From jason at cgt.duhs.duke.edu Wed Sep 1 00:17:18 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Sep 1 00:23:04 2004 Subject: [Bioperl-l] Re: [Bioperl-guts-l] genbank accession from swissprot In-Reply-To: <200408301553.46187.jjhaveri@vbi.vt.edu> References: <200408301553.46187.jjhaveri@vbi.vt.edu> Message-ID: Wow Oct 1, 2004 - futuristic annotations! This is a new feature in SProt - per Boris' email in July. It hasn't been fixed to my knowledge. http://portal.open-bio.org/pipermail/bioperl-l/2004-July/016493.html Although Boris did send me a patch (attaching if you want to give it a try), it is a bit of work to incorporate all of the necessary changes that the format changes require. Quite happy for someone to take this on as I don't currently need this for my own work it is not on the priority list... -jason -------------- next part -------------- A non-text attachment was scrubbed... Name: swiss_gn_patch Type: application/octet-stream Size: 2090 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040901/ee157b72/swiss_gn_patch.obj -------------- next part -------------- On Aug 31, 2004, at 5:53 AM, Jinal Jhaveri wrote: > Hi everyone, > > I am trying to fetch the genbank locustag from the swissprot entry. My > entry > looks like this: > > DT 01-OCT-2004 (Rel. 45, Last annotation update) > DE Protein apaG. > GN Name=apaG; OrderedLocusNames=Atu0431, AGR_C_759; > OS Agrobacterium tumefaciens (strain C58 / ATCC 33970). > OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; > OC Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium. > OX NCBI_TaxID=176299; > > > I am interested in OrderedLocusNames i.e Atu0431 from the GN line. > Currently > my code looks like follows. Its not giving me the requed field though. > Does > anyone have any links / ideas / suggestions? Am I doing anything wrong? > > Code Snippet: > > my $sprotfile = shift; #name of the input sprot file > > if ($sprotfile eq '') { > print "Please error the input swissprot file name:\n Usage perl > sprot_to_tab.pl"; > exit(1); > } > > eval { > $seqio = Bio::SeqIO->new(-file => "$sprotfile",-format => 'swiss'); > $seq = $seqio->next_seq; > }; > > if ($@ ne '') { > print "ERROR in opening the swissprot file",$@; > exit(1); > } > > > #Reading the seq_object from the sprot file > > print "NCBI:Sequence:Length\n"; > while( my $seq = $seqio->next_seq ){ > print "\nSequence is > :".$seq->seq."\tAccnumber".$seq->accession_number; > > $ac= $seq->annotation(); > foreach $key ( $ac->get_all_annotation_keys() ) { > @values = $ac->get_Annotations($key); > foreach $value ( @values ) { > print "Annotation ",$key," stringified value ", > $value->as_text,"\n"; > } > } > > ... > > > > _______________________________________________ > Bioperl-guts-l mailing list > Bioperl-guts-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-guts-l > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From james.wasmuth at ed.ac.uk Wed Sep 1 09:29:30 2004 From: james.wasmuth at ed.ac.uk (James Wasmuth) Date: Wed Sep 1 10:08:47 2004 Subject: [Bioperl-l] Re: [Bioperl-guts-l] genbank accession from swissprot In-Reply-To: <200409010921.56652.jjhaveri@vbi.vt.edu> References: <200408301553.46187.jjhaveri@vbi.vt.edu> <4135C20B.3020906@ed.ac.uk> <200409010921.56652.jjhaveri@vbi.vt.edu> Message-ID: <4135CEBA.5010009@ed.ac.uk> Oh, my mistake, Hilmar fixed this about a month ago and the updated version is in the CVS - http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/Bio/SeqIO/swiss.pm so it should now give: gene_name => Value: apaG; Atu0431; AGR_C_759 -james Jinal Jhaveri wrote: >Hi James, > >Thanks for your help. This still doesn't solve the problem of fetching >OrderedLocusNames field. > >thanks >--Jinal >On Wednesday 01 September 2004 08:35 am, you wrote: > > >>Hi Jinal, >> >>you need to delete the $seqio->next_seq from the eval block. This has >>the effect of removing the entry from the object. When you later use the >>next_seq method, $seqio is emtpy. >> >>-james >> >>Jinal Jhaveri wrote: >> >> >>>Hi everyone, >>> >>>I am trying to fetch the genbank locustag from the swissprot entry. My >>>entry looks like this: >>> >>>DT 01-OCT-2004 (Rel. 45, Last annotation update) >>>DE Protein apaG. >>>GN Name=apaG; OrderedLocusNames=Atu0431, AGR_C_759; >>>OS Agrobacterium tumefaciens (strain C58 / ATCC 33970). >>>OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; >>>OC Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium. >>>OX NCBI_TaxID=176299; >>> >>> >>>I am interested in OrderedLocusNames i.e Atu0431 from the GN line. >>>Currently my code looks like follows. Its not giving me the requed field >>>though. Does anyone have any links / ideas / suggestions? Am I doing >>>anything wrong? >>> >>>Code Snippet: >>> >>>my $sprotfile = shift; #name of the input sprot file >>> >>>if ($sprotfile eq '') { >>> print "Please error the input swissprot file name:\n Usage perl >>>sprot_to_tab.pl"; >>> exit(1); >>> } >>> >>>eval { >>> $seqio = Bio::SeqIO->new(-file => "$sprotfile",-format => 'swiss'); >>> $seq = $seqio->next_seq; >>>}; >>> >>>if ($@ ne '') { >>> print "ERROR in opening the swissprot file",$@; >>> exit(1); >>>} >>> >>> >>>#Reading the seq_object from the sprot file >>> >>>print "NCBI:Sequence:Length\n"; >>>while( my $seq = $seqio->next_seq ){ >>> print "\nSequence is :".$seq->seq."\tAccnumber".$seq->accession_number; >>> >>> $ac= $seq->annotation(); >>> foreach $key ( $ac->get_all_annotation_keys() ) { >>> @values = $ac->get_Annotations($key); >>> foreach $value ( @values ) { >>> print "Annotation ",$key," stringified value ", >>>$value->as_text,"\n"; >>> } >>> } >>> >>>... >>> >>> >>> >>>_______________________________________________ >>>Bioperl-guts-l mailing list >>>Bioperl-guts-l@portal.open-bio.org >>>http://portal.open-bio.org/mailman/listinfo/bioperl-guts-l >>> >>> -- "Until man duplicates a blade of grass, nature can laugh at his so-called scientific knowledge...." --Thomas Edison Blaxter Nematode Genomics Group | School of Biological Sciences | Ashworth Laboratories | tel: +44 131 650 7403 University of Edinburgh | web: www.nematodes.org Edinburgh | EH9 3JT | UK | From james.wasmuth at ed.ac.uk Wed Sep 1 09:35:45 2004 From: james.wasmuth at ed.ac.uk (James Wasmuth) Date: Wed Sep 1 10:08:48 2004 Subject: [Bioperl-l] Re: genbank accession from swissprot] Message-ID: <4135D031.9000501@ed.ac.uk> Oh, my mistake, Hilmar fixed this about a month ago and the updated version is in the CVS - http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/Bio/SeqIO/swiss.pm so it should now give: gene_name => Value: apaG; Atu0431; AGR_C_759 -james Jinal Jhaveri wrote: >Hi James, > >Thanks for your help. This still doesn't solve the problem of fetching >OrderedLocusNames field. > >thanks >--Jinal >On Wednesday 01 September 2004 08:35 am, you wrote: > > >>Hi Jinal, >> >>you need to delete the $seqio->next_seq from the eval block. This has >>the effect of removing the entry from the object. When you later use the >>next_seq method, $seqio is emtpy. >> >>-james >> >>Jinal Jhaveri wrote: >> >> >>>Hi everyone, >>> >>>I am trying to fetch the genbank locustag from the swissprot entry. My >>>entry looks like this: >>> >>>DT 01-OCT-2004 (Rel. 45, Last annotation update) >>>DE Protein apaG. >>>GN Name=apaG; OrderedLocusNames=Atu0431, AGR_C_759; >>>OS Agrobacterium tumefaciens (strain C58 / ATCC 33970). >>>OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; >>>OC Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium. >>>OX NCBI_TaxID=176299; >>> >>> >>>I am interested in OrderedLocusNames i.e Atu0431 from the GN line. >>>Currently my code looks like follows. Its not giving me the requed field >>>though. Does anyone have any links / ideas / suggestions? Am I doing >>>anything wrong? >>> >>>Code Snippet: >>> >>>my $sprotfile = shift; #name of the input sprot file >>> >>>if ($sprotfile eq '') { >>> print "Please error the input swissprot file name:\n Usage perl >>>sprot_to_tab.pl"; >>> exit(1); >>> } >>> >>>eval { >>> $seqio = Bio::SeqIO->new(-file => "$sprotfile",-format => 'swiss'); >>> $seq = $seqio->next_seq; >>>}; >>> >>>if ($@ ne '') { >>> print "ERROR in opening the swissprot file",$@; >>> exit(1); >>>} >>> >>> >>>#Reading the seq_object from the sprot file >>> >>>print "NCBI:Sequence:Length\n"; >>>while( my $seq = $seqio->next_seq ){ >>> print "\nSequence is :".$seq->seq."\tAccnumber".$seq->accession_number; >>> >>> $ac= $seq->annotation(); >>> foreach $key ( $ac->get_all_annotation_keys() ) { >>> @values = $ac->get_Annotations($key); >>> foreach $value ( @values ) { >>> print "Annotation ",$key," stringified value ", >>>$value->as_text,"\n"; >>> } >>> } >>> >>>... >>> >>> >>> >>>_______________________________________________ >>>Bioperl-guts-l mailing list >>>Bioperl-guts-l@portal.open-bio.org >>>http://portal.open-bio.org/mailman/listinfo/bioperl-guts-l >>> >>> -- "Until man duplicates a blade of grass, nature can laugh at his so-called scientific knowledge...." --Thomas Edison Blaxter Nematode Genomics Group | School of Biological Sciences | Ashworth Laboratories | tel: +44 131 650 7403 University of Edinburgh | web: www.nematodes.org Edinburgh | EH9 3JT | UK | -- "Until man duplicates a blade of grass, nature can laugh at his so-called scientific knowledge...." --Thomas Edison Blaxter Nematode Genomics Group | School of Biological Sciences | Ashworth Laboratories | tel: +44 131 650 7403 University of Edinburgh | web: www.nematodes.org Edinburgh | EH9 3JT | UK | From james.wasmuth at ed.ac.uk Thu Sep 2 11:29:36 2004 From: james.wasmuth at ed.ac.uk (James Wasmuth) Date: Thu Sep 2 11:40:30 2004 Subject: [Bioperl-l] Re: [Bioperl-guts-l] BPlite questions In-Reply-To: <200409021131.31512.jjhaveri@vbi.vt.edu> References: <200409021131.31512.jjhaveri@vbi.vt.edu> Message-ID: <41373C60.4070200@ed.ac.uk> Jinal, it is probably better if you use the Bio::SearchIO module. THere is a HOWTO section: http://bioperl.org/HOWTOs/SearchIO/use.html re; strand, it depends on the BLAST search you are performing but something along the lines of $hsp->query->strand will return '1' for positve frame or '-1' for negative frame. so my my $blast_frame = ($hsp->query->frame + 1) * $hsp->query->strand; hth -james Jinal Jhaveri wrote: >Hi All, > >While running BPlite for parsing a blast report, I am getting following >warnings? What does this mean >-------------------- WARNING --------------------- >MSG: Query frame (-3) did not match strand of query (1) >--------------------------------------------------- > >Also, how do I detect whether the query matches the target on +ve strand or >the -ve strand? I tried to use the $hsp->strand but I think it doesn't give >me the correct result as it doesn't tells me whether the query matches it on >+ve or -ve strand > > >thank you >--Jinal >_______________________________________________ >Bioperl-guts-l mailing list >Bioperl-guts-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-guts-l > > -- "Until man duplicates a blade of grass, nature can laugh at his so-called scientific knowledge...." --Thomas Edison Blaxter Nematode Genomics Group | School of Biological Sciences | Ashworth Laboratories | tel: +44 131 650 7403 University of Edinburgh | web: www.nematodes.org Edinburgh | EH9 3JT | UK | From hlapp at gmx.net Thu Sep 2 12:00:48 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu Sep 2 12:01:18 2004 Subject: [Bioperl-l] Re: genbank accession from swissprot In-Reply-To: Message-ID: <415ADDD2-FCF9-11D8-9A8E-000A959EB4C4@gmx.net> Sort by thread :-) http://portal.open-bio.org/pipermail/bioperl-l/2004-July/016578.html I did fix it, but since there is no context for annotations (and not a MultiTaggedValue either as Ewan suggested in a response) you lose the tags. -hilmar On Tuesday, August 31, 2004, at 09:17 PM, Jason Stajich wrote: > Wow Oct 1, 2004 - futuristic annotations! > > This is a new feature in SProt - per Boris' email in July. > > It hasn't been fixed to my knowledge. > http://portal.open-bio.org/pipermail/bioperl-l/2004-July/016493.html > > Although Boris did send me a patch (attaching if you want to give it a > try), it is a bit of work to incorporate all of the necessary changes > that the format changes require. > > Quite happy for someone to take this on as I don't currently need this > for my own work it is not on the priority list... > > -jason > > On Aug 31, 2004, at 5:53 AM, Jinal Jhaveri wrote: > >> Hi everyone, >> >> I am trying to fetch the genbank locustag from the swissprot entry. >> My entry >> looks like this: >> >> DT 01-OCT-2004 (Rel. 45, Last annotation update) >> DE Protein apaG. >> GN Name=apaG; OrderedLocusNames=Atu0431, AGR_C_759; >> OS Agrobacterium tumefaciens (strain C58 / ATCC 33970). >> OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; >> OC Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium. >> OX NCBI_TaxID=176299; >> >> >> I am interested in OrderedLocusNames i.e Atu0431 from the GN line. >> Currently >> my code looks like follows. Its not giving me the requed field >> though. Does >> anyone have any links / ideas / suggestions? Am I doing anything >> wrong? >> >> Code Snippet: >> >> my $sprotfile = shift; #name of the input sprot file >> >> if ($sprotfile eq '') { >> print "Please error the input swissprot file name:\n Usage perl >> sprot_to_tab.pl"; >> exit(1); >> } >> >> eval { >> $seqio = Bio::SeqIO->new(-file => "$sprotfile",-format => >> 'swiss'); >> $seq = $seqio->next_seq; >> }; >> >> if ($@ ne '') { >> print "ERROR in opening the swissprot file",$@; >> exit(1); >> } >> >> >> #Reading the seq_object from the sprot file >> >> print "NCBI:Sequence:Length\n"; >> while( my $seq = $seqio->next_seq ){ >> print "\nSequence is >> :".$seq->seq."\tAccnumber".