module available in Bioperl that can be used to perform >>> clustering of Gene Ontology terms from a set of Gene IDs and its >>> respective Flybase GO annotations. These Gene IDs where hits from a >>> high-throughput experiment. We would like to find the GO-Term enriched >>> areas to get better biological insight irrespective of the experimental >>> parameters. >>> >>> I am extremely sorry if this is off-topic : >>> Can you please point me towards any paper/libraries that had used Gene >>> Ontology based clustering ? >> I'm not sure what you mean by GO clustering. However, there are a >> number of packages that will look for enriched GO terms given a set of >> Gene IDs. If you are looking for programmatic support for custom >> pipelines, you can look at R/Bioconductor. >> >> Here is a website that will look for GO enrichment and takes Flybase >> IDs as the gene identifier: >> >> http://niaid.abcc.ncifcrf.gov/home.jsp >> >> Sean >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > From cjfields at uiuc.edu Thu Feb 21 09:21:14 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 21 Feb 2008 08:21:14 -0600 Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <60630.192.168.1.1.1203596941.squirrel@mail.ncbs.res.in> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> <60630.192.168.1.1.1203596941.squirrel@mail.ncbs.res.in> Message-ID: <96A3AC13-1963-4802-8ADA-77D00B393823@uiuc.edu> On Feb 21, 2008, at 6:29 AM, K. Shameer wrote: > Dear All, > > Thanks for your reply. > >> I'm not sure what you mean by GO clustering. However, there are a >> number of packages that will look for enriched GO terms given a set >> of >> Gene IDs. > > In simple terms I have a list of genes, irrespective of any > experimental > value I need to cluster them based on their GO-Terms using the Di > Acyclic > Graph data structure of the Gene ontology databases. > > I found an interesting package from CPAN : GO::TermFinder . > http://search.cpan.org/dist/GO-TermFinder/ > > I am not sure if this is a part of Bioperl :). I have tried with few > examples it is working fine but I got few wrong results. If this is > not > part of Bioperl project, I may need to write to the authors. It's not part of BioPerl, so you should contact the author. >> If you are looking for programmatic support for custom >> pipelines, you can look at R/Bioconductor. > > Thanks a lot !! I have seen a couple of R packages related to GO. > But, I > honestly wanted to do it in Perl :) !!! >> BioPerl's ontology classes are all in Bio::Ontology and Bio::OntologyIO. I would also recommend looking at Chris Mungall's go- perl: http://search.cpan.org/~cmungall/go-perl-0.08/go-perl.pod >> Here is a website that will look for GO enrichment and takes Flybase >> IDs as the gene identifier: >> http://niaid.abcc.ncifcrf.gov/home.jsp > > Thanks for the link. But I am specifically for something stand alone > due > to huge volume of my dataset. > > Cheers, > Shameer > NCBS - TIFR It's always faster to do it locally, I agree, as long as the tools are available to do so. chris From donald.jackson at bms.com Thu Feb 21 09:01:51 2008 From: donald.jackson at bms.com (Donald Jackson (Genomics)) Date: Thu, 21 Feb 2008 09:01:51 -0500 Subject: [Bioperl-l] qury In-Reply-To: <4e5ea6f60802191727x1980d2c8p4783300b4223cd5f@mail.gmail.com> References: <4e5ea6f60802191727x1980d2c8p4783300b4223cd5f@mail.gmail.com> Message-ID: <47BD844F.4070801@bms.com> Hi Somil, I get the same error from my test script. It will be a few days before I can troubleshoot and upload the fix to CVS; I'll let you know when I've posted the fix. Don Jackson Somil Dutt wrote: >Hello > >I used the SiRNA tool which is written below > > >use Bio::Tools::SiRNA; > >* > my $sirna_designer = Bio::Tools::SiRNA->new( -target => $bio_seq, > -rules => 'saigo' > ); > my @pairs = $sirna_designer->design; > > foreach $pair (@pairs) { > my $sense_oligo_sequence = $pair->sense->seq; > my $antisense_oligo_sequence = $pair->antisense->seq; > > # print out results > print join ("\t", $pair->start, $pair->end, $pair->rank, > $sense_oligo_sequence, $antisense_oligo_sequence), "\n";* > } > > >But the following problem > >------------- EXCEPTION Bio::Root::BadParameter ------------- >MSG: Target must be passed as a Bio::Seq object >STACK Bio::Tools::SiRNA::target C:/Perl/site/lib/Bio/Tools/SiRNA.pm:220 >STACK Bio::Tools::SiRNA::new C:/Perl/site/lib/Bio/Tools/SiRNA.pm:198 >STACK toplevel start.pl:32 > >I dont understand why this error is coming. > >Regards > > From shameer at ncbs.res.in Thu Feb 21 14:12:16 2008 From: shameer at ncbs.res.in (K. Shameer) Date: Fri, 22 Feb 2008 00:42:16 +0530 (IST) Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <96A3AC13-1963-4802-8ADA-77D00B393823@uiuc.edu> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> <60630.192.168.1.1.1203596941.squirrel@mail.ncbs.res.in> <96A3AC13-1963-4802-8ADA-77D00B393823@uiuc.edu> Message-ID: <39220.192.168.1.1.1203621136.squirrel@mail.ncbs.res.in> >> I am not sure if this is a part of Bioperl :). I have tried with few >> examples it is working fine but I got few wrong results. If this is >> not part of Bioperl project, I may need to write to the authors. > > It's not part of BioPerl, so you should contact the author. Thanks Chris, Is there any specific way to check installed bioperl modules ? > > BioPerl's ontology classes are all in Bio::Ontology and > Bio::OntologyIO. I would also recommend looking at Chris Mungall's go- > perl: > > http://search.cpan.org/~cmungall/go-perl-0.08/go-perl.pod Thanks for the information. > It's always faster to do it locally, I agree, as long as the tools are > available to do so. :) K. Shameer NCBS - TIFR From cjfields at uiuc.edu Thu Feb 21 23:37:54 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 21 Feb 2008 22:37:54 -0600 Subject: [Bioperl-l] Bio::Graphics and perl 5.10 Message-ID: <25A5CCCB-CE0F-4E12-8C31-451775C7FB4E@uiuc.edu> I'm getting a single failed test for Bio::Graphics in bioperl-live which appears to be perl 5.10-specific and is related to Bio::Graphics::FeatureFile: t/BioGraphics...... 1..35 ok 1 - use Bio::Graphics::FeatureFile; ok 2 - use Bio::Graphics::Panel; ok 3 not ok 4 # Failed test at t/BioGraphics.t line 49. # got: '7' # expected: '5' ok 5 ok 6 ok 7 ok 8 ... It appears to be coming from render() passing two extra tracks under perl 5.10 over what is passed in perl 5.8. If anyone is running perl 5.10, can they test this out? chris From cjfields at uiuc.edu Fri Feb 22 11:28:01 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 22 Feb 2008 10:28:01 -0600 Subject: [Bioperl-l] Bio::Graphics and perl 5.10 In-Reply-To: <25A5CCCB-CE0F-4E12-8C31-451775C7FB4E@uiuc.edu> References: <25A5CCCB-CE0F-4E12-8C31-451775C7FB4E@uiuc.edu> Message-ID: <116A7145-55FD-4254-AA94-1D1AAD8D7853@uiuc.edu> (cc'ing to gbrowse list as this pertains somewhat...) Just added a bioperl bug report for this along with the png file output from perl 5.8 and perl 5.10: http://bugzilla.open-bio.org/show_bug.cgi?id=2457 Lincoln's recent commits to Bio::Graphics::FeatureFile didn't fix the issue. However, it is now pinpointing the problem for both perl 5.8 and perl 5.10 (same warning for both, with only perl 5.10 failing): 1..35 ok 1 - use Bio::Graphics::FeatureFile; ok 2 - use Bio::Graphics::Panel; ok 3 Cosmid EST FGENESH SwissProt P-element / yk53c10.3 yk53c10.5 at Bio/ Graphics/FeatureFile.pm line 285. not ok 4 # Failed test at t/BioGraphics.t line 49. # got: '7' # expected: '5' ok 5 ok 6 ok 7 ok 8 ... chris On Feb 21, 2008, at 10:37 PM, Chris Fields wrote: > I'm getting a single failed test for Bio::Graphics in bioperl-live > which appears to be perl 5.10-specific and is related to > Bio::Graphics::FeatureFile: > > t/BioGraphics...... > 1..35 > ok 1 - use Bio::Graphics::FeatureFile; > ok 2 - use Bio::Graphics::Panel; > ok 3 > not ok 4 > > # Failed test at t/BioGraphics.t line 49. > # got: '7' > # expected: '5' > ok 5 > ok 6 > ok 7 > ok 8 > ... > > It appears to be coming from render() passing two extra tracks under > perl 5.10 over what is passed in perl 5.8. If anyone is running > perl 5.10, can they test this out? > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From heikki at sanbi.ac.za Mon Feb 25 01:18:33 2008 From: heikki at sanbi.ac.za (Heikki Lehvaslaiho) Date: Mon, 25 Feb 2008 08:18:33 +0200 Subject: [Bioperl-l] GN line parsing from Uniprot/Swiss-Prot Message-ID: <200802250818.33345.heikki@sanbi.ac.za> There has been an longstanding problem with GN (gene name) line parsing in SwissProt format. It has solved in a way that deals with all the complexity in that line but unfortunately is not backward compatible. You have to upgrade your scripts if you use bioperl-live. This documentation is now part of Bio::SeqIO::swiss.pm: =head2 GN (Gene name) line management details A Uniprot/Swiss-Prot entry holds information on one protein sequence. If that sequence is identical across genes and species, they are all merged into one entry. This creates complex needs for several annotation fields in swiss-prot format. The latest syntax for GN line is described in the user manual: http://www.expasy.ch/sprot/userman.html#GN_line Each of the possibly multiple genes in an entry can have Name, Synonyms (only if there is a name), OrderedLocusNames (names from genomic sequences) and ORFNames (temporary or cosmid names). "Name" here really means "symbol". This complexity is now dealth with the following way: Each gene is an Bio::Annotation::Collection object that is accessed like all other annotations. The tag name is 'gene_name': my @genes = $seq->annotation->get_Annotations('gene_name'); Note that if you are not interested in the complexity of multiple genes, you can easily just take the first value: my ($gene) = $seq->annotation->get_Annotations('gene_name'); None of the four categories for gene_names are obligatory, so you have to test returned objects for existence before using them: my ($name) = $gene->get_Annotations('name'); if ($name) { print "The official gene symbol is: ". $name->value. "\n"; } The can be only one name, so $name is a Bio::Annotation::SimpleValue object. In other categories (tags: synonyms, orderedlocusnames, orfnames; all lower case) there can be more than one value, so they are stored in Bio::Annotation::StructuredValue objects. There can be only one object with a given tag within a given gene. All values for that category are stored in an ordered list within the StructureValue object. e.g: if ( my ($synonyms) = $gene->get_Annotations('synonyms') ) { print "Synonyms: ". join(', ', $synonyms->get_all_values). "\n"; } Since Uniprot/Swiss-Prot format have been around for quite some time, the parser is also able to read in the older GN line syntax where genes are separated by AND and various symbols by OR. The first symbol is taken to be the name and the remaining ones are stored as synonyms. Thanks for Chris Fields for helping out, Enjoy, -Heikki -- ______ _/ _/_____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za _/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho _/ _/ _/ SANBI, South African National Bioinformatics Institute _/ _/ _/ University of Western Cape, South Africa _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 ___ _/_/_/_/_/________________________________________________________ From hangsyin at gmail.com Thu Feb 21 16:14:05 2008 From: hangsyin at gmail.com (Hang) Date: Thu, 21 Feb 2008 13:14:05 -0800 (PST) Subject: [Bioperl-l] Bio::SeqIO fastq In-Reply-To: <15601113.post@talk.nabble.com> References: <15579570.post@talk.nabble.com> <200802202212.40772.heikki@sanbi.ac.za> <15601113.post@talk.nabble.com> Message-ID: <15618960.post@talk.nabble.com> Heikki and Djodja, Many thanks for you guys' help! That code is working right now. Hang Djodja wrote: > > Hang, > > It works fine for me as well. > > My Bioperl version is: > > djodja at djodja-desktop:~$ perl -MBio::Perl -le 'print Bio::Perl->VERSION;' > > 1.005002102 > > djodja at djodja-desktop:~$ > > Maybe that is the problem. > > All the best, > > Djodja > > > -- View this message in context: http://www.nabble.com/Bio%3A%3ASeqIO-fastq-tp15579570p15618960.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From sheila.zuniga at sistemasgenomicos.com Mon Feb 25 10:48:18 2008 From: sheila.zuniga at sistemasgenomicos.com (=?iso-8859-1?Q?Sheila_Zu=F1iga_Trejos?=) Date: Mon, 25 Feb 2008 16:48:18 +0100 Subject: [Bioperl-l] bioperl installation problems with CPAN Message-ID: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Dear Sir, I'm trying to install Bioperl using CPAN but it seems impossible. I get several error messages when running cpan > install Bundle::CPAN. Please find attached a file containing these error messages. Any idea of what is happening? Thanks very much for your help, Sheila -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: error.txt URL: From rchu at coh.org Mon Feb 25 16:33:10 2008 From: rchu at coh.org (Roy) Date: Mon, 25 Feb 2008 21:33:10 +0000 (UTC) Subject: [Bioperl-l] SeqIO and large GenBank files Message-ID: Hi everyone, I want to parse some of the .gbk RefSeq files from ncbi, more specifically, ref_chr*.gbk. My script seems to open the sequence stream okay, but when I try to get the next sequence in the stream, my script spits out a lot of warnings of subroutine redefinitions. Is this file incompatible with SeqIO genbank reader? Any insight is appreciated, thanks. Roy test file: ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_01 ===start_code=== #!/usr/bin/perl -w use strict; use warnings; use Bio::Perl; use Bio::SeqIO; my $USAGE = "usage: $0 \n\n"; unless (@ARGV) { print $USAGE; exit; } my $stream = Bio::SeqIO->new(-file => $ARGV[0], -format => "genbank"); my $seq_obj = $stream->next_seq; exit; ===end_code=== ===start warnings=== Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 80, line 36. Subroutine start redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 102, line 36. Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 128, line 36. Subroutine length redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 165, line 36. Subroutine location_type redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 256, line 36. Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 303, line 36. Subroutine trunc redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 334, line 36. Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 91, line 49. Subroutine each_Location redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 123, line 49. Subroutine sub_Location redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 152, line 49. Subroutine add_sub_Location redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 221, line 49. Subroutine splittype redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 245, line 49. Subroutine is_single_sequence redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 273, line 49. Subroutine guide_strand redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 298, line 49. Subroutine strand redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 326, line 49. Subroutine flip_strand redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 367, line 49. Subroutine start redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 388, line 49. Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 407, line 49. Subroutine min_start redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 426, line 49. Subroutine max_start redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 448, line 49. Subroutine start_pos_type redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 471, line 49. Subroutine min_end redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 492, line 49. Subroutine max_end redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 515, line 49. Subroutine end_pos_type redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 539, line 49. Subroutine seq_id redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 565, line 49. Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 611, line 49. Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 134, line 747. Subroutine location_type redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 161, line 747. Subroutine start redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 223, line 747. Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 250, line 747. Subroutine min_start redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 277, line 747. Subroutine max_start redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 296, line 747. Subroutine start_pos_type redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 316, line 747. Subroutine min_end redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 346, line 747. Subroutine max_end redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 365, line 747. Subroutine end_pos_type redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 385, line 747. Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 456, line 747. Subroutine _fuzzypointdecode redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 557, line 747. ==end warnings== From cjfields at uiuc.edu Mon Feb 25 17:17:49 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 25 Feb 2008 16:17:49 -0600 Subject: [Bioperl-l] SeqIO and large GenBank files In-Reply-To: References: Message-ID: <4F9A56D3-1EAE-4916-A2F6-E10DB4CE3C18@uiuc.edu> The perl executable is overly paranoid on Windows for some reason when the '-w' flag is set on the shebang line ('#!/usr/bin/perl -w'); it doesn't like method overloading for some reason. Remove it and the warnings should go away (note: you should still leave 'use strict' and 'use warnings'). chris On Feb 25, 2008, at 3:33 PM, Roy wrote: > Hi everyone, > > I want to parse some of the .gbk RefSeq files from ncbi, more > specifically, > ref_chr*.gbk. My script seems to open the sequence stream okay, but > when I try > to get the next sequence in the stream, my script spits out a lot of > warnings of > subroutine redefinitions. Is this file incompatible with SeqIO > genbank reader? > Any insight is appreciated, thanks. > > Roy > > test file: > > ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_01 > > ===start_code=== > #!/usr/bin/perl -w > use strict; > use warnings; > use Bio::Perl; > use Bio::SeqIO; > my $USAGE = "usage: $0 \n\n"; > unless (@ARGV) { > print $USAGE; > exit; > } > my $stream = Bio::SeqIO->new(-file => $ARGV[0], -format => "genbank"); > my $seq_obj = $stream->next_seq; > exit; > ===end_code=== > > ===start warnings=== > Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Simple.pm > line 80, > line 36. > Subroutine start redefined at C:/Perl/site/lib/Bio\Location > \Simple.pm line 102, > line 36. > Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Simple.pm > line 128, > line 36. > Subroutine length redefined at C:/Perl/site/lib/Bio\Location > \Simple.pm line 165, > line 36. > Subroutine location_type redefined at C:/Perl/site/lib/Bio\Location > \Simple.pm > line 256, line 36. > Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location > \Simple.pm line > 303, line 36. > Subroutine trunc redefined at C:/Perl/site/lib/Bio\Location > \Simple.pm line 334, > line 36. > Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Split.pm > line 91, > line 49. > Subroutine each_Location redefined at C:/Perl/site/lib/Bio\Location > \Split.pm > line 123, line 49. > Subroutine sub_Location redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 152, line 49. > Subroutine add_sub_Location redefined at C:/Perl/site/lib/Bio > \Location\Split.pm > line 221, line 49. > Subroutine splittype redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 245, line 49. > Subroutine is_single_sequence redefined at > C:/Perl/site/lib/Bio\Location\Split.pm line 273, line 49. > Subroutine guide_strand redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 298, line 49. > Subroutine strand redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line 326, > line 49. > Subroutine flip_strand redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 367, line 49. > Subroutine start redefined at C:/Perl/site/lib/Bio\Location\Split.pm > line 388, > line 49. > Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Split.pm > line 407, > line 49. > Subroutine min_start redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 426, line 49. > Subroutine max_start redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 448, line 49. > Subroutine start_pos_type redefined at C:/Perl/site/lib/Bio\Location > \Split.pm > line 471, line 49. > Subroutine min_end redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line 492, > line 49. > Subroutine max_end redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line 515, > line 49. > Subroutine end_pos_type redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 539, line 49. > Subroutine seq_id redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line 565, > line 49. > Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 611, line 49. > Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm > line 134, > line 747. > Subroutine location_type redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm > line 161, line 747. > Subroutine start redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm > line 223, > line 747. > Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm > line 250, > line 747. > Subroutine min_start redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm line > 277, line 747. > Subroutine max_start redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm line > 296, line 747. > Subroutine start_pos_type redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm > line 316, line 747. > Subroutine min_end redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm line 346, > line 747. > Subroutine max_end redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm line 365, > line 747. > Subroutine end_pos_type redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm line > 385, line 747. > Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm line > 456, line 747. > Subroutine _fuzzypointdecode redefined at C:/Perl/site/lib/Bio > \Location\Fuzzy.pm > line 557, line 747. > ==end warnings== > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From Russell.Smithies at agresearch.co.nz Mon Feb 25 17:12:39 2008 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 26 Feb 2008 11:12:39 +1300 Subject: [Bioperl-l] Bio::Assembly::IO problems In-Reply-To: <000001c877c5$d8dc2d70$7000000a@sistemas.local> References: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Message-ID: Is the Bio::Assembly::IO stuff working? I want to parse some .ace files but keep getting errors: [smithiesr at impala ace_phrap]$ perl 454_read_ace.pl Can't call method "get_consensus_sequence" on an undefined value at /usr/lib/perl5/site_perl/5.8.8/Bio/Assembly/IO/ace.pm line 169, line 20. My code is: #!perl -w use Bio::Assembly::IO; use Data::Dumper; my $in = "454Contigs.ace"; $io = new Bio::Assembly::IO(-file=>$in,-format=>"ace"); $ass = $io->next_assembly; print Dumper $ass; exit; any ideas? Thanx, Russell Smithies Bioinformatics Software Developer T +64 3 489 9085 E? russell.smithies at agresearch.co.nz Invermay? Research Centre Puddle Alley, Mosgiel, New Zealand T? +64 3 489 3809?? F? +64 3 489 9174? www.agresearch.co.nz ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From cjfields at uiuc.edu Mon Feb 25 18:01:42 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 25 Feb 2008 17:01:42 -0600 Subject: [Bioperl-l] Bio::Assembly::IO problems In-Reply-To: References: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Message-ID: <5827D6E2-B798-4001-84DB-8C38586D3CF2@uiuc.edu> Russell, Using the test data from the bioperl installation appears to work, but I wouldn't be surprised if this is a bug. Can you file this as a bug along with some test data? http://bugzilla.open-bio.org/ chris On Feb 25, 2008, at 4:12 PM, Smithies, Russell wrote: > Is the Bio::Assembly::IO stuff working? > I want to parse some .ace files but keep getting errors: > > [smithiesr at impala ace_phrap]$ perl 454_read_ace.pl > Can't call method "get_consensus_sequence" on an undefined value > at /usr/lib/perl5/site_perl/5.8.8/Bio/Assembly/IO/ace.pm line 169, > line 20. > > My code is: > > #!perl -w > > use Bio::Assembly::IO; > use Data::Dumper; > > my $in = "454Contigs.ace"; > > $io = new Bio::Assembly::IO(-file=>$in,-format=>"ace"); > $ass = $io->next_assembly; > > print Dumper $ass; > exit; > > any ideas? > > Thanx, > > Russell Smithies > > Bioinformatics Software 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 > > > = > ====================================================================== > 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 Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From rchu at coh.org Mon Feb 25 18:21:26 2008 From: rchu at coh.org (Roy) Date: Mon, 25 Feb 2008 23:21:26 +0000 (UTC) Subject: [Bioperl-l] SeqIO and large GenBank files References: <4F9A56D3-1EAE-4916-A2F6-E10DB4CE3C18@uiuc.edu> Message-ID: Chris Fields uiuc.edu> writes: > > The perl executable is overly paranoid on Windows for some reason when > the '-w' flag is set on the shebang line ('#!/usr/bin/perl -w'); it > doesn't like method overloading for some reason. Remove it and the > warnings should go away (note: you should still leave 'use strict' and > 'use warnings'). > > chris Thanks Chris. Your suggestion worked. I was concerned that there may be some other error because it was taking an ungodly amount of time to process, but that resolved the problems. -Roy From Russell.Smithies at agresearch.co.nz Mon Feb 25 18:23:06 2008 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 26 Feb 2008 12:23:06 +1300 Subject: [Bioperl-l] Bio::Assembly::IO problems - FIXED! In-Reply-To: References: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Message-ID: I solved the problem :-) The contig lines in our .ace files have a lower-case 'c' in the contig name instead of upper-case so weren't being found by this regex in ace.pm line 142: (/^CO Contig(\d+) (\d+) (\d+) (\d+) (\w+)/) && do { # New contig found! e.g: CO contig00001 711 12 6 U instead of: CO Contig00001 711 12 6 U Our contigs were generated with Newbler version 1.1.01.20. so might be something to watch out for in future. Russell Smithies Bioinformatics Software Developer T +64 3 489 9085 E? russell.smithies at agresearch.co.nz Invermay? Research Centre Puddle Alley, Mosgiel, New Zealand T? +64 3 489 3809?? F? +64 3 489 9174? www.agresearch.co.nz > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open- > bio.org] On Behalf Of Smithies, Russell > Sent: Tuesday, 26 February 2008 11:13 a.m. > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] Bio::Assembly::IO problems > > Is the Bio::Assembly::IO stuff working? > I want to parse some .ace files but keep getting errors: > > [smithiesr at impala ace_phrap]$ perl 454_read_ace.pl > Can't call method "get_consensus_sequence" on an undefined value at > /usr/lib/perl5/site_perl/5.8.8/Bio/Assembly/IO/ace.pm line 169, line 20. > > My code is: > > #!perl -w > > use Bio::Assembly::IO; > use Data::Dumper; > > my $in = "454Contigs.ace"; > > $io = new Bio::Assembly::IO(-file=>$in,-format=>"ace"); > $ass = $io->next_assembly; > > print Dumper $ass; > exit; > > any ideas? > > Thanx, > > Russell Smithies > > Bioinformatics Software 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 > > > ============================================================= > ========== > 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 ======================================================================= 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 David.Messina at sbc.su.se Mon Feb 25 18:46:44 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 26 Feb 2008 00:46:44 +0100 Subject: [Bioperl-l] bioperl installation problems with CPAN In-Reply-To: <000001c877c5$d8dc2d70$7000000a@sistemas.local> References: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Message-ID: <628aabb70802251546i3f43212eo705e762bf34ec27a@mail.gmail.com> Hi Sheila, It looks like your cpan configuration has gotten messed up. It's giving invalid parameters to the make command: make: *** No hay ninguna regla para construir el objetivo `dual'. Alto. /usr/bin/make dual processor system -- NOT OK Go to the command line on your system. Enter the cpan shell: % cpan Type the following: cpan> o conf makepl_arg "" cpan> o conf commit That should reset the arguments that cpan adds to the make command. If that doesn't fix your problem, reset everything by typing cpan> o conf defaults cpan> o conf commit and see if that does it. Dave From schaffer at scripps.edu Mon Feb 25 20:04:50 2008 From: schaffer at scripps.edu (Lana Schaffer) Date: Mon, 25 Feb 2008 17:04:50 -0800 Subject: [Bioperl-l] statistics Message-ID: <8F897BD2B0EB714CB79B96D84911B30209E543@EXCHV1.lj.ad.scripps.edu> Hi, I want to know if Bioperl does t-tests and how to do it? Also, I need to get a chi-squared statistic. Thanks, Lana Schaffer Biostatistics/Informatics The Scripps Research Institute DNA Array Core Facility La Jolla, CA 92037 (858) 784-2263 (858) 784-2994 schaffer at scripps.edu From sdavis2 at mail.nih.gov Mon Feb 25 21:45:00 2008 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Mon, 25 Feb 2008 21:45:00 -0500 Subject: [Bioperl-l] statistics In-Reply-To: <8F897BD2B0EB714CB79B96D84911B30209E543@EXCHV1.lj.ad.scripps.edu> References: <8F897BD2B0EB714CB79B96D84911B30209E543@EXCHV1.lj.ad.scripps.edu> Message-ID: <264855a00802251845p25130950q5dbdc4228dbb2b93@mail.gmail.com> On Mon, Feb 25, 2008 at 8:04 PM, Lana Schaffer wrote: > Hi, > I want to know if Bioperl does t-tests and how to do it? > Also, I need to get a chi-squared statistic. Hi, Lana. I don't think bioperl offers this functionality. However, a quick search of cpan (http://search.cpan.org) turns up: http://search.cpan.org/~yunfang/Statistics-TTest-1.1.0/TTest.pm http://search.cpan.org/~dcantrell/Statistics-ChiSquare-0.5/lib/Statistics/ChiSquare.pm That said, I know you are an R user. I generally stick to R for any numerics. If you need both a parsing/data munging language and statistics, consider python, where the rpy package allows you access R from python and even does data conversion, etc. Sean From florent.angly at gmail.com Tue Feb 26 00:37:20 2008 From: florent.angly at gmail.com (Florent Angly) Date: Mon, 25 Feb 2008 21:37:20 -0800 Subject: [Bioperl-l] Bio::Assembly::IO problems - FIXED! In-Reply-To: References: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Message-ID: <47C3A590.4070204@gmail.com> As far as I know, there really isn't a specification of the ACE file format, that would rule if it is legal to have the kind of contig name (non capitalized), other that its original implementation in Phrap. According to the spirit of the ACE file format, my guess is that any contig name should be allowed. For example, on this webpage http://www.cbcb.umd.edu/research/contig_representation.shtml, the contig name is just a number. So please Russel file this as a bug so that the developers can keep track of this bug, Regards, Florent Smithies, Russell wrote: > I solved the problem :-) > The contig lines in our .ace files have a lower-case 'c' in the contig name instead of upper-case so weren't being found by this regex in ace.pm line 142: > (/^CO Contig(\d+) (\d+) (\d+) (\d+) (\w+)/) && do { # New contig found! > > e.g: > CO contig00001 711 12 6 U > instead of: > CO Contig00001 711 12 6 U > > Our contigs were generated with Newbler version 1.1.01.20. so might be something to watch out for in future. > > > Russell Smithies > > Bioinformatics Software Developer > T +64 3 489 9085 > E russell.smithies at agresearch.co.nz > > Invermay Research Centre > Puddle Alley, > Mosgiel, > New Zealand > T +64 3 489 3809 > F +64 3 489 9174 > www.agresearch.co.nz > > > > > > > > > >> -----Original Message----- >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open- >> bio.org] On Behalf Of Smithies, Russell >> Sent: Tuesday, 26 February 2008 11:13 a.m. >> To: bioperl-l at lists.open-bio.org >> Subject: [Bioperl-l] Bio::Assembly::IO problems >> >> Is the Bio::Assembly::IO stuff working? >> I want to parse some .ace files but keep getting errors: >> >> [smithiesr at impala ace_phrap]$ perl 454_read_ace.pl >> Can't call method "get_consensus_sequence" on an undefined value at >> /usr/lib/perl5/site_perl/5.8.8/Bio/Assembly/IO/ace.pm line 169, line 20. >> >> My code is: >> >> #!perl -w >> >> use Bio::Assembly::IO; >> use Data::Dumper; >> >> my $in = "454Contigs.ace"; >> >> $io = new Bio::Assembly::IO(-file=>$in,-format=>"ace"); >> $ass = $io->next_assembly; >> >> print Dumper $ass; >> exit; >> >> any ideas? >> >> Thanx, >> >> Russell Smithies >> >> Bioinformatics Software 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 >> >> >> ============================================================= >> ========== >> 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 >> > ======================================================================= > 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 David.Messina at sbc.su.se Tue Feb 26 05:47:36 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 26 Feb 2008 11:47:36 +0100 Subject: [Bioperl-l] bioperl installation problems with CPAN In-Reply-To: <000701c87857$15dd6d60$7000000a@sistemas.local> References: <628aabb70802251546i3f43212eo705e762bf34ec27a@mail.gmail.com> <000701c87857$15dd6d60$7000000a@sistemas.local> Message-ID: <628aabb70802260247h2d063d4ah489318aad66c4e6a@mail.gmail.com> Hi Sheila, Please be sure to keep bioperl-l on the Cc so that everyone can follow along the discussion. I don't think this is a BioPerl-specific problem. Can you successfully install other modules from CPAN? Could you type "o conf" in cpan and paste the results into your reply to this message? Dave On 2/26/08, Sheila Zu?iga Trejos wrote: > > Hi Dave, > I've tried the two options and in both cases I got the same error message. > I even restart the server both times in case it could make any difference > but nothing changed. > First attempt: > > Type: cpan> o conf makepl_arg "" > Return: makepl_arg > Type: cpan> o conf commit > Return: commit: wrote /etc/perl/CPAN/Config.pm > Type: cpan> install Bundle::CPAN > Return: error message attached (same as before) > > Second attempt: > > Type: cpan> o conf defaults > (did not return anything) > Type: cpan> o conf commit > Return: commit: wrote /etc/perl/CPAN/Config.pm > Type: cpan> install Bundle::CPAN > Return: error message attached (same as before) > > I installed Bioperl in Debian Sarge before and I never had any problem with CPAN but with Debian Etch...Well, I hope you have other ideas. > > Thanks very much for your help. > > Sheila > > ------------------------------ > *De:* dave at davemessina.com [mailto:dave at davemessina.com] *En nombre de *Dave > Messina > *Enviado el:* martes, 26 de febrero de 2008 0:47 > *Para:* Sheila Zu?iga Trejos > *CC:* bioperl-l at bioperl.org > *Asunto:* Re: [Bioperl-l] bioperl installation problems with CPAN > > Hi Sheila, > > It looks like your cpan configuration has gotten messed up. It's giving > invalid parameters to the make command: > > make: *** No hay ninguna regla para construir el objetivo `dual'. Alto. > > /usr/bin/make dual processor system -- NOT OK > > > > Go to the command line on your system. Enter the cpan shell: > > % cpan > > Type the following: > > cpan> o conf makepl_arg "" > cpan> o conf commit > > > That should reset the arguments that cpan adds to the make command. If > that doesn't fix your problem, reset everything by typing > > cpan> o conf defaults > cpan> o conf commit > > and see if that does it. > > > Dave > > > From David.Messina at sbc.su.se Tue Feb 26 06:43:35 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 26 Feb 2008 12:43:35 +0100 Subject: [Bioperl-l] bioperl installation problems with CPAN In-Reply-To: <001001c87868$4e11cb20$7000000a@sistemas.local> References: <628aabb70802260247h2d063d4ah489318aad66c4e6a@mail.gmail.com> <001001c87868$4e11cb20$7000000a@sistemas.local> Message-ID: <628aabb70802260343n43b216a2q580827e26266c8b6@mail.gmail.com> The following two lines show the problem: > make_arg dual processor system > make_install_arg to always uninstall potentially conflicting files > The configuration parameters are key-value pairs. So here the parameter "make_arg" is set to the value "dual processor system". "dual processor system" is not a valid command-line argument for the make program, so that's why cpan can't install BioPerl (or anything else, I would suspect). Type the following in cpan: cpan> o conf make_arg "" cpan> o conf make_install_arg "" cpan> o conf commit Then type cpan> o conf and verify that those two parameters have indeed been changed successfully. If so, then try installing BioPerl again. I think it should work, but let me know if not. Dave From sheila.zuniga at sistemasgenomicos.com Tue Feb 26 06:11:09 2008 From: sheila.zuniga at sistemasgenomicos.com (=?iso-8859-1?Q?Sheila_Zu=F1iga_Trejos?