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_lehva