$seq->accession_number; >> >> $ac= $seq->annotation(); >> foreach $key ( $ac->get_all_annotation_keys() ) { >> @values = $ac->get_Annotations($key); >> foreach $value ( @values ) { >> print "Annotation ",$key," stringified value ", >> $value->as_text,"\n"; >> } >> } >> >> ... >> >> >> >> _______________________________________________ >> Bioperl-guts-l mailing list >> Bioperl-guts-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-guts-l >> >> > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From ian.donaldson at mshri.on.ca Thu Sep 2 15:24:51 2004 From: ian.donaldson at mshri.on.ca (Ian Donaldson) Date: Thu Sep 2 15:27:59 2004 Subject: [Bioperl-l] SeqHound release v3.0 now available Message-ID: <490D0AFAF3D2D3119F6C00508B6FDF150690F790@ex.mshri.on.ca> Dear BioPerl SeqHound v3.0 is available for download now from http://www.blueprint.org/seqhound/api_help/seqhound_help_guides.html BioPerl users may be interested in using SeqHound to retrieve sequence and structure records using the remote Perl API. SeqHound has the advantage that it allows unrestricted, fast access to data supported by redundant servers and a FastCGI. SeqHound also offers access to many other data types including GO annotation, precomputed RPS-BLAST and precomputed protein BLAST results. We are interested in identifying developers who are already using SeqHound. If you are, please sign up for the seqhound.usergroup email list at http://lists.blueprint.org/mailman/listinfo/seqhound.usergroup. Feedback and discussions on future development are welcome at this list. We are also interested in incorporating SeqHound functionality into the BioPerl tree. We would like feedback to this list on those functionalities that developers would find most useful as part of BioPerl so we can direct development. A complete list of API functions is available at http://www.blueprint.org/seqhound/api_help/seqhound_help_guides.html. Best regards, Ian Ian Donaldson, Ph.D. Manager of Bioinformatics Software Development The Blueprint Initiative - North America 522 University Ave. Toronto, Ontario, Canada M5G 1W7 http://blueprint.org ian.donaldson@blueprint.org About SeqHound SeqHound is a freely available bioinformatics database warehouse resource. Over 300 Gigabytes of data is collected, integrated and updated from around the world on a nightly basis. Sources include the National Center for Biotechnology Information and the Gene Ontology Consortium. Programmers have unrestricted access to up-to-date data via a remote Application Programming Interface (API) written in Perl, Java, C and C++. Over 150 function calls allow access to the complete collection of GenBank, RefSeq and SwissProt sequences, 3-D structures, precomputed protein neighbours, redundancies and conserved domain analyses. Users may also access collected sequence annotations including taxonomy, Gene Ontology assignments and PubMed links. All functions are fully documented and tested on a daily basis. The Blueprint SeqHound server is supported by a redundant architecture (failover load-balancers, failover servers and, failover SANs) for complete fault protection against component failure and to ensure rapid response time. SeqHound encourages unrestricted 24x7 calls to its servers, to allow programmers rapid, uninterrupted, access to biological data on a global basis. SeqHound services over 700,000 hits per day. All SeqHound code is freely distributed under the GNU Public License. Find SeqHound at www.blueprint.org. From sdavis2 at mail.nih.gov Thu Sep 2 15:57:52 2004 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Thu Sep 2 15:55:55 2004 Subject: [Bioperl-l] Bio::Biblio question Message-ID: <5F9A9EE8-FD1A-11D8-8E73-000A95D7BA10@mail.nih.gov> Dear all, I have the following code (below) which works in most cases. However, sometimes, I get. The failure is due to a very large result set and fails at the get_all_ids stage. I only want the ids and I only want the first 200 or so. Is there a way to QUICKLY (ie., without retrieving the entire XML for each) get only the first 200 ids? my $biblio = Bio::Biblio->new(); my $new_biblio=$biblio->find([$gene,$mod]); my $results=$new_biblio->get_count; if ($results) { my @ids=map { $_=~ /([0-9]*$)/; $1; } @{$new_biblio->get_all_ids}; ------------- EXCEPTION ------------- MSG: --- SOAP FAULT --- SOAP-ENV:Server Exception from service object: Limit exceeded. Use iterator instead. STACK Bio::DB::Biblio::soap::__ANON__[/Library/Perl/5.8.1/Bio/DB/Biblio/ soap.pm:120] /Library/Perl/5.8.1/Bio/DB/Biblio/soap.pm:119 STACK SOAP::Lite::call /Library/Perl/SOAP/Lite.pm:2839 STACK SOAP::Lite::__ANON__[/Library/Perl/SOAP/Lite.pm:2806] /Library/Perl/SOAP/Lite.pm:2802 STACK Bio::DB::Biblio::soap::get_all_ids /Library/Perl/5.8.1/Bio/DB/Biblio/soap.pm:424 STACK toplevel pubsearch.pl:35 -------------------------------------- Bio::Root::Root::throw('Bio::DB::Biblio::soap','-text','--- SOAP FAULT ---\x{a}SOAP-ENV:Server Exception from service obj...') called at /Library/Perl/5.8.1/Bio/DB/Biblio/soap.pm line 119 Bio::DB::Biblio::soap::__ANON__[/Library/Perl/5.8.1/Bio/DB/Biblio/ soap.pm:120]('SOAP::Lite=HASH(0xb8ab08)','SOAP::SOM=HASH(0xd4616c)') called at /Library/Perl/SOAP/Lite.pm line 2839 SOAP::Lite::call('SOAP::Lite=HASH(0xb8ab08)','getAllIDs','SOAP:: Data=HASH(0xd6af78)') called at /Library/Perl/SOAP/Lite.pm line 2802 SOAP::Lite::__ANON__[/Library/Perl/SOAP/Lite.pm:2806]('SOAP:: Lite=HASH(0xb8ab08)','SOAP::Data=HASH(0xd6af78)') called at /Library/Perl/5.8.1/Bio/DB/Biblio/soap.pm line 424 Bio::DB::Biblio::soap::get_all_ids('Bio::DB::Biblio:: soap=HASH(0xd800d8)') called at pubsearch.pl line 35 Debugged program terminated. Use q to quit or R to restart, use O inhibit_exit to avoid stopping after program termination, h q, h R or h O to get additional info. my $biblio = Bio::Biblio->new(); my $new_biblio=$biblio->find([$gene,$mod]); my $results=$new_biblio->get_count; if ($results) { my @ids=map { $_=~ /([0-9]*$)/; $1; } @{$new_biblio->get_all_ids}; From satya_likesyou at hotmail.com Fri Sep 3 11:02:37 2004 From: satya_likesyou at hotmail.com (satyanarayana devaraju) Date: Fri Sep 3 11:02:56 2004 Subject: [Bioperl-l] remove from the mailing list Message-ID: please remove the id satya_likesyou@hotmail.com from this mailing list thank you, satya _________________________________________________________________ All the news that matters.All the gossip from home. http://www.msn.co.in/NRI/ Specially for NRIs! From barani_quest at rediffmail.com Thu Sep 2 02:12:20 2004 From: barani_quest at rediffmail.com (Baranidharan P) Date: Fri Sep 3 11:16:38 2004 Subject: [Bioperl-l] retrieve specific pubmed record? Message-ID: <20040902061220.20208.qmail@webmail29.rediffmail.com> Dear all, Can anyone please tell me how to retrieve a specific pubmed record without giving the pubmed id and by its title author volume and journal name.. (kind of advanced search option).. - barani From barani_quest at rediffmail.com Thu Sep 2 23:15:51 2004 From: barani_quest at rediffmail.com (Baranidharan P) Date: Fri Sep 3 11:16:39 2004 Subject: [Bioperl-l] Bio::Biblio question Message-ID: <20040903031551.29644.qmail@webmail32.rediffmail.com> Dear Mr. Davis u can try my @ids= @{ new Bio::Biblio->find ("$gene")->get_all_ids } ; foreach my $ids (@ids) { print $ids; } On Fri, 03 Sep 2004 Sean Davis wrote : >Dear all, > >I have the following code (below) which works in most cases. However, sometimes, I get. The failure is due to a very large result set and fails at the get_all_ids stage. I only want the ids and I only want the first 200 or so. Is there a way to QUICKLY (ie., without retrieving the entire XML for each) get only the first 200 ids? > > >my $biblio = Bio::Biblio->new(); > my $new_biblio=$biblio->find([$gene,$mod]); > my $results=$new_biblio->get_count; > if ($results) { > my @ids=map { $_=~ /([0-9]*$)/; $1; } @{$new_biblio->get_all_ids}; > > >------------- EXCEPTION ------------- >MSG: --- SOAP FAULT --- >SOAP-ENV:Server Exception from service object: Limit exceeded. Use iterator instead. >STACK Bio::DB::Biblio::soap::__ANON__[/Library/Perl/5.8.1/Bio/DB/Biblio/ soap.pm:120] /Library/Perl/5.8.1/Bio/DB/Biblio/soap.pm:119 >STACK SOAP::Lite::call /Library/Perl/SOAP/Lite.pm:2839 >STACK SOAP::Lite::__ANON__[/Library/Perl/SOAP/Lite.pm:2806] /Library/Perl/SOAP/Lite.pm:2802 >STACK Bio::DB::Biblio::soap::get_all_ids /Library/Perl/5.8.1/Bio/DB/Biblio/soap.pm:424 >STACK toplevel pubsearch.pl:35 > >-------------------------------------- > Bio::Root::Root::throw('Bio::DB::Biblio::soap','-text','--- SOAP FAULT ---\x{a}SOAP-ENV:Server Exception from service obj...') called at /Library/Perl/5.8.1/Bio/DB/Biblio/soap.pm line 119 > Bio::DB::Biblio::soap::__ANON__[/Library/Perl/5.8.1/Bio/DB/Biblio/ soap.pm:120]('SOAP::Lite=HASH(0xb8ab08)','SOAP::SOM=HASH(0xd4616c)') called at /Library/Perl/SOAP/Lite.pm line 2839 > SOAP::Lite::call('SOAP::Lite=HASH(0xb8ab08)','getAllIDs','SOAP:: Data=HASH(0xd6af78)') called at /Library/Perl/SOAP/Lite.pm line 2802 > SOAP::Lite::__ANON__[/Library/Perl/SOAP/Lite.pm:2806]('SOAP:: Lite=HASH(0xb8ab08)','SOAP::Data=HASH(0xd6af78)') called at /Library/Perl/5.8.1/Bio/DB/Biblio/soap.pm line 424 > Bio::DB::Biblio::soap::get_all_ids('Bio::DB::Biblio:: soap=HASH(0xd800d8)') called at pubsearch.pl line 35 >Debugged program terminated. Use q to quit or R to restart, > use O inhibit_exit to avoid stopping after program termination, > h q, h R or h O to get additional info. > > > >my $biblio = Bio::Biblio->new(); > my $new_biblio=$biblio->find([$gene,$mod]); > my $results=$new_biblio->get_count; > if ($results) { > my @ids=map { $_=~ /([0-9]*$)/; $1; } @{$new_biblio->get_all_ids}; > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l =============================== Baranidharan P Senior Project Assistant Bioinformatics Sub DIC Dept of Biotechnology Indian Institute of Technology Kharagpur - 721302 West Bengal INDIA Ph. +91 3222 281365 From barani_quest at rediffmail.com Thu Sep 2 23:15:59 2004 From: barani_quest at rediffmail.com (Baranidharan P) Date: Fri Sep 3 11:16:40 2004 Subject: [Bioperl-l] Bio::Biblio question Message-ID: <20040903031559.20685.qmail@webmail29.rediffmail.com> Dear Mr. Davis u can try my @ids= @{ new Bio::Biblio->find ("$gene")->get_all_ids } ; foreach my $ids (@ids) { print $ids; } On Fri, 03 Sep 2004 Sean Davis wrote : >Dear all, > >I have the following code (below) which works in most cases. However, sometimes, I get. The failure is due to a very large result set and fails at the get_all_ids stage. I only want the ids and I only want the first 200 or so. Is there a way to QUICKLY (ie., without retrieving the entire XML for each) get only the first 200 ids? > > >my $biblio = Bio::Biblio->new(); > my $new_biblio=$biblio->find([$gene,$mod]); > my $results=$new_biblio->get_count; > if ($results) { > my @ids=map { $_=~ /([0-9]*$)/; $1; } @{$new_biblio->get_all_ids}; > > >------------- EXCEPTION ------------- >MSG: --- SOAP FAULT --- >SOAP-ENV:Server Exception from service object: Limit exceeded. Use iterator instead. >STACK Bio::DB::Biblio::soap::__ANON__[/Library/Perl/5.8.1/Bio/DB/Biblio/ soap.pm:120] /Library/Perl/5.8.1/Bio/DB/Biblio/soap.pm:119 >STACK SOAP::Lite::call /Library/Perl/SOAP/Lite.pm:2839 >STACK SOAP::Lite::__ANON__[/Library/Perl/SOAP/Lite.pm:2806] /Library/Perl/SOAP/Lite.pm:2802 >STACK Bio::DB::Biblio::soap::get_all_ids /Library/Perl/5.8.1/Bio/DB/Biblio/soap.pm:424 >STACK toplevel pubsearch.pl:35 > >-------------------------------------- > Bio::Root::Root::throw('Bio::DB::Biblio::soap','-text','--- SOAP FAULT ---\x{a}SOAP-ENV:Server Exception from service obj...') called at /Library/Perl/5.8.1/Bio/DB/Biblio/soap.pm line 119 > Bio::DB::Biblio::soap::__ANON__[/Library/Perl/5.8.1/Bio/DB/Biblio/ soap.pm:120]('SOAP::Lite=HASH(0xb8ab08)','SOAP::SOM=HASH(0xd4616c)') called at /Library/Perl/SOAP/Lite.pm line 2839 > SOAP::Lite::call('SOAP::Lite=HASH(0xb8ab08)','getAllIDs','SOAP:: Data=HASH(0xd6af78)') called at /Library/Perl/SOAP/Lite.pm line 2802 > SOAP::Lite::__ANON__[/Library/Perl/SOAP/Lite.pm:2806]('SOAP:: Lite=HASH(0xb8ab08)','SOAP::Data=HASH(0xd6af78)') called at /Library/Perl/5.8.1/Bio/DB/Biblio/soap.pm line 424 > Bio::DB::Biblio::soap::get_all_ids('Bio::DB::Biblio:: soap=HASH(0xd800d8)') called at pubsearch.pl line 35 >Debugged program terminated. Use q to quit or R to restart, > use O inhibit_exit to avoid stopping after program termination, > h q, h R or h O to get additional info. > > > >my $biblio = Bio::Biblio->new(); > my $new_biblio=$biblio->find([$gene,$mod]); > my $results=$new_biblio->get_count; > if ($results) { > my @ids=map { $_=~ /([0-9]*$)/; $1; } @{$new_biblio->get_all_ids}; > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l =============================== Baranidharan P Senior Project Assistant Bioinformatics Sub DIC Dept of Biotechnology Indian Institute of Technology Kharagpur - 721302 West Bengal INDIA Ph. +91 3222 281365 From dag at sonsorol.org Fri Sep 3 11:14:43 2004 From: dag at sonsorol.org (Chris Dagdigian) Date: Fri Sep 3 11:16:45 2004 Subject: [Bioperl-l] remove from the mailing list In-Reply-To: References: Message-ID: <41388A63.8040501@sonsorol.org> {vent mode on} There are 1300+ people subscribed to this list and manually responding to requests like this takes valuable time away from our volunteer administrators. Especially when: o Every message sent to the list includes a link to the membership management page where you can easily unsubscribe yourself faster than I can do it through the admin interface. o You recieved an email at the first of this month (3 days ago) containing your list management password and a direct link to your personal list settings page. I can't think of a way for us to make it easier or more obvious. Should you ever join this list (or any other) again please realize that just about every modern mailing list software system in common use includes trivially easy methods for the user him/herself to handle common list subscriber settings and preferences. You've been removed BTW. -Chris satyanarayana devaraju wrote: > please remove the id satya_likesyou@hotmail.com from this mailing list > > > thank you, > > > satya -- Chris Dagdigian, BioTeam - Independent life science IT & informatics consulting Office: 617-665-6088, Mobile: 617-877-5498, Fax: 425-699-0193 PGP KeyID: 83D4310E iChat/AIM: bioteamdag Web: http://bioteam.net From sdavis2 at mail.nih.gov Fri Sep 3 11:34:19 2004 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Fri Sep 3 11:32:17 2004 Subject: [Bioperl-l] retrieve specific pubmed record? In-Reply-To: <20040902061220.20208.qmail@webmail29.rediffmail.com> References: <20040902061220.20208.qmail@webmail29.rediffmail.com> Message-ID: Check out: http://search.cpan.org/~birney/bioperl-1.4/Bio/Biblio.pm There is also a biblio script that comes in bioperl-live/scripts/biblio as an example. Sean On Sep 2, 2004, at 2:12 AM, Baranidharan P wrote: > > Dear all, > > Can anyone please tell me how to retrieve a specific pubmed record > without giving the pubmed id and by > its title author volume and journal name.. (kind of advanced search > option).. > > - barani > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From sdavis2 at mail.nih.gov Fri Sep 3 11:38:39 2004 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Fri Sep 3 11:36:36 2004 Subject: [Bioperl-l] Bio::Biblio question In-Reply-To: <20040903031559.20685.qmail@webmail29.rediffmail.com> References: <20040903031559.20685.qmail@webmail29.rediffmail.com> Message-ID: <53F94C5E-FDBF-11D8-B0B6-000A95D7BA10@mail.nih.gov> Thanks for the reply. The problem isn't getting the IDs. It is that the get_all_ids method returns a list that is prohibitively long for the SOAP service, so an exception is thrown. I can easily check to see how big the list might be before issuing get_all_ids, but I am still stuck with trying to get some of the ids back. Looking at the protocol, it appears that there is no such functionality as get_more_ids(200). Am I correct on this? The specification suggests that there might be a "format" argument for limiting what is returned by get_next, but I don't see anything except pubmed vs. medline as formats. Thanks for any more guidance. Sean On Sep 2, 2004, at 