=) Date: Tue, 26 Feb 2008 12:11:09 +0100 Subject: [Bioperl-l] bioperl installation problems with CPAN In-Reply-To: <628aabb70802260247h2d063d4ah489318aad66c4e6a@mail.gmail.com> Message-ID: <001001c87868$4e11cb20$7000000a@sistemas.local> Hi Dave, Thanks for your quick reply. Here is the output: cpan> o conf CPAN::Config options from /etc/perl/CPAN/Config.pm: commit Commit changes to disk defaults Reload defaults from disk init Interactive setting of all options build_cache 10 build_dir /root/.cpan/build cache_metadata 1 cpan_home /root/.cpan cpan_version_check 1 dontload_hash ftp /usr/bin/ftp ftp_proxy getcwd cwd gpg /usr/bin/gpg gzip /bin/gzip histfile /root/.cpan/histfile histsize 100 http_proxy inactivity_timeout 0 index_expire 1 inhibit_startup_message 0 keep_source_where /root/.cpan/sources lynx make /usr/bin/make make_arg dual processor system make_install_arg to always uninstall potentially conflicting files makepl_arg ncftpget /usr/bin/ncftpget no_proxy pager /usr/bin/less prefer_installer MB prerequisites_policy ask scan_cache atstart shell /bin/bash tar /bin/tar term_is_latin 1 unzip /usr/bin/unzip urllist ftp://ftp.rediris.es/mirror/CPAN/ wget /usr/bin/wget Sheila _____ De: dave at davemessina.com [mailto:dave at davemessina.com] En nombre de Dave Messina Enviado el: martes, 26 de febrero de 2008 11:48 Para: Sheila Zu?iga Trejos CC: bioperl-l at bioperl.org Asunto: Re: [Bioperl-l] bioperl installation problems with CPAN Hi Sheila, Please be sure to keep bioperl-l on the Cc so that everyone can follow along the discussion. I don't think this is a BioPerl-specific problem. Can you successfully install other modules from CPAN? Could you type "o conf" in cpan and paste the results into your reply to this message? Dave On 2/26/08, Sheila Zu?iga Trejos wrote: Hi Dave, I've tried the two options and in both cases I got the same error message. I even restart the server both times in case it could make any difference but nothing changed. First attempt: Type: cpan> o conf makepl_arg "" Return: makepl_arg Type: cpan> o conf commit Return: commit: wrote /etc/perl/CPAN/Config.pm Type: cpan> install Bundle::CPAN Return: error message attached (same as before) Second attempt: Type: cpan> o conf defaults (did not return anything) Type: cpan> o conf commit Return: commit: wrote /etc/perl/CPAN/Config.pm Type: cpan> install Bundle::CPAN Return: error message attached (same as before) I installed Bioperl in Debian Sarge before and I never had any problem with CPAN but with Debian Etch... Well, I hope you have other ideas. Thanks very much for your help. Sheila _____ De: dave at davemessina.com [mailto:dave at davemessina.com] En nombre de Dave Messina Enviado el: martes, 26 de febrero de 2008 0:47 Para: Sheila Zu?iga Trejos CC: bioperl-l at bioperl.org Asunto: Re: [Bioperl-l] bioperl installation problems with CPAN Hi Sheila, It looks like your cpan configuration has gotten messed up. It's giving invalid parameters to the make command: make: *** No hay ninguna regla para construir el objetivo `dual'. Alto. /usr/bin/make dual processor system -- NOT OK Go to the command line on your system. Enter the cpan shell: % cpan Type the following: cpan> o conf makepl_arg "" cpan> o conf commit That should reset the arguments that cpan adds to the make command. If that doesn't fix your problem, reset everything by typing cpan> o conf defaults cpan> o conf commit and see if that does it. Dave From sheila.zuniga at sistemasgenomicos.com Tue Feb 26 06:54:53 2008 From: sheila.zuniga at sistemasgenomicos.com (=?iso-8859-1?Q?Sheila_Zu=F1iga_Trejos?=) Date: Tue, 26 Feb 2008 12:54:53 +0100 Subject: [Bioperl-l] bioperl installation problems with CPAN In-Reply-To: <628aabb70802260343n43b216a2q580827e26266c8b6@mail.gmail.com> Message-ID: <001801c8786e$6a04bc10$7000000a@sistemas.local> Hi Dave, You're right! It works! Thanks very much for your help. Sheila _____ De: dave at davemessina.com [mailto:dave at davemessina.com] En nombre de Dave Messina Enviado el: martes, 26 de febrero de 2008 12:44 Para: Sheila Zu?iga Trejos CC: bioperl-l at bioperl.org Asunto: Re: [Bioperl-l] bioperl installation problems with CPAN The following two lines show the problem: make_arg dual processor system make_install_arg to always uninstall potentially conflicting files The configuration parameters are key-value pairs. So here the parameter "make_arg" is set to the value "dual processor system". "dual processor system" is not a valid command-line argument for the make program, so that's why cpan can't install BioPerl (or anything else, I would suspect). Type the following in cpan: cpan> o conf make_arg "" cpan> o conf make_install_arg "" cpan> o conf commit Then type cpan> o conf and verify that those two parameters have indeed been changed successfully. If so, then try installing BioPerl again. I think it should work, but let me know if not. Dave From bix at sendu.me.uk Mon Feb 25 17:35:18 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 25 Feb 2008 22:35:18 +0000 Subject: [Bioperl-l] bioperl installation problems with CPAN In-Reply-To: <000001c877c5$d8dc2d70$7000000a@sistemas.local> References: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Message-ID: <47C342A6.7090009@sendu.me.uk> Sheila Zu?iga Trejos wrote: > Dear Sir, > I'm trying to install Bioperl using CPAN but it seems impossible. I get > several error messages when running cpan > install Bundle::CPAN. Please find > attached a file containing these error messages. > Any idea of what is happening? Looks like you've given one of the CPAN options (when you first ran CPAN it asked a bunch of questions) a dodgy value: 'dual processor system'. The easiest thing to do would be to delete your .cpan directory and start over, making sure to answer all the questions carefully and correctly. From bix at sendu.me.uk Tue Feb 26 05:34:04 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 26 Feb 2008 10:34:04 +0000 Subject: [Bioperl-l] statistics In-Reply-To: <264855a00802251845p25130950q5dbdc4228dbb2b93@mail.gmail.com> References: <8F897BD2B0EB714CB79B96D84911B30209E543@EXCHV1.lj.ad.scripps.edu> <264855a00802251845p25130950q5dbdc4228dbb2b93@mail.gmail.com> Message-ID: <47C3EB1C.2000407@sendu.me.uk> Sean Davis wrote: > On Mon, Feb 25, 2008 at 8:04 PM, Lana Schaffer wrote: >> Hi, >> I want to know if Bioperl does t-tests and how to do it? >> Also, I need to get a chi-squared statistic. > > Hi, Lana. I don't think bioperl offers this functionality. However, > a quick search of cpan (http://search.cpan.org) turns up: > > http://search.cpan.org/~yunfang/Statistics-TTest-1.1.0/TTest.pm > http://search.cpan.org/~dcantrell/Statistics-ChiSquare-0.5/lib/Statistics/ChiSquare.pm > > That said, I know you are an R user. I generally stick to R for any > numerics. If you need both a parsing/data munging language and > statistics, consider python, where the rpy package allows you access R > from python and even does data conversion, etc. There's also an R interface for perl: http://www.omegahat.org/RSPerl/ From johnsonm at gmail.com Tue Feb 26 19:47:02 2008 From: johnsonm at gmail.com (Mark Johnson) Date: Tue, 26 Feb 2008 18:47:02 -0600 Subject: [Bioperl-l] Bio::Tools::Run::Fgenesh anyone? Message-ID: We've got fgenesh/fgenesh+ installed locally and I'm going to need Bio::Tools::Run::Fgenesh for a nematode annotation pipeline. Does Bio::Tools::Fgenesh still need unit tests as well? Throw 'em in genpred.t with everything else? From jay at jays.net Thu Feb 28 15:25:29 2008 From: jay at jays.net (Jay Hannah) Date: Thu, 28 Feb 2008 14:25:29 -0600 Subject: [Bioperl-l] helpdesk@open-bio.org ... User unknown References: <200802281949.m1SJnIeD000744@ferret.jays.net> Message-ID: <78E7CE4E-9633-4015-B37C-A097D7F5B411@jays.net> Did I remember that address incorrectly? I'd look it up, but... :) j Begin forwarded message: > From: Mail Delivery Subsystem > Date: February 28, 2008 1:49:18 PM CST > To: > Subject: Returned mail: see transcript for details > > The original message was received at Thu, 28 Feb 2008 13:10:05 -0600 > from host-137-197-64-194.unmc.edu [137.197.64.194] > > ----- The following addresses had permanent fatal errors ----- > > (reason: 550 5.1.1 ... User unknown) > > ----- Transcript of session follows ----- > ... while talking to open-bio.org.: >>>> DATA > <<< 550 5.1.1 ... User unknown > 550 5.1.1 ... User unknown > <<< 503 5.0.0 Need RCPT (recipient) > Reporting-MTA: dns; ferret.jays.net > Arrival-Date: Thu, 28 Feb 2008 13:10:05 -0600 > > Final-Recipient: RFC822; helpdesk at open-bio.org > Action: failed > Status: 5.1.1 > Remote-MTA: DNS; open-bio.org > Diagnostic-Code: SMTP; 550 5.1.1 ... User > unknown > Last-Attempt-Date: Thu, 28 Feb 2008 13:49:18 -0600 > > From: Jay Hannah > Date: February 28, 2008 1:09:57 PM CST > To: helpdesk at open-bio.org > Subject: Websites are down? > > > Is this the right email address to report this to? > > I can't reach: > > http://bioperl.org > http://open-bio.org > > Thanks, > > j > > > > From David.Messina at sbc.su.se Thu Feb 28 16:56:46 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Thu, 28 Feb 2008 22:56:46 +0100 Subject: [Bioperl-l] helpdesk@open-bio.org ... User unknown In-Reply-To: <78E7CE4E-9633-4015-B37C-A097D7F5B411@jays.net> References: <200802281949.m1SJnIeD000744@ferret.jays.net> <78E7CE4E-9633-4015-B37C-A097D7F5B411@jays.net> Message-ID: <628aabb70802281356w693787e0r19aa80b56079182d@mail.gmail.com> Close. :) support at helpdesk.open-bio.org > I can't reach: > > > > http://bioperl.org > > http://open-bio.org Both work for me at the moment, by the way. Perhaps 'twas transient? Dave From cjfields at uiuc.edu Fri Feb 1 19:03:36 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 1 Feb 2008 13:03:36 -0600 Subject: [Bioperl-l] Odd issue with HSP::seq_inds() Message-ID: Apologies ahead of time for the longish post! While working on a recent bug (http://bugzilla.open-bio.org/show_bug.cgi?id=2436 ) I found a pretty significant bug. It appears that seq_inds() is giving some bad return values tied specifically to reports where either or both query or hit are translated. I'll file a full bug report but I felt it might be worth bringing up here to discuss specifically what values should be expected when these reports are parsed (all three nucleotide positions or only the first for each nonmatching translated position, etc). I used the following script to track the total HSPs as well as those where seq_inds() returns positions within the HSP bounds for query and hit: ------------------------------------------- use Bio::SearchIO; use Test::More qw(no_plan); my $file = shift || die; my $io = Bio::SearchIO->new(-format => 'blast', -file => $file); my ($hsp_co, $correctq, $correcth) = (0,0,0); while (my $res = $io->next_result) { while (my $hit = $res->next_hit) { while (my $hsp = $hit->next_hsp) { $hsp_co++; my ($qs, $qe, $hs, $he) = ($hsp->start('query'),$hsp- >end('query'), $hsp->start('hit'),$hsp- >end('hit')); my @pos = $hsp->seq_inds('query','nomatch'); my @pos2 = grep {$_ >= $qs && $_ <= $qe} @pos; # should always be true if (scalar(@pos2) == scalar(@pos)) { $correctq++; } @pos = $hsp->seq_inds('hit','nomatch'); @pos2 = grep {$_ >= $hs && $_ <= $he} @pos; # should always be true if (scalar(@pos2) == scalar(@pos)) { $correcth++; } } } } is($correctq, $hsp_co, 'Query seq_inds() positions fall within HSP bounds'); is($correcth, $hsp_co, 'Subject seq_inds() positions fall within HSP bounds'); ------------------------------------------- Here are the results for the following BLAST report types (culled from test reports used in SearchIO.t): BLASTN : both pass TBLASTN : query passes, subject fails BLASTX : query fails, subject passes TBLASTX : both fail When looking at the failed query seq_inds() data for the first HSP in the TBLASTX report used in SearchIO.t (HUMBETGLOA.tblastx), I get these positions for the query: 355 364 365 367 368 370 371 373 374 375 and for the hit: 1941 1942 1943 1945 1946 1948 1949 1951 1952 1961 This is the actual first HSP for that report: ------------------------------------------- >gb|AE000479.1|AE000479 Escherichia coli K-12 MG1655 section 369 of 400 of the complete genome Length = 10934 Score = 33.6 bits (67), Expect = 0.13 Identities = 11/26 (42%), Positives = 16/26 (61%) Frame = +1 / -2 Query: 1057 SAYWSIFPPLGCWWSTLGPRGSLSPL 1134 +A W++FPP+G W L + SPL Sbjct: 5893 AAVWALFPPVGSQWGCLASQWRTSPL 5816 ------------------------------------------- It looks like it has something to do with the positions getting divided by 3 but not converted back to correspond to the nucleotide position. When fixing this (and as mentioned above), do we want to only report the first nucleotide position where the mismatch occurs, or report the three positions corresponding to that codon region? Any thoughts? chris From tthmok at gmail.com Sun Feb 3 21:54:49 2008 From: tthmok at gmail.com (Terrance Mok) Date: Sun, 3 Feb 2008 14:54:49 -0700 Subject: [Bioperl-l] Problems Installing Bioperl 1.5.2 - Windows Message-ID: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> Hi I've been trying to install bioperl on a fresh install of ActivePerl on Windows. Following the installation guide using the GUI Perl Package Manager, I add the 4 locations and all of them list 0 packages except for "Bribes http://www.Bribes.org/perl/ppm ". Then when searching for bioperl (with all package view), nothing shows up since no packages are found for all the other locations I added. I've also had problems installing on Ubuntu (helping a friend), when using CPAN and following exactly the guide on the bioperl installation it will not work. When doing the install command in CPAN, install S/SE/SENDU/bioperl- 1.5.2_102.tar.gz she gets an error that "/home/username/.cpan/build/bioperl-1.5.2_102: No such file or directory at Makefile.PL line 25." From anjan.purkayastha at gmail.com Sun Feb 3 17:10:49 2008 From: anjan.purkayastha at gmail.com (ANJAN PURKAYASTHA) Date: Sun, 3 Feb 2008 12:10:49 -0500 Subject: [Bioperl-l] sequence object question Message-ID: hi, here is the problem i'm facing. i parse a genbank file with the statement: my $gb_stream = Bio::SeqIO->new( -file => 'gb_test_file', -format => 'GenBank'); while (my $seq_obj= $gb_stream->next_seq){ ..... } presumably $seq_obj is a Bio::Seq::RichSeq object. now, when I try: my $feat_obj($seq_obj->getSeqFeatures){ ..... } i get an error message: Can't locate object method "getSeqFeatures" via package "Bio::Seq::RichSeq" at gb_file_reader.pl line 11. on reading docs I find that Bio::Seq::RichSeq does not have a getSeqFeatures method. but, RIchSeq is a child of the Seq class, which HAS a getSeqFeatures method (i presume this method is also inherited by the RichSeq class). so, why am i getting an error message and how do i go about getting the features within each genbank file? appreciate any pointers. TIA. anjan -- ANJAN PURKAYASTHA, PhD. Senior Computational Biologist ========================== 1101 King Street, Suite 310, Alexandria, VA 22314. 703.518.8040 (office) 703.740.6939 (mobile) email: anjan at vbi.vt.edu; anjan.purkayastha at gmail.com http://www.vbi.vt.edu ========================== From jason at bioperl.org Sun Feb 3 23:51:21 2008 From: jason at bioperl.org (Jason Stajich) Date: Sun, 3 Feb 2008 15:51:21 -0800 Subject: [Bioperl-l] sequence object question In-Reply-To: References: Message-ID: <212091BA-2942-4A95-9329-AB76D8F102A5@bioperl.org> It is 'get_SeqFeatures' http://doc.bioperl.org/bioperl-live/Bio/FeatureHolderI.html#POD1 Deobfuscator: http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio %3A%3ASeq&sort_order=by+method&search_string=Bio%3A%3ASeq http://bioperl.org/cgi-bin/deob_detail.cgi? method=Bio::Seq::get_SeqFeatures HOWTO: http://bioperl.org/wiki/HOWTO:Feature-Annotation On Feb 3, 2008, at 9:10 AM, ANJAN PURKAYASTHA wrote: > hi, > here is the problem i'm facing. > > i parse a genbank file with the statement: > my $gb_stream = Bio::SeqIO->new( -file => 'gb_test_file', -format => > 'GenBank'); > while (my $seq_obj= $gb_stream->next_seq){ > ..... > > } > > presumably $seq_obj is a Bio::Seq::RichSeq object. > > now, when I try: > my $feat_obj($seq_obj->getSeqFeatures){ > ..... > } > i get an error message: Can't locate object method "getSeqFeatures" > via > package "Bio::Seq::RichSeq" at gb_file_reader.pl line 11. > > > on reading docs I find that Bio::Seq::RichSeq does not have a > getSeqFeatures > method. > but, RIchSeq is a child of the Seq class, which HAS a > getSeqFeatures method > (i presume this method is also inherited by the RichSeq class). > > so, why am i getting an error message and how do i go about getting > the > features within each genbank file? > > appreciate any pointers. > > TIA. > > anjan > > -- > ANJAN PURKAYASTHA, PhD. > Senior Computational Biologist > ========================== > > 1101 King Street, Suite 310, > Alexandria, VA 22314. > 703.518.8040 (office) > 703.740.6939 (mobile) > > email: > anjan at vbi.vt.edu; > anjan.purkayastha at gmail.com > > http://www.vbi.vt.edu > > ========================== > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From anjan.purkayastha at gmail.com Mon Feb 4 04:00:33 2008 From: anjan.purkayastha at gmail.com (ANJAN PURKAYASTHA) Date: Sun, 3 Feb 2008 23:00:33 -0500 Subject: [Bioperl-l] sequence object question In-Reply-To: <212091BA-2942-4A95-9329-AB76D8F102A5@bioperl.org> References: <212091BA-2942-4A95-9329-AB76D8F102A5@bioperl.org> Message-ID: Thanks a lot! On Feb 3, 2008 6:51 PM, Jason Stajich wrote: > It is 'get_SeqFeatures' > http://doc.bioperl.org/bioperl-live/Bio/FeatureHolderI.html#POD1 > > Deobfuscator: > http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio > %3A%3ASeq&sort_order=by+method&search_string=Bio%3A%3ASeq > http://bioperl.org/cgi-bin/deob_detail.cgi? > method=Bio::Seq::get_SeqFeatures > > HOWTO: > http://bioperl.org/wiki/HOWTO:Feature-Annotation > > > On Feb 3, 2008, at 9:10 AM, ANJAN PURKAYASTHA wrote: > > > hi, > > here is the problem i'm facing. > > > > i parse a genbank file with the statement: > > my $gb_stream = Bio::SeqIO->new( -file => 'gb_test_file', -format => > > 'GenBank'); > > while (my $seq_obj= $gb_stream->next_seq){ > > ..... > > > > } > > > > presumably $seq_obj is a Bio::Seq::RichSeq object. > > > > now, when I try: > > my $feat_obj($seq_obj->getSeqFeatures){ > > ..... > > } > > i get an error message: Can't locate object method "getSeqFeatures" > > via > > package "Bio::Seq::RichSeq" at gb_file_reader.pl line 11. > > > > > > on reading docs I find that Bio::Seq::RichSeq does not have a > > getSeqFeatures > > method. > > but, RIchSeq is a child of the Seq class, which HAS a > > getSeqFeatures method > > (i presume this method is also inherited by the RichSeq class). > > > > so, why am i getting an error message and how do i go about getting > > the > > features within each genbank file? > > > > appreciate any pointers. > > > > TIA. > > > > anjan > > > > -- > > ANJAN PURKAYASTHA, PhD. > > Senior Computational Biologist > > ========================== > > > > 1101 King Street, Suite 310, > > Alexandria, VA 22314. > > 703.518.8040 (office) > > 703.740.6939 (mobile) > > > > email: > > anjan at vbi.vt.edu; > > anjan.purkayastha at gmail.com > > > > http://www.vbi.vt.edu > > > > ========================== > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- ANJAN PURKAYASTHA, PhD. Senior Computational Biologist ========================== 1101 King Street, Suite 310, Alexandria, VA 22314. 703.518.8040 (office) 703.740.6939 (mobile) email: anjan at vbi.vt.edu; anjan.purkayastha at gmail.com http://www.vbi.vt.edu ========================== From bix at sendu.me.uk Mon Feb 4 08:45:31 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 04 Feb 2008 08:45:31 +0000 Subject: [Bioperl-l] Problems Installing Bioperl 1.5.2 - Windows In-Reply-To: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> References: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> Message-ID: <47A6D0AB.7050702@sendu.me.uk> Terrance Mok wrote: > Hi I've been trying to install bioperl on a fresh install of ActivePerl on > Windows. > Following the installation guide using the GUI Perl Package Manager, I add > the 4 locations and all of them list 0 packages except for "Bribes > http://www.Bribes.org/perl/ppm ". > Then when searching for bioperl (with all package view), nothing shows up > since no packages are found for all the other locations I added. Hopefully someone else will chime in, but perhaps there's something wrong with the server? Can anyone else confirm? > I've also had problems installing on Ubuntu (helping a friend), when using > CPAN and following exactly the guide on the bioperl installation it will not > work. When doing the install command in CPAN, install S/SE/SENDU/bioperl- > 1.5.2_102.tar.gz she gets an error that > "/home/username/.cpan/build/bioperl-1.5.2_102: No such file or directory at > Makefile.PL line 25." Hard to figure out what might be wrong without complete details. Can she install anything else via CPAN? Has she run out of disc space? From darren.obbard at ed.ac.uk Mon Feb 4 08:56:06 2008 From: darren.obbard at ed.ac.uk (Darren Obbard) Date: Mon, 04 Feb 2008 08:56:06 +0000 Subject: [Bioperl-l] Problems Installing Bioperl 1.5.2 - Windows In-Reply-To: <47A6D0AB.7050702@sendu.me.uk> References: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> <47A6D0AB.7050702@sendu.me.uk> Message-ID: <47A6D326.40103@ed.ac.uk> Hi, > Terrance Mok wrote: >> Then when searching for bioperl (with all package view), nothing >> shows up >> since no packages are found for all the other locations I added. > Hopefully someone else will chime in, but perhaps there's something > wrong with the server? Can anyone else confirm? Just to note that I too have had the same problem. From ca. 2 weeks ago I could see no packages on the recommended bioperl repository. I just assumed I was doing something wrong, and thought I'd wait until my need became urgent. -- Darren Obbard University of Edinburgh, UK From darren.obbard at ed.ac.uk Mon Feb 4 11:07:23 2008 From: darren.obbard at ed.ac.uk (Darren Obbard) Date: Mon, 04 Feb 2008 11:07:23 +0000 Subject: [Bioperl-l] Problems Installing Bioperl 1.5.2 - Windows In-Reply-To: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> References: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> Message-ID: <47A6F1EB.8060806@ed.ac.uk> Hi again, Having just looked, it seems fine on this machine (XP proffessional, sp2). The problem I was (and am) having are on a clean install of Vista (ultimate). Perhaps this is a vista/activestate issue? What versions of windows/activeperl are people having problems with? From cjfields at uiuc.edu Mon Feb 4 17:53:08 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 4 Feb 2008 11:53:08 -0600 Subject: [Bioperl-l] Problems Installing Bioperl 1.5.2 - Windows In-Reply-To: <47A6D0AB.7050702@sendu.me.uk> References: <883c74d20802031354j6efd59f4m6327537333c8efcd@mail.gmail.com> <47A6D0AB.7050702@sendu.me.uk> Message-ID: <8863D982-5CEF-4E0E-8840-FC8850D96F06@uiuc.edu> On Feb 4, 2008, at 2:45 AM, Sendu Bala wrote: > Terrance Mok wrote: >> Hi I've been trying to install bioperl on a fresh install of >> ActivePerl on >> Windows. >> Following the installation guide using the GUI Perl Package >> Manager, I add >> the 4 locations and all of them list 0 packages except for "Bribes >> http://www.Bribes.org/perl/ppm ". >> Then when searching for bioperl (with all package view), nothing >> shows up >> since no packages are found for all the other locations I added. > > Hopefully someone else will chime in, but perhaps there's something > wrong with the server? Can anyone else confirm? I haven't used ActivePerl in a while personally since switching to OS X (even when using perl 5.10). Terrance, did you follow the ActivePerl instructions or our installation instructions? Also, we don't guarantee that it will work with AtcivePerl's 5.10 port but it's worth a try; if not downgrade to the latest 5.8 build. >> I've also had problems installing on Ubuntu (helping a friend), >> when using >> CPAN and following exactly the guide on the bioperl installation it >> will not >> work. When doing the install command in CPAN, install S/SE/SENDU/ >> bioperl- >> 1.5.2_102.tar.gz she gets an error that >> "/home/username/.cpan/build/bioperl-1.5.2_102: No such file or >> directory at >> Makefile.PL line 25." > > Hard to figure out what might be wrong without complete details. Can > she install anything else via CPAN? Has she run out of disc space? Haven't seen that before but it works for me using cpan and perl 5.8 and perl 5.10. chris From jay at jays.net Mon Feb 4 19:42:17 2008 From: jay at jays.net (Jay Hannah) Date: Mon, 04 Feb 2008 13:42:17 -0600 Subject: [Bioperl-l] SVN server trouble? Message-ID: <47A76A99.2080307@jays.net> I'm getting this error trying to check out trunk, from 2 different servers on 2 different networks: $ svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk bioperl-live svn: Can't find a temporary directory: Error string not specified yet Is this an SVN server problem of some sort, or is it just me somehow? ( Oh, and come hang out with us: irc.freenode.net #bioperl ) Thanks, Jay Hannah http://clab.ist.unomaha.edu/CLAB/index.php/User:Jhannah From David.Messina at sbc.su.se Mon Feb 4 21:35:42 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Mon, 4 Feb 2008 22:35:42 +0100 Subject: [Bioperl-l] SVN server trouble? In-Reply-To: <47A76A99.2080307@jays.net> References: <47A76A99.2080307@jays.net> Message-ID: <628aabb70802041335o300dca9dha7b75d4e0037ef54@mail.gmail.com> Not just you, Jay. I'm getting the same error trying to 'svn update' on a previously-checked-out working copy. Dave From cjfields at uiuc.edu Mon Feb 4 21:48:00 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 4 Feb 2008 15:48:00 -0600 Subject: [Bioperl-l] SVN server trouble? In-Reply-To: <628aabb70802041335o300dca9dha7b75d4e0037ef54@mail.gmail.com> References: <47A76A99.2080307@jays.net> <628aabb70802041335o300dca9dha7b75d4e0037ef54@mail.gmail.com> Message-ID: I went ahead and reported it to support. It's an odd issue, but a checkout works from dev (for those with dev accounts), so it has to be something wonky on code.open-bio.org. chris On Feb 4, 2008, at 3:35 PM, Dave Messina wrote: > Not just you, Jay. I'm getting the same error trying to 'svn update' > on a > previously-checked-out working copy. > Dave From jason at bioperl.org Mon Feb 4 22:11:14 2008 From: jason at bioperl.org (Jason Stajich) Date: Mon, 4 Feb 2008 14:11:14 -0800 Subject: [Bioperl-l] SVN server trouble? In-Reply-To: References: <47A76A99.2080307@jays.net> <628aabb70802041335o300dca9dha7b75d4e0037ef54@mail.gmail.com> Message-ID: ChrisD says that something with is eating up free space on the host so /tmp is full causing the problem(s). Will report in when it's been fixed and we can figure out whether the SVNweb runaway svn diffs are creating the glut of big files. -jason On Feb 4, 2008, at 1:48 PM, Chris Fields wrote: > I went ahead and reported it to support. It's an odd issue, but a > checkout works from dev (for those with dev accounts), so it has to > be something wonky on code.open-bio.org. > > chris > > On Feb 4, 2008, at 3:35 PM, Dave Messina wrote: > >> Not just you, Jay. I'm getting the same error trying to 'svn >> update' on a >> previously-checked-out working copy. >> Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From luisecarracedo at hotmail.com Tue Feb 5 17:59:33 2008 From: luisecarracedo at hotmail.com (luis esteban) Date: Tue, 5 Feb 2008 19:59:33 +0200 Subject: [Bioperl-l] Eland report Message-ID: Hi to everibody!! Is there anybody working in any project tryng to convert Blat or Blast reports in Eland reports. Any Idea, any sugestions would be apreciated. Thanks a Lot Luis Esteban PhD _________________________________________________________________ ?Aburrido? Ingres? ya y divertite como nunca en MSN Juegos. http://juegos.ar.msn.com/ From jason at bioperl.org Tue Feb 5 19:22:14 2008 From: jason at bioperl.org (Jason Stajich) Date: Tue, 5 Feb 2008 11:22:14 -0800 Subject: [Bioperl-l] Eland report In-Reply-To: References: Message-ID: You mean print out eland reports from a BLAST/BLAT/table report? I really hope eland report doesn't become the standard though... -jason On Feb 5, 2008, at 9:59 AM, luis esteban wrote: > > Hi to everibody!! > Is there anybody working in any project tryng to convert Blat or > Blast reports in Eland reports. > Any Idea, any sugestions would be apreciated. > Thanks a Lot > Luis Esteban PhD > _________________________________________________________________ > ?Aburrido? Ingres? ya y divertite como nunca en MSN Juegos. > http://juegos.ar.msn.com/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From sjmiller at email.arizona.edu Tue Feb 5 20:23:28 2008 From: sjmiller at email.arizona.edu (Susan J. Miller) Date: Tue, 05 Feb 2008 13:23:28 -0700 Subject: [Bioperl-l] Bioperl-l Digest, Vol 57, Issue 10 In-Reply-To: References: Message-ID: <47A8C5C0.7040401@email.arizona.edu> bioperl-l-request at lists.open-bio.org wrote: > > Message: 2 > Date: Thu, 31 Jan 2008 10:34:31 +0100 > From: Georg Otto > Subject: Re: [Bioperl-l] Bio::DB::GenBank and large number of requests > To: bioperl-l at bioperl.org > Message-ID: > Content-Type: text/plain; charset=us-ascii > > Hi, > > I succeeded with a similar task using the seqhound database. I had a > list of > 200,000 gid numbers, but I guess it can work in a similar > fashion using accession numbers. Hi Georg, How recently have you used the SeqHound database? We installed it from CPAN but when we try to run the following test script this error occurs: MSG: HTTP::Request error: 500 Can't connect to seqhound.blueprint.org:80 (Bad hostname 'seqhound.blueprint.org') Script: #!/usr/local/bin/perl use warnings; use Bio::SeqIO; use Bio::DB::SeqHound; my $sh = Bio::DB::SeqHound->new(); my $seq = $sh->get_Seq_by_acc("CAA28783"); print $seq->display_name, "\n"; Do you know if SeqHound has moved? Is there a way to comfigure it so that it works? Thanks, -susan Susan J. Miller Manager, Scientific Data Analysis Biotechnology Computing Facility Arizona Research Laboratories (520) 626-2597 From cjfields at uiuc.edu Tue Feb 5 21:38:31 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 5 Feb 2008 15:38:31 -0600 Subject: [Bioperl-l] SeqHound In-Reply-To: <47A8C5C0.7040401@email.arizona.edu> References: <47A8C5C0.7040401@email.arizona.edu> Message-ID: <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> The URL has changed. I'll fix this in bioperl-live. You can fix this in your script directly for now (though I hate globals): use Bio::DB::SeqHound; $Bio::DB::SeqHound::HOSTBASE = 'http://dogboxonline.unleashedinformatics.com/' ; my $sh = Bio::DB::SeqHound->new(); my $seq = $sh->get_Seq_by_acc("CAA28783"); print $seq->display_name, "\n"; chris On Feb 5, 2008, at 2:23 PM, Susan J. Miller wrote: > bioperl-l-request at lists.open-bio.org wrote: >> >> Message: 2 >> Date: Thu, 31 Jan 2008 10:34:31 +0100 >> From: Georg Otto >> Subject: Re: [Bioperl-l] Bio::DB::GenBank and large number of >> requests >> To: bioperl-l at bioperl.org >> Message-ID: >> Content-Type: text/plain; charset=us-ascii >> Hi, >> I succeeded with a similar task using the seqhound database. I had a >> list of > 200,000 gid numbers, but I guess it can work in a similar >> fashion using accession numbers. > > Hi Georg, > > How recently have you used the SeqHound database? We installed it > from CPAN but when we try to run the following test script this > error occurs: > > MSG: HTTP::Request error: 500 Can't connect to > seqhound.blueprint.org:80 (Bad hostname 'seqhound.blueprint.org') > > Script: > #!/usr/local/bin/perl > use warnings; > use Bio::SeqIO; > use Bio::DB::SeqHound; > > my $sh = Bio::DB::SeqHound->new(); > my $seq = $sh->get_Seq_by_acc("CAA28783"); > print $seq->display_name, "\n"; > > > Do you know if SeqHound has moved? Is there a way to comfigure it > so that it works? > > Thanks, > -susan > > Susan J. Miller > Manager, Scientific Data Analysis > Biotechnology Computing Facility > Arizona Research Laboratories > (520) 626-2597 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Tue Feb 5 22:59:48 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 5 Feb 2008 16:59:48 -0600 Subject: [Bioperl-l] SeqHound In-Reply-To: <47A8E3BF.7000308@email.arizona.edu> References: <47A8C5C0.7040401@email.arizona.edu> <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> <47A8E3BF.7000308@email.arizona.edu> Message-ID: <025C4E5C-CD77-442F-AEB1-ACC265B36017@uiuc.edu> On Feb 5, 2008, at 4:31 PM, Susan J. Miller wrote: > Chris Fields wrote: >> The URL has changed. I'll fix this in bioperl-live. >> You can fix this in your script directly for now (though I hate >> globals): >> use Bio::DB::SeqHound; >> $Bio::DB::SeqHound::HOSTBASE = 'http://dogboxonline.unleashedinformatics.com/' >> ; > > Thanks Chris, that helps a little bit, but I'm still not having much > luck with the SeqHound DB. The CPAN SeqHound.pm documentation for > the get_Stream_by_Query method says: > ... No problem. It was an easy fix. ... > I get the error: > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Id list has been truncated even after maxids requested > STACK: Error::throw > STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/ > Root/Root.pm:359 > STACK: Bio::DB::Query::WebQuery::_fetch_ids /usr/lib/perl5/site_perl/ > 5.8.8/Bio/DB/Query/WebQuery.pm:236 > STACK: Bio::DB::Query::WebQuery::ids /usr/lib/perl5/site_perl/5.8.8/ > Bio/DB/Query/WebQuery.pm:200 > STACK: Bio::DB::SeqHound::get_Stream_by_query /usr/lib/perl5/ > site_perl/5.8.8/Bio/DB/SeqHound.pm:314 > STACK: SeqHoundQuery.pl:21 > > There are only 5013 sequences that match this query so it seems odd > that the Id list is too long...or am I using SeqHound improperly? > > (My reason for trying SeqHound is that I want to set up a monthly > cron job to download nucest fasta sequences for drosphila > melanogaster, and I've tried NCBI E-Utilities and the script > generated by the NCBI ebot and in both cases some of the 570828 > records get dropped, even after running repeated attempts.) > > > Thanks, > -susan The URL is likely way too long (a common problem when using a GET as opposed to a POST with LWP). NCBI's efetch has the same problem, which is why using epost is a good idea (except it only takes GI's!). You will have to loop through the IDs in bunches of 250-500 max to get what you want. Don't know if there is a way to post to SeqHound but it might be worth investigating at some point. I also see they have a SOAP interface up. chris From sjmiller at email.arizona.edu Tue Feb 5 22:31:27 2008 From: sjmiller at email.arizona.edu (Susan J. Miller) Date: Tue, 05 Feb 2008 15:31:27 -0700 Subject: [Bioperl-l] SeqHound In-Reply-To: <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> References: <47A8C5C0.7040401@email.arizona.edu> <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> Message-ID: <47A8E3BF.7000308@email.arizona.edu> Chris Fields wrote: > The URL has changed. I'll fix this in bioperl-live. > > You can fix this in your script directly for now (though I hate globals): > > use Bio::DB::SeqHound; > > $Bio::DB::SeqHound::HOSTBASE = > 'http://dogboxonline.unleashedinformatics.com/'; > Thanks Chris, that helps a little bit, but I'm still not having much luck with the SeqHound DB. The CPAN SeqHound.pm documentation for the get_Stream_by_Query method says: Title : get_Stream_by_query Usage : $seq = $db->get_Stream_by_query($query); Function: Retrieves Seq objects from Entrez 'en masse', rather than one at a time. For large numbers of sequences, this is far superior than get_Stream_by_[id/acc](). Example : $query_string = 'Candida maltosa 26S ribosomal RNA gene'; However, when I try: $query_string = 'drosophila simulans[orgn]'; $query = Bio::DB::Query::GenBank->new(-db=>'nucest', -query=>$query_string); $stream = $sh->get_Stream_by_query($query); I get the error: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Id list has been truncated even after maxids requested STACK: Error::throw STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359 STACK: Bio::DB::Query::WebQuery::_fetch_ids /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Query/WebQuery.pm:236 STACK: Bio::DB::Query::WebQuery::ids /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Query/WebQuery.pm:200 STACK: Bio::DB::SeqHound::get_Stream_by_query /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqHound.pm:314 STACK: SeqHoundQuery.pl:21 There are only 5013 sequences that match this query so it seems odd that the Id list is too long...or am I using SeqHound improperly? (My reason for trying SeqHound is that I want to set up a monthly cron job to download nucest fasta sequences for drosphila melanogaster, and I've tried NCBI E-Utilities and the script generated by the NCBI ebot and in both cases some of the 570828 records get dropped, even after running repeated attempts.) Thanks, -susan Susan J. Miller Manager, Scientific Data Analysis Biotechnology Computing Facility Arizona Research Laboratories (520) 626-2597 From lincoln.stein at gmail.com Tue Feb 5 23:43:06 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 5 Feb 2008 18:43:06 -0500 Subject: [Bioperl-l] ActiveState Perl problems Message-ID: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> Hi Scott, Bioperl folk, I'm afraid that the ActiveState ppm install of BioPerl no longer works. Using the current ActiveState (perl version 5.10), I added the Bribes, Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates repositories. However, when I synched up, all but the Bribes reps showed up empty in the ppm tool. In addition, there's nothing in the release candidate rep any longer. I used to use this to get at Bioperl 1.5. Perhaps the architecture needs to be changed? Lincoln -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From cjfields at uiuc.edu Wed Feb 6 00:13:29 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 5 Feb 2008 18:13:29 -0600 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> Message-ID: I'll try changing out package.xml on portal. The one in RC appears to be blank now (which explains why you can't use that one). chris On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: > Hi Scott, Bioperl folk, > > I'm afraid that the ActiveState ppm install of BioPerl no longer > works. > Using the current ActiveState (perl version 5.10), I added the Bribes, > Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates > repositories. However, when I synched up, all but the Bribes reps > showed up > empty in the ppm tool. > > In addition, there's nothing in the release candidate rep any > longer. I used > to use this to get at Bioperl 1.5. > > Perhaps the architecture needs to be changed? > > Lincoln > > > > -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > (516) 367-8380 (voice) > (516) 367-8389 (fax) > FOR URGENT MESSAGES & SCHEDULING, > PLEASE CONTACT MY ASSISTANT, > SANDRA MICHELSEN, AT michelse at cshl.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From golharam at umdnj.edu Tue Feb 5 23:15:43 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Tue, 05 Feb 2008 18:15:43 -0500 Subject: [Bioperl-l] Bio::SeqIO object for GenBank XML format? Message-ID: <47A8EE1F.7050100@umdnj.edu> Is there a SeqIO module for the XML format for GenBank records? The "http://www.bioperl.org/wiki/HOWTO:SeqIO" page doesn't show one listed. From Kevin.M.Brown at asu.edu Wed Feb 6 00:25:58 2008 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Tue, 5 Feb 2008 17:25:58 -0700 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> Message-ID: <1A4207F8295607498283FE9E93B775B4045AA97F@EX02.asurite.ad.asu.edu> Well, Kobes seems to have two different ppm repos. One for 8xx builds of activestate perl and one for 10xx builds. So, Bioperl probably needs to be rebuilt for 5.10 to get it to show in the 5.10 repos. I just opened up Activestate perl 5.8 and I see 1.5.2_100 listed in it from the Regular Release site. > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Lincoln Stein > Sent: Tuesday, February 05, 2008 4:43 PM > To: Scott Cain > Cc: bioperl-l > Subject: [Bioperl-l] ActiveState Perl problems > > Hi Scott, Bioperl folk, > > I'm afraid that the ActiveState ppm install of BioPerl no > longer works. > Using the current ActiveState (perl version 5.10), I added the Bribes, > Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates > repositories. However, when I synched up, all but the Bribes > reps showed up > empty in the ppm tool. > > In addition, there's nothing in the release candidate rep any > longer. I used > to use this to get at Bioperl 1.5. > > Perhaps the architecture needs to be changed? > > Lincoln > > > > -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > (516) 367-8380 (voice) > (516) 367-8389 (fax) > FOR URGENT MESSAGES & SCHEDULING, > PLEASE CONTACT MY ASSISTANT, > SANDRA MICHELSEN, AT michelse at cshl.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From jason at bioperl.org Wed Feb 6 00:45:35 2008 From: jason at bioperl.org (Jason Stajich) Date: Tue, 5 Feb 2008 16:45:35 -0800 Subject: [Bioperl-l] Bio::SeqIO object for GenBank XML format? In-Reply-To: <47A8EE1F.7050100@umdnj.edu> References: <47A8EE1F.7050100@umdnj.edu> Message-ID: <67216BC0-8F2F-432C-B94F-C9A92640E01A@bioperl.org> Then there probably isn't - the codebase Bo/SeqIO directory would tell you otherwise I guess. Does anyone use the format and want to write one? On Feb 5, 2008, at 3:15 PM, Ryan Golhar wrote: > Is there a SeqIO module for the XML format for GenBank records? > The "http://www.bioperl.org/wiki/HOWTO:SeqIO" page doesn't show one > listed. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bosborne11 at verizon.net Tue Feb 5 23:52:57 2008 From: bosborne11 at verizon.net (Brian Osborne) Date: Tue, 05 Feb 2008 18:52:57 -0500 Subject: [Bioperl-l] SeqHound In-Reply-To: <47A8E3BF.7000308@email.arizona.edu> References: <47A8C5C0.7040401@email.arizona.edu> <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> <47A8E3BF.7000308@email.arizona.edu> Message-ID: <4D3A27D3-D535-4F34-8A7F-966F30B51F86@verizon.net> Susan, It sounds like you could use rsync though perhaps there's some detail that I missed. A typical command would look something like this: rsync -av ftp.ncbi.nlm.nih.gov::blast/db/FASTA/ /local/data/FASTA/ Brian O. On Feb 5, 2008, at 5:31 PM, Susan J. Miller wrote: > (My reason for trying SeqHound is that I want to set up a monthly > cron job to download nucest fasta sequences for drosphila > melanogaster, and I've tried NCBI E-Utilities and the script > generated by the NCBI ebot and in both cases some of the 570828 > records get dropped, even after running repeated attempts.) From barry.moore at genetics.utah.edu Wed Feb 6 01:09:56 2008 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Tue, 5 Feb 2008 18:09:56 -0700 Subject: [Bioperl-l] SeqHound In-Reply-To: <47A8E3BF.7000308@email.arizona.edu> References: <47A8C5C0.7040401@email.arizona.edu> <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> <47A8E3BF.7000308@email.arizona.edu> Message-ID: Susan, I'm joining this discussion late so my apologies if I'm missing the original point. If you're trying to routinely download thousands of sequences from GenBank or SeqHound you probably want to be using ftp to download the flat files and query/parse locally. If you're trying to stay on top of the latest Drosophila ESTs, then how about setting up a nightly cron job to download the incremental updates from NCBIs ftp (ftp://ftp.ncbi.nih.gov/genbank/daily-nc) and parse that for Drosophila EST sequences. The EST division is huge, but I would think nightly incrementals should be manageable. Barry On Feb 5, 2008, at 3:31 PM, Susan J. Miller wrote: > Chris Fields wrote: >> The URL has changed. I'll fix this in bioperl-live. >> >> You can fix this in your script directly for now (though I hate >> globals): >> >> use Bio::DB::SeqHound; >> >> $Bio::DB::SeqHound::HOSTBASE = >> 'http://dogboxonline.unleashedinformatics.com/'; >> > > Thanks Chris, that helps a little bit, but I'm still not having much > luck with the SeqHound DB. The CPAN SeqHound.pm documentation for the > get_Stream_by_Query method says: > > Title : get_Stream_by_query > Usage : $seq = $db->get_Stream_by_query($query); > Function: Retrieves Seq objects from Entrez 'en masse', rather than > one at a time. For large numbers of sequences, this is far superior > than get_Stream_by_[id/acc](). > Example : $query_string = 'Candida maltosa 26S ribosomal RNA gene'; > > However, when I try: > > $query_string = 'drosophila simulans[orgn]'; > $query = Bio::DB::Query::GenBank->new(-db=>'nucest', > -query=>$query_string); > $stream = $sh->get_Stream_by_query($query); > > I get the error: > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Id list has been truncated even after maxids requested > STACK: Error::throw > STACK: Bio::Root::Root::throw > /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359 > STACK: Bio::DB::Query::WebQuery::_fetch_ids > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Query/WebQuery.pm:236 > STACK: Bio::DB::Query::WebQuery::ids > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Query/WebQuery.pm:200 > STACK: Bio::DB::SeqHound::get_Stream_by_query > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqHound.pm:314 > STACK: SeqHoundQuery.pl:21 > > There are only 5013 sequences that match this query so it seems odd > that > the Id list is too long...or am I using SeqHound improperly? > > (My reason for trying SeqHound is that I want to set up a monthly cron > job to download nucest fasta sequences for drosphila melanogaster, and > I've tried NCBI E-Utilities and the script generated by the NCBI ebot > and in both cases some of the 570828 records get dropped, even after > running repeated attempts.) > > > Thanks, > -susan > > Susan J. Miller > Manager, Scientific Data Analysis > Biotechnology Computing Facility > Arizona Research Laboratories > (520) 626-2597 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at uiuc.edu Wed Feb 6 01:19:16 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 5 Feb 2008 19:19:16 -0600 Subject: [Bioperl-l] Bio::SeqIO object for GenBank XML format? In-Reply-To: <67216BC0-8F2F-432C-B94F-C9A92640E01A@bioperl.org> References: <47A8EE1F.7050100@umdnj.edu> <67216BC0-8F2F-432C-B94F-C9A92640E01A@bioperl.org> Message-ID: <9F54378C-9905-4E90-88B9-F539B1E933DF@uiuc.edu> Could probably base it off of the BSML parser. Might be better to write up a general INSDC XML parser, which GenBank/EMBL/DDBJ all use now: http://www.insdc.org/page.php?page=documents&sid=fa24a7d177ab7a687e87a85db6822c01 chris On Feb 5, 2008, at 6:45 PM, Jason Stajich wrote: > Then there probably isn't - the codebase Bo/SeqIO directory would > tell you otherwise I guess. > Does anyone use the format and want to write one? > > On Feb 5, 2008, at 3:15 PM, Ryan Golhar wrote: > >> Is there a SeqIO module for the XML format for GenBank records? >> The "http://www.bioperl.org/wiki/HOWTO:SeqIO" page doesn't show one >> listed. >> >> _______________________________________________ >> 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 Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Feb 6 01:32:52 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 5 Feb 2008 19:32:52 -0600 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <1A4207F8295607498283FE9E93B775B4045AA97F@EX02.asurite.ad.asu.edu> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> <1A4207F8295607498283FE9E93B775B4045AA97F@EX02.asurite.ad.asu.edu> Message-ID: <3BFD59BB-152C-4D43-B8E7-96DC293D8C34@uiuc.edu> Kobes keeps two separate repos because there are several binary-only modules (DBD::mysql, GD, etc) which are incompatible with older major perl releases (5.6, 5.8, 5.10). If the modules are pure perl then there shouldn't be a problem. Saying that, there is one issue which tanks Bio::SeqIO::entrezgene parsing (which mistakenly made pseudohashes) which Stefan and I fixed recently; that'll tank in perl 5.10. chris On Feb 5, 2008, at 6:25 PM, Kevin Brown wrote: > Well, Kobes seems to have two different ppm repos. One for 8xx builds > of activestate perl and one for 10xx builds. So, Bioperl probably > needs > to be rebuilt for 5.10 to get it to show in the 5.10 repos. I just > opened up Activestate perl 5.8 and I see 1.5.2_100 listed in it from > the > Regular Release site. > >> -----Original Message----- >> From: bioperl-l-bounces at lists.open-bio.org >> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of >> Lincoln Stein >> Sent: Tuesday, February 05, 2008 4:43 PM >> To: Scott Cain >> Cc: bioperl-l >> Subject: [Bioperl-l] ActiveState Perl problems >> >> Hi Scott, Bioperl folk, >> >> I'm afraid that the ActiveState ppm install of BioPerl no >> longer works. >> Using the current ActiveState (perl version 5.10), I added the >> Bribes, >> Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates >> repositories. However, when I synched up, all but the Bribes >> reps showed up >> empty in the ppm tool. >> >> In addition, there's nothing in the release candidate rep any >> longer. I used >> to use this to get at Bioperl 1.5. >> >> Perhaps the architecture needs to be changed? >> >> Lincoln >> >> >> >> -- >> Lincoln D. Stein >> Cold Spring Harbor Laboratory >> 1 Bungtown Road >> Cold Spring Harbor, NY 11724 >> (516) 367-8380 (voice) >> (516) 367-8389 (fax) >> FOR URGENT MESSAGES & SCHEDULING, >> PLEASE CONTACT MY ASSISTANT, >> SANDRA MICHELSEN, AT michelse at cshl.edu >> _______________________________________________ >> 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 Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From golharam at umdnj.edu Wed Feb 6 00:54:24 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Tue, 05 Feb 2008 19:54:24 -0500 Subject: [Bioperl-l] Bio::SeqIO object for GenBank XML format? In-Reply-To: <67216BC0-8F2F-432C-B94F-C9A92640E01A@bioperl.org> References: <47A8EE1F.7050100@umdnj.edu> <67216BC0-8F2F-432C-B94F-C9A92640E01A@bioperl.org> Message-ID: <47A90540.9060002@umdnj.edu> If no one else has already built one, then I'd be happy to based on the genbank and chaosxml/tigrxml modules. Ryan Jason Stajich wrote: > Then there probably isn't - the codebase Bo/SeqIO directory would tell > you otherwise I guess. > Does anyone use the format and want to write one? > > On Feb 5, 2008, at 3:15 PM, Ryan Golhar wrote: > >> Is there a SeqIO module for the XML format for GenBank records? The >> "http://www.bioperl.org/wiki/HOWTO:SeqIO" page doesn't show one listed. >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > From cjfields at uiuc.edu Wed Feb 6 03:06:06 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 5 Feb 2008 21:06:06 -0600 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> Message-ID: <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> According to this page you can remove the tags and it will assume the files are for any OS: http://aspn.activestate.com/ASPN/docs/ActivePerl/5.10/lib/ActivePerl/PPM/PPD.html#ppd_xml_format I have moved the old package.xml to package.bak and replaced it with one w/o those tags; I can now pick it up on Mac OS X using ActiveState perl 5.10: ppm> search * Downloading bioperl.org packlist...not modified 1: Bio-ASN1-EntrezGene v1.09 2: Bundle-BioPerl-Core v1.5.2_100 3: Bundle-BioPerl-Db v1.5.2_100 4: Bundle-BioPerl-Network v1.5.2_100 5: Bundle-BioPerl-Run v1.5.2_100 6: Class-AutoClass v1.01 7: GD-SVG v0.25 8: Graph v0.80 9: SVG-Graph v0.01 10: bioperl v1.5.2_100 11: bioperl-db v1.5.2_100 12: bioperl-network v1.5.2_100 13: bioperl-run v1.5.2_100 I'll add ARCHITECTURE versioning tags back when we know it's working (maybe tomorrow, when I can get on to WinXP to test it). chris On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: > Hi Scott, Bioperl folk, > > I'm afraid that the ActiveState ppm install of BioPerl no longer > works. > Using the current ActiveState (perl version 5.10), I added the Bribes, > Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates > repositories. However, when I synched up, all but the Bribes reps > showed up > empty in the ppm tool. > > In addition, there's nothing in the release candidate rep any > longer. I used > to use this to get at Bioperl 1.5. > > Perhaps the architecture needs to be changed? > > Lincoln > > > > -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > (516) 367-8380 (voice) > (516) 367-8389 (fax) > FOR URGENT MESSAGES & SCHEDULING, > PLEASE CONTACT MY ASSISTANT, > SANDRA MICHELSEN, AT michelse at cshl.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From lincoln.stein at gmail.com Wed Feb 6 04:25:27 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 5 Feb 2008 23:25:27 -0500 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> Message-ID: <6dce9a0b0802052025y1243b7den4d19ed4dd1d71ff9@mail.gmail.com> Wow, nice fast work! Thanks all. Lincoln On Feb 5, 2008 10:06 PM, Chris Fields wrote: > According to this page you can remove the tags and it > will assume the files are for any OS: > > > http://aspn.activestate.com/ASPN/docs/ActivePerl/5.10/lib/ActivePerl/PPM/PPD.html#ppd_xml_format > > I have moved the old package.xml to package.bak and replaced it with > one w/o those tags; I can now pick it up on Mac OS X using ActiveState > perl 5.10: > > ppm> search * > Downloading bioperl.org packlist...not modified > 1: Bio-ASN1-EntrezGene v1.09 > 2: Bundle-BioPerl-Core v1.5.2_100 > 3: Bundle-BioPerl-Db v1.5.2_100 > 4: Bundle-BioPerl-Network v1.5.2_100 > 5: Bundle-BioPerl-Run v1.5.2_100 > 6: Class-AutoClass v1.01 > 7: GD-SVG v0.25 > 8: Graph v0.80 > 9: SVG-Graph v0.01 > 10: bioperl v1.5.2_100 > 11: bioperl-db v1.5.2_100 > 12: bioperl-network v1.5.2_100 > 13: bioperl-run v1.5.2_100 > > I'll add ARCHITECTURE versioning tags back when we know it's working > (maybe tomorrow, when I can get on to WinXP to test it). > > chris > > On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: > > > Hi Scott, Bioperl folk, > > > > I'm afraid that the ActiveState ppm install of BioPerl no longer > > works. > > Using the current ActiveState (perl version 5.10), I added the Bribes, > > Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates > > repositories. However, when I synched up, all but the Bribes reps > > showed up > > empty in the ppm tool. > > > > In addition, there's nothing in the release candidate rep any > > longer. I used > > to use this to get at Bioperl 1.5. > > > > Perhaps the architecture needs to be changed? > > > > Lincoln > > > > > > > > -- > > Lincoln D. Stein > > Cold Spring Harbor Laboratory > > 1 Bungtown Road > > Cold Spring Harbor, NY 11724 > > (516) 367-8380 (voice) > > (516) 367-8389 (fax) > > FOR URGENT MESSAGES & SCHEDULING, > > PLEASE CONTACT MY ASSISTANT, > > SANDRA MICHELSEN, AT michelse at cshl.edu > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From bioinfo21 at gmail.com Wed Feb 6 07:04:37 2008 From: bioinfo21 at gmail.com (Priya) Date: Wed, 6 Feb 2008 12:34:37 +0530 Subject: [Bioperl-l] Bioperl Message-ID: <98af6e260802052304y66add58fi65e289cb4b9069f7@mail.gmail.com> Hi all I am new to Bioperl. I have installed Bioperl in Linux. I am trying to use one of the sample programs in bioperl. I couldnt figure out where to set the http proxy authentication. I tried to follow the manual for installation. Still I am not getting it right . Let me know how to set the proxy authentication and where exactly it should be set. I tried to set env variables for http in .bashrc. Still its not working. Help me out. Thanks in advance. Regards Priya.. From lincoln.stein at gmail.com Wed Feb 6 15:03:31 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Wed, 6 Feb 2008 10:03:31 -0500 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> Message-ID: <6dce9a0b0802060703j231704acta813715265f1fab5@mail.gmail.com> Sadly, bioperl still won't install under ActiveState 5.10 because it can't find a repository with the SOAP::Lite prerequisite. Lincoln On Feb 5, 2008 10:06 PM, Chris Fields wrote: > According to this page you can remove the tags and it > will assume the files are for any OS: > > > http://aspn.activestate.com/ASPN/docs/ActivePerl/5.10/lib/ActivePerl/PPM/PPD.html#ppd_xml_format > > I have moved the old package.xml to package.bak and replaced it with > one w/o those tags; I can now pick it up on Mac OS X using ActiveState > perl 5.10: > > ppm> search * > Downloading bioperl.org packlist...not modified > 1: Bio-ASN1-EntrezGene v1.09 > 2: Bundle-BioPerl-Core v1.5.2_100 > 3: Bundle-BioPerl-Db v1.5.2_100 > 4: Bundle-BioPerl-Network v1.5.2_100 > 5: Bundle-BioPerl-Run v1.5.2_100 > 6: Class-AutoClass v1.01 > 7: GD-SVG v0.25 > 8: Graph v0.80 > 9: SVG-Graph v0.01 > 10: bioperl v1.5.2_100 > 11: bioperl-db v1.5.2_100 > 12: bioperl-network v1.5.2_100 > 13: bioperl-run v1.5.2_100 > > I'll add ARCHITECTURE versioning tags back when we know it's working > (maybe tomorrow, when I can get on to WinXP to test it). > > chris > > On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: > > > Hi Scott, Bioperl folk, > > > > I'm afraid that the ActiveState ppm install of BioPerl no longer > > works. > > Using the current ActiveState (perl version 5.10), I added the Bribes, > > Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates > > repositories. However, when I synched up, all but the Bribes reps > > showed up > > empty in the ppm tool. > > > > In addition, there's nothing in the release candidate rep any > > longer. I used > > to use this to get at Bioperl 1.5. > > > > Perhaps the architecture needs to be changed? > > > > Lincoln > > > > > > > > -- > > Lincoln D. Stein > > Cold Spring Harbor Laboratory > > 1 Bungtown Road > > Cold Spring Harbor, NY 11724 > > (516) 367-8380 (voice) > > (516) 367-8389 (fax) > > FOR URGENT MESSAGES & SCHEDULING, > > PLEASE CONTACT MY ASSISTANT, > > SANDRA MICHELSEN, AT michelse at cshl.edu > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From cjfields at uiuc.edu Wed Feb 6 15:55:00 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 6 Feb 2008 09:55:00 -0600 Subject: [Bioperl-l] BOSC 2008? Message-ID: <1182EAB9-7A75-498F-B91B-C14771DFD607@uiuc.edu> Anyone have information on the where/when for BOSC 2008? chris From n.haigh at sheffield.ac.uk Wed Feb 6 16:36:19 2008 From: n.haigh at sheffield.ac.uk (Nathan S Haigh) Date: Wed, 06 Feb 2008 16:36:19 +0000 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <6dce9a0b0802060703j231704acta813715265f1fab5@mail.gmail.com> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> <6dce9a0b0802060703j231704acta813715265f1fab5@mail.gmail.com> Message-ID: <47A9E203.3080008@sheffield.