11:15 PM, Baranidharan P wrote: > Dear Mr. Davis > > u can try > my @ids= @{ new Bio::Biblio->find ("$gene")->get_all_ids } ; > > foreach my $ids (@ids) > { > print $ids; > } > > > On Fri, 03 Sep 2004 Sean Davis wrote : >> Dear all, >> >> I have the following code (below) which works in most cases. However, > sometimes, I get. The failure is due to a very large result set and > fails at the get_all_ids stage. I only want the ids and I only want > the first 200 or so. Is there a way to QUICKLY (ie., without > retrieving the entire XML for each) get only the first 200 ids? >> >> >> my $biblio = Bio::Biblio->new(); >> my $new_biblio=$biblio->find([$gene,$mod]); >> my $results=$new_biblio->get_count; >> if ($results) { >> my @ids=map { $_=~ /([0-9]*$)/; $1; } > @{$new_biblio->get_all_ids}; >> >> >> ------------- EXCEPTION ------------- >> MSG: --- SOAP FAULT --- >> SOAP-ENV:Server Exception from service object: Limit exceeded. Use > iterator instead. >> STACK > Bio::DB::Biblio::soap::__ANON__[/Library/Perl/5.8.1/Bio/DB/Biblio/ > soap.pm:120] /Library/Perl/5.8.1/Bio/DB/Biblio/soap.pm:119 >> STACK SOAP::Lite::call /Library/Perl/SOAP/Lite.pm:2839 >> STACK SOAP::Lite::__ANON__[/Library/Perl/SOAP/Lite.pm:2806] > /Library/Perl/SOAP/Lite.pm:2802 >> STACK Bio::DB::Biblio::soap::get_all_ids > /Library/Perl/5.8.1/Bio/DB/Biblio/soap.pm:424 >> STACK toplevel pubsearch.pl:35 >> >> -------------------------------------- >> Bio::Root::Root::throw('Bio::DB::Biblio::soap','-text','--- > SOAP FAULT ---\x{a}SOAP-ENV:Server Exception from service obj...') > called at /Library/Perl/5.8.1/Bio/DB/Biblio/soap.pm line 119 >> > Bio::DB::Biblio::soap::__ANON__[/Library/Perl/5.8.1/Bio/DB/Biblio/ > soap.pm:120]('SOAP::Lite=HASH(0xb8ab08)','SOAP::SOM=HASH(0xd4616c)') > called at /Library/Perl/SOAP/Lite.pm line 2839 >> > SOAP::Lite::call('SOAP::Lite=HASH(0xb8ab08)','getAllIDs','SOAP:: > Data=HASH(0xd6af78)') called at /Library/Perl/SOAP/Lite.pm line 2802 >> SOAP::Lite::__ANON__[/Library/Perl/SOAP/Lite.pm:2806]('SOAP:: > Lite=HASH(0xb8ab08)','SOAP::Data=HASH(0xd6af78)') called at > /Library/Perl/5.8.1/Bio/DB/Biblio/soap.pm line 424 >> Bio::DB::Biblio::soap::get_all_ids('Bio::DB::Biblio:: > soap=HASH(0xd800d8)') called at pubsearch.pl line 35 >> Debugged program terminated. Use q to quit or R to restart, >> use O inhibit_exit to avoid stopping after program termination, >> h q, h R or h O to get additional info. >> >> >> >> my $biblio = Bio::Biblio->new(); >> my $new_biblio=$biblio->find([$gene,$mod]); >> my $results=$new_biblio->get_count; >> if ($results) { >> my @ids=map { $_=~ /([0-9]*$)/; $1; } > @{$new_biblio->get_all_ids}; >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > =============================== > > Baranidharan P > > Senior Project Assistant > > Bioinformatics Sub DIC > > Dept of Biotechnology > > Indian Institute of Technology > > Kharagpur - 721302 > > West Bengal > > INDIA > > Ph. +91 3222 281365 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From brian_osborne at cognia.com Fri Sep 3 11:45:04 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Fri Sep 3 11:45:50 2004 Subject: [Bioperl-l] retrieve specific pubmed record? In-Reply-To: <20040902061220.20208.qmail@webmail29.rediffmail.com> Message-ID: Barani, The script examples/biblio/biblio_examples.pl has examples like this. Not exactly this, but with a little recombination... Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Baranidharan P Sent: Thursday, September 02, 2004 2:12 AM To: bioperl-l@portal.open-bio.org Subject: [Bioperl-l] retrieve specific pubmed record? Dear all, Can anyone please tell me how to retrieve a specific pubmed record without giving the pubmed id and by its title author volume and journal name.. (kind of advanced search option).. - barani From lstein at cshl.edu Fri Sep 3 17:20:21 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Fri Sep 3 17:22:02 2004 Subject: [Bioperl-l] Das version In-Reply-To: References: Message-ID: <200409031720.21083.lstein@cshl.edu> Try CPAN. Lincoln On Thursday 05 August 2004 08:42 am, Sean Davis wrote: > A quick question: > > I was just trying out a script (make_das_conf.pl) from the Gbrowse > distribution that asks for Das version 0.96, but CVS from > bioperl-live has only 0.94. Is there another branch from CVS that > I should be using? > > Thanks, > Sean > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From fernan at iib.unsam.edu.ar Sat Sep 4 16:48:22 2004 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Sat Sep 4 16:49:22 2004 Subject: [Bioperl-l] build Align object from scratch? Message-ID: <20040904204822.GA29480@iib.unsam.edu.ar> Hi! is it possible to build an alignment object without reading an alignment from a file, a filehandle etc? I'm reading the pods for AlignIO, AlignI, SimpleAlign, etc and I don't see this as a possibility. What I'm doing is reading gapped sequences from tables in a MySQL database (i.e. already aligned sequences). I need to recreate the alignment in my program to then take some portions of these sequences based on their overlappings. Examples of the kind of sequences that I'll be reading are: ATGGTATGGAGTGATGAGTGTGTGA ----TATGGAGTGATGAGT------ ATGGTATGGAGTG------------ --------------TGAGTGTGTGA Essentially this looks like an aligned FASTA ... of course I could write an alignment in this format to a tmp file and then read it again using AlignIO ... but given that I already have this info available to my program, I just thought this was not the most elegant way to do it. Is there another? thanks in advance for any tip, Fernan -- Fernan Aguero - fernan at iib.unsam.edu.ar Phone: +54 11 4580-7255/7 ext 310, Fax: +54 11 4752-9639 Check http://genoma.unsam.edu.ar/~fernan for more info. From jason.stajich at duke.edu Sat Sep 4 17:16:06 2004 From: jason.stajich at duke.edu (Jason Stajich) Date: Sat Sep 4 17:16:40 2004 Subject: [Bioperl-l] build Align object from scratch? In-Reply-To: <20040904204822.GA29480@iib.unsam.edu.ar> References: <20040904204822.GA29480@iib.unsam.edu.ar> Message-ID: So you want to use the code in Bio::AlignIO::fasta as your guide here. If you just follow what is going on in next_aln you'll see how a sequence is parsed, built into a sequence object, and added to a SimpleAlign object. The basics: # create an alignment object to hold the aligned sequences my $aln = Bio::SimpleAlign->new(); # create a sequence object my $seq = Bio::LocatableSeq->new(-start => $start, -end => $end, -seq => $seqwithgaps, -description => $mydesc, -display_id=> $displayid); # add it to the alignment $aln->add_seq($seq); Add all your seqs and you have an alignment reconstituted from your database. -jason On Sep 5, 2004, at 6:48 AM, Fernan Aguero wrote: > Hi! > > is it possible to build an alignment object without reading an > alignment from a file, a filehandle etc? > > I'm reading the pods for AlignIO, AlignI, SimpleAlign, etc > and I don't see this as a possibility. > > What I'm doing is reading gapped sequences from tables in > a MySQL database (i.e. already aligned sequences). I need to > recreate the alignment in my program to then take some > portions of these sequences based on their overlappings. > > Examples of the kind of sequences that I'll be reading are: > > ATGGTATGGAGTGATGAGTGTGTGA > ----TATGGAGTGATGAGT------ > ATGGTATGGAGTG------------ > --------------TGAGTGTGTGA > > Essentially this looks like an aligned FASTA ... of course I > could write an alignment in this format to a tmp file and > then read it again using AlignIO ... but given that I > already have this info available to my program, I just > thought this was not the most elegant way to do it. > > Is there another? > > thanks in advance for any tip, > > Fernan > > -- > Fernan Aguero - fernan at iib.unsam.edu.ar > Phone: +54 11 4580-7255/7 ext 310, Fax: +54 11 4752-9639 > Check http://genoma.unsam.edu.ar/~fernan for more info. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Jason Stajich jason.stajich at duke.edu http://www.duke.edu/~jes12/ From smarkel at scitegic.com Sat Sep 4 17:24:42 2004 From: smarkel at scitegic.com (Scott Markel) Date: Sat Sep 4 17:25:05 2004 Subject: [Bioperl-l] build Align object from scratch? In-Reply-To: <20040904204822.GA29480@iib.unsam.edu.ar> References: <20040904204822.GA29480@iib.unsam.edu.ar> Message-ID: <413A329A.5090901@scitegic.com> Fernan, I did something like this recently. I used Bio::SimpleAlign, created Bio::LocatableSeq objects for each member sequence and added them using $alignment->add_seq(). Worked fine. Scott Fernan Aguero wrote: > Hi! > > is it possible to build an alignment object without reading an > alignment from a file, a filehandle etc? > > I'm reading the pods for AlignIO, AlignI, SimpleAlign, etc > and I don't see this as a possibility. > > What I'm doing is reading gapped sequences from tables in > a MySQL database (i.e. already aligned sequences). I need to > recreate the alignment in my program to then take some > portions of these sequences based on their overlappings. > > Examples of the kind of sequences that I'll be reading are: > > ATGGTATGGAGTGATGAGTGTGTGA > ----TATGGAGTGATGAGT------ > ATGGTATGGAGTG------------ > --------------TGAGTGTGTGA > > Essentially this looks like an aligned FASTA ... of course I > could write an alignment in this format to a tmp file and > then read it again using AlignIO ... but given that I > already have this info available to my program, I just > thought this was not the most elegant way to do it. > > Is there another? > > thanks in advance for any tip, > > Fernan > -- Scott Markel, Ph.D. Principal Bioinformatics Architect email: smarkel@scitegic.com SciTegic Inc. mobile: +1 858 205 3653 9665 Chesapeake Drive, Suite 401 voice: +1 858 279 8800, ext. 253 San Diego, CA 92123 fax: +1 858 279 8804 USA web: http://www.scitegic.com From fernan at iib.unsam.edu.ar Sun Sep 5 16:00:39 2004 From: fernan at iib.unsam.edu.ar (Fernan Aguero) Date: Sun Sep 5 16:02:04 2004 Subject: [Bioperl-l] Displaying an alignment using Bio::Graphics In-Reply-To: <4118DB65.8030000@gradient.cis.upenn.edu> References: <4118DB65.8030000@gradient.cis.upenn.edu> Message-ID: <20040905200039.GA32581@iib.unsam.edu.ar> +----[ Josh Burdick (10.Aug.2004 11:45): | | I wrote a Perl module to write out DNA (or an arbitrary string), | with HTML tags around some regions. Hi Josh, this is a late reply ... I remembered reading this thread but at that time i was not trying to colorize sequences in HTML. Now I am :) | Don't know if this is useful in your case, since it's only for one | string. If anyone wants to adapt it for use in bioperl, feel free. | It's attached at the end of this message. Yes, it is useful. I'm dealing with alignments too, but will be colorizing the consensus sequence to mark some features. [snipped] | This code is a bit more efficient, since it only adds tags | at the beginning and end of where things are colored, or | otherwise tagged. It has some weird bugs, though, if you | add non-nested regions. Yes, I'm seeing some weird things regarding the place where the tag is added. I guess I've corrected the behaviour, at least for my particular example. Don't know if it'll work for other cases. Below is the explanation and fix. I'm trying to colorize two non-nested regions: ------------xxxxxxxxxxxxxxxxxx--------------- so I want the regions marked with '-' to be colored and the central region (x) to be in plain black. The central region is a CDS (ATG...TGA), so it's easy to see if the ranges are being colorized OK. My range objects (-) have start=>1, end=>80, start=>573,end=>623 The first base is a 'G' and after getting the output from ColoredSeq, it looks like this: g------ATGxxxxxxTGAt------ So it seems that it is putting the opening tag _after_ the position indicated as a 'start'. The closing tags appear to be OK. Is this the bug you mentioned for non-nested regions? What I'd like is to have that base also colored. I guessed that this was because you have: $a = $_->start + 1; in your add_tag method. Now if I change it to $a = $_->start; then the opening tag is positioned OK (at least for this simple example). Perhaps this change breaks other cases (nested tags)? | Browsers typically won't complain, but exactly which tag | will have precedence where is unpredictable. I guess you are referring to the last tag. This is not being printed ... in my case it does not matter since there's nothing in the HTML file after it (the browser will not complain). Anyway I could just print a closing tag after calling ColoredSeq ... Thanks for sharing your code, Fernan [snipped] | Josh | | -- | Josh Burdick | jburdick@gradient.cis.upenn.edu | http://www.cis.upenn.edu/~jburdick | cut here | -------------- | | # Write a sequence, with bits of it colored as HTML. | | package local::Bio::ColoredSeq; | | # Constructor. | # Args: | # Seq object containing the Seq in question | sub new { | my($type, $seq) = @_; | my $self = (); | | $self->{'seq'} = $seq; | my %h = (); | $self->{'tags'} = \%h; | return bless $self, $type; | } | | # Add a tag around a certain region of the sequence text. | # Args: | # opening_tag, closing_tag - the HTML tags to put around | # that chunk of sequence. | # loc - ref. to list of things implementing RangeI | # Note that currently, later tags override earlier tags. | sub add_tag { | my($self, $opening_tag, $closing_tag, $locs) = @_; | | foreach (@$locs) { | my $a = $_->start + 1; | my $b = $_->end + 1; | # print "$a $b $opening_tag $closing_tag\n"; | next if ($a == $b); | $self->{'tags'}->{$a} = $self->{'tags'}->{$a} . $opening_tag; | $self->{'tags'}->{$b} = $closing_tag . $self->{'tags'}->{$b}; | } | } | | # HTML, showing bits of the sequence in various colors. | sub as_html { | my($self) = @_; | my $line_length = 50; | my $s = ""; | | my $seq = $self->{'seq'}; | my %tags = %{$self->{'tags'}}; | | foreach my $i (1..($seq->length)) { | if (defined $tags{$i}) { | $s = $s . $tags{$i}; | } | if ($i % $line_length == 1) { | $s = $s . "