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Last time I was playing with Windows PPM packages, I seem to remember having to build some packages for inclusion in the BioPerl repo so that all dependencies were satisfied. Unfortunately, I don't have time to do this myself, but it's a work around if someone has time to do it? Alternatively, contact one of the other repo's and see if they can do something about it as it will/should be available for at least an older version of ActivePerl. Sorry I can't be more help. Nath Lincoln Stein wrote: > Sadly, bioperl still won't install under ActiveState 5.10 because it can't > find a repository with the SOAP::Lite prerequisite. > > Lincoln > > On Feb 5, 2008 10:06 PM, Chris Fields wrote: > >> According to this page you can remove the tags and it >> will assume the files are for any OS: >> >> >> http://aspn.activestate.com/ASPN/docs/ActivePerl/5.10/lib/ActivePerl/PPM/PPD.html#ppd_xml_format >> >> I have moved the old package.xml to package.bak and replaced it with >> one w/o those tags; I can now pick it up on Mac OS X using ActiveState >> perl 5.10: >> >> ppm> search * >> Downloading bioperl.org packlist...not modified >> 1: Bio-ASN1-EntrezGene v1.09 >> 2: Bundle-BioPerl-Core v1.5.2_100 >> 3: Bundle-BioPerl-Db v1.5.2_100 >> 4: Bundle-BioPerl-Network v1.5.2_100 >> 5: Bundle-BioPerl-Run v1.5.2_100 >> 6: Class-AutoClass v1.01 >> 7: GD-SVG v0.25 >> 8: Graph v0.80 >> 9: SVG-Graph v0.01 >> 10: bioperl v1.5.2_100 >> 11: bioperl-db v1.5.2_100 >> 12: bioperl-network v1.5.2_100 >> 13: bioperl-run v1.5.2_100 >> >> I'll add ARCHITECTURE versioning tags back when we know it's working >> (maybe tomorrow, when I can get on to WinXP to test it). >> >> chris >> >> On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: >> >>> Hi Scott, Bioperl folk, >>> >>> I'm afraid that the ActiveState ppm install of BioPerl no longer >>> works. >>> Using the current ActiveState (perl version 5.10), I added the Bribes, >>> Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates >>> repositories. However, when I synched up, all but the Bribes reps >>> showed up >>> empty in the ppm tool. >>> >>> In addition, there's nothing in the release candidate rep any >>> longer. I used >>> to use this to get at Bioperl 1.5. >>> >>> Perhaps the architecture needs to be changed? >>> >>> Lincoln >>> >>> >>> >>> -- >>> Lincoln D. Stein >>> Cold Spring Harbor Laboratory >>> 1 Bungtown Road >>> Cold Spring Harbor, NY 11724 >>> (516) 367-8380 (voice) >>> (516) 367-8389 (fax) >>> FOR URGENT MESSAGES & SCHEDULING, >>> PLEASE CONTACT MY ASSISTANT, >>> SANDRA MICHELSEN, AT michelse at cshl.edu >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> >> > > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHqeID9gTv6QYzVL4RAsyqAJ0XkCJgdKu6SHzci4XGww4OofRBzgCfQqCL MxylCxJflKjtscupJ5cRHKk= =Brpe -----END PGP SIGNATURE----- From cjfields at uiuc.edu Wed Feb 6 17:09:40 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 6 Feb 2008 11:09:40 -0600 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <47A9E203.3080008@sheffield.ac.uk> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> <6dce9a0b0802060703j231704acta813715265f1fab5@mail.gmail.com> <47A9E203.3080008@sheffield.ac.uk> Message-ID: <0E379930-B25F-42F5-8706-B39C64D6D2EB@uiuc.edu> SOAP::Lite is pretty complicated; I'm not sure if it is pure perl either (which makes it problematic for WinXP). I'll do some checking around to see if there is a perl 5.10 build for Windows. I'm toying around with the idea of setting up a nightly PPM archives of the bioperl distributions in their own directory, along with nightly tar balls. Just need to get time to work on it! chris On Feb 6, 2008, at 10:36 AM, Nathan S Haigh wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Last time I was playing with Windows PPM packages, I seem to > remember having to build some packages for inclusion in the BioPerl > repo so that all > dependencies were satisfied. Unfortunately, I don't have time to do > this myself, but it's a work around if someone has time to do it? > Alternatively, > contact one of the other repo's and see if they can do something > about it as it will/should be available for at least an older > version of ActivePerl. > > Sorry I can't be more help. > Nath > > > Lincoln Stein wrote: >> Sadly, bioperl still won't install under ActiveState 5.10 because >> it can't >> find a repository with the SOAP::Lite prerequisite. >> >> Lincoln >> >> On Feb 5, 2008 10:06 PM, Chris Fields wrote: >> >>> According to this page you can remove the tags and it >>> will assume the files are for any OS: >>> >>> >>> http://aspn.activestate.com/ASPN/docs/ActivePerl/5.10/lib/ActivePerl/PPM/PPD.html#ppd_xml_format >>> >>> I have moved the old package.xml to package.bak and replaced it with >>> one w/o those tags; I can now pick it up on Mac OS X using >>> ActiveState >>> perl 5.10: >>> >>> ppm> search * >>> Downloading bioperl.org packlist...not modified >>> 1: Bio-ASN1-EntrezGene v1.09 >>> 2: Bundle-BioPerl-Core v1.5.2_100 >>> 3: Bundle-BioPerl-Db v1.5.2_100 >>> 4: Bundle-BioPerl-Network v1.5.2_100 >>> 5: Bundle-BioPerl-Run v1.5.2_100 >>> 6: Class-AutoClass v1.01 >>> 7: GD-SVG v0.25 >>> 8: Graph v0.80 >>> 9: SVG-Graph v0.01 >>> 10: bioperl v1.5.2_100 >>> 11: bioperl-db v1.5.2_100 >>> 12: bioperl-network v1.5.2_100 >>> 13: bioperl-run v1.5.2_100 >>> >>> I'll add ARCHITECTURE versioning tags back when we know it's working >>> (maybe tomorrow, when I can get on to WinXP to test it). >>> >>> chris >>> >>> On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: >>> >>>> Hi Scott, Bioperl folk, >>>> >>>> I'm afraid that the ActiveState ppm install of BioPerl no longer >>>> works. >>>> Using the current ActiveState (perl version 5.10), I added the >>>> Bribes, >>>> Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates >>>> repositories. However, when I synched up, all but the Bribes reps >>>> showed up >>>> empty in the ppm tool. >>>> >>>> In addition, there's nothing in the release candidate rep any >>>> longer. I used >>>> to use this to get at Bioperl 1.5. >>>> >>>> Perhaps the architecture needs to be changed? >>>> >>>> Lincoln >>>> >>>> >>>> >>>> -- >>>> Lincoln D. Stein >>>> Cold Spring Harbor Laboratory >>>> 1 Bungtown Road >>>> Cold Spring Harbor, NY 11724 >>>> (516) 367-8380 (voice) >>>> (516) 367-8389 (fax) >>>> FOR URGENT MESSAGES & SCHEDULING, >>>> PLEASE CONTACT MY ASSISTANT, >>>> SANDRA MICHELSEN, AT michelse at cshl.edu >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> Christopher Fields >>> Postdoctoral Researcher >>> Lab of Dr. Robert Switzer >>> Dept of Biochemistry >>> University of Illinois Urbana-Champaign >>> >>> >>> >>> >> >> > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.6 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFHqeID9gTv6QYzVL4RAsyqAJ0XkCJgdKu6SHzci4XGww4OofRBzgCfQqCL > MxylCxJflKjtscupJ5cRHKk= > =Brpe > -----END PGP SIGNATURE----- Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Feb 6 17:54:16 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 6 Feb 2008 11:54:16 -0600 Subject: [Bioperl-l] ActiveState Perl problems In-Reply-To: <47A9E203.3080008@sheffield.ac.uk> References: <6dce9a0b0802051543w574ab2co694d49f513e84d1e@mail.gmail.com> <01E32E6E-20A0-42C5-BE0E-91D3B231589A@uiuc.edu> <6dce9a0b0802060703j231704acta813715265f1fab5@mail.gmail.com> <47A9E203.3080008@sheffield.ac.uk> Message-ID: <48143927-C57B-4525-9025-A6FDC5A49070@uiuc.edu> Just an update: I have installed ActivePerl 5.10 on my WinXP box and added the following repos to PPM4 (in the following order, just in case it matters): Kobes: http://cpan.uwinnipeg.ca/PPMPackages/10xx/ Bribes: http://www.bribes.org/perl/ppm BioPerl: http://bioperl.org/DIST Note that the above Kobes repo is 5.10-specific. SOAP::Lite is in both Kobes and Bribes for perl 5.10. I then ran into issues with XML::SAX::ExpatXS and XML::SAX::Writer (the former is a binary-only, so likely failed with the ActiveState autobuild process; the latter should work though, so it might be worth hosting a version in BioPerl). I removed both dependencies from package.xml on the server and everything appears to install fine now using PPM4. I'll see if Randy Kobes can get an XML::SAX::ExpatXS version up. It is only required for 1.5.2; bioperl-live no longer requires it (just XML::SAX). chris On Feb 6, 2008, at 10:36 AM, Nathan S Haigh wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Last time I was playing with Windows PPM packages, I seem to > remember having to build some packages for inclusion in the BioPerl > repo so that all > dependencies were satisfied. Unfortunately, I don't have time to do > this myself, but it's a work around if someone has time to do it? > Alternatively, > contact one of the other repo's and see if they can do something > about it as it will/should be available for at least an older > version of ActivePerl. > > Sorry I can't be more help. > Nath > > > Lincoln Stein wrote: >> Sadly, bioperl still won't install under ActiveState 5.10 because >> it can't >> find a repository with the SOAP::Lite prerequisite. >> >> Lincoln >> >> On Feb 5, 2008 10:06 PM, Chris Fields wrote: >> >>> According to this page you can remove the tags and it >>> will assume the files are for any OS: >>> >>> >>> http://aspn.activestate.com/ASPN/docs/ActivePerl/5.10/lib/ActivePerl/PPM/PPD.html#ppd_xml_format >>> >>> I have moved the old package.xml to package.bak and replaced it with >>> one w/o those tags; I can now pick it up on Mac OS X using >>> ActiveState >>> perl 5.10: >>> >>> ppm> search * >>> Downloading bioperl.org packlist...not modified >>> 1: Bio-ASN1-EntrezGene v1.09 >>> 2: Bundle-BioPerl-Core v1.5.2_100 >>> 3: Bundle-BioPerl-Db v1.5.2_100 >>> 4: Bundle-BioPerl-Network v1.5.2_100 >>> 5: Bundle-BioPerl-Run v1.5.2_100 >>> 6: Class-AutoClass v1.01 >>> 7: GD-SVG v0.25 >>> 8: Graph v0.80 >>> 9: SVG-Graph v0.01 >>> 10: bioperl v1.5.2_100 >>> 11: bioperl-db v1.5.2_100 >>> 12: bioperl-network v1.5.2_100 >>> 13: bioperl-run v1.5.2_100 >>> >>> I'll add ARCHITECTURE versioning tags back when we know it's working >>> (maybe tomorrow, when I can get on to WinXP to test it). >>> >>> chris >>> >>> On Feb 5, 2008, at 5:43 PM, Lincoln Stein wrote: >>> >>>> Hi Scott, Bioperl folk, >>>> >>>> I'm afraid that the ActiveState ppm install of BioPerl no longer >>>> works. >>>> Using the current ActiveState (perl version 5.10), I added the >>>> Bribes, >>>> Kobes, BioPerl-Regular Releases, and BioPerl-Release Candidates >>>> repositories. However, when I synched up, all but the Bribes reps >>>> showed up >>>> empty in the ppm tool. >>>> >>>> In addition, there's nothing in the release candidate rep any >>>> longer. I used >>>> to use this to get at Bioperl 1.5. >>>> >>>> Perhaps the architecture needs to be changed? >>>> >>>> Lincoln >>>> >>>> >>>> >>>> -- >>>> Lincoln D. Stein >>>> Cold Spring Harbor Laboratory >>>> 1 Bungtown Road >>>> Cold Spring Harbor, NY 11724 >>>> (516) 367-8380 (voice) >>>> (516) 367-8389 (fax) >>>> FOR URGENT MESSAGES & SCHEDULING, >>>> PLEASE CONTACT MY ASSISTANT, >>>> SANDRA MICHELSEN, AT michelse at cshl.edu >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> Christopher Fields >>> Postdoctoral Researcher >>> Lab of Dr. Robert Switzer >>> Dept of Biochemistry >>> University of Illinois Urbana-Champaign >>> >>> >>> >>> >> >> > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.6 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFHqeID9gTv6QYzVL4RAsyqAJ0XkCJgdKu6SHzci4XGww4OofRBzgCfQqCL > MxylCxJflKjtscupJ5cRHKk= > =Brpe > -----END PGP SIGNATURE----- > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From sjmiller at email.arizona.edu Wed Feb 6 20:57:35 2008 From: sjmiller at email.arizona.edu (Susan J. Miller) Date: Wed, 06 Feb 2008 13:57:35 -0700 Subject: [Bioperl-l] SeqHound In-Reply-To: References: <47A8C5C0.7040401@email.arizona.edu> <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> <47A8E3BF.7000308@email.arizona.edu> Message-ID: <47AA1F3F.9000404@email.arizona.edu> Barry Moore wrote: > Susan, > > I'm joining this discussion late so my apologies if I'm missing the > original point. If you're trying to routinely download thousands of > sequences from GenBank or SeqHound you probably want to be using ftp to > download the flat files and query/parse locally. If you're trying to > stay on top of the latest Drosophila ESTs, then how about setting up a > nightly cron job to download the incremental updates from NCBIs ftp > (ftp://ftp.ncbi.nih.gov/genbank/daily-nc) and parse that for Drosophila > EST sequences. The EST division is huge, but I would think nightly > incrementals should be manageable. Hi Barry, I'll try your suggestion. I guess my interpretation of the documentation for SeqHound was erroneous. (Who knows what 'large numbers of sequences' means?) I tried using SeqHound's get_Stream_by_id method to fetch 10000 sequences, 500 at a time, and got a timeout error. -- Regards, -susan Susan J. Miller Manager, Scientific Data Analysis Biotechnology Computing Facility Arizona Research Laboratories (520) 626-2597 From David.Messina at sbc.su.se Wed Feb 6 21:17:46 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 6 Feb 2008 22:17:46 +0100 Subject: [Bioperl-l] BOSC 2008? In-Reply-To: <1182EAB9-7A75-498F-B91B-C14771DFD607@uiuc.edu> References: <1182EAB9-7A75-498F-B91B-C14771DFD607@uiuc.edu> Message-ID: <628aabb70802061317n2f0d1103w9367346166bf8c3f@mail.gmail.com> Hey Chris, Isn't it usually in conjunction with ISMB (which is Toronto 7/19-23 this year)? From cjfields at uiuc.edu Wed Feb 6 21:22:20 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 6 Feb 2008 15:22:20 -0600 Subject: [Bioperl-l] BOSC 2008? In-Reply-To: <628aabb70802061317n2f0d1103w9367346166bf8c3f@mail.gmail.com> References: <1182EAB9-7A75-498F-B91B-C14771DFD607@uiuc.edu> <628aabb70802061317n2f0d1103w9367346166bf8c3f@mail.gmail.com> Message-ID: <9C6A22B1-9E84-4F17-8459-CBBDCB2110D4@uiuc.edu> Yep. I found this out earlier from Darin London. Just trying to plan for it ahead of time! chris On Feb 6, 2008, at 3:17 PM, Dave Messina wrote: > Hey Chris, > > Isn't it usually in conjunction with ISMB (which is Toronto 7/19-23 > this year)? > > Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Feb 6 21:48:45 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 6 Feb 2008 15:48:45 -0600 Subject: [Bioperl-l] SeqHound In-Reply-To: <47AA1F3F.9000404@email.arizona.edu> References: <47A8C5C0.7040401@email.arizona.edu> <111DD141-75F8-4437-9EAD-E049BBADB515@uiuc.edu> <47A8E3BF.7000308@email.arizona.edu> <47AA1F3F.9000404@email.arizona.edu> Message-ID: <78824D84-B8B7-4A5C-BD81-7224F26D32E9@uiuc.edu> On Feb 6, 2008, at 2:57 PM, Susan J. Miller wrote: > Barry Moore wrote: >> Susan, >> I'm joining this discussion late so my apologies if I'm missing the >> original point. If you're trying to routinely download thousands >> of sequences from GenBank or SeqHound you probably want to be using >> ftp to download the flat files and query/parse locally. If you're >> trying to stay on top of the latest Drosophila ESTs, then how about >> setting up a nightly cron job to download the incremental updates >> from NCBIs ftp (ftp://ftp.ncbi.nih.gov/genbank/daily-nc) and parse >> that for Drosophila EST sequences. The EST division is huge, but I >> would think nightly incrementals should be manageable. > > > Hi Barry, > > I'll try your suggestion. I guess my interpretation of the > documentation for SeqHound was erroneous. (Who knows what 'large > numbers of sequences' means?) I tried using SeqHound's > get_Stream_by_id method to fetch 10000 sequences, 500 at a time, and > got a timeout error. > > > -- > Regards, > -susan Barry's and Brian's suggestions make more sense. You could also possibly automate a Entrez query to limit retrievals to a period of time instead of munging through the last releases; it all depends on how many sequences you need to parse through. The SeqHound timeout may be set up on their end to prevent a single server from spamming them with tons of requests. NCBI is a bit more tolerant but can be brittle with busy server traffic. chris From barry.moore at genetics.utah.edu Wed Feb 6 21:50:53 2008 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Wed, 6 Feb 2008 14:50:53 -0700 Subject: [Bioperl-l] Fwd: SeqHound References: <6CA6C310-E23C-47ED-9206-7F914BCA689E@genetics.utah.edu> Message-ID: <7167DD26-92F7-4D44-B111-E6CAA30BFB1E@genetics.utah.edu> Susan- Yeah, I used them several years ago, and it seemed like quite a good project at the time. I see that it has recently moved to a new location with a start up company, and I couldn't make heads or tails of their new sight. I wonder if the SeqHound side of their work hasn't suffered - perhaps only temporarily - from their recent move from academia to the brave new world of .com start-up. B On Feb 6, 2008, at 1:57 PM, Susan J. Miller wrote: > Barry Moore wrote: >> Susan, >> >> I'm joining this discussion late so my apologies if I'm missing the >> original point. If you're trying to routinely download thousands of >> sequences from GenBank or SeqHound you probably want to be using >> ftp to >> download the flat files and query/parse locally. If you're trying to >> stay on top of the latest Drosophila ESTs, then how about setting >> up a >> nightly cron job to download the incremental updates from NCBIs ftp >> (ftp://ftp.ncbi.nih.gov/genbank/daily-nc) and parse that for >> Drosophila >> EST sequences. The EST division is huge, but I would think nightly >> incrementals should be manageable. > > > Hi Barry, > > I'll try your suggestion. I guess my interpretation of the > documentation for SeqHound was erroneous. (Who knows what 'large > numbers of sequences' means?) I tried using SeqHound's > get_Stream_by_id > method to fetch 10000 sequences, 500 at a time, and got a timeout > error. > > > -- > Regards, > -susan > > Susan J. Miller > Manager, Scientific Data Analysis > Biotechnology Computing Facility > Arizona Research Laboratories > (520) 626-2597 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From oliverpelz at googlemail.com Thu Feb 7 17:24:38 2008 From: oliverpelz at googlemail.com (Oliver Pelz) Date: Thu, 7 Feb 2008 18:24:38 +0100 Subject: [Bioperl-l] Found dead links in PDoc and a little improvement Message-ID: Hello everybody, I am a beginner in bioperl and currently working heavily with the PDoc's. In this doc here: http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Variation/IO/flat.html the two links to the EBI in the description field are dead. I have looked to find other information but there is nothing available about this pseudo embl format. Has someone the old descriptions and can edit/paste them in this documentation. Another thing would help beginners. At the Bio::SeqIO documentation there are those examples for world fastest ... converter. It would be cool to add a $out->close() to those examples because I was very frustrated in the beginning when the outfiles were empty after the script had finished. Thanks for reading Oliver From bosborne11 at verizon.net Thu Feb 7 18:41:48 2008 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 07 Feb 2008 13:41:48 -0500 Subject: [Bioperl-l] Found dead links in PDoc and a little improvement In-Reply-To: References: Message-ID: Oliver, Removed those dead links, thank you for that. The reason there's no close() in most code examples is that Perl programmers don't usually use this function. The filehandle is closed automatically when open() is called again or when the Perl script finishes. Brian O. On Feb 7, 2008, at 12:24 PM, Oliver Pelz wrote: > Hello everybody, > I am a beginner in bioperl and currently working heavily with the > PDoc's. > > In this doc here: > http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Variation/IO/flat.html > > the two links to the EBI in the description field are dead. I have > looked to > find other information > but there is nothing available about this pseudo embl format. > Has someone the old descriptions and can edit/paste them in this > documentation. > > Another thing would help beginners. > At the Bio::SeqIO documentation there are those examples for world > fastest > ... converter. > It would be cool to add a $out->close() to those examples because I > was very > frustrated in the > beginning when the outfiles were empty after the script had finished. > > Thanks for reading > > Oliver > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From golharam at umdnj.edu Thu Feb 7 21:24:16 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 07 Feb 2008 16:24:16 -0500 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser Message-ID: <47AB7700.8030801@umdnj.edu> Is there a SeqIO parser module for GenBank ASN.1 format? I thought it would have been genbank or entrezgene, but neither of them work. From cjfields at uiuc.edu Thu Feb 7 21:48:25 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 7 Feb 2008 15:48:25 -0600 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <47AB7700.8030801@umdnj.edu> References: <47AB7700.8030801@umdnj.edu> Message-ID: No. The only ASN.1 parser is entrezgene. You could probably try building one using the same ASN.1 parser that SeqIO::entrezgene uses (Bio::ASN1::EntrezGene); it includes a parser for sequences: http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm chris On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: > Is there a SeqIO parser module for GenBank ASN.1 format? I thought > it would have been genbank or entrezgene, but neither of them work. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jason at bioperl.org Thu Feb 7 22:46:41 2008 From: jason at bioperl.org (Jason Stajich) Date: Thu, 7 Feb 2008 14:46:41 -0800 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: References: <47AB7700.8030801@umdnj.edu> Message-ID: <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> ugh - why parse ASN.1? NCBI provides converter application in the ncbi toolkit to many formats : genbank, XML, etc. On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: > No. The only ASN.1 parser is entrezgene. You could probably try > building one using the same ASN.1 parser that SeqIO::entrezgene > uses (Bio::ASN1::EntrezGene); it includes a parser for sequences: > > http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ > ASN1/Sequence.pm > > chris > > On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: > >> Is there a SeqIO parser module for GenBank ASN.1 format? I >> thought it would have been genbank or entrezgene, but neither of >> them work. >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From golharam at umdnj.edu Thu Feb 7 23:00:33 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 07 Feb 2008 18:00:33 -0500 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> Message-ID: <47AB8D91.9080201@umdnj.edu> That I can use from Perl? Such as???? I need to retrieve Gene Ontology information (classification and GO id) from the Entrez Gene record. I thought it would be easiest using BioPerl to do this. BioPerl only has an ASN.1 parser, entrezgene. When I use this to load the Gene record, I'm using: my $io = Bio::SeqIO->new(-file => ' "entrezgene" ); my $seq_obj = $io->next_seq; Something is not working with the second line. I get an error: "Use of uninitialized value in string eq at /home/golharam/bioperl/bioperl-1.5.1//Bio/SeqIO/entrezgene.pm line 244" It sort of makes sense because, well, the Entrez Gene record doesn't have a sequence...it has information about a gene. I figure I must be doing something wrong but I haven't seen anything in BioPerl about parsing entrez gene records any other way. Ryan Jason Stajich wrote: > ugh - why parse ASN.1? NCBI provides converter application in the ncbi > toolkit to many formats : genbank, XML, etc. > On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: > >> No. The only ASN.1 parser is entrezgene. You could probably try >> building one using the same ASN.1 parser that SeqIO::entrezgene uses >> (Bio::ASN1::EntrezGene); it includes a parser for sequences: >> >> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm >> >> >> chris >> >> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >> >>> Is there a SeqIO parser module for GenBank ASN.1 format? I thought >>> it would have been genbank or entrezgene, but neither of them work. >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > From luciap at sas.upenn.edu Thu Feb 7 22:37:46 2008 From: luciap at sas.upenn.edu (Lucia Peixoto) Date: Thu, 07 Feb 2008 17:37:46 -0500 Subject: [Bioperl-l] How to add branch labels for PAML codeml branch models Message-ID: <1202423866.47ab883ab02a3@webmail.sas.upenn.edu> Just a small question in order to label the branches to use model 2 of PAML branch models can I use add_tag_value of Bio::Tree Node? or there's some other way to do it with bioperl? thanks Lucia Peixoto Department of Biology,SAS University of Pennsylvania From cjfields at uiuc.edu Thu Feb 7 23:39:11 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 7 Feb 2008 17:39:11 -0600 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <47AB8E92.4000307@umdnj.edu> References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8E92.4000307@umdnj.edu> Message-ID: Bio::SeqIO::entrezgene should do this. Any dbxrefs (including GO IDs) should be stored in the annotation collection, but I'm not sure how it is parsed; you'll have to test it out. I agree with Jason; ASN.1 isn't a very friendly format. Don't know why NCBI sticks with it, but I'm sure they have their reasons (I think this may have been discussed before on the list). chris On Feb 7, 2008, at 5:04 PM, Ryan Golhar wrote: > Let me re-phrase then - I want to parse an entry such as this: > > http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 > > to retrieve the text of the Gene Ontology entries and the associated > GO IDs for those entries. Is this possible with BioPerl? If so, > how can I do this with BioPerl? > > Ryan > > > > Jason Stajich wrote: >> ugh - why parse ASN.1? NCBI provides converter application in the >> ncbi toolkit to many formats : genbank, XML, etc. >> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: >>> No. The only ASN.1 parser is entrezgene. You could probably try >>> building one using the same ASN.1 parser that SeqIO::entrezgene >>> uses (Bio::ASN1::EntrezGene); it includes a parser for sequences: >>> >>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm >>> >>> chris >>> >>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >>> >>>> Is there a SeqIO parser module for GenBank ASN.1 format? I >>>> thought it would have been genbank or entrezgene, but neither of >>>> them work. >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> Christopher Fields >>> Postdoctoral Researcher >>> Lab of Dr. Robert Switzer >>> Dept of Biochemistry >>> University of Illinois Urbana-Champaign >>> >>> >>> >>> _______________________________________________ >>> 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 > Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From golharam at umdnj.edu Thu Feb 7 23:04:50 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 07 Feb 2008 18:04:50 -0500 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> Message-ID: <47AB8E92.4000307@umdnj.edu> Let me re-phrase then - I want to parse an entry such as this: http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 to retrieve the text of the Gene Ontology entries and the associated GO IDs for those entries. Is this possible with BioPerl? If so, how can I do this with BioPerl? Ryan Jason Stajich wrote: > ugh - why parse ASN.1? NCBI provides converter application in the ncbi > toolkit to many formats : genbank, XML, etc. > On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: > >> No. The only ASN.1 parser is entrezgene. You could probably try >> building one using the same ASN.1 parser that SeqIO::entrezgene uses >> (Bio::ASN1::EntrezGene); it includes a parser for sequences: >> >> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm >> >> >> chris >> >> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >> >>> Is there a SeqIO parser module for GenBank ASN.1 format? I thought >>> it would have been genbank or entrezgene, but neither of them work. >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> >> _______________________________________________ >> 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 golharam at umdnj.edu Thu Feb 7 23:09:06 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 07 Feb 2008 18:09:06 -0500 Subject: [Bioperl-l] BioPipe links don't work Message-ID: <47AB8F92.2030006@umdnj.edu> The links to BioPipe on the HOWTO page do not work. They all lead to http://www.sedoparking.com/biopipe.org From barry.moore at genetics.utah.edu Fri Feb 8 00:31:53 2008 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Thu, 7 Feb 2008 17:31:53 -0700 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <47AB8E92.4000307@umdnj.edu> References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8E92.4000307@umdnj.edu> Message-ID: Ryan, I you have a list of NCBI Gene IDs then you can grab the flatfile gene2go from NCBIs ftp site ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2go.gz. That will give you tax_id, gene_id, go_id, evidence code, qualifier, category etc. From there you can get the description from the GO OBO file http://www.geneontology.org/ontology/ gene_ontology_edit.obo. If all you need is the description then the file is pretty easy to parse on the fly, but if you need to traverse the graphs or if you want an already written parser then add go-perl http://search.cpan.org/~cmungall/go-perl/go-perl.pod Barry On Feb 7, 2008, at 4:04 PM, Ryan Golhar wrote: > Let me re-phrase then - I want to parse an entry such as this: > > http://www.ncbi.nlm.nih.gov/sites/entrez? > db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 > > to retrieve the text of the Gene Ontology entries and the > associated GO > IDs for those entries. Is this possible with BioPerl? If so, how > can I > do this with BioPerl? > > Ryan > > > > Jason Stajich wrote: >> ugh - why parse ASN.1? NCBI provides converter application in the >> ncbi >> toolkit to many formats : genbank, XML, etc. >> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: >> >>> No. The only ASN.1 parser is entrezgene. You could probably try >>> building one using the same ASN.1 parser that SeqIO::entrezgene uses >>> (Bio::ASN1::EntrezGene); it includes a parser for sequences: >>> >>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/ >>> Bio/ASN1/Sequence.pm >>> >>> >>> chris >>> >>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >>> >>>> Is there a SeqIO parser module for GenBank ASN.1 format? I thought >>>> it would have been genbank or entrezgene, but neither of them work. >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> Christopher Fields >>> Postdoctoral Researcher >>> Lab of Dr. Robert Switzer >>> Dept of Biochemistry >>> University of Illinois Urbana-Champaign >>> >>> >>> >>> _______________________________________________ >>> 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 golharam at umdnj.edu Fri Feb 8 00:46:21 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 07 Feb 2008 19:46:21 -0500 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8E92.4000307@umdnj.edu> Message-ID: <47ABA65D.1000705@umdnj.edu> Thank Barry. I did try using go-perl but it is slow when processing queries. I didn't know about ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz. I think that is exactly what I'm looking for. Ryan Barry Moore wrote: > Ryan, > > I you have a list of NCBI Gene IDs then you can grab the flatfile > gene2go from NCBIs ftp site > ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz. That will give you > tax_id, gene_id, go_id, evidence code, qualifier, category etc. From > there you can get the description from the GO OBO file > http://www.geneontology.org/ontology/gene_ontology_edit.obo. If all you > need is the description then the file is pretty easy to parse on the > fly, but if you need to traverse the graphs or if you want an already > written parser then add go-perl > http://search.cpan.org/~cmungall/go-perl/go-perl.pod > > Barry > > > > On Feb 7, 2008, at 4:04 PM, Ryan Golhar wrote: > >> Let me re-phrase then - I want to parse an entry such as this: >> >> http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 >> >> >> to retrieve the text of the Gene Ontology entries and the associated GO >> IDs for those entries. Is this possible with BioPerl? If so, how can I >> do this with BioPerl? >> >> Ryan >> >> >> >> Jason Stajich wrote: >>> ugh - why parse ASN.1? NCBI provides converter application in the ncbi >>> toolkit to many formats : genbank, XML, etc. >>> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: >>> >>>> No. The only ASN.1 parser is entrezgene. You could probably try >>>> building one using the same ASN.1 parser that SeqIO::entrezgene uses >>>> (Bio::ASN1::EntrezGene); it includes a parser for sequences: >>>> >>>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm >>>> >>>> >>>> >>>> chris >>>> >>>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >>>> >>>>> Is there a SeqIO parser module for GenBank ASN.1 format? I thought >>>>> it would have been genbank or entrezgene, but neither of them work. >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> Christopher Fields >>>> Postdoctoral Researcher >>>> Lab of Dr. Robert Switzer >>>> Dept of Biochemistry >>>> University of Illinois Urbana-Champaign >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 golharam at umdnj.edu Thu Feb 7 23:59:52 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 07 Feb 2008 18:59:52 -0500 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8E92.4000307@umdnj.edu> Message-ID: <47AB9B78.5090907@umdnj.edu> That's what I thought too. However, I'm getting errors with a parser. I found Bio::ASN1::EntrezGene online and am using that module outside of Bioperl as it works well for what I'm doing. I've already changed my code and don't want to deal with tracking down the errors I had with BioPerl (I've already spend enough time on this) but they were easy enough to reproduce. Ryan Chris Fields wrote: > Bio::SeqIO::entrezgene should do this. Any dbxrefs (including GO IDs) > should be stored in the annotation collection, but I'm not sure how it > is parsed; you'll have to test it out. > > I agree with Jason; ASN.1 isn't a very friendly format. Don't know why > NCBI sticks with it, but I'm sure they have their reasons (I think this > may have been discussed before on the list). > > chris > > On Feb 7, 2008, at 5:04 PM, Ryan Golhar wrote: > >> Let me re-phrase then - I want to parse an entry such as this: >> >> http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 >> >> >> to retrieve the text of the Gene Ontology entries and the associated >> GO IDs for those entries. Is this possible with BioPerl? If so, how >> can I do this with BioPerl? >> >> Ryan >> >> >> >> Jason Stajich wrote: >>> ugh - why parse ASN.1? NCBI provides converter application in the >>> ncbi toolkit to many formats : genbank, XML, etc. >>> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: >>>> No. The only ASN.1 parser is entrezgene. You could probably try >>>> building one using the same ASN.1 parser that SeqIO::entrezgene uses >>>> (Bio::ASN1::EntrezGene); it includes a parser for sequences: >>>> >>>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm >>>> >>>> >>>> chris >>>> >>>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >>>> >>>>> Is there a SeqIO parser module for GenBank ASN.1 format? I thought >>>>> it would have been genbank or entrezgene, but neither of them work. >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> Christopher Fields >>>> Postdoctoral Researcher >>>> Lab of Dr. Robert Switzer >>>> Dept of Biochemistry >>>> University of Illinois Urbana-Champaign >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >> > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > > From cjfields at uiuc.edu Fri Feb 8 01:32:18 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 7 Feb 2008 19:32:18 -0600 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <47AB9B78.5090907@umdnj.edu> References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8E92.4000307@umdnj.edu> <47AB9B78.5090907@umdnj.edu> Message-ID: <1001C6BB-24D5-4BB8-B135-0E9D2952B49A@uiuc.edu> It's possible that has been fixed in bioperl-live. However, just in case, if you are getting errors could you file a bug report along with the relevant code demonstrating it? chris On Feb 7, 2008, at 5:59 PM, Ryan Golhar wrote: > That's what I thought too. However, I'm getting errors with a parser. > > I found Bio::ASN1::EntrezGene online and am using that module > outside of Bioperl as it works well for what I'm doing. > > I've already changed my code and don't want to deal with tracking > down the errors I had with BioPerl (I've already spend enough time > on this) but they were easy enough to reproduce. > > Ryan > > > Chris Fields wrote: >> Bio::SeqIO::entrezgene should do this. Any dbxrefs (including GO >> IDs) should be stored in the annotation collection, but I'm not >> sure how it is parsed; you'll have to test it out. >> I agree with Jason; ASN.1 isn't a very friendly format. Don't know >> why NCBI sticks with it, but I'm sure they have their reasons (I >> think this may have been discussed before on the list). >> chris >> On Feb 7, 2008, at 5:04 PM, Ryan Golhar wrote: >>> Let me re-phrase then - I want to parse an entry such as this: >>> >>> http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 >>> >>> to retrieve the text of the Gene Ontology entries and the >>> associated GO IDs for those entries. Is this possible with >>> BioPerl? If so, how can I do this with BioPerl? >>> >>> Ryan >>> >>> >>> >>> Jason Stajich wrote: >>>> ugh - why parse ASN.1? NCBI provides converter application in the >>>> ncbi toolkit to many formats : genbank, XML, etc. >>>> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: >>>>> No. The only ASN.1 parser is entrezgene. You could probably >>>>> try building one using the same ASN.1 parser that >>>>> SeqIO::entrezgene uses (Bio::ASN1::EntrezGene); it includes a >>>>> parser for sequences: >>>>> >>>>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm >>>>> >>>>> chris >>>>> >>>>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >>>>> >>>>>> Is there a SeqIO parser module for GenBank ASN.1 format? I >>>>>> thought it would have been genbank or entrezgene, but neither >>>>>> of them work. >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> Christopher Fields >>>>> Postdoctoral Researcher >>>>> Lab of Dr. Robert Switzer >>>>> Dept of Biochemistry >>>>> University of Illinois Urbana-Champaign >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From jason at bioperl.org Fri Feb 8 01:52:39 2008 From: jason at bioperl.org (Jason Stajich) Date: Thu, 7 Feb 2008 17:52:39 -0800 Subject: [Bioperl-l] How to add branch labels for PAML codeml branch models In-Reply-To: <1202423866.47ab883ab02a3@webmail.sas.upenn.edu> References: <1202423866.47ab883ab02a3@webmail.sas.upenn.edu> Message-ID: It will work if you just change the node's ID to be something like: 'ID #1' (for tips) and for the internal nodes just set the id to ("#1"), etc... I added some code to demonstrate this one the wiki: http://bioperl.org/wiki/HOWTO:PAML#Setting_up_Branch-specific_labels The format is nonstandard so you have to hack the output some to get what you want, hence the extra part that requires you strip out the " since they are required for escaping space characters. -jason On Feb 7, 2008, at 2:37 PM, Lucia Peixoto wrote: > Just a small question > in order to label the branches to use model 2 of PAML branch models > can I use add_tag_value of Bio::Tree Node? > or there's some other way to do it with bioperl? > > thanks > > Lucia Peixoto > Department of Biology,SAS > University of Pennsylvania > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjm at fruitfly.org Fri Feb 8 02:14:20 2008 From: cjm at fruitfly.org (Chris Mungall) Date: Thu, 7 Feb 2008 18:14:20 -0800 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8E92.4000307@umdnj.edu> Message-ID: Just to add to Barry's suggestions: You can query the database directly: http://www.berkeleybop.org/goose You can also use the go-db-perl API and point it at the mysql port of one of the mirrors; see http://www.geneontology.org/GO.database.shtml On Feb 7, 2008, at 4:31 PM, Barry Moore wrote: > Ryan, > > I you have a list of NCBI Gene IDs then you can grab the flatfile > gene2go from NCBIs ftp site ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ > gene2go.gz. That will give you tax_id, gene_id, go_id, evidence > code, qualifier, category etc. From there you can get the > description from the GO OBO file http://www.geneontology.org/ > ontology/gene_ontology_edit.obo. If all you need is the > description then the file is pretty easy to parse on the fly, but > if you need to traverse the graphs or if you want an already > written parser then add go-perl http://search.cpan.org/~cmungall/go- > perl/go-perl.pod > > Barry > > > > On Feb 7, 2008, at 4:04 PM, Ryan Golhar wrote: > >> Let me re-phrase then - I want to parse an entry such as this: >> >> http://www.ncbi.nlm.nih.gov/sites/entrez? >> db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 >> >> to retrieve the text of the Gene Ontology entries and the >> associated GO >> IDs for those entries. Is this possible with BioPerl? If so, how >> can I >> do this with BioPerl? >> >> Ryan >> >> >> >> Jason Stajich wrote: >>> ugh - why parse ASN.1? NCBI provides converter application in the >>> ncbi >>> toolkit to many formats : genbank, XML, etc. >>> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote: >>> >>>> No. The only ASN.1 parser is entrezgene. You could probably try >>>> building one using the same ASN.1 parser that SeqIO::entrezgene >>>> uses >>>> (Bio::ASN1::EntrezGene); it includes a parser for sequences: >>>> >>>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/ >>>> Bio/ASN1/Sequence.pm >>>> >>>> >>>> chris >>>> >>>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote: >>>> >>>>> Is there a SeqIO parser module for GenBank ASN.1 format? I >>>>> thought >>>>> it would have been genbank or entrezgene, but neither of them >>>>> work. >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> Christopher Fields >>>> Postdoctoral Researcher >>>> Lab of Dr. Robert Switzer >>>> Dept of Biochemistry >>>> University of Illinois Urbana-Champaign >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 hlapp at gmx.net Fri Feb 8 02:45:48 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 7 Feb 2008 21:45:48 -0500 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: <47AB8D91.9080201@umdnj.edu> References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8D91.9080201@umdnj.edu> Message-ID: On Feb 7, 2008, at 6:00 PM, Ryan Golhar wrote: > Something is not working with the second line. I get an error: > > "Use of uninitialized value in string eq at > /home/golharam/bioperl/bioperl-1.5.1//Bio/SeqIO/ > entrezgene.pm line 244" This isn't an error, is it - it's a warning, no? -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Fri Feb 8 03:24:45 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 7 Feb 2008 21:24:45 -0600 Subject: [Bioperl-l] GenBank ASN.1 SeqIO parser In-Reply-To: References: <47AB7700.8030801@umdnj.edu> <65B8B6F0-5058-4D88-AEE6-5A381A9ED1B1@bioperl.org> <47AB8D91.9080201@umdnj.edu> Message-ID: I agree. I also noticed Ryan's running bioperl 1.5.1. Probably worth trying the latest code from Subversion. chris On Feb 7, 2008, at 8:45 PM, Hilmar Lapp wrote: > > On Feb 7, 2008, at 6:00 PM, Ryan Golhar wrote: > >> Something is not working with the second line. I get an error: >> >> "Use of uninitialized value in string eq at >> /home/golharam/bioperl/bioperl-1.5.1//Bio/SeqIO/ >> entrezgene.pm line 244" > > > This isn't an error, is it - it's a warning, no? > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From David.Messina at sbc.su.se Fri Feb 8 09:00:05 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Fri, 8 Feb 2008 10:00:05 +0100 Subject: [Bioperl-l] BioPipe links don't work In-Reply-To: <47AB8F92.2030006@umdnj.edu> References: <47AB8F92.2030006@umdnj.edu> Message-ID: <628aabb70802080100g43c02f0btdc8c8065c576ff3d@mail.gmail.com> BioPipe, as far as I can tell, is dead, and indeed the HOWTO is no longer active. Therefore I've removed the BioPipe entry entirely. If anyone would prefer it stay, please let me know and I'll revert the change and update the links to point to the GMOD "BioPipe is no longer supported" page. Dave From luciap at sas.upenn.edu Fri Feb 8 15:53:36 2008 From: luciap at sas.upenn.edu (Lucia Peixoto) Date: Fri, 08 Feb 2008 10:53:36 -0500 Subject: [Bioperl-l] How to add branch labels for PAML codeml branch models In-Reply-To: References: <1202423866.47ab883ab02a3@webmail.sas.upenn.edu> Message-ID: <1202486016.47ac7b003b860@webmail.sas.upenn.edu> Hi as I have my trees right now the bootstrap support ends up as the node ID so I guess I have to assign node ID to bootstrap first and then change? Lucia Quoting Jason Stajich : > It will work if you just change the node's ID to be something like: > 'ID #1' (for tips) and for the internal nodes just set the id to > ("#1"), etc... > > I added some code to demonstrate this one the wiki: > http://bioperl.org/wiki/HOWTO:PAML#Setting_up_Branch-specific_labels > > The format is nonstandard so you have to hack the output some to get > what you want, hence the extra part that requires you strip out the " > since they are required for escaping space characters. > > -jason > On Feb 7, 2008, at 2:37 PM, Lucia Peixoto wrote: > > > Just a small question > > in order to label the branches to use model 2 of PAML branch models > > can I use add_tag_value of Bio::Tree Node? > > or there's some other way to do it with bioperl? > > > > thanks > > > > Lucia Peixoto > > Department of Biology,SAS > > University of Pennsylvania > > _______________________________________________ > > 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 > Lucia Peixoto Department of Biology,SAS University of Pennsylvania From jason at bioperl.org Fri Feb 8 18:18:59 2008 From: jason at bioperl.org (Jason Stajich) Date: Fri, 8 Feb 2008 10:18:59 -0800 Subject: [Bioperl-l] How to add branch labels for PAML codeml branch models In-Reply-To: <1202486016.47ac7b003b860@webmail.sas.upenn.edu> References: <1202423866.47ab883ab02a3@webmail.sas.upenn.edu> <1202486016.47ac7b003b860@webmail.sas.upenn.edu> Message-ID: <793E2862-7D2F-4936-93E3-960BD6D74EB3@bioperl.org> http://bioperl.org/wiki/HOWTO:Trees#Reading_and_Writing_Trees Remember that in newick format bootstrap and internal node ids are effectively the same thing - that we store in them separate slots in bioperl is that fact that other formats can separate out this data but there is no standard in newick format. In sometime cases formats do accept the node labels that look like NODEID[BOOTSTRAP] for internal nodes (and BioPerl parses those out nicely) but most programs don't recognize that. On parsing, unless you tell Bioperl that the internal IDs are bootstrap values it is going to store that data as an ID. You will want to clear the bootstraps anyways to write PAML trees anyways. -jason On Feb 8, 2008, at 7:53 AM, Lucia Peixoto wrote: > Hi > as I have my trees right now the bootstrap support ends up as the > node ID > so I guess I have to assign node ID to bootstrap first and then > change? > > > Lucia > > Quoting Jason Stajich : > >> It will work if you just change the node's ID to be something like: >> 'ID #1' (for tips) and for the internal nodes just set the id to >> ("#1"), etc... >> >> I added some code to demonstrate this one the wiki: >> http://bioperl.org/wiki/HOWTO:PAML#Setting_up_Branch- >> specific_labels >> >> The format is nonstandard so you have to hack the output some to get >> what you want, hence the extra part that requires you strip out the " >> since they are required for escaping space characters. >> >> -jason >> On Feb 7, 2008, at 2:37 PM, Lucia Peixoto wrote: >> >>> Just a small question >>> in order to label the branches to use model 2 of PAML branch models >>> can I use add_tag_value of Bio::Tree Node? >>> or there's some other way to do it with bioperl? >>> >>> thanks >>> >>> Lucia Peixoto >>> Department of Biology,SAS >>> University of Pennsylvania >>> _______________________________________________ >>> 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 >> > > > Lucia Peixoto > Department of Biology,SAS > University of Pennsylvania From golharam at umdnj.edu Sat Feb 9 02:01:45 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 08 Feb 2008 21:01:45 -0500 Subject: [Bioperl-l] error in build.pl of bioperl-live Message-ID: <47AD0989.1050904@umdnj.edu> I just obtained the latest build of bioperl from svn. When I run 'perl Build.pl', I get an error "Use of uninitialized value in concatenation (.) or string at Build.PL line 184.". Here's the output I see (The error is at the end): [golharam at hydrogen bioperl-live]$ perl Build.PL Checking prerequisites... Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] * Optional prerequisite Ace is not installed (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF:: Adaptor::ace) * Optional prerequisite Algorithm::Munkres is not installed (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) * Optional prerequisite Math::Random is not installed (wanted for Random Phylogenetic Networks, used by Bio::PhyloNetwork::RandomFactory) * Optional prerequisite GraphViz is not installed (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz) * Class::AutoClass (0.091) is installed, but we prefer to have 1 (wanted for creating objects, used by Bio::Graph::SimpleGraph, Bio::Graph::SimpleGraph::Traversal and Bio::Graph::ProteinGraph) * Optional prerequisite Array::Compare is not installed (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Checking features: Network..................enabled BioDBSeqFeature_mysql....enabled BioDBGFF.................enabled BioDBSeqFeature_BDB......enabled Do you want to run the BioDBGFF or BioDBSeqFeature_mysql live database tests? y/ n [n] n - will not run the BioDBGFF live database tests Use of uninitialized value in concatenation (.) or string at Build.PL line 184. Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] From golharam at umdnj.edu Sat Feb 9 02:08:30 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 08 Feb 2008 21:08:30 -0500 Subject: [Bioperl-l] error in build.pl of bioperl-live In-Reply-To: <47AD0989.1050904@umdnj.edu> References: <47AD0989.1050904@umdnj.edu> Message-ID: <47AD0B1E.3050200@umdnj.edu> In addition, if I continue past the error and run './Build test', I get a bunch of errors like this: BEGIN failed--compilation aborted at t/lib/BioperlTest.pm line 109. Compilation failed in require at t/Allele.t line 9. BEGIN failed--compilation aborted at t/Allele.t line 9. t/Allele.......................... Dubious, test returned 255 (wstat 65280, 0xff00) No subtests run All the tests fail. The last few lines read: Files=257, Tests=0, 19 wallclock secs ( 0.77 usr 0.51 sys + 12.18 cusr 1.75 csys = 15.21 CPU) Result: FAIL Failed 255/257 test programs. 0/0 subtests failed. Am I missing something? This can't be related to the missing prereqs as all the tests are failing. Ryan Golhar wrote: > I just obtained the latest build of bioperl from svn. When I run 'perl > Build.pl', I get an error "Use of uninitialized value in concatenation > (.) or string at Build.PL line 184.". Here's the output I see (The > error is at the end): > > [golharam at hydrogen bioperl-live]$ perl Build.PL > Checking prerequisites... > Install [a]ll optional external modules, [n]one, or choose > [i]nteractively? [n] > * Optional prerequisite Ace is not installed > (wanted for access of ACeDB database, used by Bio::DB::Ace and > Bio::DB::GFF:: > Adaptor::ace) > * Optional prerequisite Algorithm::Munkres is not installed > (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) > * Optional prerequisite Math::Random is not installed > (wanted for Random Phylogenetic Networks, used by > Bio::PhyloNetwork::RandomFactory) > * Optional prerequisite GraphViz is not installed > (wanted for Phylogenetic Network Visulization, used by > Bio::PhyloNetwork::GraphViz) > * Class::AutoClass (0.091) is installed, but we prefer to have 1 > (wanted for creating objects, used by Bio::Graph::SimpleGraph, > Bio::Graph::SimpleGraph::Traversal and Bio::Graph::ProteinGraph) > * Optional prerequisite Array::Compare is not installed > (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) > > ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the > versions > of the modules indicated above before proceeding with this installation > > Checking features: > Network..................enabled > BioDBSeqFeature_mysql....enabled > BioDBGFF.................enabled > BioDBSeqFeature_BDB......enabled > > Do you want to run the BioDBGFF or BioDBSeqFeature_mysql live database > tests? y/ > n [n] n > - will not run the BioDBGFF live database tests > > Use of uninitialized value in concatenation (.) or string at Build.PL > line 184. > Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? > [a] > From hlapp at gmx.net Sat Feb 9 03:33:55 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 8 Feb 2008 22:33:55 -0500 Subject: [Bioperl-l] error in build.pl of bioperl-live In-Reply-To: <47AD0989.1050904@umdnj.edu> References: <47AD0989.1050904@umdnj.edu> Message-ID: Hi Ryan, On Feb 8, 2008, at 9:01 PM, Ryan Golhar wrote: > I get an error "Use of uninitialized value in concatenation (.) or > string at Build.PL line 184.". do keep in mind that this kind of message is almost never an error. It's simply a warning that you wouldn't even see w/o -w. All that it means is that a scalar with an undefined value is being evaluated to a string (which results, by default, in an empty string). Is the build failing or halting at this point for you? That said, it's indeed a good to point those out, as someone either should have initialized a scalar when it wasn't, or that someone was expecting the scalar to always have a value, and so the absence of it may indicate an unexpected condition resulting from an error elsewhere. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From golharam at umdnj.edu Sat Feb 9 03:58:02 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Fri, 08 Feb 2008 22:58:02 -0500 Subject: [Bioperl-l] error in build.pl of bioperl-live In-Reply-To: References: <47AD0989.1050904@umdnj.edu> Message-ID: <47AD24CA.2050102@umdnj.edu> Hi Hilmar, The script doesn't halt, but the tests do fail. I sent another message with the errors I am seeing. I do not know if they are related to this or not. Ryan Hilmar Lapp wrote: > Hi Ryan, > > On Feb 8, 2008, at 9:01 PM, Ryan Golhar wrote: > >> I get an error "Use of uninitialized value in concatenation (.) or >> string at Build.PL line 184.". > > > do keep in mind that this kind of message is almost never an error. It's > simply a warning that you wouldn't even see w/o -w. All that it means is > that a scalar with an undefined value is being evaluated to a string > (which results, by default, in an empty string). > > Is the build failing or halting at this point for you? > > That said, it's indeed a good to point those out, as someone either > should have initialized a scalar when it wasn't, or that someone was > expecting the scalar to always have a value, and so the absence of it > may indicate an unexpected condition resulting from an error elsewhere. > > -hilmar From hlapp at gmx.net Sat Feb 9 04:07:31 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 8 Feb 2008 23:07:31 -0500 Subject: [Bioperl-l] error in build.pl of bioperl-live In-Reply-To: <47AD24CA.2050102@umdnj.edu> References: <47AD0989.1050904@umdnj.edu> <47AD24CA.2050102@umdnj.edu> Message-ID: On Feb 8, 2008, at 10:58 PM, Ryan Golhar wrote: > The script doesn't halt, but the tests do fail. I sent another > message with the errors I am seeing. I do not know if they are > related to this or not. Yep I saw that. They might be related if, for example, the issue is related to not finding BioPerl? Can you run one test in verbose mode? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Sat Feb 9 04:47:08 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 8 Feb 2008 22:47:08 -0600 Subject: [Bioperl-l] error in build.pl of bioperl-live In-Reply-To: <47AD24CA.2050102@umdnj.edu> References: <47AD0989.1050904@umdnj.edu> <47AD24CA.2050102@umdnj.edu> Message-ID: Ryan, I don't see either the 'Use of initialized' error or the massive failed test issue using Mac OS X (perl 5.8). I get a different set of warnings using perl 5.10 related to Data::Dumper but not this (and everything runs fine). It might be of help to know what perl version, OS, etc. you are using. It also might be worth upgrading Module::Build and Test::Harness as well (though the Build.PL script should catch that and warn you). chris On Feb 8, 2008, at 9:58 PM, Ryan Golhar wrote: > Hi Hilmar, > > The script doesn't halt, but the tests do fail. I sent another > message with the errors I am seeing. I do not know if they are > related to this or not. > > Ryan > > > Hilmar Lapp wrote: >> Hi Ryan, >> On Feb 8, 2008, at 9:01 PM, Ryan Golhar wrote: >>> I get an error "Use of uninitialized value in concatenation (.) or >>> string at Build.PL line 184.". >> do keep in mind that this kind of message is almost never an error. >> It's simply a warning that you wouldn't even see w/o -w. All that >> it means is that a scalar with an undefined value is being >> evaluated to a string (which results, by default, in an empty >> string). >> Is the build failing or halting at this point for you? >> That said, it's indeed a good to point those out, as someone either >> should have initialized a scalar when it wasn't, or that someone >> was expecting the scalar to always have a value, and so the absence >> of it may indicate an unexpected condition resulting from an error >> elsewhere. >> -hilmar > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Sat Feb 9 04:49:14 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 8 Feb 2008 22:49:14 -0600 Subject: [Bioperl-l] error in build.pl of bioperl-live In-Reply-To: References: <47AD0989.1050904@umdnj.edu> <47AD24CA.2050102@umdnj.edu> Message-ID: <35C30475-6CC6-470E-B40B-DF13E65FC8A3@uiuc.edu> On Feb 8, 2008, at 10:07 PM, Hilmar Lapp wrote: > > On Feb 8, 2008, at 10:58 PM, Ryan Golhar wrote: > >> The script doesn't halt, but the tests do fail. I sent another >> message with the errors I am seeing. I do not know if they are >> related to this or not. > > > Yep I saw that. They might be related if, for example, the issue is > related to not finding BioPerl? > > Can you run one test in verbose mode? > > -hilmar To add to that, 'perl -I. t/SearchIO.t' should also still work for most (but not all). chris From heikki at sanbi.ac.za Tue Feb 12 08:25:32 2008 From: heikki at sanbi.ac.za (Heikki Lehvaslaiho) Date: Tue, 12 Feb 2008 10:25:32 +0200 Subject: [Bioperl-l] BioHackathon 2008 Message-ID: <200802121025.32797.heikki@sanbi.ac.za> Hi all, BioHackathon 2008 is happening right now in Tokyo, Japan. See http://hackathon.dbcls.jp/ The focus is on web services but some direct work on Bio* projects is getting done, too. See page: http://hackathon.dbcls.jp/wiki/OpenBio* for ideas thrown in the air. I just had a look how well the most common sequence file formats survive reading from a flat file into BioPerl objects and writing back into the same format: http://hackathon.dbcls.jp/wiki/BioPerlRoundTripFirstPass -Heikki -- ______ _/ _/_____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za _/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho _/ _/ _/ SANBI, South African National Bioinformatics Institute _/ _/ _/ University of Western Cape, South Africa _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 ___ _/_/_/_/_/________________________________________________________ From lenski at mdc-berlin.de Tue Feb 12 09:54:25 2008 From: lenski at mdc-berlin.de (Ulf Lenski) Date: Tue, 12 Feb 2008 10:54:25 +0100 Subject: [Bioperl-l] fetch protein-na-complexes from pdb Message-ID: <47B16CD1.2060307@mdc-berlin.de> is there a bioperl modul for fetching protein-na-complexes from the pdb? and can i distinguish ss-dna from dna chains without parsing the pdb files and go through the coordinates (calculate distances etc...)? tx - ulf. -------------- next part -------------- A non-text attachment was scrubbed... Name: lenski.vcf Type: text/x-vcard Size: 216 bytes Desc: not available URL: From bernd.web at gmail.com Tue Feb 12 12:45:51 2008 From: bernd.web at gmail.com (Bernd Web) Date: Tue, 12 Feb 2008 13:45:51 +0100 Subject: [Bioperl-l] fetch protein-na-complexes from pdb In-Reply-To: <47B16CD1.2060307@mdc-berlin.de> References: <47B16CD1.2060307@mdc-berlin.de> Message-ID: <716af09c0802120445n6d477c7dj5de7819408eb2c48@mail.gmail.com> Hi Ulf, At rcsb.org you can get a list of PDB IDs for Protein/NA complexes and even download the entries there. See http://www.rcsb.org/pdb/statistics/holdings.do Also see "webdownload" on the RCSB site. Alternatively, you could fetch the files one by one (e.g. with wget). The file "ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_entry_type.txt" contains the entry type of all PDB entries (i.e.: prot/nuc/prot-nuc and diffraction/NMR). Regards, Bernd 2008/2/12 Ulf Lenski : > is there a bioperl modul for fetching protein-na-complexes from the pdb? > and can i distinguish ss-dna from dna chains without parsing the pdb > files and go through the coordinates (calculate distances etc...)? > > tx - ulf. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From lenski at mdc-berlin.de Tue Feb 12 13:43:51 2008 From: lenski at mdc-berlin.de (Ulf Lenski) Date: Tue, 12 Feb 2008 14:43:51 +0100 Subject: [Bioperl-l] fetch protein-na-complexes from pdb In-Reply-To: <716af09c0802120445n6d477c7dj5de7819408eb2c48@mail.gmail.com> References: <47B16CD1.2060307@mdc-berlin.de> <716af09c0802120445n6d477c7dj5de7819408eb2c48@mail.gmail.com> Message-ID: <47B1A297.7030406@mdc-berlin.de> hi bernd, thanks a lot - that helps me for my first question. but how can I distinguish the nuc chains? How I can find out the type of a single chain? ss-rna ss-dna ds-rna ds-dna regards, ulf. Bernd Web schrieb: > Hi Ulf, > > At rcsb.org you can get a list of PDB IDs for Protein/NA complexes and > even download the entries there. See > http://www.rcsb.org/pdb/statistics/holdings.do > Also see "webdownload" on the RCSB site. > > Alternatively, you could fetch the files one by one (e.g. with wget). > The file "ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_entry_type.txt" > contains the entry type of all PDB entries (i.e.: prot/nuc/prot-nuc > and diffraction/NMR). > > Regards, > Bernd > > > 2008/2/12 Ulf Lenski : > >> is there a bioperl modul for fetching protein-na-complexes from the pdb? >> and can i distinguish ss-dna from dna chains without parsing the pdb >> files and go through the coordinates (calculate distances etc...)? >> >> tx - ulf. >> >> _______________________________________________ >> 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 > > -------------- next part -------------- A non-text attachment was scrubbed... Name: lenski.vcf Type: text/x-vcard Size: 216 bytes Desc: not available URL: From cjfields at uiuc.edu Tue Feb 12 17:02:13 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 12 Feb 2008 11:02:13 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release Message-ID: Now that SVN migration is complete and a BioSQL 1.0 release is imminent (congrats Hilmar and Heikki), I would like to get a new bioperl core release out the door soon, preferably by the next BOSC meeting, end of summer by the latest. One major issue that all the core devs have right now is time, or a serious lack thereof. I, for instance, will be moving into a new research position in the next few months or so. I'm assuming Jason, Hilmar, Heikki, Sendu, and the other core developers are facing similar time constraints. In that light, we need to decide whether we are planning a new 1.5 release, or if we want to start a new stable (1.6) release. With the latter, we need to define very specifically what needs to be accomplished for that release, and it needs to be realistic with the timeframe above in mind. I would also like to extend the invitation for anyone who wishes to help to join in. For my vote, I would like to release a new stable 1.6; 1.5.x has been around for too long and the end goals were never really defined clearly (something we need to keep in mind for the next dev release). I also vote for separating out experimental/untested/undocumented/ unmaintained modules into a separate 'bioperl-dev' release (the 'here be dragons' of bioperl). I believe it would help the core release cycle tremendously. Issues raised in the past just off the top of my head (add more as needed): * perl 5.10 compliance (appears to mostly work now) * outstanding bugs (core only) * GFF/GFF3 compliance * BioSQL 1.0 compliance (impending) * POD and test coverage * smoke tests for bioperl-live/db/etc. * smaller, more focused core (less dependencies) * separating out experimental or poorly maintained modules into a separate 'bioperl-dev' distribution * bioperl-db issues with Bio::Species changes * module maintenance * sequence format roundtripping (i.e. genbank, embl, swissetc) * additional sequence parsers (insdcxml, etc) * enhancement requests in bugzilla (Albert?) chris From hangsyin at gmail.com Tue Feb 12 16:50:33 2008 From: hangsyin at gmail.com (Hang) Date: Tue, 12 Feb 2008 08:50:33 -0800 (PST) Subject: [Bioperl-l] BLAT in memory Message-ID: <15435321.post@talk.nabble.com> Dear all, I wonder whether it is a way that allows me to BLAT sequences and retrieve the result without writing to a file. Thank you! Best, Hang -- View this message in context: http://www.nabble.com/BLAT-in-memory-tp15435321p15435321.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From jason at bioperl.org Tue Feb 12 17:49:56 2008 From: jason at bioperl.org (Jason Stajich) Date: Tue, 12 Feb 2008 09:49:56 -0800 Subject: [Bioperl-l] BLAT in memory In-Reply-To: <15435321.post@talk.nabble.com> References: <15435321.post@talk.nabble.com> Message-ID: <63C04F95-2EFB-433B-91F8-7907829E18CB@bioperl.org> Specify 'stdout' as the filename. -jason On Feb 12, 2008, at 8:50 AM, Hang wrote: > > Dear all, > > I wonder whether it is a way that allows me to BLAT sequences and > retrieve > the result without writing to a file. Thank you! > > Best, > Hang > -- > View this message in context: http://www.nabble.com/BLAT-in-memory- > tp15435321p15435321.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 bix at sendu.me.uk Tue Feb 12 18:10:52 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 12 Feb 2008 18:10:52 +0000 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: Message-ID: <47B1E12C.9010708@sendu.me.uk> Chris Fields wrote: > * perl 5.10 compliance (appears to mostly work now) > * outstanding bugs (core only) > * POD and test coverage I'm fine with everything you said, but I'll just say that, at a minimum, the above is what needs to be done. Someone needs to step up and organise that 3rd point, since it will require a lot of work. As I've already done work on the test suite, if no one else expresses an interest I might look into it myself. > Now that SVN migration is complete Speaking of which, is there a way a file (like, oh, I don't know, bioperl-live/trunk/t/lib/BioperlTest.pm) can exist just once in SVN but be seen in other locations (like bioperl-run/trunk/t/lib/BioperlTest.pm)? Such that a commit to the version in bioperl-run also affects the version in bioperl-live? Or is there some appropriate other way to organise where cross-repository files are kept and dealt with? From cjfields at uiuc.edu Tue Feb 12 18:51:57 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 12 Feb 2008 12:51:57 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <47B1E12C.9010708@sendu.me.uk> References: <47B1E12C.9010708@sendu.me.uk> Message-ID: <9424A11E-7541-442C-B53E-C791A2D8C6FB@uiuc.edu> On Feb 12, 2008, at 12:10 PM, Sendu Bala wrote: > Chris Fields wrote: >> * perl 5.10 compliance (appears to mostly work now) >> * outstanding bugs (core only) >> * POD and test coverage > > I'm fine with everything you said, but I'll just say that, at a > minimum, the above is what needs to be done. I think we should also try to get bioperl-db up to speed for the BioSQL 1.0 release (at least Bio::Species-related issues). > Someone needs to step up and organise that 3rd point, since it will > require a lot of work. As I've already done work on the test suite, > if no one else expresses an interest I might look into it myself. Jason and I discussed it off list (along with Nathan Haigh). We also brought up the idea of smoke tests, which should pinpoint how stable bioperl-live distributions are. Having those set up would pinpoint modules we think need to stay in core or should go into a separate 'dev/extras' distribution. We could test smoke/coverage/POD on those as well. >> Now that SVN migration is complete > > Speaking of which, is there a way a file (like, oh, I don't know, > bioperl-live/trunk/t/lib/BioperlTest.pm) can exist just once in SVN > but be seen in other locations (like bioperl-run/trunk/t/lib/ > BioperlTest.pm)? Such that a commit to the version in bioperl-run > also affects the version in bioperl-live? Or is there some > appropriate other way to organise where cross-repository files are > kept and dealt with? Maybe using external definitions, though I haven't messed with it personally. http://svnbook.red-bean.com/en/1.4/svn.advanced.externals.html One of the outstanding issues on SVN migration is the use of aliases for a checkout ('bioperl-all'); that would probably require setting svn:externals in some way. chris From hlapp at gmx.net Tue Feb 12 23:24:31 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 13 Feb 2008 08:24:31 +0900 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <47B1E12C.9010708@sendu.me.uk> References: <47B1E12C.9010708@sendu.me.uk> Message-ID: On Feb 13, 2008, at 3:10 AM, Sendu Bala wrote: > Speaking of which, is there a way a file (like, oh, I don't know, > bioperl-live/trunk/t/lib/BioperlTest.pm) can exist just once in SVN > but be seen in other locations (like bioperl-run/trunk/t/lib/ > BioperlTest.pm)? svn supposedly supports symlinks (though I haven't tested that myself yet), and since bioperl-live and bioperl-run are under the same svn root (aren't they?) you could make a symbolic link. The downside of this is that if someone only checks out bioperl-run the link would presumably be dangling. Though maybe not, not sure how super-smart svn is in this regard. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Wed Feb 13 02:10:23 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 13 Feb 2008 11:10:23 +0900 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <9424A11E-7541-442C-B53E-C791A2D8C6FB@uiuc.edu> References: <47B1E12C.9010708@sendu.me.uk> <9424A11E-7541-442C-B53E-C791A2D8C6FB@uiuc.edu> Message-ID: <66FBC084-74E4-458D-9F46-FCAD124AB8DE@gmx.net> On Feb 13, 2008, at 3:51 AM, Chris Fields wrote: > I think we should also try to get bioperl-db up to speed for the > BioSQL 1.0 release (at least Bio::Species-related issues). I agree. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From n.haigh at sheffield.ac.uk Wed Feb 13 08:46:02 2008 From: n.haigh at sheffield.ac.uk (Nathan S Haigh) Date: Wed, 13 Feb 2008 08:46:02 +0000 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <9424A11E-7541-442C-B53E-C791A2D8C6FB@uiuc.edu> References: <47B1E12C.9010708@sendu.me.uk> <9424A11E-7541-442C-B53E-C791A2D8C6FB@uiuc.edu> Message-ID: <47B2AE4A.3040509@sheffield.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Chris Fields wrote: > On Feb 12, 2008, at 12:10 PM, Sendu Bala wrote: > >> Chris Fields wrote: >>> * perl 5.10 compliance (appears to mostly work now) >>> * outstanding bugs (core only) >>> * POD and test coverage >> >> I'm fine with everything you said, but I'll just say that, at a >> minimum, the above is what needs to be done. > > I think we should also try to get bioperl-db up to speed for the BioSQL > 1.0 release (at least Bio::Species-related issues). > >> Someone needs to step up and organise that 3rd point, since it will >> require a lot of work. As I've already done work on the test suite, if >> no one else expresses an interest I might look into it myself. > > Jason and I discussed it off list (along with Nathan Haigh). We also > brought up the idea of smoke tests, which should pinpoint how stable > bioperl-live distributions are. Having those set up would pinpoint > modules we think need to stay in core or should go into a separate > 'dev/extras' distribution. We could test smoke/coverage/POD on those as > well. > I've moved away from Perl coding over the past 6-12 months but try to keep an eye on the BioPerl mailing list and chip in when I can. The last time the Devel::Cover module came up, it was lacking the ability to sort the coverage report table by each of the coverage metrics - which was a problem for us as we have so many modules and it was time consuming to find those with poor coverage. However, this feature were implemented in Devel::Cover 0.62, so it makes things slightly easier/neater. I'm not sure if the problem of failing tests still mess up the completion of the coverage report or not. >>> Now that SVN migration is complete >> >> Speaking of which, is there a way a file (like, oh, I don't know, >> bioperl-live/trunk/t/lib/BioperlTest.pm) can exist just once in SVN >> but be seen in other locations (like >> bioperl-run/trunk/t/lib/BioperlTest.pm)? Such that a commit to the >> version in bioperl-run also affects the version in bioperl-live? Or is >> there some appropriate other way to organise where cross-repository >> files are kept and dealt with? > See the subversion FAQs: http://subversion.tigris.org/faq.html#symlinks > Maybe using external definitions, though I haven't messed with it > personally. > > http://svnbook.red-bean.com/en/1.4/svn.advanced.externals.html > > One of the outstanding issues on SVN migration is the use of aliases for > a checkout ('bioperl-all'); that would probably require setting > svn:externals in some way. > > chris -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHsq5K9gTv6QYzVL4RAuJWAKCM/eEEXL5LqTsG/fGAmGIM6+dW9QCfe/6w T2a/dKg6d8HHXNXrOnSbdcs= =T8pz -----END PGP SIGNATURE----- From David.Messina at sbc.su.se Wed Feb 13 11:06:58 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 13 Feb 2008 12:06:58 +0100 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: Message-ID: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> I agree with Chris that the next BioPerl release should be 1.6. Shunting abandoned, experimental, and less-developed code to "bioperl-dev" would be extremely beneficial. As Chris stated, not only does it reduce the number of modules needing full test coverage, but the most important core modules are the ones most likely to have good test coverage already. And it would make BioPerl easier to grok for newcomers, too, which is always nice. I've made a first go at dividing the current bioperl core along these lines here: http://www.bioperl.org/wiki/Proposed_1.6_core_modules It's a very rough cut, so those with more familiarity with the bioperl corpus, please go in and rearrange as you see fit. Dave From n.haigh at sheffield.ac.uk Wed Feb 13 12:07:16 2008 From: n.haigh at sheffield.ac.uk (Nathan S Haigh) Date: Wed, 13 Feb 2008 12:07:16 +0000 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> Message-ID: <47B2DD74.5020503@sheffield.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I remember a conversion about how/if to split bioperl modules up in the past. If I remember rightly, there was talk of splitting all modules up and then creating a CPAN bundle for the core modules. I don't know if this make the admin really complex, but this allows people to install just those modules they require rather than the whole bioperl-core. For example, if I write a script or a module that wants to make use of BioPerl's SeqIO abilities, the end user has to download and install a load of modules that he/she may never use. Instead, it would be nicer to simply install SeqIO and it's dependecies. If I want to install all the BioPerl core, I can install a CPAN bundle. Just a thought. Nath Dave Messina wrote: > I agree with Chris that the next BioPerl release should be 1.6. > > Shunting abandoned, experimental, and less-developed code to "bioperl-dev" > would be extremely beneficial. As Chris stated, not only does it reduce the > number of modules needing full test coverage, but the most important core > modules are the ones most likely to have good test coverage already. And it > would make BioPerl easier to grok for newcomers, too, which is always nice. > > I've made a first go at dividing the current bioperl core along these lines > here: > http://www.bioperl.org/wiki/Proposed_1.6_core_modules > > It's a very rough cut, so those with more familiarity with the bioperl > corpus, please go in and rearrange as you see fit. > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHst109gTv6QYzVL4RAvmAAKCmJa5X0dvyPiQ6lADQ0BBk/tu3OQCg1cNC ZZVlnTSKc6dcCbYJ5JgUGjA= =bvUu -----END PGP SIGNATURE----- From bosborne11 at verizon.net Wed Feb 13 15:08:36 2008 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 13 Feb 2008 10:08:36 -0500 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> Message-ID: Dave, A few of those modules are supposed to be removed in 1.6, according to the notes in the DEPRECATED file. I've marked them. Brian O. On Feb 13, 2008, at 6:06 AM, Dave Messina wrote: > I've made a first go at dividing the current bioperl core along > these lines > here: > http://www.bioperl.org/wiki/Proposed_1.6_core_modules From cjfields at uiuc.edu Wed Feb 13 16:58:03 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 13 Feb 2008 10:58:03 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> Message-ID: I've added/modified the page as well; moved Bio::FeatureIO and Bio::SeqFeature::Annotated over to the bioperl-dev for now, along with Bio::Assembly and Bio::Restriction. We'll have to test out removing those modules to see what blows up. chris On Feb 13, 2008, at 9:08 AM, Brian Osborne wrote: > Dave, > > A few of those modules are supposed to be removed in 1.6, according > to the notes in the DEPRECATED file. I've marked them. > > Brian O. > > > On Feb 13, 2008, at 6:06 AM, Dave Messina wrote: > >> I've made a first go at dividing the current bioperl core along >> these lines >> here: >> http://www.bioperl.org/wiki/Proposed_1.6_core_modules > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From cjfields at uiuc.edu Wed Feb 13 19:11:34 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 13 Feb 2008 13:11:34 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> Message-ID: <8C98F03E-0424-4383-A08C-F227745DBEF6@uiuc.edu> On Feb 13, 2008, at 12:32 PM, Brian Osborne wrote: > Chris, > > You should be careful about the names of these packages. For > example, Bio::Biblio and Bio::Restriction are not "in development" > as the term bioperl-dev implies. They're tried and true. And there > may be sets of modules that are experimental in "bioperl-dev", of > course. Is it possible to have 2 packages, "dev" and "tools"? Or > something along those lines? > > Calling things by the wrong names leads to confusion, witness the > Bioperl newcomers who would install an antiquated version 1.4 > because it was labelled 'stable'. > > BIO I agree the name 'dev' is misleading. 'tools' or 'extras' sounds better, maybe using 'dev' for experimental implementations, such as Jason's SeqFeature::Slim or my SeqIO driver/handler modules. The problem with the two namespaces you mention is lack of maintenance and documentation, though I agree they're stable (so maybe in those cases maintenance isn't an issue). We do need to clean up documentation issues with those classes as well as many more (mine included); POD/test coverage will help out there. chris From bosborne11 at verizon.net Wed Feb 13 18:32:46 2008 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 13 Feb 2008 13:32:46 -0500 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> Message-ID: <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> Chris, You should be careful about the names of these packages. For example, Bio::Biblio and Bio::Restriction are not "in development" as the term bioperl-dev implies. They're tried and true. And there may be sets of modules that are experimental in "bioperl-dev", of course. Is it possible to have 2 packages, "dev" and "tools"? Or something along those lines? Calling things by the wrong names leads to confusion, witness the Bioperl newcomers who would install an antiquated version 1.4 because it was labelled 'stable'. BIO On Feb 13, 2008, at 11:58 AM, Chris Fields wrote: > I've added/modified the page as well; moved Bio::FeatureIO and > Bio::SeqFeature::Annotated over to the bioperl-dev for now, along > with Bio::Assembly and Bio::Restriction. We'll have to test out > removing those modules to see what blows up. From David.Messina at sbc.su.se Wed Feb 13 19:55:26 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 13 Feb 2008 20:55:26 +0100 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> Message-ID: <628aabb70802131155q73674b72qad547c55c5443e2d@mail.gmail.com> Great, thanks guys. From bix at sendu.me.uk Wed Feb 13 20:19:01 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Wed, 13 Feb 2008 20:19:01 +0000 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> Message-ID: <47B350B5.3060501@sendu.me.uk> Brian Osborne wrote: > You should be careful about the names of these packages. For example, > Bio::Biblio and Bio::Restriction are not "in development" as the term > bioperl-dev implies. They're tried and true. And there may be sets of > modules that are experimental in "bioperl-dev", of course. Is it > possible to have 2 packages, "dev" and "tools"? Or something along those > lines? > > Calling things by the wrong names leads to confusion, witness the > Bioperl newcomers who would install an antiquated version 1.4 because it > was labelled 'stable'. On the topic of confusion, I think 'bioperl-tools' is a very bad choice since we have Bio::Tools. Why would Bio::Microarray (for example) be in there? (And then we have Bio::Microarray::Tools ...) Can all of the non Bio::Tools modules currently in the bioperl-tools section of the wiki page be annotated as to why they're there and not in core? Then maybe we can come up with a better name to categorize them all under. Perhaps we could also annotate the things in core to justify why they should be in core? Is anyone good at creating maps so we can easily see what Bioperl modules are most used (by other Bioperl modules)? Or is the split intended to be 'core' == "anything and everything that was in 1.4", '????' == "everything else"? In which case, what's a good name for "modules created after 1.4"? 'crust'? ;) From cjfields at uiuc.edu Wed Feb 13 21:05:16 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Wed, 13 Feb 2008 15:05:16 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <47B350B5.3060501@sendu.me.uk> References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> <47B350B5.3060501@sendu.me.uk> Message-ID: <477CF001-FF35-4A08-A360-C9FA2031E353@uiuc.edu> On Feb 13, 2008, at 2:19 PM, Sendu Bala wrote: > Brian Osborne wrote: >> You should be careful about the names of these packages. For >> example, Bio::Biblio and Bio::Restriction are not "in development" >> as the term bioperl-dev implies. They're tried and true. And there >> may be sets of modules that are experimental in "bioperl-dev", of >> course. Is it possible to have 2 packages, "dev" and "tools"? Or >> something along those lines? >> Calling things by the wrong names leads to confusion, witness the >> Bioperl newcomers who would install an antiquated version 1.4 >> because it was labelled 'stable'. > > On the topic of confusion, I think 'bioperl-tools' is a very bad > choice since we have Bio::Tools. Why would Bio::Microarray (for > example) be in there? (And then we have Bio::Microarray::Tools ...) > > Can all of the non Bio::Tools modules currently in the bioperl-tools > section of the wiki page be annotated as to why they're there and > not in core? Then maybe we can come up with a better name to > categorize them all under. > > Perhaps we could also annotate the things in core to justify why > they should be in core? Is anyone good at creating maps so we can > easily see what Bioperl modules are most used (by other Bioperl > modules)? Frankly, it will be hard for a handful of people (Dave, Brian, and I) to justify the existence for every bioperl module or it's placement in bioperl-?, but at least we have a start on it. The page is open for editing by anyone (Dave, Brian, and I have already added quite a bit). There is also a discussion page to add to, which is a good place for proposals and to sketch out ideas. I think we should take some time on this to stew over the options available, maybe a month or two, and set some deadline for starting up. > Or is the split intended to be 'core' == "anything and everything > that was in 1.4", '????' == "everything else"? In which case, what's > a good name for "modules created after 1.4"? 'crust'? ;) I personally take the extreme view of having a very tight core with just the basic sequence, feature, alignment, and annotation classes (just for maintenance sake); everything else just uses those base classes anyway, so I don't necessarily consider them core. I don't think paring down to that level is feasible for a 1.6 release, but moving some of the unmaintained cruft out into a separate installation would be a good start. chris From pengchy at yahoo.com.cn Thu Feb 14 01:26:21 2008 From: pengchy at yahoo.com.cn (Åô³Ì) Date: 14 Feb 2008 01:26:21 -0000 Subject: Åô³ÌÑûÇëÄú¼ÓÈëÈô±ÈÁÚ Message-ID: <20080214012621.30230.qmail@zorpia.com> Hi bioperl! Your friend ?? from ??, just invited you to online photo albums and journals at Zorpia.com. So what is Zorpia? It is an online community that allows you to upload unlimited amount of photos, write journals and make friends. We also have a variety of skins in store for you so that you can customize your homepage freely. Join now for free! Please click the following link to join Zorpia: http://cn.signup.zorpia.com/signup?invitation_key=200802c0d8af2b64f8ef03d6417e4ab4&referral=pengchy This message was delivered with the ??'s initiation. If you wish to discontinue receiving invitations from us, please click the following link: http://cn.signup.zorpia.com/email/optout/bioperl-l at lists.open-bio.org From hangsyin at gmail.com Thu Feb 14 03:10:54 2008 From: hangsyin at gmail.com (Hang) Date: Wed, 13 Feb 2008 19:10:54 -0800 (PST) Subject: [Bioperl-l] Re trieve ID tag in GFF3 Message-ID: <15473188.post@talk.nabble.com> Dear All, I wonder what method I should call to retrieve values of ID tags in GFF3 format. For example, a GFF3 entry in the database is like this: 4 FlyBase gene 24068 25621 . + . ID=FBgn0040037;Name=ABC;Ontology_term=... I'd like to retrieve the scalar value 'FBgn0040037' to compare with another value. Please complete the code below: use Bio::DB::SeqFeature::Store; my $db = Bio::DB::SeqFeature::Store->new(-adaptor => 'DBI::mysql', -dsn => 'dbi:mysql:XXX_gff', -user => 'XXX', -pass => 'XXX')|| die "Database open failed"; ??? Thanks alot! Hang -- View this message in context: http://www.nabble.com/Retrieve-ID-tag-in-GFF3-tp15473188p15473188.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From cjfields at uiuc.edu Thu Feb 14 20:36:27 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 14 Feb 2008 14:36:27 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <47B350B5.3060501@sendu.me.uk> References: <628aabb70802130306p36975008y4b095f1f512d5f00@mail.gmail.com> <38D42814-D806-458C-B2C6-9FF276DC7092@verizon.net> <47B350B5.3060501@sendu.me.uk> Message-ID: <3C0A6ADA-AABC-4D7A-B858-CEB8E87AFDDE@uiuc.edu> On Feb 13, 2008, at 2:19 PM, Sendu Bala wrote: > Brian Osborne wrote: >> You should be careful about the names of these packages. For >> example, Bio::Biblio and Bio::Restriction are not "in development" >> as the term bioperl-dev implies. They're tried and true. And there >> may be sets of modules that are experimental in "bioperl-dev", of >> course. Is it possible to have 2 packages, "dev" and "tools"? Or >> something along those lines? >> Calling things by the wrong names leads to confusion, witness the >> Bioperl newcomers who would install an antiquated version 1.4 >> because it was labelled 'stable'. > > On the topic of confusion, I think 'bioperl-tools' is a very bad > choice since we have Bio::Tools. Why would Bio::Microarray (for > example) be in there? (And then we have Bio::Microarray::Tools ...) > > Can all of the non Bio::Tools modules currently in the bioperl-tools > section of the wiki page be annotated as to why they're there and > not in core? Then maybe we can come up with a better name to > categorize them all under. > > Perhaps we could also annotate the things in core to justify why > they should be in core? Is anyone good at creating maps so we can > easily see what Bioperl modules are most used (by other Bioperl > modules)? > > > Or is the split intended to be 'core' == "anything and everything > that was in 1.4", '????' == "everything else"? In which case, what's > a good name for "modules created after 1.4"? 'crust'? ;) I added a modified proposal to the Talk page for the Release: http://www.bioperl.org/wiki/Talk:Proposed_1.6_core_modules I'm pretty flexible on any of that; it's a proposal only and I think some of it may be wrongheaded, but hey, I'm willing to take a few rotten tomatoes. The key issue is we should try to work out what we mean by 'core' or the core library. I have a rather extreme view of it as being the bare essentials without external, non-perl core dependencies (only SeqI/PrimarySeqI, AlignI, AnnotationI, SeqFeatureI and required modules for those classes) but I'm sure others would lump in parsers, DB functionality, etc. I basically suggest placing those (and any stable but potentially non-core code) in a 'bioperl-main', with any unstable or untested code going into a 'bioperl-unstable'. In essence, bioperl-main would require core and resemble a stable release; bioperl-unstable would require bioperl-main (and core) and resemble a dev release. Not sure how versioning would go or if this is a viable option at all, but it's worth discussing. chris From aaron.j.mackey at gsk.com Fri Feb 15 18:06:58 2008 From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com) Date: Fri, 15 Feb 2008 13:06:58 -0500 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <47B350B5.3060501@sendu.me.uk> Message-ID: > Or is the split intended to be 'core' == "anything and everything that > was in 1.4", '????' == "everything else"? In which case, what's a good > name for "modules created after 1.4"? 'crust'? ;) Nah, "icing". a module "use" map might be very useful to help identify "core" vs. other layers of mantle/crust/icing. http://www.perlmonks.org/?node_id=87329 http://search.cpan.org/src/NEILB/pmusage-1.2/ Some more serious alternatives to "bioperl-dev" and "-tools" might be: "-accessory" or "-optional" or "-other" or "-addons", etc. -Aaron From lincoln.stein at gmail.com Fri Feb 15 20:17:31 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Fri, 15 Feb 2008 15:17:31 -0500 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: Message-ID: <6dce9a0b0802151217t59e41ccq2bcb10c68b8aede1@mail.gmail.com> > * perl 5.10 compliance (appears to mostly work now) > * GFF/GFF3 compliance I've been doing a lot of work on this recently. I think it's much improved. No problems with 5.10 for the modules that I use frequently. Lincoln > > * BioSQL 1.0 compliance (impending) > * POD and test coverage > * smoke tests for bioperl-live/db/etc. > * smaller, more focused core (less dependencies) > * separating out experimental or poorly maintained modules into a > separate 'bioperl-dev' distribution > * bioperl-db issues with Bio::Species changes > * module maintenance > * sequence format roundtripping (i.e. genbank, embl, swissetc) > * additional sequence parsers (insdcxml, etc) > * enhancement requests in bugzilla (Albert?) > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse at cshl.edu From cjfields at uiuc.edu Fri Feb 15 21:43:42 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 15 Feb 2008 15:43:42 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: <6dce9a0b0802151217t59e41ccq2bcb10c68b8aede1@mail.gmail.com> References: <6dce9a0b0802151217t59e41ccq2bcb10c68b8aede1@mail.gmail.com> Message-ID: On Feb 15, 2008, at 2:17 PM, Lincoln Stein wrote: >> * perl 5.10 compliance (appears to mostly work now) >> * GFF/GFF3 compliance > > > I've been doing a lot of work on this recently. I think it's much > improved. > No problems with 5.10 for the modules that I use frequently. > > Lincoln I think bioperl works now for perl 5.10. The only significant issue we ran into were problems with Bio::SeqIO::entrezgene. The parser looped and created a pseudohash under some conditions, which threw all sorts of errors with 5.8. Stefan and I fixed that one in Subversion. There were some odd Data::Dumper-related messages popping up with 'perl Build.PL' using perl 5.10; not sure what's going on there, but it appears harmless: Encountered CODE ref, using dummy placeholder at /opt/perl/lib/5.10.0/ darwin-2level/Data/Dumper.pm line 190. chris From cjfields at uiuc.edu Fri Feb 15 21:49:33 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 15 Feb 2008 15:49:33 -0600 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: Message-ID: On Feb 15, 2008, at 12:06 PM, aaron.j.mackey at gsk.com wrote: >> Or is the split intended to be 'core' == "anything and everything >> that >> was in 1.4", '????' == "everything else"? In which case, what's a >> good >> name for "modules created after 1.4"? 'crust'? ;) > > Nah, "icing". > > a module "use" map might be very useful to help identify "core" vs. > other > layers of mantle/crust/icing. > > http://www.perlmonks.org/?node_id=87329 > http://search.cpan.org/src/NEILB/pmusage-1.2/ > > Some more serious alternatives to "bioperl-dev" and "-tools" might be: > "-accessory" or "-optional" or "-other" or "-addons", etc. > > -Aaron 'bioperl-extras' (Ricky Gervais fan myself) chris From hlapp at gmx.net Fri Feb 15 22:14:10 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 16 Feb 2008 07:14:10 +0900 Subject: [Bioperl-l] Priorities for a bioperl-1.6 release In-Reply-To: References: Message-ID: <82E17B18-32D9-4858-9245-EEF9D143DA11@gmx.net> On Feb 16, 2008, at 6:49 AM, Chris Fields wrote: >> >> Some more serious alternatives to "bioperl-dev" and "-tools" might >> be: >> "-accessory" or "-optional" or "-other" or "-addons", etc. >> >> -Aaron > > 'bioperl-extras' (Ricky Gervais fan myself) > Actually I like bioperl-opt - sounds somehow reminiscent of the /opt directory we all know (often containing the best things :) -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at uiuc.edu Sun Feb 17 14:07:20 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Sun, 17 Feb 2008 08:07:20 -0600 Subject: [Bioperl-l] [Bioperl-guts-l] [14510] bioperl-live/trunk/Bio/SeqIO/swiss.pm: GN line output now follows the new format. In-Reply-To: <200802171000.m1HA0oGq003135@dev.open-bio.org> References: <200802171000.m1HA0oGq003135@dev.open-bio.org> Message-ID: Heikki, See bug 1825: http://bugzilla.open-bio.org/show_bug.cgi?id=1825 Hilmar's final comments about restructuring Bio::Annotation::StructuredValue using Data::Stag should work. chris On Feb 17, 2008, at 4:00 AM, Heikki Lehvaslaiho wrote: > Revision: 14510 > Author: heikki > Date: 2008-02-17 05:00:50 -0500 (Sun, 17 Feb 2008) > > Log Message: > ----------- > GN line output now follows the new format. BioPerl would need new > objects to store all infomation so for now only the official name > (Name=) and synonym categories are kept. ORFNames and > OrderedLocusNames are treated as synonyms. > > Modified Paths: > -------------- > bioperl-live/trunk/Bio/SeqIO/swiss.pm > > Modified: bioperl-live/trunk/Bio/SeqIO/swiss.pm > =================================================================== > --- bioperl-live/trunk/Bio/SeqIO/swiss.pm 2008-02-17 09:48:07 UTC > (rev 14509) > +++ bioperl-live/trunk/Bio/SeqIO/swiss.pm 2008-02-17 10:00:50 UTC > (rev 14510) > @@ -494,16 +494,13 @@ > #Definition lines > $self->_write_line_swissprot_regex("DE ","DE ",$seq- > >desc(),"\\s\+\|\$",$LINE_LENGTH); > > - #Gene name > - if ((my @genes = $seq->annotation- > >get_Annotations('gene_name') ) ) { > - $self->_print("GN ", > - join(' OR ', > - map { > - $_->isa("Bio::Annotation::StructuredValue") ? > - $_->value(-joins => [" AND ", " OR "]) : > - $_->value(); > - } @genes), > - ".\n"); > + #Gene name; print out new format but only two categories: Name > and Synonyms > + if ( my @genes = $seq->annotation- > >get_Annotations('gene_name') ) { > + my @gene_names = map { $_->get_all_values} @genes; > + my $gn_string = 'Name='. shift(@gene_names). ';'; > + $gn_string .= ' Synonyms='. join(', ', @gene_names). ";" if > scalar @gene_names; > + $self->_write_line_swissprot_regex("GN ","GN ", > $gn_string,"\\s\+\|\$",$LINE_LENGTH); > + > } > > # Organism lines > @@ -1267,7 +1264,6 @@ > } > > my $subl = $length - (length $pre1) -1 ; > - my @lines; > > my $first_line = 1; > while($line =~ m/(.{1,$subl})($regex)/g) { > > > _______________________________________________ > Bioperl-guts-l mailing list > Bioperl-guts-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From heikki at sanbi.ac.za Mon Feb 18 08:12:11 2008 From: heikki at sanbi.ac.za (Heikki Lehvaslaiho) Date: Mon, 18 Feb 2008 10:12:11 +0200 Subject: [Bioperl-l] [Bioperl-guts-l] [14510] bioperl-live/trunk/Bio/SeqIO/swiss.pm: GN line output now follows the new format. In-Reply-To: References: <200802171000.m1HA0oGq003135@dev.open-bio.org> Message-ID: <200802181012.11295.heikki@sanbi.ac.za> Thanks for pointing this out to me. Looks like I've solved the first level: "Problem #1 is to have all the value tokens available from the created object, regardless of their tags." Anybody want to go on to the next level and code in the complete representation of the GN line? -Heikki On Sunday 17 February 2008 16:07:20 Chris Fields wrote: > Heikki, > > See bug 1825: > > http://bugzilla.open-bio.org/show_bug.cgi?id=1825 > > Hilmar's final comments about restructuring > Bio::Annotation::StructuredValue using Data::Stag should work. > > chris > > On Feb 17, 2008, at 4:00 AM, Heikki Lehvaslaiho wrote: > > Revision: 14510 > > Author: heikki > > Date: 2008-02-17 05:00:50 -0500 (Sun, 17 Feb 2008) > > > > Log Message: > > ----------- > > GN line output now follows the new format. BioPerl would need new > > objects to store all infomation so for now only the official name > > (Name=) and synonym categories are kept. ORFNames and > > OrderedLocusNames are treated as synonyms. > > > > Modified Paths: > > -------------- > > bioperl-live/trunk/Bio/SeqIO/swiss.pm > > > > Modified: bioperl-live/trunk/Bio/SeqIO/swiss.pm > > =================================================================== > > --- bioperl-live/trunk/Bio/SeqIO/swiss.pm 2008-02-17 09:48:07 UTC > > (rev 14509) > > +++ bioperl-live/trunk/Bio/SeqIO/swiss.pm 2008-02-17 10:00:50 UTC > > (rev 14510) > > @@ -494,16 +494,13 @@ > > #Definition lines > > $self->_write_line_swissprot_regex("DE ","DE ",$seq- > > > > >desc(),"\\s\+\|\$",$LINE_LENGTH); > > > > - #Gene name > > - if ((my @genes = $seq->annotation- > > > > >get_Annotations('gene_name') ) ) { > > > > - $self->_print("GN ", > > - join(' OR ', > > - map { > > - $_->isa("Bio::Annotation::StructuredValue") ? > > - $_->value(-joins => [" AND ", " OR "]) : > > - $_->value(); > > - } @genes), > > - ".\n"); > > + #Gene name; print out new format but only two categories: Name > > and Synonyms > > + if ( my @genes = $seq->annotation- > > > > >get_Annotations('gene_name') ) { > > > > + my @gene_names = map { $_->get_all_values} @genes; > > + my $gn_string = 'Name='. shift(@gene_names). ';'; > > + $gn_string .= ' Synonyms='. join(', ', @gene_names). ";" if > > scalar @gene_names; > > + $self->_write_line_swissprot_regex("GN ","GN ", > > $gn_string,"\\s\+\|\$",$LINE_LENGTH); > > + > > } > > > > # Organism lines > > @@ -1267,7 +1264,6 @@ > > } > > > > my $subl = $length - (length $pre1) -1 ; > > - my @lines; > > > > my $first_line = 1; > > while($line =~ m/(.{1,$subl})($regex)/g) { > > > > > > _______________________________________________ > > Bioperl-guts-l mailing list > > Bioperl-guts-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za _/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho _/ _/ _/ SANBI, South African National Bioinformatics Institute _/ _/ _/ University of Western Cape, South Africa _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 ___ _/_/_/_/_/________________________________________________________ From cjfields at uiuc.edu Mon Feb 18 18:56:32 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 18 Feb 2008 12:56:32 -0600 Subject: [Bioperl-l] [Bioperl-guts-l] [14510] bioperl-live/trunk/Bio/SeqIO/swiss.pm: GN line output now follows the new format. In-Reply-To: <200802181012.11295.heikki@sanbi.ac.za> References: <200802171000.m1HA0oGq003135@dev.open-bio.org> <200802181012.11295.heikki@sanbi.ac.za> Message-ID: <670A1145-D1A6-4245-A621-750E0F4FFB6E@uiuc.edu> I may try working on the next. I had indicated that I would do this in the past, just never got around to it; time is the enemy of us all. chris On Feb 18, 2008, at 2:12 AM, Heikki Lehvaslaiho wrote: > Thanks for pointing this out to me. Looks like I've solved the first > level: > > "Problem #1 is to have all the value tokens > available from the created object, regardless of their tags." > > Anybody want to go on to the next level and code in the complete > representation of the GN line? > > -Heikki > > > On Sunday 17 February 2008 16:07:20 Chris Fields wrote: >> Heikki, >> >> See bug 1825: >> >> http://bugzilla.open-bio.org/show_bug.cgi?id=1825 >> >> Hilmar's final comments about restructuring >> Bio::Annotation::StructuredValue using Data::Stag should work. >> >> chris >> >> On Feb 17, 2008, at 4:00 AM, Heikki Lehvaslaiho wrote: >>> Revision: 14510 >>> Author: heikki >>> Date: 2008-02-17 05:00:50 -0500 (Sun, 17 Feb 2008) >>> >>> Log Message: >>> ----------- >>> GN line output now follows the new format. BioPerl would need new >>> objects to store all infomation so for now only the official name >>> (Name=) and synonym categories are kept. ORFNames and >>> OrderedLocusNames are treated as synonyms. >>> >>> Modified Paths: >>> -------------- >>> bioperl-live/trunk/Bio/SeqIO/swiss.pm >>> >>> Modified: bioperl-live/trunk/Bio/SeqIO/swiss.pm >>> =================================================================== >>> --- bioperl-live/trunk/Bio/SeqIO/swiss.pm 2008-02-17 09:48:07 UTC >>> (rev 14509) >>> +++ bioperl-live/trunk/Bio/SeqIO/swiss.pm 2008-02-17 10:00:50 UTC >>> (rev 14510) >>> @@ -494,16 +494,13 @@ >>> #Definition lines >>> $self->_write_line_swissprot_regex("DE ","DE ",$seq- >>> >>>> desc(),"\\s\+\|\$",$LINE_LENGTH); >>> >>> - #Gene name >>> - if ((my @genes = $seq->annotation- >>> >>>> get_Annotations('gene_name') ) ) { >>> >>> - $self->_print("GN ", >>> - join(' OR ', >>> - map { >>> - $_->isa("Bio::Annotation::StructuredValue") ? >>> - $_->value(-joins => [" AND ", " OR "]) : >>> - $_->value(); >>> - } @genes), >>> - ".\n"); >>> + #Gene name; print out new format but only two categories: Name >>> and Synonyms >>> + if ( my @genes = $seq->annotation- >>> >>>> get_Annotations('gene_name') ) { >>> >>> + my @gene_names = map { $_->get_all_values} @genes; >>> + my $gn_string = 'Name='. shift(@gene_names). ';'; >>> + $gn_string .= ' Synonyms='. join(', ', @gene_names). ";" if >>> scalar @gene_names; >>> + $self->_write_line_swissprot_regex("GN ","GN ", >>> $gn_string,"\\s\+\|\$",$LINE_LENGTH); >>> + >>> } >>> >>> # Organism lines >>> @@ -1267,7 +1264,6 @@ >>> } >>> >>> my $subl = $length - (length $pre1) -1 ; >>> - my @lines; >>> >>> my $first_line = 1; >>> while($line =~ m/(.{1,$subl})($regex)/g) { >>> >>> >>> _______________________________________________ >>> Bioperl-guts-l mailing list >>> Bioperl-guts-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l >> >> Christopher Fields >> Postdoctoral Researcher >> Lab of Dr. Robert Switzer >> Dept of Biochemistry >> University of Illinois Urbana-Champaign >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > -- > ______ _/ _/_____________________________________________________ > _/ _/ > _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za > _/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho > _/ _/ _/ SANBI, South African National Bioinformatics Institute > _/ _/ _/ University of Western Cape, South Africa > _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 > ___ _/_/_/_/_/________________________________________________________ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From hlapp at gmx.net Mon Feb 18 22:14:33 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 18 Feb 2008 17:14:33 -0500 Subject: [Bioperl-l] BOSC 2008? In-Reply-To: <9C6A22B1-9E84-4F17-8459-CBBDCB2110D4@uiuc.edu> References: <1182EAB9-7A75-498F-B91B-C14771DFD607@uiuc.edu> <628aabb70802061317n2f0d1103w9367346166bf8c3f@mail.gmail.com> <9C6A22B1-9E84-4F17-8459-CBBDCB2110D4@uiuc.edu> Message-ID: As an aside, I've posted the (so far "unofficial") update on the news.open-bio.org blog. -hilmar On Feb 6, 2008, at 4:22 PM, Chris Fields wrote: > Yep. I found this out earlier from Darin London. Just trying to > plan for it ahead of time! > > chris > > On Feb 6, 2008, at 3:17 PM, Dave Messina wrote: > >> Hey Chris, >> >> Isn't it usually in conjunction with ISMB (which is Toronto >> 7/19-23 this year)? >> >> > > Christopher Fields > Postdoctoral Researcher > Lab of Dr. Robert Switzer > Dept of Biochemistry > University of Illinois Urbana-Champaign > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From johan.nilsson at sh.se Tue Feb 19 14:42:52 2008 From: johan.nilsson at sh.se (Johan Nilsson) Date: Tue, 19 Feb 2008 15:42:52 +0100 Subject: [Bioperl-l] Dumping a MSA from BLAST results Message-ID: <47BAEAEC.5080203@sh.se> Hello, I have a question regarding the conversion from a Blast search result (PSI-blast using blastpgp, to be more exact) to a multiple sequence alignment file. I'm running the Bio::Tools::Run::StandAloneBlast and I retrieve the HSPs from the resulting Bio::Search::Hit::HitI objects. I have no problems obtaining each HSP alignment using $hit->get_aln. However, rather than dumping many local alignments, I would like to write a single result file where the HSPs are interleaved. I guess this shouldn't be too hard, but nevertheless I haven't found out how to do this in a simple way. Any suggestions would be highly appreciated! Best Regards /Johan Nilsson From jason at bioperl.org Tue Feb 19 16:17:32 2008 From: jason at bioperl.org (Jason Stajich) Date: Tue, 19 Feb 2008 08:17:32 -0800 Subject: [Bioperl-l] Dumping a MSA from BLAST results In-Reply-To: <47BAEAEC.5080203@sh.se> References: <47BAEAEC.5080203@sh.se> Message-ID: <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> All the individual pairwise alignments won't necessarily be an alignment of the same region and the gap insertions can be different in each instance of the query sequence that is participating in the pairwise alns so it won't fit into an MSA. It makes more sense to extract the aligned part of the hit sequences identified and a subsequence of the query which is the min and max region aligned. Run this through a MSA program. -jason On Feb 19, 2008, at 6:42 AM, Johan Nilsson wrote: > Hello, > > I have a question regarding the conversion from a Blast search > result (PSI-blast using blastpgp, to be more exact) to a multiple > sequence alignment file. I'm running the > Bio::Tools::Run::StandAloneBlast and I retrieve the HSPs from the > resulting Bio::Search::Hit::HitI objects. I have no problems > obtaining each HSP alignment using $hit->get_aln. However, rather > than dumping many local alignments, I would like to write a single > result file where the HSPs are interleaved. > > I guess this shouldn't be too hard, but nevertheless I haven't > found out how to do this in a simple way. Any suggestions would be > highly appreciated! > > Best Regards > /Johan Nilsson > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at uiuc.edu Tue Feb 19 17:18:34 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Tue, 19 Feb 2008 11:18:34 -0600 Subject: [Bioperl-l] Dumping a MSA from BLAST results In-Reply-To: <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> Message-ID: One could use an alternative blastall output format (like -m1 to -m6), which give various anchored alignments. None of these are parsed via bioperl as far as I know; might be worth getting something up and running if there is enough interest in it. chris PS. Here's example output using 'blastall -p blastp -i test2.faa -d CP000560.faa -m6', which is query-anchored, flat, blunt ends: BLASTP 2.2.16 [Mar-25-2007] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= gi|1373160|gb|AAB57770.1| PyrR (173 letters) Database: CP000560.faa 3693 sequences; 1,147,568 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gb|ABS73893.1| PyrR [Bacillus amyloliquefaciens FZB42] 322 1e-89 gb|ABS75590.1| ComFC [Bacillus amyloliquefaciens FZB42] 37 6e-04 gb|ABS72500.1| Prs [Bacillus amyloliquefaciens FZB42] 28 0.22 gb|ABS72703.1| YcdA [Bacillus amyloliquefaciens FZB42] 27 0.49 gb|ABS74832.1| Apt [Bacillus amyloliquefaciens FZB42] 26 1.1 gb|ABS75734.1| Upp [Bacillus amyloliquefaciens FZB42] 26 1.4 gb|ABS74081.1| NrdE [Bacillus amyloliquefaciens FZB42] 25 1.9 gb|ABS76054.1| RocD [Bacillus amyloliquefaciens FZB42] 24 4.1 gb|ABS74744.1| Gpr [Bacillus amyloliquefaciens FZB42] 24 5.4 gb|ABS74336.1| UvrX [Bacillus amyloliquefaciens FZB42] 23 7.1 gb|ABS74825.1| YrvM [Bacillus amyloliquefaciens FZB42] 23 9.2 gb|ABS72555.1| RpoB [Bacillus amyloliquefaciens FZB42] 23 9.2 1_0 1 MNQKAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKR--- LAER---- 53 ABS73893 1 MNQKAVILDEQAIRRALTRIAHEMIERNKGMNDCILVGIKTRGIYLAKR--- LAER---- 53 ABS75590 116 ------------------------------- NTHTLIPIPLSGERLAERGFNQSEL---- 140 ABS72500 164 ----------------------------KDLKDIVIVSPDHGGVTRARK--- LADR---- 188 ABS72703 55 ----------------------------------------------ALK--- VTVT---- 61 ABS74832 ------------------------------------------------------------ ABS75734 ------------------------------------------------------------ ABS74081 ------------------------------------------------------------ ABS74081 502 -----------------------------------------RSAELAKE--- KGET---- 513 ABS76054 305 ------VLEEEGLAERSLQLGRYFKEELEKIDNPIIKDVRGRGLFIGVE--- LTEAARPY 355 ABS74744 43 -------------------------ERDKG-------GIKVRTVDITKE--- GAEL---- 63 ABS74336 ------------------------------------------------------------ ABS74825 ------------------------------------------------------------ ABS72555 ------------------------------------------------------------ 1_0 54 IEQIEGNPVTVGEIDITLYRDDLSKKTSNDEPLVKGADIP-V--DITD--- QKVILVDDV 107 ABS73893 54 IEQIEGNPVTVGEIDITLYRDDLTKKTSNEEPLVKGADIP-A--DITD--- QKVIVVDDV 107 ABS75590 141 LASLLGMPVISPLIRLNNEKQSKKSKTDRLSAEKKFSAAE-N--SATG--- MNVILIDDI 194 ABS72500 189 LKA----PIAI---------IDKRRPRPNE---VEVMNIV-G--NVEG--- KTAILIDDI 226 ABS72703 62 VKNTGKDPLTVKSSDFSLYQDD--AKTAK-----------------TD--- KEDLMQSGT 99 ABS74832 112 --------------------------------------------------- QRVLITDDL 120 ABS75734 100 ---------------VGLYRDPETLK-----PVEYYVKLP-S--DVEE--- REFIVVDPM 133 ABS74081 386 -----------------LQASQVSAYTDYDEEDEIGLDIS-C--NLGS--- LNILNVMKH 422 ABS74081 514 FEHYEGSTYATGEYFNKYIEKEFSPAYEKIAALFEGMHIP-TIEDWKE--- LKAFVAENG 569 ABS76054 356 CEKLKGEGLLCKETHDTVIR---------------------------------------- 375 ABS74744 64 SGKKQGRYVTIEAQGVREHDSDMQEKVT-------------------------------- 91 ABS74336 109 ----------------------------------KTIDLP-T-- NITMDIYRYCLILFDK 131 ABS74825 199 ------------------- REDVRKEVGNDEAKIRKAQMP-------------------- 219 ABS72555 1090 -----GAAYTLQEI-LTVKSDDVVGRVKTYEAIVKGDNVPEP--GVPE--- SFKVLIKEL 1138 1_0 108 LYTGRTVRAGMDALVDVGRPSSIQLAVLVDRGHRELPIRADYIGKNIPTSKSEKVMVQLD 167 ABS73893 108 LYTGRTVRAAMDALVDVGRPSSIQLAVLVDRGHRELPIRADYIGKNIPTSKAEKVMVQLS 167 ABS75590 195 YTTGATLHQAAEVLLTAGKASSVSSFTLI------------------------------- 223 ABS72500 227 IDTAGTITLAANALVENG------------------------------------------ 244 ABS72703 100 LHAGKTVTGNLYFTADEGK----------------------------------------- 118 ABS74832 121 LATGGTIEATIKLVEELG------------------------------------------ 138 ABS75734 134 LATGGSAVEAINSL---------------------------------------------- 147 ABS74081 423 KSIERTVKLATDSLTHVSETTDIRNAPAVRRANKAM------------------------ 458 ABS74081 570 MY---------------------------------------------------------- 571 ABS76054 374 ------------------------------------------------------------ 375 ABS74744 90 ------------------------------------------------------------ 91 ABS74336 132 FYTGKTVRS--------------------------------------------------- 140 ABS74825 218 ------------------------------------------------------------ 219 ABS72555 1139 ------ QSLGMDVKILSGDEEEIEMRDLED------------------------------ 1162 1_0 168 EVDQND 173 ABS73893 168 EVDQTD 173 ABS75590 222 ------ 223 ABS72500 243 ------ 244 ABS72703 117 ------ 118 ABS74832 137 ------ 138 ABS75734 146 ------ 147 ABS74081 457 ------ 458 ABS74081 570 ------ 571 ABS76054 374 ------ 375 ABS74744 90 ------ 91 ABS74336 139 ------ 140 ABS74825 218 ------ 219 ABS72555 1161 ------ 1162 On Feb 19, 2008, at 10:17 AM, Jason Stajich wrote: > All the individual pairwise alignments won't necessarily be an > alignment of the same region and the gap insertions can be different > in each instance of the query sequence that is participating in the > pairwise alns so it won't fit into an MSA. > > It makes more sense to extract the aligned part of the hit sequences > identified and a subsequence of the query which is the min and max > region aligned. Run this through a MSA program. > > -jason > On Feb 19, 2008, at 6:42 AM, Johan Nilsson wrote: > >> Hello, >> >> I have a question regarding the conversion from a Blast search >> result (PSI-blast using blastpgp, to be more exact) to a multiple >> sequence alignment file. I'm running the >> Bio::Tools::Run::StandAloneBlast and I retrieve the HSPs from the >> resulting Bio::Search::Hit::HitI objects. I have no problems >> obtaining each HSP alignment using $hit->get_aln. However, rather >> than dumping many local alignments, I would like to write a single >> result file where the HSPs are interleaved. >> >> I guess this shouldn't be too hard, but nevertheless I haven't >> found out how to do this in a simple way. Any suggestions would be >> highly appreciated! >> >> Best Regards >> /Johan Nilsson >> _______________________________________________ >> 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 Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From hangsyin at gmail.com Wed Feb 20 00:20:18 2008 From: hangsyin at gmail.com (Hang) Date: Tue, 19 Feb 2008 16:20:18 -0800 (PST) Subject: [Bioperl-l] Bio::SeqIO fastq Message-ID: <15579570.post@talk.nabble.com> Hi, I'd like to read and write fastq entry. I don't know what is wrong with the following code: use Bio::SeqIO; my $in = Bio::SeqIO->new(-format => "fastq", -file => "test.fq"); while( my $seq = $in->next_seq ) { my $qual = $seq->qual; print $qual; } my test.fq file: @test AAAAA +test IIIII I got "Can't locate method 'qual' via package "AAAAA", perhaps you forgot to load "AAAAA?" at line XX ". Thanks Hang -- View this message in context: http://www.nabble.com/Bio%3A%3ASeqIO-fastq-tp15579570p15579570.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From heikki at sanbi.ac.za Wed Feb 20 20:12:40 2008 From: heikki at sanbi.ac.za (Heikki Lehvaslaiho) Date: Wed, 20 Feb 2008 22:12:40 +0200 Subject: [Bioperl-l] Bio::SeqIO fastq In-Reply-To: <15579570.post@talk.nabble.com> References: <15579570.post@talk.nabble.com> Message-ID: <200802202212.40772.heikki@sanbi.ac.za> Hang, It works for me. The last statement should be print "@$qual", "\n"; to print out readable values. Maybe you have an old version of BioPerl? Try: perl -MBio::Perl -le 'print Bio::Perl->VERSION;' I recommend installing the latest from CVS/SVN. -Heikki On Wednesday 20 February 2008 02:20:18 Hang wrote: > Hi, > > I'd like to read and write fastq entry. I don't know what is wrong with the > following code: > > use Bio::SeqIO; > my $in = Bio::SeqIO->new(-format => "fastq", > -file => "test.fq"); > while( my $seq = $in->next_seq ) { > my $qual = $seq->qual; > print $qual; > } > > my test.fq file: > @test > AAAAA > +test > IIIII > > I got "Can't locate method 'qual' via package "AAAAA", perhaps you forgot > to load "AAAAA?" at line XX ". > > Thanks > Hang -- ______ _/ _/_____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za _/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho _/ _/ _/ SANBI, South African National Bioinformatics Institute _/ _/ _/ University of Western Cape, South Africa _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 ___ _/_/_/_/_/________________________________________________________ From j.s.soares at gmail.com Wed Feb 20 23:04:35 2008 From: j.s.soares at gmail.com (Djodja) Date: Wed, 20 Feb 2008 15:04:35 -0800 (PST) Subject: [Bioperl-l] Bio::SeqIO fastq In-Reply-To: <200802202212.40772.heikki@sanbi.ac.za> References: <15579570.post@talk.nabble.com> <200802202212.40772.heikki@sanbi.ac.za> Message-ID: <15601113.post@talk.nabble.com> Hang, It works fine for me as well. My Bioperl version is: djodja at djodja-desktop:~$ perl -MBio::Perl -le 'print Bio::Perl->VERSION;' 1.005002102 djodja at djodja-desktop:~$ Maybe that is the problem. All the best, Djodja -- View this message in context: http://www.nabble.com/Bio%3A%3ASeqIO-fastq-tp15579570p15601113.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From shameer at ncbs.res.in Wed Feb 20 09:35:43 2008 From: shameer at ncbs.res.in (K. Shameer) Date: Wed, 20 Feb 2008 15:05:43 +0530 (IST) Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> Message-ID: <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> Dear All, Is there any module available in Bioperl that can be used to perform clustering of Gene Ontology terms from a set of Gene IDs and its respective Flybase GO annotations. These Gene IDs where hits from a high-throughput experiment. We would like to find the GO-Term enriched areas to get better biological insight irrespective of the experimental parameters. I am extremely sorry if this is off-topic : Can you please point me towards any paper/libraries that had used Gene Ontology based clustering ? Many thanks in advance, -- K. Shameer Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group National Centre for Biological Sciences (TIFR) GKVK Campus, Bangalore - 65, Karnataka - India T - 91-080-23666001 EXT - 6251 W - http://www.ncbs.res.in From sdavis2 at mail.nih.gov Thu Feb 21 11:54:47 2008 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Thu, 21 Feb 2008 06:54:47 -0500 Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> Message-ID: <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> On Wed, Feb 20, 2008 at 4:35 AM, K. Shameer wrote: > Dear All, > > Is there any module available in Bioperl that can be used to perform > clustering of Gene Ontology terms from a set of Gene IDs and its > respective Flybase GO annotations. These Gene IDs where hits from a > high-throughput experiment. We would like to find the GO-Term enriched > areas to get better biological insight irrespective of the experimental > parameters. > > I am extremely sorry if this is off-topic : > Can you please point me towards any paper/libraries that had used Gene > Ontology based clustering ? I'm not sure what you mean by GO clustering. However, there are a number of packages that will look for enriched GO terms given a set of Gene IDs. If you are looking for programmatic support for custom pipelines, you can look at R/Bioconductor. Here is a website that will look for GO enrichment and takes Flybase IDs as the gene identifier: http://niaid.abcc.ncifcrf.gov/home.jsp Sean From thiago.venancio at gmail.com Thu Feb 21 12:00:10 2008 From: thiago.venancio at gmail.com (Thiago M. Venancio) Date: Thu, 21 Feb 2008 09:00:10 -0300 Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> Message-ID: <44255ea80802210400u6e5242fdpae4c724621395f05@mail.gmail.com> Hi, This is off topic, but here we go. For enrichment analysis, I use Ontologizer: http://www.charite.de/ch/medgen/ontologizer/ But I am also not sure what do you mean by clustering. Best. T On Thu, Feb 21, 2008 at 8:54 AM, Sean Davis wrote: > On Wed, Feb 20, 2008 at 4:35 AM, K. Shameer wrote: > > Dear All, > > > > Is there any module available in Bioperl that can be used to perform > > clustering of Gene Ontology terms from a set of Gene IDs and its > > respective Flybase GO annotations. These Gene IDs where hits from a > > high-throughput experiment. We would like to find the GO-Term enriched > > areas to get better biological insight irrespective of the experimental > > parameters. > > > > I am extremely sorry if this is off-topic : > > Can you please point me towards any paper/libraries that had used Gene > > Ontology based clustering ? > > I'm not sure what you mean by GO clustering. However, there are a > number of packages that will look for enriched GO terms given a set of > Gene IDs. If you are looking for programmatic support for custom > pipelines, you can look at R/Bioconductor. > > Here is a website that will look for GO enrichment and takes Flybase > IDs as the gene identifier: > > http://niaid.abcc.ncifcrf.gov/home.jsp > > Sean > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- "At the center of your being you have the answer; You know who you are and you know what you want." Lao Tzu ======================== Thiago Motta Venancio, M.Sc., PhD Laboratory of Bioinformatics University of Sao Paulo ======================== From shameer at ncbs.res.in Thu Feb 21 12:29:01 2008 From: shameer at ncbs.res.in (K. Shameer) Date: Thu, 21 Feb 2008 17:59:01 +0530 (IST) Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> Message-ID: <60630.192.168.1.1.1203596941.squirrel@mail.ncbs.res.in> Dear All, Thanks for your reply. > I'm not sure what you mean by GO clustering. However, there are a > number of packages that will look for enriched GO terms given a set of > Gene IDs. In simple terms I have a list of genes, irrespective of any experimental value I need to cluster them based on their GO-Terms using the Di Acyclic Graph data structure of the Gene ontology databases. I found an interesting package from CPAN : GO::TermFinder . http://search.cpan.org/dist/GO-TermFinder/ I am not sure if this is a part of Bioperl :). I have tried with few examples it is working fine but I got few wrong results. If this is not part of Bioperl project, I may need to write to the authors. > If you are looking for programmatic support for custom > pipelines, you can look at R/Bioconductor. Thanks a lot !! I have seen a couple of R packages related to GO. But, I honestly wanted to do it in Perl :) !!! > > Here is a website that will look for GO enrichment and takes Flybase > IDs as the gene identifier: > http://niaid.abcc.ncifcrf.gov/home.jsp Thanks for the link. But I am specifically for something stand alone due to huge volume of my dataset. Cheers, Shameer NCBS - TIFR From golharam at umdnj.edu Thu Feb 21 12:26:58 2008 From: golharam at umdnj.edu (Ryan Golhar) Date: Thu, 21 Feb 2008 07:26:58 -0500 Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <44255ea80802210400u6e5242fdpae4c724621395f05@mail.gmail.com> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> <44255ea80802210400u6e5242fdpae4c724621395f05@mail.gmail.com> Message-ID: <47BD6E12.3000808@umdnj.edu> ArrayTrack is a good tool to do this, available from the FDA. It has some nice output and performs some statistical analysis for you. I'm using it now to cluster GO terms. Thiago M. Venancio wrote: > Hi, > This is off topic, but here we go. > For enrichment analysis, I use Ontologizer: > > http://www.charite.de/ch/medgen/ontologizer/ > > But I am also not sure what do you mean by clustering. > > Best. > > T > > On Thu, Feb 21, 2008 at 8:54 AM, Sean Davis wrote: > >> On Wed, Feb 20, 2008 at 4:35 AM, K. Shameer wrote: >>> Dear All, >>> >>> Is there any module available in Bioperl that can be used to perform >>> clustering of Gene Ontology terms from a set of Gene IDs and its >>> respective Flybase GO annotations. These Gene IDs where hits from a >>> high-throughput experiment. We would like to find the GO-Term enriched >>> areas to get better biological insight irrespective of the experimental >>> parameters. >>> >>> I am extremely sorry if this is off-topic : >>> Can you please point me towards any paper/libraries that had used Gene >>> Ontology based clustering ? >> I'm not sure what you mean by GO clustering. However, there are a >> number of packages that will look for enriched GO terms given a set of >> Gene IDs. If you are looking for programmatic support for custom >> pipelines, you can look at R/Bioconductor. >> >> Here is a website that will look for GO enrichment and takes Flybase >> IDs as the gene identifier: >> >> http://niaid.abcc.ncifcrf.gov/home.jsp >> >> Sean >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > From cjfields at uiuc.edu Thu Feb 21 14:21:14 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 21 Feb 2008 08:21:14 -0600 Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <60630.192.168.1.1.1203596941.squirrel@mail.ncbs.res.in> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> <60630.192.168.1.1.1203596941.squirrel@mail.ncbs.res.in> Message-ID: <96A3AC13-1963-4802-8ADA-77D00B393823@uiuc.edu> On Feb 21, 2008, at 6:29 AM, K. Shameer wrote: > Dear All, > > Thanks for your reply. > >> I'm not sure what you mean by GO clustering. However, there are a >> number of packages that will look for enriched GO terms given a set >> of >> Gene IDs. > > In simple terms I have a list of genes, irrespective of any > experimental > value I need to cluster them based on their GO-Terms using the Di > Acyclic > Graph data structure of the Gene ontology databases. > > I found an interesting package from CPAN : GO::TermFinder . > http://search.cpan.org/dist/GO-TermFinder/ > > I am not sure if this is a part of Bioperl :). I have tried with few > examples it is working fine but I got few wrong results. If this is > not > part of Bioperl project, I may need to write to the authors. It's not part of BioPerl, so you should contact the author. >> If you are looking for programmatic support for custom >> pipelines, you can look at R/Bioconductor. > > Thanks a lot !! I have seen a couple of R packages related to GO. > But, I > honestly wanted to do it in Perl :) !!! >> BioPerl's ontology classes are all in Bio::Ontology and Bio::OntologyIO. I would also recommend looking at Chris Mungall's go- perl: http://search.cpan.org/~cmungall/go-perl-0.08/go-perl.pod >> Here is a website that will look for GO enrichment and takes Flybase >> IDs as the gene identifier: >> http://niaid.abcc.ncifcrf.gov/home.jsp > > Thanks for the link. But I am specifically for something stand alone > due > to huge volume of my dataset. > > Cheers, > Shameer > NCBS - TIFR It's always faster to do it locally, I agree, as long as the tools are available to do so. chris From donald.jackson at bms.com Thu Feb 21 14:01:51 2008 From: donald.jackson at bms.com (Donald Jackson (Genomics)) Date: Thu, 21 Feb 2008 09:01:51 -0500 Subject: [Bioperl-l] qury In-Reply-To: <4e5ea6f60802191727x1980d2c8p4783300b4223cd5f@mail.gmail.com> References: <4e5ea6f60802191727x1980d2c8p4783300b4223cd5f@mail.gmail.com> Message-ID: <47BD844F.4070801@bms.com> Hi Somil, I get the same error from my test script. It will be a few days before I can troubleshoot and upload the fix to CVS; I'll let you know when I've posted the fix. Don Jackson Somil Dutt wrote: >Hello > >I used the SiRNA tool which is written below > > >use Bio::Tools::SiRNA; > >* > my $sirna_designer = Bio::Tools::SiRNA->new( -target => $bio_seq, > -rules => 'saigo' > ); > my @pairs = $sirna_designer->design; > > foreach $pair (@pairs) { > my $sense_oligo_sequence = $pair->sense->seq; > my $antisense_oligo_sequence = $pair->antisense->seq; > > # print out results > print join ("\t", $pair->start, $pair->end, $pair->rank, > $sense_oligo_sequence, $antisense_oligo_sequence), "\n";* > } > > >But the following problem > >------------- EXCEPTION Bio::Root::BadParameter ------------- >MSG: Target must be passed as a Bio::Seq object >STACK Bio::Tools::SiRNA::target C:/Perl/site/lib/Bio/Tools/SiRNA.pm:220 >STACK Bio::Tools::SiRNA::new C:/Perl/site/lib/Bio/Tools/SiRNA.pm:198 >STACK toplevel start.pl:32 > >I dont understand why this error is coming. > >Regards > > From shameer at ncbs.res.in Thu Feb 21 19:12:16 2008 From: shameer at ncbs.res.in (K. Shameer) Date: Fri, 22 Feb 2008 00:42:16 +0530 (IST) Subject: [Bioperl-l] Clustering of Gene Ontology Terms In-Reply-To: <96A3AC13-1963-4802-8ADA-77D00B393823@uiuc.edu> References: <47BAEAEC.5080203@sh.se> <6F6166DB-06C1-4316-A12D-D7A08F6850E6@bioperl.org> <51593.192.168.1.1.1203500143.squirrel@mail.ncbs.res.in> <264855a00802210354r3c0b9e59lbad69471a3cb522f@mail.gmail.com> <60630.192.168.1.1.1203596941.squirrel@mail.ncbs.res.in> <96A3AC13-1963-4802-8ADA-77D00B393823@uiuc.edu> Message-ID: <39220.192.168.1.1.1203621136.squirrel@mail.ncbs.res.in> >> I am not sure if this is a part of Bioperl :). I have tried with few >> examples it is working fine but I got few wrong results. If this is >> not part of Bioperl project, I may need to write to the authors. > > It's not part of BioPerl, so you should contact the author. Thanks Chris, Is there any specific way to check installed bioperl modules ? > > BioPerl's ontology classes are all in Bio::Ontology and > Bio::OntologyIO. I would also recommend looking at Chris Mungall's go- > perl: > > http://search.cpan.org/~cmungall/go-perl-0.08/go-perl.pod Thanks for the information. > It's always faster to do it locally, I agree, as long as the tools are > available to do so. :) K. Shameer NCBS - TIFR From cjfields at uiuc.edu Fri Feb 22 04:37:54 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Thu, 21 Feb 2008 22:37:54 -0600 Subject: [Bioperl-l] Bio::Graphics and perl 5.10 Message-ID: <25A5CCCB-CE0F-4E12-8C31-451775C7FB4E@uiuc.edu> I'm getting a single failed test for Bio::Graphics in bioperl-live which appears to be perl 5.10-specific and is related to Bio::Graphics::FeatureFile: t/BioGraphics...... 1..35 ok 1 - use Bio::Graphics::FeatureFile; ok 2 - use Bio::Graphics::Panel; ok 3 not ok 4 # Failed test at t/BioGraphics.t line 49. # got: '7' # expected: '5' ok 5 ok 6 ok 7 ok 8 ... It appears to be coming from render() passing two extra tracks under perl 5.10 over what is passed in perl 5.8. If anyone is running perl 5.10, can they test this out? chris From cjfields at uiuc.edu Fri Feb 22 16:28:01 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Fri, 22 Feb 2008 10:28:01 -0600 Subject: [Bioperl-l] Bio::Graphics and perl 5.10 In-Reply-To: <25A5CCCB-CE0F-4E12-8C31-451775C7FB4E@uiuc.edu> References: <25A5CCCB-CE0F-4E12-8C31-451775C7FB4E@uiuc.edu> Message-ID: <116A7145-55FD-4254-AA94-1D1AAD8D7853@uiuc.edu> (cc'ing to gbrowse list as this pertains somewhat...) Just added a bioperl bug report for this along with the png file output from perl 5.8 and perl 5.10: http://bugzilla.open-bio.org/show_bug.cgi?id=2457 Lincoln's recent commits to Bio::Graphics::FeatureFile didn't fix the issue. However, it is now pinpointing the problem for both perl 5.8 and perl 5.10 (same warning for both, with only perl 5.10 failing): 1..35 ok 1 - use Bio::Graphics::FeatureFile; ok 2 - use Bio::Graphics::Panel; ok 3 Cosmid EST FGENESH SwissProt P-element / yk53c10.3 yk53c10.5 at Bio/ Graphics/FeatureFile.pm line 285. not ok 4 # Failed test at t/BioGraphics.t line 49. # got: '7' # expected: '5' ok 5 ok 6 ok 7 ok 8 ... chris On Feb 21, 2008, at 10:37 PM, Chris Fields wrote: > I'm getting a single failed test for Bio::Graphics in bioperl-live > which appears to be perl 5.10-specific and is related to > Bio::Graphics::FeatureFile: > > t/BioGraphics...... > 1..35 > ok 1 - use Bio::Graphics::FeatureFile; > ok 2 - use Bio::Graphics::Panel; > ok 3 > not ok 4 > > # Failed test at t/BioGraphics.t line 49. > # got: '7' > # expected: '5' > ok 5 > ok 6 > ok 7 > ok 8 > ... > > It appears to be coming from render() passing two extra tracks under > perl 5.10 over what is passed in perl 5.8. If anyone is running > perl 5.10, can they test this out? > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From heikki at sanbi.ac.za Mon Feb 25 06:18:33 2008 From: heikki at sanbi.ac.za (Heikki Lehvaslaiho) Date: Mon, 25 Feb 2008 08:18:33 +0200 Subject: [Bioperl-l] GN line parsing from Uniprot/Swiss-Prot Message-ID: <200802250818.33345.heikki@sanbi.ac.za> There has been an longstanding problem with GN (gene name) line parsing in SwissProt format. It has solved in a way that deals with all the complexity in that line but unfortunately is not backward compatible. You have to upgrade your scripts if you use bioperl-live. This documentation is now part of Bio::SeqIO::swiss.pm: =head2 GN (Gene name) line management details A Uniprot/Swiss-Prot entry holds information on one protein sequence. If that sequence is identical across genes and species, they are all merged into one entry. This creates complex needs for several annotation fields in swiss-prot format. The latest syntax for GN line is described in the user manual: http://www.expasy.ch/sprot/userman.html#GN_line Each of the possibly multiple genes in an entry can have Name, Synonyms (only if there is a name), OrderedLocusNames (names from genomic sequences) and ORFNames (temporary or cosmid names). "Name" here really means "symbol". This complexity is now dealth with the following way: Each gene is an Bio::Annotation::Collection object that is accessed like all other annotations. The tag name is 'gene_name': my @genes = $seq->annotation->get_Annotations('gene_name'); Note that if you are not interested in the complexity of multiple genes, you can easily just take the first value: my ($gene) = $seq->annotation->get_Annotations('gene_name'); None of the four categories for gene_names are obligatory, so you have to test returned objects for existence before using them: my ($name) = $gene->get_Annotations('name'); if ($name) { print "The official gene symbol is: ". $name->value. "\n"; } The can be only one name, so $name is a Bio::Annotation::SimpleValue object. In other categories (tags: synonyms, orderedlocusnames, orfnames; all lower case) there can be more than one value, so they are stored in Bio::Annotation::StructuredValue objects. There can be only one object with a given tag within a given gene. All values for that category are stored in an ordered list within the StructureValue object. e.g: if ( my ($synonyms) = $gene->get_Annotations('synonyms') ) { print "Synonyms: ". join(', ', $synonyms->get_all_values). "\n"; } Since Uniprot/Swiss-Prot format have been around for quite some time, the parser is also able to read in the older GN line syntax where genes are separated by AND and various symbols by OR. The first symbol is taken to be the name and the remaining ones are stored as synonyms. Thanks for Chris Fields for helping out, Enjoy, -Heikki -- ______ _/ _/_____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za _/_/_/_/_/ Senior Scientist skype: heikki_lehvaslaiho _/ _/ _/ SANBI, South African National Bioinformatics Institute _/ _/ _/ University of Western Cape, South Africa _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 ___ _/_/_/_/_/________________________________________________________ From hangsyin at gmail.com Thu Feb 21 21:14:05 2008 From: hangsyin at gmail.com (Hang) Date: Thu, 21 Feb 2008 13:14:05 -0800 (PST) Subject: [Bioperl-l] Bio::SeqIO fastq In-Reply-To: <15601113.post@talk.nabble.com> References: <15579570.post@talk.nabble.com> <200802202212.40772.heikki@sanbi.ac.za> <15601113.post@talk.nabble.com> Message-ID: <15618960.post@talk.nabble.com> Heikki and Djodja, Many thanks for you guys' help! That code is working right now. Hang Djodja wrote: > > Hang, > > It works fine for me as well. > > My Bioperl version is: > > djodja at djodja-desktop:~$ perl -MBio::Perl -le 'print Bio::Perl->VERSION;' > > 1.005002102 > > djodja at djodja-desktop:~$ > > Maybe that is the problem. > > All the best, > > Djodja > > > -- View this message in context: http://www.nabble.com/Bio%3A%3ASeqIO-fastq-tp15579570p15618960.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From sheila.zuniga at sistemasgenomicos.com Mon Feb 25 15:48:18 2008 From: sheila.zuniga at sistemasgenomicos.com (=?iso-8859-1?Q?Sheila_Zu=F1iga_Trejos?=) Date: Mon, 25 Feb 2008 16:48:18 +0100 Subject: [Bioperl-l] bioperl installation problems with CPAN Message-ID: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Dear Sir, I'm trying to install Bioperl using CPAN but it seems impossible. I get several error messages when running cpan > install Bundle::CPAN. Please find attached a file containing these error messages. Any idea of what is happening? Thanks very much for your help, Sheila -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: error.txt URL: From rchu at coh.org Mon Feb 25 21:33:10 2008 From: rchu at coh.org (Roy) Date: Mon, 25 Feb 2008 21:33:10 +0000 (UTC) Subject: [Bioperl-l] SeqIO and large GenBank files Message-ID: Hi everyone, I want to parse some of the .gbk RefSeq files from ncbi, more specifically, ref_chr*.gbk. My script seems to open the sequence stream okay, but when I try to get the next sequence in the stream, my script spits out a lot of warnings of subroutine redefinitions. Is this file incompatible with SeqIO genbank reader? Any insight is appreciated, thanks. Roy test file: ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_01 ===start_code=== #!