\n"; | } | $s = $s . $seq->subseq($i, $i); | } | | return $s; | } | | 1; | +----] -- Fernan Aguero - fernan at iib.unsam.edu.ar Phone: +54 11 4580-7255/7 ext 310, Fax: +54 11 4752-9639 Check http://genoma.unsam.edu.ar/~fernan for more info. From Alex.Zelensky at anu.edu.au Mon Sep 6 01:30:00 2004 From: Alex.Zelensky at anu.edu.au (Alex Zelensky) Date: Mon Sep 6 01:30:53 2004 Subject: [Bioperl-l] bioperl-db performance Message-ID: Hi, I have a project which is based on the bioperl-db. Till now I've been using the old (bioperl-1.1 branch) version of the code and schema, but it is becoming unacceptable (mainly because of the way taxonomy is stored), so I decided to upgrade to the current version. The new code is a huge leap forward in terms of design, clarity and consistency. However, I am experiencing severe performance problems. For example, retrieving a locally stored GenPept entry consistently takes 16-17 seconds (by primary or unique key, doesn't matter), compared 2-3'' it takes to get it directly from SRS using Bio::DB::GenBank or ~ 1'' from the old bioperl-db. Also, getting a species object (I use them a lot) from a local database (new bioperl-db) that contains nothing but an import of NCBI taxonomy takes >15'', compared to <1'' with the old bioperl-db. In both cases I use a mysql 4.0.16 on a dual 866 Mhz PowerPC G4 with 768 Mb RAM. So, my questions are: 1. Is this performance drop an expected behavior (due to increased complexity of the code and new schema)? 2. If the answer to (1) is yes, then what is the way to improve it and how big an improvement can be achieved? 3. If the answer to (1) is no, where should I look for my problem source? There was a related question on this list in May 2004, but it described sequence loading performance on a significantly slower machine, and the suggestion was to increase the horsepower. Thanks in advance! Regards, Alex. From ram at i122server.vu-wien.ac.at Mon Sep 6 15:00:36 2004 From: ram at i122server.vu-wien.ac.at (Rambabu Gudavalli) Date: Mon Sep 6 15:01:35 2004 Subject: [Bioperl-l] please add me Message-ID: <0960787F-0037-11D9-9239-000A95EBF744@i122server.vu-wien.ac.at> Dear Sirs, please add me to the bioperl mailing list. thanks Ram From lstein at cshl.edu Mon Sep 6 17:04:56 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Mon Sep 6 17:05:19 2004 Subject: [Bioperl-l] Displaying an alignment using Bio::Graphics In-Reply-To: <20040905200039.GA32581@iib.unsam.edu.ar> References: <4118DB65.8030000@gradient.cis.upenn.edu> <20040905200039.GA32581@iib.unsam.edu.ar> Message-ID: <200409061704.56354.lstein@cshl.edu> Hi, Just so that people know, there is a library in gbrowse (http://www.gmod.org/ggb) called Bio::Graphics::Browser::Markup that handles nested HTML tags correctly (including doing hue addition when two colors overlap). Here is the synopsis: use Bio::Graphics::Browser::Markup; my $string = join '','a'..'z','a'..'z','a'..'z'; my $markup = Bio::Graphics::Browser::Markup->new; $markup->add_style(cds=>'UPPERCASE'); $markup->add_style(exon =>'Text-decoration: underline'); $markup->add_style(variation=>'Font-weight: bold'); $markup->add_style(italic=>'Font-style: oblique'); $markup->add_style(yellow=>'BGCOLOR blue'); $markup->add_style(green=>'BGCOLOR red'); $markup->add_style(orange=>'BGCOLOR orange'); $markup->add_style(mango=>'FGCOLOR red'); $markup->add_style(br=>'
'); $markup->markup(\$string,[ ['cds',1=>10], ['cds',12=>15], ['variation',20=>41], ['exon',0=>29], ['exon',32=>40], ['italic',18=>29], ['yellow',5=>40], ['green',20=>50], ['orange',30=>60], ['mango',0=>36], ['br',10=>10], ['br',20=>20], ['br',30=>30], ['br',40=>40], ['br',50=>50], ['br',60=>60], ]); print $string,"\n"; Then there is another module called Bio::Graphics::Browser::PadAlignment which uses this code to generate colorized multiple alignments that are correctly gapped, etc. An example of this running is here: http://www.wormbase.org/db/seq/show_mult_align?name=WP%3ACE31390;class=Protein Lincoln On Sunday 05 September 2004 04:00 pm, Fernan Aguero wrote: > +----[ Josh Burdick (10.Aug.2004 11:45): > | I wrote a Perl module to write out DNA (or an arbitrary string), > | with HTML tags around some regions. > > Hi Josh, > > this is a late reply ... I remembered reading this thread > but at that time i was not trying to colorize sequences in > HTML. Now I am :) > > | Don't know if this is useful in your case, since it's only for one > | string. If anyone wants to adapt it for use in bioperl, feel free. > | It's attached at the end of this message. > > Yes, it is useful. I'm dealing with alignments too, but will > be colorizing the consensus sequence to mark some features. > > [snipped] > > | This code is a bit more efficient, since it only adds tags > | at the beginning and end of where things are colored, or > | otherwise tagged. It has some weird bugs, though, if you > | add non-nested regions. > > Yes, I'm seeing some weird things regarding the place where > the tag is added. I guess I've corrected the behaviour, at > least for my particular example. Don't know if it'll work > for other cases. Below is the explanation and fix. > > I'm trying to colorize two non-nested regions: > > ------------xxxxxxxxxxxxxxxxxx--------------- > > so I want the regions marked with '-' to be colored and the > central region (x) to be in plain black. > > The central region is a CDS (ATG...TGA), so it's easy to see > if the ranges are being colorized OK. > > My range objects (-) have start=>1, end=>80, start=>573,end=>623 > The first base is a 'G' and after getting the output from > ColoredSeq, it looks like this: > > g------ATGxxxxxxTGAt------ > > So it seems that it is putting the opening tag _after_ the > position indicated as a 'start'. The closing tags appear to > be OK. Is this the bug you mentioned for non-nested regions? > > What I'd like is to have that base also colored. I guessed > that this was because you have: > $a = $_->start + 1; > in your add_tag method. Now if I change it to > $a = $_->start; > then the opening tag is positioned OK (at least for this > simple example). > > Perhaps this change breaks other cases (nested tags)? > > | Browsers typically won't complain, but exactly which tag > | will have precedence where is unpredictable. > > I guess you are referring to the last tag. This is not being > printed ... in my case it does not matter since there's > nothing in the HTML file after it (the browser will not > complain). Anyway I could just print a closing tag after > calling ColoredSeq ... > > Thanks for sharing your code, > > Fernan > > [snipped] > > | Josh > | > | -- > | Josh Burdick > | jburdick@gradient.cis.upenn.edu > | http://www.cis.upenn.edu/~jburdick > | > | > | cut here > | -------------- > | > | # Write a sequence, with bits of it colored as HTML. > | > | package local::Bio::ColoredSeq; > | > | # Constructor. > | # Args: > | # Seq object containing the Seq in question > | sub new { > | my($type, $seq) = @_; > | my $self = (); > | > | $self->{'seq'} = $seq; > | my %h = (); > | $self->{'tags'} = \%h; > | return bless $self, $type; > | } > | > | # Add a tag around a certain region of the sequence text. > | # Args: > | # opening_tag, closing_tag - the HTML tags to put around > | # that chunk of sequence. > | # loc - ref. to list of things implementing RangeI > | # Note that currently, later tags override earlier tags. > | sub add_tag { > | my($self, $opening_tag, $closing_tag, $locs) = @_; > | > | foreach (@$locs) { > | my $a = $_->start + 1; > | my $b = $_->end + 1; > | # print "$a $b $opening_tag $closing_tag\n"; > | next if ($a == $b); > | $self->{'tags'}->{$a} = $self->{'tags'}->{$a} . $opening_tag; > | $self->{'tags'}->{$b} = $closing_tag . $self->{'tags'}->{$b}; > | } > | } > | > | # HTML, showing bits of the sequence in various colors. > | sub as_html { > | my($self) = @_; > | my $line_length = 50; > | my $s = ""; > | > | my $seq = $self->{'seq'}; > | my %tags = %{$self->{'tags'}}; > | > | foreach my $i (1..($seq->length)) { > | if (defined $tags{$i}) { > | $s = $s . $tags{$i}; > | } > | if ($i % $line_length == 1) { > | $s = $s . "
\n"; > | } > | $s = $s . $seq->subseq($i, $i); > | } > | > | return $s; > | } > | > | 1; > > +----] -- Lincoln Stein lstein@cshl.edu Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) From Alex.Zelensky at anu.edu.au Tue Sep 7 00:58:24 2004 From: Alex.Zelensky at anu.edu.au (Alex Zelensky) Date: Tue Sep 7 01:00:29 2004 Subject: [Bioperl-l] bioperl-db performance In-Reply-To: References: Message-ID: <8C24E7BE-008A-11D9-8E94-000393BC6874@anu.edu.au> Hi again, Ok, I found one bottleneck which if removed significantly speeds up species (and hence sequence) object retrieval from bioperl-db, at least in my case (mysql 4.0.20). For the reasons I don't understand, SQL statement in the Bio::DB::BioSQL::mysql::SpeciesAdaptorDriver::get_classification works about 10x faster if " ORDER BY node.left_value" is removed from it and sorting of the classification array is done with perl (left_value has to be included into the list of returned fields). An even higher speedup (from >16'' to <1'') can be achieved by replacing the complex request with a dumb perl loop that fetches parent nodes one by one with a simple select by primary key. I didn't check whether this behavior is specific to mysql or the particular versions of it that I have (4.0.16 and 4.0.20), but since mysql is popular and 4.0.20 is the current production version, I think it's better to fix this. Regards, Alex. On 06/09/2004, at 3:30 PM, Alex Zelensky wrote: > Hi, > > I have a project which is based on the bioperl-db. Till now I've been > using the old (bioperl-1.1 branch) version of the code and schema, but > it is becoming unacceptable (mainly because of the way taxonomy is > stored), so I decided to upgrade to the current version. The new code > is a huge leap forward in terms of design, clarity and consistency. > However, I am experiencing severe performance problems. > > For example, retrieving a locally stored GenPept entry consistently > takes 16-17 seconds (by primary or unique key, doesn't matter), > compared 2-3'' it takes to get it directly from SRS using > Bio::DB::GenBank or ~ 1'' from the old bioperl-db. Also, getting a > species object (I use them a lot) from a local database (new > bioperl-db) that contains nothing but an import of NCBI taxonomy takes > >15'', compared to <1'' with the old bioperl-db. In both cases I use a > mysql 4.0.16 on a dual 866 Mhz PowerPC G4 with 768 Mb RAM. > > So, my questions are: > 1. Is this performance drop an expected behavior (due to increased > complexity of the code and new schema)? > 2. If the answer to (1) is yes, then what is the way to improve it and > how big an improvement can be achieved? > 3. If the answer to (1) is no, where should I look for my problem > source? > > There was a related question on this list in May 2004, but it > described sequence loading performance on a significantly slower > machine, and the suggestion was to increase the horsepower. > > Thanks in advance! > > Regards, > Alex. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > From tex at biosysadmin.com Tue Sep 7 01:06:12 2004 From: tex at biosysadmin.com (James Thompson) Date: Tue Sep 7 17:18:08 2004 Subject: [Bioperl-l] PSI-BLAST Matrix Parser? Message-ID: Dear Bioperl-ers, I'd like to parse the output of a PSI-BLAST matrix, and I was wondering if there was a Bioperl way of parsing these files. If not, I'd like to make my code general enough to be committed, and I'd like some advice on where exactly to put such a module. From my cursory knowledge of Bioperl, I think that adding another format parser to Bio::Matrix::PSM::IO would be a good way to go. I have a couple of questions: - Does anyone know what the PSI-BLAST matrix format is called? - Is this the correct place in which to put code for parsing this type of files? The file format represents a position-specific scoring matrix with some added statistical information, here's a general overview of the information available from the matrix file: Last position-specific scoring matrix computed, weighted observed percentages rounded down, information per position, and relative weight of gapless real matches to p seudocounts. Any help is greatly appreciated. James Thompson From skirov at utk.edu Tue Sep 7 20:12:40 2004 From: skirov at utk.edu (Stefan A Kirov) Date: Tue Sep 7 20:13:02 2004 Subject: [Bioperl-l] PSI-BLAST Matrix Parser? In-Reply-To: References: Message-ID: I am not sure what object you are going to store your data in... Are you going to develop your own class to hold the data or use an existing one? Also is there any reason not to use Bio::AlignIO (it reads PSI-Blast as far as I know)? Stefan On Tue, 7 Sep 2004, James Thompson wrote: >Dear Bioperl-ers, > >I'd like to parse the output of a PSI-BLAST matrix, and I was wondering if >there was a Bioperl way of parsing these files. If not, I'd like to make my >code general enough to be committed, and I'd like some advice on where exactly >to put such a module. From my cursory knowledge of Bioperl, I think that adding >another format parser to Bio::Matrix::PSM::IO would be a good way to go. > >I have a couple of questions: >- Does anyone know what the PSI-BLAST matrix format is called? >- Is this the correct place in which to put code for parsing this type of files? > >The file format represents a position-specific scoring matrix with some added >statistical information, here's a general overview of the information available >from the matrix file: > >Last position-specific scoring matrix computed, weighted observed percentages >rounded down, information per position, and relative weight of gapless real >matches to p seudocounts. > >Any help is greatly appreciated. > >James Thompson > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > From tex at biosysadmin.com Tue Sep 7 21:19:54 2004 From: tex at biosysadmin.com (James Thompson) Date: Wed Sep 8 13:31:52 2004 Subject: [Bioperl-l] PSI-BLAST Matrix Parser? In-Reply-To: Message-ID: Stefan, Thanks for the response. For reading in the actual alignment I would use Bio::AlignIO to read the PSI-BLAST output as it's just another alignment file, but the matrix file that I'm talking about is slightly different. Now that I've perused CVS more and learned more about how the Bio::Matrix::PSM modules work, I think I have a more clear picture of what I'd like to do. If you run PSI-BLAST with the -Q option, will take the matrix that it used for the position-specific search and output it to a file. I've put up a link to one of my matrix files up here if you'd like to look at it: http://bioinformatics.rit.edu/~tex/atp1.matrix Basically I'd like to make some Bio::Matrix::PSM::Psm objects (or at least a PsmI-compliant object), and I think that the correct way to do this would be to add a file format parser to Bio::Matrix::PSM::IO. Currently in Bioperl there are three format parsers: - mast - meme - transfac None of these work with the PSI-BLAST matrix files. I'd like to write a new matrix file parser (perhaps called psi-blast?) in the spirit of the three other parsers. If I were to write this, could someone commit it for me? James Thompson On Tue, 7 Sep 2004, Stefan A Kirov wrote: > I am not sure what object you are going to store your data in... Are you > going to develop your own class to hold the data or use an existing one? > Also is there any reason not to use Bio::AlignIO (it reads PSI-Blast as > far as I know)? > Stefan > > > On Tue, 7 Sep 2004, James Thompson wrote: > > >Dear Bioperl-ers, > > > >I'd like to parse the output of a PSI-BLAST matrix, and I was wondering if > >there was a Bioperl way of parsing these files. If not, I'd like to make my > >code general enough to be committed, and I'd like some advice on where exactly > >to put such a module. From my cursory knowledge of Bioperl, I think that adding > >another format parser to Bio::Matrix::PSM::IO would be a good way to go. > > > >I have a couple of questions: > >- Does anyone know what the PSI-BLAST matrix format is called? > >- Is this the correct place in which to put code for parsing this type of files? > > > >The file format represents a position-specific scoring matrix with some added > >statistical information, here's a general overview of the information available > >from the matrix file: > > > >Last position-specific scoring matrix computed, weighted observed percentages > >rounded down, information per position, and relative weight of gapless real > >matches to p seudocounts. > > > >Any help is greatly appreciated. > > > >James Thompson > > > >_______________________________________________ > >Bioperl-l mailing list > >Bioperl-l@portal.open-bio.org > >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > From brian_osborne at cognia.com Wed Sep 8 13:49:22 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Wed Sep 8 13:50:30 2004 Subject: [Bioperl-l] PSI-BLAST Matrix Parser? In-Reply-To: Message-ID: James, >If I were to write this, could someone commit it for me? Certainly. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of James Thompson Sent: Tuesday, September 07, 2004 9:20 PM To: Stefan A Kirov Cc: bioperl-l@portal.open-bio.org Subject: Re: [Bioperl-l] PSI-BLAST Matrix Parser? Stefan, Thanks for the response. For reading in the actual alignment I would use Bio::AlignIO to read the PSI-BLAST output as it's just another alignment file, but the matrix file that I'm talking about is slightly different. Now that I've perused CVS more and learned more about how the Bio::Matrix::PSM modules work, I think I have a more clear picture of what I'd like to do. If you run PSI-BLAST with the -Q option, will take the matrix that it used for the position-specific search and output it to a file. I've put up a link to one of my matrix files up here if you'd like to look at it: http://bioinformatics.rit.edu/~tex/atp1.matrix Basically I'd like to make some Bio::Matrix::PSM::Psm objects (or at least a PsmI-compliant object), and I think that the correct way to do this would be to add a file format parser to Bio::Matrix::PSM::IO. Currently in Bioperl there are three format parsers: - mast - meme - transfac None of these work with the PSI-BLAST matrix files. I'd like to write a new matrix file parser (perhaps called psi-blast?) in the spirit of the three other parsers. If I were to write this, could someone commit it for me? James Thompson On Tue, 7 Sep 2004, Stefan A Kirov wrote: > I am not sure what object you are going to store your data in... Are you > going to develop your own class to hold the data or use an existing one? > Also is there any reason not to use Bio::AlignIO (it reads PSI-Blast as > far as I know)? > Stefan > > > On Tue, 7 Sep 2004, James Thompson wrote: > > >Dear Bioperl-ers, > > > >I'd like to parse the output of a PSI-BLAST matrix, and I was wondering if > >there was a Bioperl way of parsing these files. If not, I'd like to make my > >code general enough to be committed, and I'd like some advice on where exactly > >to put such a module. From my cursory knowledge of Bioperl, I think that adding > >another format parser to Bio::Matrix::PSM::IO would be a good way to go. > > > >I have a couple of questions: > >- Does anyone know what the PSI-BLAST matrix format is called? > >- Is this the correct place in which to put code for parsing this type of files? > > > >The file format represents a position-specific scoring matrix with some added > >statistical information, here's a general overview of the information available > >from the matrix file: > > > >Last position-specific scoring matrix computed, weighted observed percentages > >rounded down, information per position, and relative weight of gapless real > >matches to p seudocounts. > > > >Any help is greatly appreciated. > > > >James Thompson > > > >_______________________________________________ > >Bioperl-l mailing list > >Bioperl-l@portal.open-bio.org > >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From skirov at utk.edu Wed Sep 8 14:07:21 2004 From: skirov at utk.edu (Stefan Kirov) Date: Wed Sep 8 14:07:40 2004 Subject: [Bioperl-l] PSI-BLAST Matrix Parser? In-Reply-To: References: Message-ID: <413F4A59.1040409@utk.edu> This seems reasonable to me. The one thing you need to consider is the structure that should contain the matrix. The current design of Bio::Matrix::PSM::Psm and Bio::Matrix::PSM::SiteMatrix does not allow this as SiteMatrix is a DNA only object. There are two ways to go: Either change SiteMatrix to accept protein matrix data or add a protein matrix class to Bio::Matrix::PSM (say Bio::Matrix::PSM::ProtMatrix), which will hold the data and make Bio::Matrix::PSM::Psm inherit from the class and be able to contain the object (as it is actually a container right now). So you will have something like: my $psmIO= new Bio::Matrix::PSM::IO(-file=>$file, -format=>'psi-blast'); #this will call the actual parser (Bio::Matrix::PSM::IO::psiblast) my $header=$psmIO->.... #I guess there will be some header data while (my $psm=$psmIO->next_psm) { my $psimatrix=$psm->protmatrix; #This will be Bio::Matrix::PSM::ProtMatrix object $psimatrix->.....; #Now process the data parsed into this object through its methods... } If you do this maybe you should get an account and commit it yourself? Does this make sense to you? Stefan James Thompson wrote: >Stefan, > >Thanks for the response. For reading in the actual alignment I would use >Bio::AlignIO to read the PSI-BLAST output as it's just another alignment file, >but the matrix file that I'm talking about is slightly different. Now that >I've perused CVS more and learned more about how the Bio::Matrix::PSM modules >work, I think I have a more clear picture of what I'd like to do. > >If you run PSI-BLAST with the -Q option, will take the matrix that it >used for the position-specific search and output it to a file. I've put up a >link to one of my matrix files up here if you'd like to look at it: > >http://bioinformatics.rit.edu/~tex/atp1.matrix > >Basically I'd like to make some Bio::Matrix::PSM::Psm objects (or at least >a PsmI-compliant object), and I think that the correct way to do this would >be to add a file format parser to Bio::Matrix::PSM::IO. Currently in Bioperl >there are three format parsers: > - mast > - meme > - transfac > >None of these work with the PSI-BLAST matrix files. I'd like to write a new >matrix file parser (perhaps called psi-blast?) in the spirit of the three other >parsers. > >If I were to write this, could someone commit it for me? > >James Thompson > >On Tue, 7 Sep 2004, Stefan A Kirov wrote: > > > >>I am not sure what object you are going to store your data in... Are you >>going to develop your own class to hold the data or use an existing one? >>Also is there any reason not to use Bio::AlignIO (it reads PSI-Blast as >>far as I know)? >>Stefan >> >> >>On Tue, 7 Sep 2004, James Thompson wrote: >> >> >> >>>Dear Bioperl-ers, >>> >>>I'd like to parse the output of a PSI-BLAST matrix, and I was wondering if >>>there was a Bioperl way of parsing these files. If not, I'd like to make my >>>code general enough to be committed, and I'd like some advice on where exactly >>>to put such a module. From my cursory knowledge of Bioperl, I think that adding >>>another format parser to Bio::Matrix::PSM::IO would be a good way to go. >>> >>>I have a couple of questions: >>>- Does anyone know what the PSI-BLAST matrix format is called? >>>- Is this the correct place in which to put code for parsing this type of files? >>> >>>The file format represents a position-specific scoring matrix with some added >>>statistical information, here's a general overview of the information available >>> >>> >>>from the matrix file: >> >> >>>Last position-specific scoring matrix computed, weighted observed percentages >>>rounded down, information per position, and relative weight of gapless real >>>matches to p seudocounts. >>> >>>Any help is greatly appreciated. >>> >>>James Thompson >>> >>>_______________________________________________ >>>Bioperl-l mailing list >>>Bioperl-l@portal.open-bio.org >>>http://portal.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >>> > > > > -- Stefan Kirov, Ph.D. University of Tennessee/Oak Ridge National Laboratory 1060 Commerce Park, Oak Ridge TN 37830-8026 USA tel +865 576 5120 fax +865 241 1965 e-mail: skirov@utk.edu sao@ornl.gov From bucket_ospam at lycos.com Wed Sep 8 17:16:18 2004 From: bucket_ospam at lycos.com (Gabriel Berriz) Date: Wed Sep 8 17:16:35 2004 Subject: [Bioperl-l] Gene/protein ID synonyms Message-ID: <20040908211618.D9DEE86AE9@ws7-1.us4.outblaze.com> One recurrent headache for much of our bioinformatics development comes from the fact that for most model organisms any one gene or protein can be identified by several different IDs (e.g. for yeast genes one has common names, ORF names, SGD IDs, etc.). We want to give users the option to refer to genes and proteins according to as many standards as possible, which means that our software has to be able to translate between all these standards and its own internal representation. Moreover, this translation facility has to keep pace with updates to the source databases. Are there Bioperl modules to deal with this problem? If not, what would be a better mailing list or forum to enquire about available solutions to this problem? I am aware of SRS, which some people find very useful for this kind of translation, but I'd like to learn more about what else is out there. Many thanks, Gabriel -- _______________________________________________ Find what you are looking for with the Lycos Yellow Pages http://r.lycos.com/r/yp_emailfooter/http://yellowpages.lycos.com/default.asp?SRC=lycos10 From skirov at utk.edu Wed Sep 8 19:01:20 2004 From: skirov at utk.edu (Stefan A Kirov) Date: Wed Sep 8 19:01:32 2004 Subject: [Bioperl-l] Gene/protein ID synonyms In-Reply-To: <20040908211618.D9DEE86AE9@ws7-1.us4.outblaze.com> References: <20040908211618.D9DEE86AE9@ws7-1.us4.outblaze.com> Message-ID: Gabriel, I believe there are several things to consider. Are you talking just about yeast? If not I think EnsMART is the best place to start (go to www.ensembl.org, and go to the documentation link). I think this is the most comprehensive and at the same time easy way to accomplish what you need to do. You may also look at BioSQL. There is something we developed: genereg.ornl.gov/gkdb, but it is restricted to the organisms in LocusLink (to become Entrez Gene). As you say it is hard to syncrhonize with the source but there is really no other way I believe. Stefan On Wed, 8 Sep 2004, Gabriel Berriz wrote: >One recurrent headache for much of our bioinformatics development comes from the fact that for most model organisms any one gene or protein can be identified by several different IDs (e.g. for yeast genes one has common names, ORF names, SGD IDs, etc.). We want to give users the option to refer to genes and proteins according to as many standards as possible, which means that our software has to be able to translate between all these standards and its own internal representation. Moreover, this translation facility has to keep pace with updates to the source databases. > >Are there Bioperl modules to deal with this problem? If not, what would be a better mailing list or forum to enquire about available solutions to this problem? I am aware of SRS, which some people find very useful for this kind of translation, but I'd like to learn more about what else is out there. > >Many thanks, > >Gabriel > >-- >_______________________________________________ >Find what you are looking for with the Lycos Yellow Pages >http://r.lycos.com/r/yp_emailfooter/http://yellowpages.lycos.com/default.asp?SRC=lycos10 > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > From boris.steipe at utoronto.ca Wed Sep 8 19:29:41 2004 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Wed Sep 8 19:29:45 2004 Subject: [Bioperl-l] Gene/protein ID synonyms In-Reply-To: Message-ID: Gabriel - The seqhound remote API should have the functions you need. See Regards, Boris > On Wed, 8 Sep 2004, Gabriel Berriz wrote: > >> One recurrent headache for much of our bioinformatics development >> comes from the fact that for most model organisms any one gene or >> protein can be identified by several different IDs (e.g. for yeast >> genes one has common names, ORF names, SGD IDs, etc.). We want to >> give users the option to refer to genes and proteins according to as >> many standards as possible, which means that our software has to be >> able to translate between all these standards and its own internal >> representation. Moreover, this translation facility has to keep pace >> with updates to the source databases. >> >> Are there Bioperl modules to deal with this problem? If not, what >> would be a better mailing list or forum to enquire about available >> solutions to this problem? I am aware of SRS, which some people find >> very useful for this kind of translation, but I'd like to learn more >> about what else is out there. >> >> Many thanks, >> >> Gabriel >> >> -- >> _______________________________________________ >> Find what you are looking for with the Lycos Yellow Pages >> http://r.lycos.com/r/yp_emailfooter/http://yellowpages.lycos.com/ >> default.asp?SRC=lycos10 >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From Karolina.Zavisek at zg.htnet.hr Thu Sep 9 12:19:59 2004 From: Karolina.Zavisek at zg.htnet.hr (Karolina Zavisek) Date: Thu Sep 9 13:35:41 2004 Subject: [Bioperl-l] howto save blast parser output Message-ID: <200409091019.i89AJxsW007790@ls413.htnet.hr> Hi, Can someone please help me with this little problem I'm having with my BLAST parser. Parser works fine but I don't know how to make him save output that he prints out on my screen. I would like to save it to some file. Oh, and must I mention that I'm new to perl and bioperl. Thanks! First part of the program executes remote BLAST and retrieves report which is saved in to the file which is later used by parser. So this is code: #!/usr/bin/perl -w use strict; use Bio::SeqIO; use Bio::Tools::Run::RemoteBlast; use Bio::SearchIO; use Bio::SearchIO::Writer::HTMLResultWriter; use Bio::AlignIO; my $prog = 'blastp'; my $db = 'nr'; my $e_val = '1e-10'; my @params = ('-program'=> $prog, '-data'=> $db, '-expect'=> $e_val, 'readmethod' => 'SearchIO'); my $factory = Bio::Tools::Run::RemoteBlast -> new (@params); my $v = 1; my $str = Bio::SeqIO -> new (-file => 'ketosynt.fasta', -format => 'fasta'); my $r = $factory -> submit_blast ('ketosynt.fasta'); print STDERR "waiting..." if( $v > 0 ); while ( my @rids = $factory->each_rid ) { foreach my $rid ( @rids ) { my $rc = $factory->retrieve_blast($rid); if( !ref($rc) ) { if( $rc < 0 ) { $factory->remove_rid($rid); } print STDERR "**\n" if ( $v > 0 ); sleep 5; } else { my $result = $rc->next_result(); #save the output my $filename = $result->query_name()."