/usr/bin/perl -w use strict; use warnings; use Bio::Perl; use Bio::SeqIO; my $USAGE = "usage: $0 \n\n"; unless (@ARGV) { print $USAGE; exit; } my $stream = Bio::SeqIO->new(-file => $ARGV[0], -format => "genbank"); my $seq_obj = $stream->next_seq; exit; ===end_code=== ===start warnings=== Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 80, line 36. Subroutine start redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 102, line 36. Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 128, line 36. Subroutine length redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 165, line 36. Subroutine location_type redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 256, line 36. Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 303, line 36. Subroutine trunc redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 334, line 36. Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 91, line 49. Subroutine each_Location redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 123, line 49. Subroutine sub_Location redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 152, line 49. Subroutine add_sub_Location redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 221, line 49. Subroutine splittype redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 245, line 49. Subroutine is_single_sequence redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 273, line 49. Subroutine guide_strand redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 298, line 49. Subroutine strand redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 326, line 49. Subroutine flip_strand redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 367, line 49. Subroutine start redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 388, line 49. Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 407, line 49. Subroutine min_start redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 426, line 49. Subroutine max_start redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 448, line 49. Subroutine start_pos_type redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 471, line 49. Subroutine min_end redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 492, line 49. Subroutine max_end redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 515, line 49. Subroutine end_pos_type redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 539, line 49. Subroutine seq_id redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 565, line 49. Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 611, line 49. Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 134, line 747. Subroutine location_type redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 161, line 747. Subroutine start redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 223, line 747. Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 250, line 747. Subroutine min_start redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 277, line 747. Subroutine max_start redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 296, line 747. Subroutine start_pos_type redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 316, line 747. Subroutine min_end redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 346, line 747. Subroutine max_end redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 365, line 747. Subroutine end_pos_type redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 385, line 747. Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 456, line 747. Subroutine _fuzzypointdecode redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 557, line 747. ==end warnings== From cjfields at uiuc.edu Mon Feb 25 22:17:49 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 25 Feb 2008 16:17:49 -0600 Subject: [Bioperl-l] SeqIO and large GenBank files In-Reply-To: References: Message-ID: <4F9A56D3-1EAE-4916-A2F6-E10DB4CE3C18@uiuc.edu> The perl executable is overly paranoid on Windows for some reason when the '-w' flag is set on the shebang line ('#!/usr/bin/perl -w'); it doesn't like method overloading for some reason. Remove it and the warnings should go away (note: you should still leave 'use strict' and 'use warnings'). chris On Feb 25, 2008, at 3:33 PM, Roy wrote: > Hi everyone, > > I want to parse some of the .gbk RefSeq files from ncbi, more > specifically, > ref_chr*.gbk. My script seems to open the sequence stream okay, but > when I try > to get the next sequence in the stream, my script spits out a lot of > warnings of > subroutine redefinitions. Is this file incompatible with SeqIO > genbank reader? > Any insight is appreciated, thanks. > > Roy > > test file: > > ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_01 > > ===start_code=== > #!/usr/bin/perl -w > use strict; > use warnings; > use Bio::Perl; > use Bio::SeqIO; > my $USAGE = "usage: $0 \n\n"; > unless (@ARGV) { > print $USAGE; > exit; > } > my $stream = Bio::SeqIO->new(-file => $ARGV[0], -format => "genbank"); > my $seq_obj = $stream->next_seq; > exit; > ===end_code=== > > ===start warnings=== > Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Simple.pm > line 80, > line 36. > Subroutine start redefined at C:/Perl/site/lib/Bio\Location > \Simple.pm line 102, > line 36. > Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Simple.pm > line 128, > line 36. > Subroutine length redefined at C:/Perl/site/lib/Bio\Location > \Simple.pm line 165, > line 36. > Subroutine location_type redefined at C:/Perl/site/lib/Bio\Location > \Simple.pm > line 256, line 36. > Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location > \Simple.pm line > 303, line 36. > Subroutine trunc redefined at C:/Perl/site/lib/Bio\Location > \Simple.pm line 334, > line 36. > Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Split.pm > line 91, > line 49. > Subroutine each_Location redefined at C:/Perl/site/lib/Bio\Location > \Split.pm > line 123, line 49. > Subroutine sub_Location redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 152, line 49. > Subroutine add_sub_Location redefined at C:/Perl/site/lib/Bio > \Location\Split.pm > line 221, line 49. > Subroutine splittype redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 245, line 49. > Subroutine is_single_sequence redefined at > C:/Perl/site/lib/Bio\Location\Split.pm line 273, line 49. > Subroutine guide_strand redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 298, line 49. > Subroutine strand redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line 326, > line 49. > Subroutine flip_strand redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 367, line 49. > Subroutine start redefined at C:/Perl/site/lib/Bio\Location\Split.pm > line 388, > line 49. > Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Split.pm > line 407, > line 49. > Subroutine min_start redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 426, line 49. > Subroutine max_start redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 448, line 49. > Subroutine start_pos_type redefined at C:/Perl/site/lib/Bio\Location > \Split.pm > line 471, line 49. > Subroutine min_end redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line 492, > line 49. > Subroutine max_end redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line 515, > line 49. > Subroutine end_pos_type redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 539, line 49. > Subroutine seq_id redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line 565, > line 49. > Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location > \Split.pm line > 611, line 49. > Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm > line 134, > line 747. > Subroutine location_type redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm > line 161, line 747. > Subroutine start redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm > line 223, > line 747. > Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm > line 250, > line 747. > Subroutine min_start redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm line > 277, line 747. > Subroutine max_start redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm line > 296, line 747. > Subroutine start_pos_type redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm > line 316, line 747. > Subroutine min_end redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm line 346, > line 747. > Subroutine max_end redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm line 365, > line 747. > Subroutine end_pos_type redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm line > 385, line 747. > Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location > \Fuzzy.pm line > 456, line 747. > Subroutine _fuzzypointdecode redefined at C:/Perl/site/lib/Bio > \Location\Fuzzy.pm > line 557, line 747. > ==end warnings== > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From Russell.Smithies at agresearch.co.nz Mon Feb 25 22:12:39 2008 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 26 Feb 2008 11:12:39 +1300 Subject: [Bioperl-l] Bio::Assembly::IO problems In-Reply-To: <000001c877c5$d8dc2d70$7000000a@sistemas.local> References: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Message-ID: Is the Bio::Assembly::IO stuff working? I want to parse some .ace files but keep getting errors: [smithiesr at impala ace_phrap]$ perl 454_read_ace.pl Can't call method "get_consensus_sequence" on an undefined value at /usr/lib/perl5/site_perl/5.8.8/Bio/Assembly/IO/ace.pm line 169, line 20. My code is: #!perl -w use Bio::Assembly::IO; use Data::Dumper; my $in = "454Contigs.ace"; $io = new Bio::Assembly::IO(-file=>$in,-format=>"ace"); $ass = $io->next_assembly; print Dumper $ass; exit; any ideas? Thanx, Russell Smithies Bioinformatics Software Developer T +64 3 489 9085 E? russell.smithies at agresearch.co.nz Invermay? Research Centre Puddle Alley, Mosgiel, New Zealand T? +64 3 489 3809?? F? +64 3 489 9174? www.agresearch.co.nz ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From cjfields at uiuc.edu Mon Feb 25 23:01:42 2008 From: cjfields at uiuc.edu (Chris Fields) Date: Mon, 25 Feb 2008 17:01:42 -0600 Subject: [Bioperl-l] Bio::Assembly::IO problems In-Reply-To: References: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Message-ID: <5827D6E2-B798-4001-84DB-8C38586D3CF2@uiuc.edu> Russell, Using the test data from the bioperl installation appears to work, but I wouldn't be surprised if this is a bug. Can you file this as a bug along with some test data? http://bugzilla.open-bio.org/ chris On Feb 25, 2008, at 4:12 PM, Smithies, Russell wrote: > Is the Bio::Assembly::IO stuff working? > I want to parse some .ace files but keep getting errors: > > [smithiesr at impala ace_phrap]$ perl 454_read_ace.pl > Can't call method "get_consensus_sequence" on an undefined value > at /usr/lib/perl5/site_perl/5.8.8/Bio/Assembly/IO/ace.pm line 169, > line 20. > > My code is: > > #!perl -w > > use Bio::Assembly::IO; > use Data::Dumper; > > my $in = "454Contigs.ace"; > > $io = new Bio::Assembly::IO(-file=>$in,-format=>"ace"); > $ass = $io->next_assembly; > > print Dumper $ass; > exit; > > any ideas? > > Thanx, > > Russell Smithies > > Bioinformatics Software 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 > > > = > ====================================================================== > 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 Christopher Fields Postdoctoral Researcher Lab of Dr. Robert Switzer Dept of Biochemistry University of Illinois Urbana-Champaign From rchu at coh.org Mon Feb 25 23:21:26 2008 From: rchu at coh.org (Roy) Date: Mon, 25 Feb 2008 23:21:26 +0000 (UTC) Subject: [Bioperl-l] SeqIO and large GenBank files References: <4F9A56D3-1EAE-4916-A2F6-E10DB4CE3C18@uiuc.edu> Message-ID: Chris Fields uiuc.edu> writes: > > The perl executable is overly paranoid on Windows for some reason when > the '-w' flag is set on the shebang line ('#!/usr/bin/perl -w'); it > doesn't like method overloading for some reason. Remove it and the > warnings should go away (note: you should still leave 'use strict' and > 'use warnings'). > > chris Thanks Chris. Your suggestion worked. I was concerned that there may be some other error because it was taking an ungodly amount of time to process, but that resolved the problems. -Roy From Russell.Smithies at agresearch.co.nz Mon Feb 25 23:23:06 2008 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 26 Feb 2008 12:23:06 +1300 Subject: [Bioperl-l] Bio::Assembly::IO problems - FIXED! In-Reply-To: References: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Message-ID: I solved the problem :-) The contig lines in our .ace files have a lower-case 'c' in the contig name instead of upper-case so weren't being found by this regex in ace.pm line 142: (/^CO Contig(\d+) (\d+) (\d+) (\d+) (\w+)/) && do { # New contig found! e.g: CO contig00001 711 12 6 U instead of: CO Contig00001 711 12 6 U Our contigs were generated with Newbler version 1.1.01.20. so might be something to watch out for in future. Russell Smithies Bioinformatics Software Developer T +64 3 489 9085 E? russell.smithies at agresearch.co.nz Invermay? Research Centre Puddle Alley, Mosgiel, New Zealand T? +64 3 489 3809?? F? +64 3 489 9174? www.agresearch.co.nz > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open- > bio.org] On Behalf Of Smithies, Russell > Sent: Tuesday, 26 February 2008 11:13 a.m. > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] Bio::Assembly::IO problems > > Is the Bio::Assembly::IO stuff working? > I want to parse some .ace files but keep getting errors: > > [smithiesr at impala ace_phrap]$ perl 454_read_ace.pl > Can't call method "get_consensus_sequence" on an undefined value at > /usr/lib/perl5/site_perl/5.8.8/Bio/Assembly/IO/ace.pm line 169, line 20. > > My code is: > > #!perl -w > > use Bio::Assembly::IO; > use Data::Dumper; > > my $in = "454Contigs.ace"; > > $io = new Bio::Assembly::IO(-file=>$in,-format=>"ace"); > $ass = $io->next_assembly; > > print Dumper $ass; > exit; > > any ideas? > > Thanx, > > Russell Smithies > > Bioinformatics Software 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 > > > ============================================================= > ========== > 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 ======================================================================= 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 David.Messina at sbc.su.se Mon Feb 25 23:46:44 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 26 Feb 2008 00:46:44 +0100 Subject: [Bioperl-l] bioperl installation problems with CPAN In-Reply-To: <000001c877c5$d8dc2d70$7000000a@sistemas.local> References: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Message-ID: <628aabb70802251546i3f43212eo705e762bf34ec27a@mail.gmail.com> Hi Sheila, It looks like your cpan configuration has gotten messed up. It's giving invalid parameters to the make command: make: *** No hay ninguna regla para construir el objetivo `dual'. Alto. /usr/bin/make dual processor system -- NOT OK Go to the command line on your system. Enter the cpan shell: % cpan Type the following: cpan> o conf makepl_arg "" cpan> o conf commit That should reset the arguments that cpan adds to the make command. If that doesn't fix your problem, reset everything by typing cpan> o conf defaults cpan> o conf commit and see if that does it. Dave From schaffer at scripps.edu Tue Feb 26 01:04:50 2008 From: schaffer at scripps.edu (Lana Schaffer) Date: Mon, 25 Feb 2008 17:04:50 -0800 Subject: [Bioperl-l] statistics Message-ID: <8F897BD2B0EB714CB79B96D84911B30209E543@EXCHV1.lj.ad.scripps.edu> Hi, I want to know if Bioperl does t-tests and how to do it? Also, I need to get a chi-squared statistic. Thanks, Lana Schaffer Biostatistics/Informatics The Scripps Research Institute DNA Array Core Facility La Jolla, CA 92037 (858) 784-2263 (858) 784-2994 schaffer at scripps.edu From sdavis2 at mail.nih.gov Tue Feb 26 02:45:00 2008 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Mon, 25 Feb 2008 21:45:00 -0500 Subject: [Bioperl-l] statistics In-Reply-To: <8F897BD2B0EB714CB79B96D84911B30209E543@EXCHV1.lj.ad.scripps.edu> References: <8F897BD2B0EB714CB79B96D84911B30209E543@EXCHV1.lj.ad.scripps.edu> Message-ID: <264855a00802251845p25130950q5dbdc4228dbb2b93@mail.gmail.com> On Mon, Feb 25, 2008 at 8:04 PM, Lana Schaffer wrote: > Hi, > I want to know if Bioperl does t-tests and how to do it? > Also, I need to get a chi-squared statistic. Hi, Lana. I don't think bioperl offers this functionality. However, a quick search of cpan (http://search.cpan.org) turns up: http://search.cpan.org/~yunfang/Statistics-TTest-1.1.0/TTest.pm http://search.cpan.org/~dcantrell/Statistics-ChiSquare-0.5/lib/Statistics/ChiSquare.pm That said, I know you are an R user. I generally stick to R for any numerics. If you need both a parsing/data munging language and statistics, consider python, where the rpy package allows you access R from python and even does data conversion, etc. Sean From florent.angly at gmail.com Tue Feb 26 05:37:20 2008 From: florent.angly at gmail.com (Florent Angly) Date: Mon, 25 Feb 2008 21:37:20 -0800 Subject: [Bioperl-l] Bio::Assembly::IO problems - FIXED! In-Reply-To: References: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Message-ID: <47C3A590.4070204@gmail.com> As far as I know, there really isn't a specification of the ACE file format, that would rule if it is legal to have the kind of contig name (non capitalized), other that its original implementation in Phrap. According to the spirit of the ACE file format, my guess is that any contig name should be allowed. For example, on this webpage http://www.cbcb.umd.edu/research/contig_representation.shtml, the contig name is just a number. So please Russel file this as a bug so that the developers can keep track of this bug, Regards, Florent Smithies, Russell wrote: > I solved the problem :-) > The contig lines in our .ace files have a lower-case 'c' in the contig name instead of upper-case so weren't being found by this regex in ace.pm line 142: > (/^CO Contig(\d+) (\d+) (\d+) (\d+) (\w+)/) && do { # New contig found! > > e.g: > CO contig00001 711 12 6 U > instead of: > CO Contig00001 711 12 6 U > > Our contigs were generated with Newbler version 1.1.01.20. so might be something to watch out for in future. > > > Russell Smithies > > Bioinformatics Software Developer > T +64 3 489 9085 > E russell.smithies at agresearch.co.nz > > Invermay Research Centre > Puddle Alley, > Mosgiel, > New Zealand > T +64 3 489 3809 > F +64 3 489 9174 > www.agresearch.co.nz > > > > > > > > > >> -----Original Message----- >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open- >> bio.org] On Behalf Of Smithies, Russell >> Sent: Tuesday, 26 February 2008 11:13 a.m. >> To: bioperl-l at lists.open-bio.org >> Subject: [Bioperl-l] Bio::Assembly::IO problems >> >> Is the Bio::Assembly::IO stuff working? >> I want to parse some .ace files but keep getting errors: >> >> [smithiesr at impala ace_phrap]$ perl 454_read_ace.pl >> Can't call method "get_consensus_sequence" on an undefined value at >> /usr/lib/perl5/site_perl/5.8.8/Bio/Assembly/IO/ace.pm line 169, line 20. >> >> My code is: >> >> #!perl -w >> >> use Bio::Assembly::IO; >> use Data::Dumper; >> >> my $in = "454Contigs.ace"; >> >> $io = new Bio::Assembly::IO(-file=>$in,-format=>"ace"); >> $ass = $io->next_assembly; >> >> print Dumper $ass; >> exit; >> >> any ideas? >> >> Thanx, >> >> Russell Smithies >> >> Bioinformatics Software 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 >> >> >> ============================================================= >> ========== >> 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 >> > ======================================================================= > 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 David.Messina at sbc.su.se Tue Feb 26 10:47:36 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 26 Feb 2008 11:47:36 +0100 Subject: [Bioperl-l] bioperl installation problems with CPAN In-Reply-To: <000701c87857$15dd6d60$7000000a@sistemas.local> References: <628aabb70802251546i3f43212eo705e762bf34ec27a@mail.gmail.com> <000701c87857$15dd6d60$7000000a@sistemas.local> Message-ID: <628aabb70802260247h2d063d4ah489318aad66c4e6a@mail.gmail.com> Hi Sheila, Please be sure to keep bioperl-l on the Cc so that everyone can follow along the discussion. I don't think this is a BioPerl-specific problem. Can you successfully install other modules from CPAN? Could you type "o conf" in cpan and paste the results into your reply to this message? Dave On 2/26/08, Sheila Zu?iga Trejos wrote: > > Hi Dave, > I've tried the two options and in both cases I got the same error message. > I even restart the server both times in case it could make any difference > but nothing changed. > First attempt: > > Type: cpan> o conf makepl_arg "" > Return: makepl_arg > Type: cpan> o conf commit > Return: commit: wrote /etc/perl/CPAN/Config.pm > Type: cpan> install Bundle::CPAN > Return: error message attached (same as before) > > Second attempt: > > Type: cpan> o conf defaults > (did not return anything) > Type: cpan> o conf commit > Return: commit: wrote /etc/perl/CPAN/Config.pm > Type: cpan> install Bundle::CPAN > Return: error message attached (same as before) > > I installed Bioperl in Debian Sarge before and I never had any problem with CPAN but with Debian Etch...Well, I hope you have other ideas. > > Thanks very much for your help. > > Sheila > > ------------------------------ > *De:* dave at davemessina.com [mailto:dave at davemessina.com] *En nombre de *Dave > Messina > *Enviado el:* martes, 26 de febrero de 2008 0:47 > *Para:* Sheila Zu?iga Trejos > *CC:* bioperl-l at bioperl.org > *Asunto:* Re: [Bioperl-l] bioperl installation problems with CPAN > > Hi Sheila, > > It looks like your cpan configuration has gotten messed up. It's giving > invalid parameters to the make command: > > make: *** No hay ninguna regla para construir el objetivo `dual'. Alto. > > /usr/bin/make dual processor system -- NOT OK > > > > Go to the command line on your system. Enter the cpan shell: > > % cpan > > Type the following: > > cpan> o conf makepl_arg "" > cpan> o conf commit > > > That should reset the arguments that cpan adds to the make command. If > that doesn't fix your problem, reset everything by typing > > cpan> o conf defaults > cpan> o conf commit > > and see if that does it. > > > Dave > > > From David.Messina at sbc.su.se Tue Feb 26 11:43:35 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 26 Feb 2008 12:43:35 +0100 Subject: [Bioperl-l] bioperl installation problems with CPAN In-Reply-To: <001001c87868$4e11cb20$7000000a@sistemas.local> References: <628aabb70802260247h2d063d4ah489318aad66c4e6a@mail.gmail.com> <001001c87868$4e11cb20$7000000a@sistemas.local> Message-ID: <628aabb70802260343n43b216a2q580827e26266c8b6@mail.gmail.com> The following two lines show the problem: > make_arg dual processor system > make_install_arg to always uninstall potentially conflicting files > The configuration parameters are key-value pairs. So here the parameter "make_arg" is set to the value "dual processor system". "dual processor system" is not a valid command-line argument for the make program, so that's why cpan can't install BioPerl (or anything else, I would suspect). Type the following in cpan: cpan> o conf make_arg "" cpan> o conf make_install_arg "" cpan> o conf commit Then type cpan> o conf and verify that those two parameters have indeed been changed successfully. If so, then try installing BioPerl again. I think it should work, but let me know if not. Dave From sheila.zuniga at sistemasgenomicos.com Tue Feb 26 11:11:09 2008 From: sheila.zuniga at sistemasgenomicos.com (=?iso-8859-1?Q?Sheila_Zu=F1iga_Trejos?=) Date: Tue, 26 Feb 2008 12:11:09 +0100 Subject: [Bioperl-l] bioperl installation problems with CPAN In-Reply-To: <628aabb70802260247h2d063d4ah489318aad66c4e6a@mail.gmail.com> Message-ID: <001001c87868$4e11cb20$7000000a@sistemas.local> Hi Dave, Thanks for your quick reply. Here is the output: cpan> o conf CPAN::Config options from /etc/perl/CPAN/Config.pm: commit Commit changes to disk defaults Reload defaults from disk init Interactive setting of all options build_cache 10 build_dir /root/.cpan/build cache_metadata 1 cpan_home /root/.cpan cpan_version_check 1 dontload_hash ftp /usr/bin/ftp ftp_proxy getcwd cwd gpg /usr/bin/gpg gzip /bin/gzip histfile /root/.cpan/histfile histsize 100 http_proxy inactivity_timeout 0 index_expire 1 inhibit_startup_message 0 keep_source_where /root/.cpan/sources lynx make /usr/bin/make make_arg dual processor system make_install_arg to always uninstall potentially conflicting files makepl_arg ncftpget /usr/bin/ncftpget no_proxy pager /usr/bin/less prefer_installer MB prerequisites_policy ask scan_cache atstart shell /bin/bash tar /bin/tar term_is_latin 1 unzip /usr/bin/unzip urllist ftp://ftp.rediris.es/mirror/CPAN/ wget /usr/bin/wget Sheila _____ De: dave at davemessina.com [mailto:dave at davemessina.com] En nombre de Dave Messina Enviado el: martes, 26 de febrero de 2008 11:48 Para: Sheila Zu?iga Trejos CC: bioperl-l at bioperl.org Asunto: Re: [Bioperl-l] bioperl installation problems with CPAN Hi Sheila, Please be sure to keep bioperl-l on the Cc so that everyone can follow along the discussion. I don't think this is a BioPerl-specific problem. Can you successfully install other modules from CPAN? Could you type "o conf" in cpan and paste the results into your reply to this message? Dave On 2/26/08, Sheila Zu?iga Trejos wrote: Hi Dave, I've tried the two options and in both cases I got the same error message. I even restart the server both times in case it could make any difference but nothing changed. First attempt: Type: cpan> o conf makepl_arg "" Return: makepl_arg Type: cpan> o conf commit Return: commit: wrote /etc/perl/CPAN/Config.pm Type: cpan> install Bundle::CPAN Return: error message attached (same as before) Second attempt: Type: cpan> o conf defaults (did not return anything) Type: cpan> o conf commit Return: commit: wrote /etc/perl/CPAN/Config.pm Type: cpan> install Bundle::CPAN Return: error message attached (same as before) I installed Bioperl in Debian Sarge before and I never had any problem with CPAN but with Debian Etch... Well, I hope you have other ideas. Thanks very much for your help. Sheila _____ De: dave at davemessina.com [mailto:dave at davemessina.com] En nombre de Dave Messina Enviado el: martes, 26 de febrero de 2008 0:47 Para: Sheila Zu?iga Trejos CC: bioperl-l at bioperl.org Asunto: Re: [Bioperl-l] bioperl installation problems with CPAN Hi Sheila, It looks like your cpan configuration has gotten messed up. It's giving invalid parameters to the make command: make: *** No hay ninguna regla para construir el objetivo `dual'. Alto. /usr/bin/make dual processor system -- NOT OK Go to the command line on your system. Enter the cpan shell: % cpan Type the following: cpan> o conf makepl_arg "" cpan> o conf commit That should reset the arguments that cpan adds to the make command. If that doesn't fix your problem, reset everything by typing cpan> o conf defaults cpan> o conf commit and see if that does it. Dave From sheila.zuniga at sistemasgenomicos.com Tue Feb 26 11:54:53 2008 From: sheila.zuniga at sistemasgenomicos.com (=?iso-8859-1?Q?Sheila_Zu=F1iga_Trejos?=) Date: Tue, 26 Feb 2008 12:54:53 +0100 Subject: [Bioperl-l] bioperl installation problems with CPAN In-Reply-To: <628aabb70802260343n43b216a2q580827e26266c8b6@mail.gmail.com> Message-ID: <001801c8786e$6a04bc10$7000000a@sistemas.local> Hi Dave, You're right! It works! Thanks very much for your help. Sheila _____ De: dave at davemessina.com [mailto:dave at davemessina.com] En nombre de Dave Messina Enviado el: martes, 26 de febrero de 2008 12:44 Para: Sheila Zu?iga Trejos CC: bioperl-l at bioperl.org Asunto: Re: [Bioperl-l] bioperl installation problems with CPAN The following two lines show the problem: make_arg dual processor system make_install_arg to always uninstall potentially conflicting files The configuration parameters are key-value pairs. So here the parameter "make_arg" is set to the value "dual processor system". "dual processor system" is not a valid command-line argument for the make program, so that's why cpan can't install BioPerl (or anything else, I would suspect). Type the following in cpan: cpan> o conf make_arg "" cpan> o conf make_install_arg "" cpan> o conf commit Then type cpan> o conf and verify that those two parameters have indeed been changed successfully. If so, then try installing BioPerl again. I think it should work, but let me know if not. Dave From bix at sendu.me.uk Mon Feb 25 22:35:18 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 25 Feb 2008 22:35:18 +0000 Subject: [Bioperl-l] bioperl installation problems with CPAN In-Reply-To: <000001c877c5$d8dc2d70$7000000a@sistemas.local> References: <000001c877c5$d8dc2d70$7000000a@sistemas.local> Message-ID: <47C342A6.7090009@sendu.me.uk> Sheila Zu?iga Trejos wrote: > Dear Sir, > I'm trying to install Bioperl using CPAN but it seems impossible. I get > several error messages when running cpan > install Bundle::CPAN. Please find > attached a file containing these error messages. > Any idea of what is happening? Looks like you've given one of the CPAN options (when you first ran CPAN it asked a bunch of questions) a dodgy value: 'dual processor system'. The easiest thing to do would be to delete your .cpan directory and start over, making sure to answer all the questions carefully and correctly. From bix at sendu.me.uk Tue Feb 26 10:34:04 2008 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 26 Feb 2008 10:34:04 +0000 Subject: [Bioperl-l] statistics In-Reply-To: <264855a00802251845p25130950q5dbdc4228dbb2b93@mail.gmail.com> References: <8F897BD2B0EB714CB79B96D84911B30209E543@EXCHV1.lj.ad.scripps.edu> <264855a00802251845p25130950q5dbdc4228dbb2b93@mail.gmail.com> Message-ID: <47C3EB1C.2000407@sendu.me.uk> Sean Davis wrote: > On Mon, Feb 25, 2008 at 8:04 PM, Lana Schaffer wrote: >> Hi, >> I want to know if Bioperl does t-tests and how to do it? >> Also, I need to get a chi-squared statistic. > > Hi, Lana. I don't think bioperl offers this functionality. However, > a quick search of cpan (http://search.cpan.org) turns up: > > http://search.cpan.org/~yunfang/Statistics-TTest-1.1.0/TTest.pm > http://search.cpan.org/~dcantrell/Statistics-ChiSquare-0.5/lib/Statistics/ChiSquare.pm > > That said, I know you are an R user. I generally stick to R for any > numerics. If you need both a parsing/data munging language and > statistics, consider python, where the rpy package allows you access R > from python and even does data conversion, etc. There's also an R interface for perl: http://www.omegahat.org/RSPerl/ From johnsonm at gmail.com Wed Feb 27 00:47:02 2008 From: johnsonm at gmail.com (Mark Johnson) Date: Tue, 26 Feb 2008 18:47:02 -0600 Subject: [Bioperl-l] Bio::Tools::Run::Fgenesh anyone? Message-ID: We've got fgenesh/fgenesh+ installed locally and I'm going to need Bio::Tools::Run::Fgenesh for a nematode annotation pipeline. Does Bio::Tools::Fgenesh still need unit tests as well? Throw 'em in genpred.t with everything else? From jay at jays.net Thu Feb 28 20:25:29 2008 From: jay at jays.net (Jay Hannah) Date: Thu, 28 Feb 2008 14:25:29 -0600 Subject: [Bioperl-l] helpdesk@open-bio.org ... User unknown References: <200802281949.m1SJnIeD000744@ferret.jays.net> Message-ID: <78E7CE4E-9633-4015-B37C-A097D7F5B411@jays.net> Did I remember that address incorrectly? I'd look it up, but... :) j Begin forwarded message: > From: Mail Delivery Subsystem > Date: February 28, 2008 1:49:18 PM CST > To: > Subject: Returned mail: see transcript for details > > The original message was received at Thu, 28 Feb 2008 13:10:05 -0600 > from host-137-197-64-194.unmc.edu [137.197.64.194] > > ----- The following addresses had permanent fatal errors ----- > > (reason: 550 5.1.1 ... User unknown) > > ----- Transcript of session follows ----- > ... while talking to open-bio.org.: >>>> DATA > <<< 550 5.1.1 ... User unknown > 550 5.1.1 ... User unknown > <<< 503 5.0.0 Need RCPT (recipient) > Reporting-MTA: dns; ferret.jays.net > Arrival-Date: Thu, 28 Feb 2008 13:10:05 -0600 > > Final-Recipient: RFC822; helpdesk at open-bio.org > Action: failed > Status: 5.1.1 > Remote-MTA: DNS; open-bio.org > Diagnostic-Code: SMTP; 550 5.1.1 ... User > unknown > Last-Attempt-Date: Thu, 28 Feb 2008 13:49:18 -0600 > > From: Jay Hannah > Date: February 28, 2008 1:09:57 PM CST > To: helpdesk at open-bio.org > Subject: Websites are down? > > > Is this the right email address to report this to? > > I can't reach: > > http://bioperl.org > http://open-bio.org > > Thanks, > > j > > > > From David.Messina at sbc.su.se Thu Feb 28 21:56:46 2008 From: David.Messina at sbc.su.se (Dave Messina) Date: Thu, 28 Feb 2008 22:56:46 +0100 Subject: [Bioperl-l] helpdesk@open-bio.org ... User unknown In-Reply-To: <78E7CE4E-9633-4015-B37C-A097D7F5B411@jays.net> References: <200802281949.m1SJnIeD000744@ferret.jays.net> <78E7CE4E-9633-4015-B37C-A097D7F5B411@jays.net> Message-ID: <628aabb70802281356w693787e0r19aa80b56079182d@mail.gmail.com> Close. :) support at helpdesk.open-bio.org > I can't reach: > > > > http://bioperl.org > > http://open-bio.org Both work for me at the moment, by the way. Perhaps 'twas transient? Dave