\.out"; $factory->save_output('my_result.bls'); $factory->remove_rid($rid); } } } ################### PARSER 1 ########################################### my $in = new Bio::SearchIO(-format => 'blast', -file => 'my_result.bls'); while( my $result = $in->next_result ) { while( my $hit = $result->query_description ) { while( $hit = $result->query_accession ) { while( $hit = $result->next_hit ) { while( my $hsp = $hit->next_hsp ) { my $aln = $hsp->get_aln(); if( $hsp->length('total') > 100 ) { if ( $hsp->percent_identity >= 75 ) { print "Hit= ", $hit->name, ",\nLength=", $hsp->length('total'), #this is part which output I want to #save ",\nPercent_id=", $hsp->percent_identity, # ",\nAccession_number=", $hit->accession, # ",\nDescription=", $hit->description,"\n\n"; # # my $alnIO = Bio::AlignIO->new(-format=>'fasta'); # my $alignment_as_string = $alnIO->write_aln($aln); # # change BLAST report from text format to html######################## my $writer = new Bio::SearchIO::Writer::HTMLResultWriter; $in = new Bio::SearchIO(-format => 'blast', -file => 'my_result.bls'); my $out = new Bio::SearchIO(-writer => $writer, -file => '>my_result2.html'); $out->write_result($in->next_result); } } } } } } } ---------------------- H T n e t - - W e b M a i l ---------------------- Ova poruka poslana je upotrebom HTnet WebMail usluge. http://www.htnet.hr/webmail From ukg100 at yahoo.com Wed Sep 8 17:46:27 2004 From: ukg100 at yahoo.com (unni krishnan) Date: Thu Sep 9 13:36:07 2004 Subject: [Bioperl-l] data conversion Message-ID: <20040908214627.17565.qmail@web14311.mail.yahoo.com> Is there any way to convert the accession ids (given below) to a single ID (Unigene, genbank, locuslink, swissport, genpept, GI number, any of them will do). These data are proteins and wanted to know whether bioperl can query . Accession # gb|AAA40936.1 gb|AAA41660.1 pir|JC1039 pir|S37300 rf|NP_036686.1 rf|NP_036737.1 rf|XP_345137.1 sp|P04764 sp|P11981 sp|P17209 spt|P00564 spt|P02563 spt|Q63679 spt|Q9WVK7 trm|Q924K3 trm|Q9ER34 trm|Q9JJ79 Thanks uk --------------------------------- Do you Yahoo!? Shop for Back-to-School deals on Yahoo! Shopping. From dag at sonsorol.org Thu Sep 9 14:40:44 2004 From: dag at sonsorol.org (Chris Dagdigian) Date: Thu Sep 9 15:53:26 2004 Subject: [Bioperl-l] [Fwd: fixed bug... how do I submit the code?] Message-ID: <4140A3AC.9040605@sonsorol.org> -------------- next part -------------- An embedded message was scrubbed... From: Martin Suchorolski Subject: fixed bug... how do I submit the code? Date: Thu, 09 Sep 2004 11:29:40 -0700 Size: 10136 Url: http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040909/4dcb1684/fixedbug...eml From skirov at utk.edu Thu Sep 9 16:23:52 2004 From: skirov at utk.edu (Stefan A Kirov) Date: Thu Sep 9 16:24:09 2004 Subject: [Bioperl-l] [Fwd: fixed bug... how do I submit the code?] In-Reply-To: <4140A3AC.9040605@sonsorol.org> References: <4140A3AC.9040605@sonsorol.org> Message-ID: On Thu, 9 Sep 2004, Chris Dagdigian wrote: > > From skirov at utk.edu Thu Sep 9 16:26:48 2004 From: skirov at utk.edu (Stefan A Kirov) Date: Thu Sep 9 16:26:57 2004 Subject: [Bioperl-l] [Fwd: fixed bug... how do I submit the code?] In-Reply-To: <4140A3AC.9040605@sonsorol.org> References: <4140A3AC.9040605@sonsorol.org> Message-ID: Chris, This bug was fixed few months ago by Jason Stajich and me. It is in bioperl-live and it's been there for a long time. I also added this to the bug report. Stefan Date: Thu, 09 Sep 2004 11:29:40 -0700 From: Martin Suchorolski To: dag@sonsorol.org Subject: fixed bug... how do I submit the code? I just fixed a bug(#1693) and would like to commit the change to your CVS archive. How do I do this? Is there a process by which the fix needs to be reviewed? I am attaching the fixed code (Bio/Matrix/PSM/IO/meme.pm) , if this is only allowed by Bioperl developers Cheers, -Martin From sdavis2 at mail.nih.gov Fri Sep 10 06:23:12 2004 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Fri Sep 10 06:21:47 2004 Subject: [Bioperl-l] data conversion In-Reply-To: <20040908214627.17565.qmail@web14311.mail.yahoo.com> References: <20040908214627.17565.qmail@web14311.mail.yahoo.com> Message-ID: <6B63690F-0313-11D9-8801-000A95D7BA10@mail.nih.gov> I would map them to unigene. The NCBI ftp site (ftp.ncbi.nih.gov) has some files in the unigene repository that you will need. You will proabably have to write some code to do it, though. Sean On Sep 8, 2004, at 5:46 PM, unni krishnan wrote: > > Is there any way to convert the accession ids (given below) to a single > ID (Unigene, genbank, locuslink, swissport, genpept, GI number, any of > them will do). These data are proteins and wanted to know whether > bioperl can query . > > Accession # > > gb|AAA40936.1 > > gb|AAA41660.1 > > pir|JC1039 > > pir|S37300 > > rf|NP_036686.1 > > rf|NP_036737.1 > > rf|XP_345137.1 > > sp|P04764 > > sp|P11981 > > sp|P17209 > > spt|P00564 > > spt|P02563 > > spt|Q63679 > > spt|Q9WVK7 > > trm|Q924K3 > > trm|Q9ER34 > trm|Q9JJ79 > > Thanks > > uk > > > --------------------------------- > Do you Yahoo!? > Shop for Back-to-School deals on Yahoo! Shopping. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From holger.klein at molgen.mpg.de Fri Sep 10 09:05:18 2004 From: holger.klein at molgen.mpg.de (Holger Klein) Date: Fri Sep 10 09:05:46 2004 Subject: [Bioperl-l] Blat running/parsing problem Message-ID: <4141A68E.4060703@molgen.mpg.de> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello all, I have a problem using blat from within bioperl-run. Using my $inseq = Bio::SeqIO->new( '-file' => "<$queryfile", '-format' => "fasta" ); my $seq = $inseq->next_seq; my $seqname = $seq->id(); # $subject is a string containing the location of another fasta file my $blat_fac = Bio::Tools::Run::Alignment::Blat->new( "program_dir" => $BLAT_dir, "DB" => $subject) ; my @feats = $blat_fac->run($seq); for my $f (@feats) { while (my $r = $f->next_result()) { print $r."\n"; } I get the following error message: - -->%-- Argument "2.2.4" isn't numeric in addition (+) at /usr/local/lib/perl5/site_perl/5.8.3/Bio/SearchIO/psl.pm line 191, line 1. Argument "BLASTN" isn't numeric in addition (+) at /usr/local/lib/perl5/site_perl/5.8.3/Bio/SearchIO/psl.pm line 191, line 1. Argument "[blat]" isn't numeric in addition (+) at /usr/local/lib/perl5/site_perl/5.8.3/Bio/SearchIO/psl.pm line 191, line 1. Use of uninitialized value in division (/) at /usr/local/lib/perl5/site_perl/5.8.3/Bio/SearchIO/psl.pm line 191, line 1. Illegal division by zero at /usr/local/lib/perl5/site_perl/5.8.3/Bio/SearchIO/psl.pm line 191, line 1. - --%<-- Looking at the output of the blat run, it seems as if it was called with the option -out=blast by bioperl, while $f, the element which is given back from $blat_fac->run($seq) above is of type Bio::SearchIO::psl=HASH(0x858ad8c). So it seems to me, that Bio::Tools::Run::Alignment::Blat tries to parse blast-like output with a psl-parser. I tried to give an output type parameter to my blat-factory with: my $blat_fac = Bio::Tools::Run::Alignment::Blat->new( "program_dir" => $BLAT_dir, "DB" => $subject, "out" => "psl"); which resulted in: - -->%-- - ------------- EXCEPTION ------------- MSG: Unallowed parameter: OUT ! STACK Bio::Tools::Run::Alignment::Blat::AUTOLOAD /usr/local/lib/perl5/site_perl/5.8.3/Bio/Tools/Run/Alignment/Blat.pm:110 STACK Bio::Tools::Run::Alignment::Blat::new /usr/local/lib/perl5/site_perl/5.8.3/Bio/Tools/Run/Alignment/Blat.pm:137 - --%<-- Can anybody tell me what I'm doing wrong here or point me to a piece of code, where I can see how running blat and parsing it's output is really done? BTW: all of this happens in bioperl-run-1.4 and bioperl-1.4. Regards, Holger - -- Holger Klein computational molecular biology - MPI for molecular genetics http://www.molgen.mpg.de/~klein_h | room #334 holger.klein@molgen.mpg.de | fon +49 (0)30 8413-1170 / fax -1152 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFBQaaSqKu/1Xw0J4wRAvKNAJ9Rfrm9Wk81sMGhx6Hp4LbXPDdmGgCfUeAR ljzkyPjv0wPyKlAfhFdsdnA= =A1VQ -----END PGP SIGNATURE----- From panther_k at hotmail.com Fri Sep 10 05:30:49 2004 From: panther_k at hotmail.com (kavitha venugopal) Date: Fri Sep 10 09:47:39 2004 Subject: [Bioperl-l] bio Message-ID: hai bioperl i m doin my postgraduation in bioinformatics.i require detail about application of bioperl in bioinformatics.i kindly request you to enclose the detail _________________________________________________________________ Cool ringtones, snazzy logos! Expressive cards, fun games! http://www.msn.co.in/Mobile/ Get it all at MSN mobile! From tan10 at psu.edu Fri Sep 10 12:17:27 2004 From: tan10 at psu.edu (Todd Naumann) Date: Fri Sep 10 12:15:37 2004 Subject: [Bioperl-l] Re: how to save blast parser output Message-ID: Karolina, To redirect the output from the screen into a file can be done by adding: open OUT, ">filename"; #can be placed anywhere before the print statement # then simply add print OUT "Hit = ", $hit->name, # adding OUT after print directs everything to file filename. Using this method you would need to manually add the desired filename to the program before each run. If you want to use the program often and write lots of separate files it is easier to: my $filename = shift @ARGV; #this sets $filename to first command line argument open OUT, ">$filename"; #sets OUT to name of file supplied on command line print OUT, "Hit=", $hit->name, Then you can just supply the desired filename as a command line argument. perl program_name.pl argument -Todd From popgen23 at mac.com Sun Sep 12 12:15:32 2004 From: popgen23 at mac.com (Michael S. Robeson II) Date: Sun Sep 12 12:15:36 2004 Subject: [Bioperl-l] Help installing BioPerl Message-ID: I have successfully installed BioPerl on several machines running Mac OS X (10.3.5) w/o any trouble. However one of my machines (same OS) the install is not working. Basically I keep getting "Error 2" problems at the end of an install. I've used the "perl -MCPAN -eshell" as both a normal user and root and it still does not work. I've tried this while installing the "Bundle::BioPerl and the "B/BI/BIRNEY/bioperl-run-1.4.tar.gz". Basically what it amounts to is that I get an error that says "Can't locate Bio/Perl.pm in @INC". I basically know what this means but I am not so sure how to fix this or what to do. Any help would be greatly appreciated. -Thanks -Mike From brian_osborne at cognia.com Mon Sep 13 08:08:06 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Mon Sep 13 08:08:12 2004 Subject: [Bioperl-l] Help installing BioPerl In-Reply-To: Message-ID: Mike, Do you mean that the test for Bio::Perl is failing? Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Michael S. Robeson II Sent: Sunday, September 12, 2004 12:16 PM To: bioperl-l@portal.open-bio.org Subject: [Bioperl-l] Help installing BioPerl I have successfully installed BioPerl on several machines running Mac OS X (10.3.5) w/o any trouble. However one of my machines (same OS) the install is not working. Basically I keep getting "Error 2" problems at the end of an install. I've used the "perl -MCPAN -eshell" as both a normal user and root and it still does not work. I've tried this while installing the "Bundle::BioPerl and the "B/BI/BIRNEY/bioperl-run-1.4.tar.gz". Basically what it amounts to is that I get an error that says "Can't locate Bio/Perl.pm in @INC". I basically know what this means but I am not so sure how to fix this or what to do. Any help would be greatly appreciated. -Thanks -Mike _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From popgen23 at mac.com Mon Sep 13 12:58:42 2004 From: popgen23 at mac.com (Michael Robeson) Date: Mon Sep 13 12:58:47 2004 Subject: [Bioperl-l] Help installing BioPerl In-Reply-To: References: Message-ID: <2AF263C1-05A6-11D9-81EE-000393539070@mac.com> In a sense , yes. When I try to run any script using Bio::Perl I get this error: "Can't locate Bio/Perl.pm in @INC". -Mike On Sep 13, 2004, at 6:08 AM, Brian Osborne wrote: > Mike, > > Do you mean that the test for Bio::Perl is failing? > > Brian O. > > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org > [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Michael S. > Robeson II > Sent: Sunday, September 12, 2004 12:16 PM > To: bioperl-l@portal.open-bio.org > Subject: [Bioperl-l] Help installing BioPerl > > I have successfully installed BioPerl on several machines running Mac > OS X (10.3.5) w/o any trouble. However one of my machines (same OS) the > install is not working. Basically I keep getting "Error 2" problems at > the end of an install. > > I've used the "perl -MCPAN -eshell" as both a normal user and root and > it still does not work. I've tried this while installing the > "Bundle::BioPerl and the "B/BI/BIRNEY/bioperl-run-1.4.tar.gz". > > Basically what it amounts to is that I get an error that says "Can't > locate Bio/Perl.pm in @INC". I basically know what this means but I am > not so sure how to fix this or what to do. > > Any help would be greatly appreciated. > > -Thanks > -Mike > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > From jsun at utdallas.edu Mon Sep 13 13:12:06 2004 From: jsun at utdallas.edu (Sun, Jian) Date: Mon Sep 13 13:12:12 2004 Subject: [Bioperl-l] perl moudules for Degenerate Primer Design Message-ID: Dear all; Could anybody give me some directions or suggestions that are there any BioPerl Moudules have been developed and povided for degenerate primer design? Thanks in advance Jian From jason.stajich at duke.edu Mon Sep 13 13:16:22 2004 From: jason.stajich at duke.edu (Jason Stajich) Date: Mon Sep 13 13:16:27 2004 Subject: [Bioperl-l] Help installing BioPerl In-Reply-To: <2AF263C1-05A6-11D9-81EE-000393539070@mac.com> References: <2AF263C1-05A6-11D9-81EE-000393539070@mac.com> Message-ID: But are you sure you installed bioperl-1.4.tar.gz....it doesn't sound like it. "B/BI/BIRNEY/bioperl-1.4.tar.gz" Does this return anything? % perldoc Bio::Perl On Sep 13, 2004, at 12:58 PM, Michael Robeson wrote: > In a sense , yes. > > When I try to run any script using Bio::Perl I get this error: > > "Can't locate Bio/Perl.pm in @INC". > > -Mike > > On Sep 13, 2004, at 6:08 AM, Brian Osborne wrote: > >> Mike, >> >> Do you mean that the test for Bio::Perl is failing? >> >> Brian O. >> >> -----Original Message----- >> From: bioperl-l-bounces@portal.open-bio.org >> [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Michael S. >> Robeson II >> Sent: Sunday, September 12, 2004 12:16 PM >> To: bioperl-l@portal.open-bio.org >> Subject: [Bioperl-l] Help installing BioPerl >> >> I have successfully installed BioPerl on several machines running Mac >> OS X (10.3.5) w/o any trouble. However one of my machines (same OS) >> the >> install is not working. Basically I keep getting "Error 2" problems at >> the end of an install. >> >> I've used the "perl -MCPAN -eshell" as both a normal user and root and >> it still does not work. I've tried this while installing the >> "Bundle::BioPerl and the "B/BI/BIRNEY/bioperl-run-1.4.tar.gz". >> >> Basically what it amounts to is that I get an error that says "Can't >> locate Bio/Perl.pm in @INC". I basically know what this means but I am >> not so sure how to fix this or what to do. >> >> Any help would be greatly appreciated. >> >> -Thanks >> -Mike >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Jason Stajich jason.stajich at duke.edu http://www.duke.edu/~jes12/ From brian_osborne at cognia.com Mon Sep 13 13:22:37 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Mon Sep 13 13:22:50 2004 Subject: [Bioperl-l] Help installing BioPerl In-Reply-To: <2AF263C1-05A6-11D9-81EE-000393539070@mac.com> Message-ID: Mike, One fix is to put a "use lib ;" line into your scripts, another fix is to set the PERL5LIB variable to the Bioperl home directory, a third fix is to do the CPAN-based install again but set the installation directory to a location known to Perl (see the INSTALL file for the specific CPAN command). Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Michael Robeson Sent: Monday, September 13, 2004 12:59 PM To: Brian Osborne Cc: bioperl-l@portal.open-bio.org Subject: Re: [Bioperl-l] Help installing BioPerl In a sense , yes. When I try to run any script using Bio::Perl I get this error: "Can't locate Bio/Perl.pm in @INC". -Mike On Sep 13, 2004, at 6:08 AM, Brian Osborne wrote: > Mike, > > Do you mean that the test for Bio::Perl is failing? > > Brian O. > > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org > [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Michael S. > Robeson II > Sent: Sunday, September 12, 2004 12:16 PM > To: bioperl-l@portal.open-bio.org > Subject: [Bioperl-l] Help installing BioPerl > > I have successfully installed BioPerl on several machines running Mac > OS X (10.3.5) w/o any trouble. However one of my machines (same OS) the > install is not working. Basically I keep getting "Error 2" problems at > the end of an install. > > I've used the "perl -MCPAN -eshell" as both a normal user and root and > it still does not work. I've tried this while installing the > "Bundle::BioPerl and the "B/BI/BIRNEY/bioperl-run-1.4.tar.gz". > > Basically what it amounts to is that I get an error that says "Can't > locate Bio/Perl.pm in @INC". I basically know what this means but I am > not so sure how to fix this or what to do. > > Any help would be greatly appreciated. > > -Thanks > -Mike > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From popgen23 at mac.com Mon Sep 13 13:24:18 2004 From: popgen23 at mac.com (Michael Robeson) Date: Mon Sep 13 13:24:24 2004 Subject: [Bioperl-l] Help installing BioPerl In-Reply-To: References: <2AF263C1-05A6-11D9-81EE-000393539070@mac.com> Message-ID: Actually the file on the CPAN was: "B/BI/BIRNEY/bioperl-run-1.4.tar.gz" Maybe that's it? This file with the added "-run-" in the name might be something different? But, yes "perldoc Bio::Perl" does return the Bio::Perl synopsis. -Mike On Sep 13, 2004, at 11:16 AM, Jason Stajich wrote: > But are you sure you installed bioperl-1.4.tar.gz....it doesn't sound > like it. > "B/BI/BIRNEY/bioperl-1.4.tar.gz" > > Does this return anything? > % perldoc Bio::Perl > > On Sep 13, 2004, at 12:58 PM, Michael Robeson wrote: > >> In a sense , yes. >> >> When I try to run any script using Bio::Perl I get this error: >> >> "Can't locate Bio/Perl.pm in @INC". >> >> -Mike >> >> On Sep 13, 2004, at 6:08 AM, Brian Osborne wrote: >> >>> Mike, >>> >>> Do you mean that the test for Bio::Perl is failing? >>> >>> Brian O. >>> >>> -----Original Message----- >>> From: bioperl-l-bounces@portal.open-bio.org >>> [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Michael S. >>> Robeson II >>> Sent: Sunday, September 12, 2004 12:16 PM >>> To: bioperl-l@portal.open-bio.org >>> Subject: [Bioperl-l] Help installing BioPerl >>> >>> I have successfully installed BioPerl on several machines running Mac >>> OS X (10.3.5) w/o any trouble. However one of my machines (same OS) >>> the >>> install is not working. Basically I keep getting "Error 2" problems >>> at >>> the end of an install. >>> >>> I've used the "perl -MCPAN -eshell" as both a normal user and root >>> and >>> it still does not work. I've tried this while installing the >>> "Bundle::BioPerl and the "B/BI/BIRNEY/bioperl-run-1.4.tar.gz". >>> >>> Basically what it amounts to is that I get an error that says "Can't >>> locate Bio/Perl.pm in @INC". I basically know what this means but I >>> am >>> not so sure how to fix this or what to do. >>> >>> Any help would be greatly appreciated. >>> >>> -Thanks >>> -Mike >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l@portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> > -- > Jason Stajich > jason.stajich at duke.edu > http://www.duke.edu/~jes12/ > From sdavis2 at mail.nih.gov Mon Sep 13 13:40:50 2004 From: sdavis2 at mail.nih.gov (Davis, Sean (NIH/NHGRI)) Date: Mon Sep 13 13:40:54 2004 Subject: [Bioperl-l] perl moudules for Degenerate Primer Design Message-ID: <0E3E7E8F6E23DF4C8127A063568356B50473B104@nihexchange12.nih.gov> See: http://search.cpan.org/~birney/bioperl-1.4/Bio/Tools/Primer3.pm Sean -----Original Message----- From: Sun, Jian To: bioperl-l@bioperl.org Sent: 9/13/2004 1:12 PM Subject: [Bioperl-l] perl moudules for Degenerate Primer Design Dear all; Could anybody give me some directions or suggestions that are there any BioPerl Moudules have been developed and povided for degenerate primer design? Thanks in advance Jian _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From brian_osborne at cognia.com Mon Sep 13 13:47:21 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Mon Sep 13 13:47:36 2004 Subject: [Bioperl-l] perl moudules for Degenerate Primer Design In-Reply-To: Message-ID: Jian, Yes, you can run Primer3 using the bioperl-run library and parse the resulting files with Bio::Tools::Primer3.pm. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Sun, Jian Sent: Monday, September 13, 2004 1:12 PM To: bioperl-l@bioperl.org Subject: [Bioperl-l] perl moudules for Degenerate Primer Design Dear all; Could anybody give me some directions or suggestions that are there any BioPerl Moudules have been developed and povided for degenerate primer design? Thanks in advance Jian _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From popgen23 at mac.com Mon Sep 13 13:47:32 2004 From: popgen23 at mac.com (Michael Robeson) Date: Mon Sep 13 13:47:38 2004 Subject: [Bioperl-l] Help installing BioPerl In-Reply-To: References: Message-ID: I'd rather not add lines to my scripts because I distribute them among colleagues and it would be a pain to alter them every time a make a script. Well, being that I am still new to BioPerl and Perl in general, I do not have any experience in manipulating this PERL5LIB variable or how to do that. I have re-ran the CPAN-based install 4 times to no avail (as root even). How do I find a location that is known to PERL and where do I find this INSTALL file? Hmm, seems like I should just write things from scratch rather than use BioPerl. Much less troubleshooting, ehh? Naa, I'd still rather try installing/using BioPerl :-) Sorry, about this but I am trying to learn. I am trying to follow along with the "perl for bioinformatics" books but they are of no use when it comes to trouble shooting bio::perl. -Thanks -Mike On Sep 13, 2004, at 11:22 AM, Brian Osborne wrote: > Mike, > > One fix is to put a "use lib ;" line into your > scripts, another fix is to set the PERL5LIB variable to the Bioperl > home > directory, a third fix is to do the CPAN-based install again but set > the > installation directory to a location known to Perl (see the INSTALL > file for > the specific CPAN command). > > Brian O. > > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org > [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Michael > Robeson > Sent: Monday, September 13, 2004 12:59 PM > To: Brian Osborne > Cc: bioperl-l@portal.open-bio.org > Subject: Re: [Bioperl-l] Help installing BioPerl > > In a sense , yes. > > When I try to run any script using Bio::Perl I get this error: > > "Can't locate Bio/Perl.pm in @INC". > > -Mike > > On Sep 13, 2004, at 6:08 AM, Brian Osborne wrote: > >> Mike, >> >> Do you mean that the test for Bio::Perl is failing? >> >> Brian O. >> >> -----Original Message----- >> From: bioperl-l-bounces@portal.open-bio.org >> [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Michael S. >> Robeson II >> Sent: Sunday, September 12, 2004 12:16 PM >> To: bioperl-l@portal.open-bio.org >> Subject: [Bioperl-l] Help installing BioPerl >> >> I have successfully installed BioPerl on several machines running Mac >> OS X (10.3.5) w/o any trouble. However one of my machines (same OS) >> the >> install is not working. Basically I keep getting "Error 2" problems at >> the end of an install. >> >> I've used the "perl -MCPAN -eshell" as both a normal user and root and >> it still does not work. I've tried this while installing the >> "Bundle::BioPerl and the "B/BI/BIRNEY/bioperl-run-1.4.tar.gz". >> >> Basically what it amounts to is that I get an error that says "Can't >> locate Bio/Perl.pm in @INC". I basically know what this means but I am >> not so sure how to fix this or what to do. >> >> Any help would be greatly appreciated. >> >> -Thanks >> -Mike >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > From jason.stajich at duke.edu Mon Sep 13 13:58:12 2004 From: jason.stajich at duke.edu (Jason Stajich) Date: Mon Sep 13 13:58:14 2004 Subject: [Bioperl-l] Help installing BioPerl In-Reply-To: References: <2AF263C1-05A6-11D9-81EE-000393539070@mac.com> Message-ID: <7AB93019-05AE-11D9-80C1-000393C44276@duke.edu> They are 2 different things. See the website and FAQ for more information about the "core" and "run" distributions. There may have been some issues with the dependancies of Bio::Perl and LWP in the 1.4 release I cannot remember. If you want to make CPAN install something, just force the install. This will ignore the failed tests and still install the modules. cpan>force install Bio::Perl cpan>force install Bio::Tools::Run::Alignment::Clustalw Setting PERL5LIB isn't that hard though and is what most people do when they can't get CPAN to behave or if they want to work with the most up-to-date version of the code. % tar zxf ~/bioperl-1.4.tar.gz % cd bioperl-1.4 % perl Makefile.PL LIB=$HOME/lib/perl % make install Add this to your .bashrc export PERL5LIB=$HOME/lib/perl An install without using CPAN. This is useful if you want to get the bugfixes that have been released since 1.4 which you can get via CVS. -jason On Sep 13, 2004, at 1:24 PM, Michael Robeson wrote: > Actually the file on the CPAN was: > "B/BI/BIRNEY/bioperl-run-1.4.tar.gz" > > Maybe that's it? This file with the added "-run-" in the name might be > something different? > > But, yes "perldoc Bio::Perl" does return the Bio::Perl synopsis. > > -Mike > > > On Sep 13, 2004, at 11:16 AM, Jason Stajich wrote: > >> But are you sure you installed bioperl-1.4.tar.gz....it doesn't sound >> like it. >> "B/BI/BIRNEY/bioperl-1.4.tar.gz" >> >> Does this return anything? >> % perldoc Bio::Perl >> >> On Sep 13, 2004, at 12:58 PM, Michael Robeson wrote: >> >>> In a sense , yes. >>> >>> When I try to run any script using Bio::Perl I get this error: >>> >>> "Can't locate Bio/Perl.pm in @INC". >>> >>> -Mike >>> >>> On Sep 13, 2004, at 6:08 AM, Brian Osborne wrote: >>> >>>> Mike, >>>> >>>> Do you mean that the test for Bio::Perl is failing? >>>> >>>> Brian O. >>>> >>>> -----Original Message----- >>>> From: bioperl-l-bounces@portal.open-bio.org >>>> [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Michael >>>> S. >>>> Robeson II >>>> Sent: Sunday, September 12, 2004 12:16 PM >>>> To: bioperl-l@portal.open-bio.org >>>> Subject: [Bioperl-l] Help installing BioPerl >>>> >>>> I have successfully installed BioPerl on several machines running >>>> Mac >>>> OS X (10.3.5) w/o any trouble. However one of my machines (same OS) >>>> the >>>> install is not working. Basically I keep getting "Error 2" problems >>>> at >>>> the end of an install. >>>> >>>> I've used the "perl -MCPAN -eshell" as both a normal user and root >>>> and >>>> it still does not work. I've tried this while installing the >>>> "Bundle::BioPerl and the "B/BI/BIRNEY/bioperl-run-1.4.tar.gz". >>>> >>>> Basically what it amounts to is that I get an error that says "Can't >>>> locate Bio/Perl.pm in @INC". I basically know what this means but I >>>> am >>>> not so sure how to fix this or what to do. >>>> >>>> Any help would be greatly appreciated. >>>> >>>> -Thanks >>>> -Mike >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l@portal.open-bio.org >>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l@portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> -- >> Jason Stajich >> jason.stajich at duke.edu >> http://www.duke.edu/~jes12/ >> > > -- Jason Stajich jason.stajich at duke.edu http://www.duke.edu/~jes12/ From sanges at biogem.it Mon Sep 13 14:04:01 2004 From: sanges at biogem.it (Remo Sanges) Date: Mon Sep 13 14:04:18 2004 Subject: [Bioperl-l] Help installing BioPerl In-Reply-To: References: Message-ID: <4A6E1BA6-05AF-11D9-BDF5-000A95B95F88@biogem.it> On Sep 13, 2004, at 7:47 PM, Michael Robeson wrote: > Hmm, seems like I should just write things from scratch rather than > use BioPerl. Much less troubleshooting, ehh? Naa, I'd still rather try > installing/using BioPerl :-) > > Sorry, about this but I am trying to learn. I am trying to follow > along with the "perl for bioinformatics" books but they are of no use > when it comes to trouble shooting bio::perl. I' m not sure but it seems that you are triyng to install bioperl-run before than bioperl, rigth? They are two different packages and you should install them in the rigth order... if you perform a search in cpan you will find: cpan> i /bioperl/ Bundle Bundle::BioPerl (C/CR/CRAFFI/Bundle-BioPerl-2.1.5.tar.gz) Distribution A/AL/ALLENDAY/bioperl-microarray-0.1.tar.gz Distribution B/BI/BIRNEY/bioperl-0.05.1.tar.gz Distribution B/BI/BIRNEY/bioperl-0.6.2.tar.gz Distribution B/BI/BIRNEY/bioperl-0.7.0.tar.gz Distribution B/BI/BIRNEY/bioperl-1.0.2.tar.gz Distribution B/BI/BIRNEY/bioperl-1.0.tar.gz Distribution B/BI/BIRNEY/bioperl-1.2.1.tar.gz Distribution B/BI/BIRNEY/bioperl-1.2.2.tar.gz Distribution B/BI/BIRNEY/bioperl-1.2.3.tar.gz Distribution B/BI/BIRNEY/bioperl-1.2.tar.gz Distribution B/BI/BIRNEY/bioperl-1.4.tar.gz Distribution B/BI/BIRNEY/bioperl-db-0.1.tar.gz Distribution B/BI/BIRNEY/bioperl-ext-1.4.tar.gz Distribution B/BI/BIRNEY/bioperl-gui-0.7.tar.gz Distribution B/BI/BIRNEY/bioperl-run-1.2.2.tar.gz Distribution B/BI/BIRNEY/bioperl-run-1.4.tar.gz Distribution C/CR/CRAFFI/Bundle-BioPerl-2.1.5.tar.gz Module Bio::LiveSeq::IO::BioPerl (B/BI/BIRNEY/bioperl-1.2.3.tar.gz) So you should install in this order: - Bundle::BioPerl - bioperl-1.4.tar.gz and then - bioperl-run-1.4.tar.gz Consider always as a reference: - the bioperl website http://bioperl.org/ - the bioperl tutorial http://www.bioperl.org/Core/Latest/bptutorial.html - the bioperl how-to http://bioperl.org/HOWTOs/ HTH Remo From popgen23 at mac.com Mon Sep 13 14:07:11 2004 From: popgen23 at mac.com (Michael Robeson) Date: Mon Sep 13 14:07:19 2004 Subject: [Bioperl-l] Help installing BioPerl In-Reply-To: <4A6E1BA6-05AF-11D9-BDF5-000A95B95F88@biogem.it> References: <4A6E1BA6-05AF-11D9-BDF5-000A95B95F88@biogem.it> Message-ID: Ok, thanks guys. Must have been sleepy when installing on that last computer! :-) When I get back to that computer tonight I will try it again w/o the correct files in the right order. I'll keep you posted as to the results. - Thanks for your help! I am sure I'll be back soon. - Mike (Bioperl newbie) On Sep 13, 2004, at 12:04 PM, Remo Sanges wrote: > On Sep 13, 2004, at 7:47 PM, Michael Robeson wrote: > >> Hmm, seems like I should just write things from scratch rather than >> use BioPerl. Much less troubleshooting, ehh? Naa, I'd still rather >> try installing/using BioPerl :-) >> >> Sorry, about this but I am trying to learn. I am trying to follow >> along with the "perl for bioinformatics" books but they are of no use >> when it comes to trouble shooting bio::perl. > > I' m not sure but it seems that you are triyng to install bioperl-run > before than bioperl, rigth? > They are two different packages and you should install them in > the rigth order... > > if you perform a search in cpan you will find: > > cpan> i /bioperl/ > Bundle Bundle::BioPerl > (C/CR/CRAFFI/Bundle-BioPerl-2.1.5.tar.gz) > Distribution A/AL/ALLENDAY/bioperl-microarray-0.1.tar.gz > Distribution B/BI/BIRNEY/bioperl-0.05.1.tar.gz > Distribution B/BI/BIRNEY/bioperl-0.6.2.tar.gz > Distribution B/BI/BIRNEY/bioperl-0.7.0.tar.gz > Distribution B/BI/BIRNEY/bioperl-1.0.2.tar.gz > Distribution B/BI/BIRNEY/bioperl-1.0.tar.gz > Distribution B/BI/BIRNEY/bioperl-1.2.1.tar.gz > Distribution B/BI/BIRNEY/bioperl-1.2.2.tar.gz > Distribution B/BI/BIRNEY/bioperl-1.2.3.tar.gz > Distribution B/BI/BIRNEY/bioperl-1.2.tar.gz > Distribution B/BI/BIRNEY/bioperl-1.4.tar.gz > Distribution B/BI/BIRNEY/bioperl-db-0.1.tar.gz > Distribution B/BI/BIRNEY/bioperl-ext-1.4.tar.gz > Distribution B/BI/BIRNEY/bioperl-gui-0.7.tar.gz > Distribution B/BI/BIRNEY/bioperl-run-1.2.2.tar.gz > Distribution B/BI/BIRNEY/bioperl-run-1.4.tar.gz > Distribution C/CR/CRAFFI/Bundle-BioPerl-2.1.5.tar.gz > Module Bio::LiveSeq::IO::BioPerl > (B/BI/BIRNEY/bioperl-1.2.3.tar.gz) > > So you should install in this order: > > - Bundle::BioPerl > - bioperl-1.4.tar.gz > and then > - bioperl-run-1.4.tar.gz > > Consider always as a reference: > > - the bioperl website http://bioperl.org/ > - the bioperl tutorial > http://www.bioperl.org/Core/Latest/bptutorial.html > - the bioperl how-to http://bioperl.org/HOWTOs/ > > > HTH > > Remo > From wes.barris at csiro.au Tue Sep 14 01:20:00 2004 From: wes.barris at csiro.au (Wes Barris) Date: Tue Sep 14 01:20:50 2004 Subject: [Bioperl-l] validate_species_name Message-ID: <41467F80.50007@csiro.au> I am converting back and forth between genbank and fasta formats. The NCBI accession "AY374167" is one of many genbank entries whos ORGANISM is flagged as invalid when creating genbank output. The bioperl error thrown is this: ------------- EXCEPTION ------------- MSG: Invalid species name 'rosenbergii-Australia' STACK Bio::Species::validate_species_name /usr/lib/perl5/site_perl/5.8.0/Bio/Species.pm:321 STACK Bio::Species::classification /usr/lib/perl5/site_perl/5.8.0/Bio/Species.pm:151 STACK toplevel /home/wes/proj/genbank/fastatogenbank.pl:29 -------------------------------------- The first few lines of the genbank file that I am trying to match are: LOCUS AY374167 867 bp DNA linear INV 31-OCT-2003 DEFINITION Macrobrachium rosenbergii-Australia 18S ribosomal RNA gene, partial sequence. ACCESSION AY374167 VERSION AY374167.1 GI:37675510 KEYWORDS . SOURCE Macrobrachium rosenbergii-Australia ORGANISM Macrobrachium rosenbergii-Australia Eukaryota; Metazoa; Arthropoda; Crustacea; Malacostraca; Eumalacostraca; Eucarida; Decapoda; Pleocyemata; Caridea; Palaemonoidea; Palaemonidae; Macrobrachium. The relevant piece of bioperl code (Species.pm) is: sub validate_species_name { my( $self, $string ) = @_; return 1 if $string eq "sp."; return 1 if $string =~ /^[a-z][\w\s]+$/i; $self->throw("Invalid species name '$string'"); } I believe that a '-' could be added to the string test like this: return 1 if $string =~ /^[a-z][\w\s-]+$/i; bioperl-live (as of today), redhat 8. -- Wes Barris E-Mail: Wes.Barris@csiro.au From simon.mcgowan at molecular-medicine.oxford.ac.uk Tue Sep 14 04:30:51 2004 From: simon.mcgowan at molecular-medicine.oxford.ac.uk (Simon McGowan) Date: Tue Sep 14 04:30:53 2004 Subject: [Bioperl-l] pad individual tracks using panel Message-ID: Hi, After reading in the features of two GenBank files using Bio::SeqIO, I am attempting to render them as a single image using Bio::Graphics::Panel. My question is, is there a way to pad all the coordinates of a single track by a given amount? This would allow me to produce a very basic alignment by lining up the contents of two tracks at a common feature within both files. I can pad the entire panel using '-offset', and I guess I need a similar option for '-add_track'. Could someone please let me know if this is possible? Thanks, Simon ------------------------------------ Simon McGowan Computational Biology Research Group University of Oxford OX1 3RE www.compbio.ox.ac.uk From nathanhaigh at ukonline.co.uk Tue Sep 14 09:00:15 2004 From: nathanhaigh at ukonline.co.uk (Nathan Haigh) Date: Tue Sep 14 09:00:30 2004 Subject: [Bioperl-l] remote blast - plain text blast report Message-ID: Hi, I am running a remote BLAST, and I just want to be able to get the plain text version of the report as returned from NCBI - how do I do this? Some previous code I had, was a follows - how should I modify this to enable me to get the plain text report in a string? Thanks Nathan my @params = ( -prog => $blast_prog, -expect => $blast_expect, -readmethod => 'SearchIO', -database => $blast_database, ); my $factory = Bio::Tools::Run::RemoteBlast->new(@params); $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = $blast_entrez_query; $Bio::Tools::Run::RemoteBlast::HEADER{'MATRIX_NAME'} = $blast_matrix; my $r = $factory->submit_blast($seq_array_ref); while (my @rids = $factory->each_rid ) { foreach my $rid ( @rids ) { my $rc = $factory->retrieve_blast($rid); if ( !ref($rc) ) { if ($rc<0) { $factory->remove_rid($rid); # the sequence failed for some reason! } sleep 5; # wait 5 secs before making another request } else { my $result = $rc->next_result(); push @results, $result; $factory->remove_rid($rid); } } } # at this point @results stores the results of all the submitted seqs as returned from $rc->next_result() From jason.stajich at duke.edu Tue Sep 14 09:35:01 2004 From: jason.stajich at duke.edu (Jason Stajich) Date: Tue Sep 14 09:35:07 2004 Subject: [Bioperl-l] remote blast - plain text blast report In-Reply-To: References: Message-ID: 2 ways. 1. Set verbose = 1 @paras = ( -verbose => 1, .... rest of your params); my $plaintextfile = $factory->file; This will be the filename where the temp report is stored, this is overwritten on each blast retrieval. 2. use Bio::SearchIO::Writer::TextResultWriter to turn the SearchIO object back into a Text Report (or use HTMLResultWriter to make it HTML). On Sep 14, 2004, at 9:00 AM, Nathan Haigh wrote: > Hi, > > I am running a remote BLAST, and I just want to be able to get the > plain > text version of the report as returned from NCBI - how do I do this? > Some previous code I had, was a follows - how should I modify this to > enable > me to get the plain text report in a string? > > Thanks > Nathan > > my @params = ( > -prog => $blast_prog, > -expect => $blast_expect, > -readmethod => 'SearchIO', > -database => $blast_database, > ); > my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > > $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = > $blast_entrez_query; > $Bio::Tools::Run::RemoteBlast::HEADER{'MATRIX_NAME'} = $blast_matrix; > > my $r = $factory->submit_blast($seq_array_ref); > > while (my @rids = $factory->each_rid ) { > foreach my $rid ( @rids ) { > my $rc = $factory->retrieve_blast($rid); > if ( !ref($rc) ) { > if ($rc<0) { > $factory->remove_rid($rid); # the sequence > failed for some reason! > } > sleep 5; # wait 5 secs before making another > request > } else { > my $result = $rc->next_result(); > push @results, $result; > $factory->remove_rid($rid); > } > } > } > > # at this point @results stores the results of all the submitted seqs > as > returned from $rc->next_result() > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Jason Stajich jason.stajich at duke.edu http://www.duke.edu/~jes12/ From brian_osborne at cognia.com Tue Sep 14 11:41:04 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Tue Sep 14 11:41:22 2004 Subject: [Bioperl-l] validate_species_name In-Reply-To: <41467F80.50007@csiro.au> Message-ID: Wes, Added "-" to that regular expression. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Wes Barris Sent: Tuesday, September 14, 2004 1:20 AM To: Bioperl Mailing List Subject: [Bioperl-l] validate_species_name I am converting back and forth between genbank and fasta formats. The NCBI accession "AY374167" is one of many genbank entries whos ORGANISM is flagged as invalid when creating genbank output. The bioperl error thrown is this: ------------- EXCEPTION ------------- MSG: Invalid species name 'rosenbergii-Australia' STACK Bio::Species::validate_species_name /usr/lib/perl5/site_perl/5.8.0/Bio/Species.pm:321 STACK Bio::Species::classification /usr/lib/perl5/site_perl/5.8.0/Bio/Species.pm:151 STACK toplevel /home/wes/proj/genbank/fastatogenbank.pl:29 -------------------------------------- The first few lines of the genbank file that I am trying to match are: LOCUS AY374167 867 bp DNA linear INV 31-OCT-2003 DEFINITION Macrobrachium rosenbergii-Australia 18S ribosomal RNA gene, partial sequence. ACCESSION AY374167 VERSION AY374167.1 GI:37675510 KEYWORDS . SOURCE Macrobrachium rosenbergii-Australia ORGANISM Macrobrachium rosenbergii-Australia Eukaryota; Metazoa; Arthropoda; Crustacea; Malacostraca; Eumalacostraca; Eucarida; Decapoda; Pleocyemata; Caridea; Palaemonoidea; Palaemonidae; Macrobrachium. The relevant piece of bioperl code (Species.pm) is: sub validate_species_name { my( $self, $string ) = @_; return 1 if $string eq "sp."; return 1 if $string =~ /^[a-z][\w\s]+$/i; $self->throw("Invalid species name '$string'"); } I believe that a '-' could be added to the string test like this: return 1 if $string =~ /^[a-z][\w\s-]+$/i; bioperl-live (as of today), redhat 8. -- Wes Barris E-Mail: Wes.Barris@csiro.au _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From jdw at ou.edu Tue Sep 14 12:49:16 2004 From: jdw at ou.edu (James D. White) Date: Tue Sep 14 12:51:25 2004 Subject: [Bioperl-l] Options for Compiling Perl 5.8.5 Running on an UltraSparc with Solaris 2.9? Message-ID: <4147210C.1265C87E@ou.edu> I am looking at upgrading my present Perl compiler from version 5.6.1 to version 5.8.5. The new version will be built with GCC 3.3 into a shared /usr/local running on a cluster of various UltraSparc models running Solaris 9. I am looking for advice on options for building the new Perl to ensure that it is compatible with the modules I will be adding to the base Perl 5.8.5, including BioPerl. For the new 5.8.5, I am considering enabling use64bitall and thread support (but which type of threads?). One of the systems has 32GB RAM, so use64bitall would enable the running of applications needing a lot of memory. Neither of these options is a requirement for the production applications I am getting ready to deploy, but I would like to build a stable Perl environment that will last quite a while without having to reinstall Perl and all of the modules again. If either use64bitall or threads will cause a problem in building and installing my add-on modules, then I probably need to avoid enabling these options. If Perl and all of the modules I wish to install can be built, tested, and installed with these options turned on, but problems arise only when using multiple threads or a large amount of memory with BioPerl, then I just need to avoid using these features with BioPerl. I am hoping someone has some experience using Perl and BioPerl in this type of environment. If someone can tell me that things will work, then that is great, and I can proceed. If someone can tell me that these features are not yet compatible, then I will build the new Perl without the extras and I won't waste time trying something that is not going to work. The major Perl modules I presently have installed and plan to run with the new compiler include: Apache with mod_perl, BioPerl, CGI, DBI, DBD::Mysql, DBD::Oracle, Tk, and all of their prerequisites and subcomponents. The existing Perl 5.6.1 was built with the following (Perl -V output listed at end of message): -compiled with GCC 2.95.2 -thread support disabled -large file support enabled -use64bitint=undef -use64bitall=undef -uselongdouble=undef -- James D. White (jdw@ou.edu) Director of Bioinformatics Department of Chemistry and Biochemistry/ACGT University of Oklahoma 101 David L. Boren Blvd., SRTC 2100 Norman, OK 73019 Phone: (405) 325-4912, FAX: (405) 325-7762 ================ perl -V output for old 5.6.1 compiler =============== Summary of my perl5 (revision 5.0 version 6 subversion 1) configuration: Platform: osname=solaris, osvers=2.8, archname=sun4-solaris uname='sunos dna2.chem.ou.edu 5.8 generic_108528-08 sun4u sparc sunw,ultra-5_10 ' config_args='-Dcc=gcc' hint=previous, useposix=true, d_sigaction=define usethreads=undef use5005threads=undef useithreads=undef usemultiplicity=undef useperlio=undef d_sfio=undef uselargefiles=define usesocks=undef use64bitint=undef use64bitall=undef uselongdouble=undef Compiler: cc='gcc', ccflags ='-fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64', optimize='-O', cppflags='-fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64' ccversion='', gccversion='2.95.2 19991024 (release)', gccosandvers='solaris2.7' intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=4321 d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16 ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8 alignbytes=8, usemymalloc=n, prototype=define Linker and Libraries: ld='gcc', ldflags =' -L/usr/local/lib ' libpth=/usr/local/lib /usr/lib /usr/ccs/lib libs=-lsocket -lnsl -ldl -lm -lc perllibs=-lsocket -lnsl -ldl -lm -lc libc=/lib/libc.so, so=so, useshrplib=false, libperl=libperl.a Dynamic Linking: dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags=' ' cccdlflags='-fPIC', lddlflags='-G -L/usr/local/lib' Characteristics of this binary (from libperl): Compile-time options: USE_LARGE_FILES Built under solaris Compiled at Sep 24 2003 13:52:02 @INC: /usr/local/lib/perl5/5.6.1/sun4-solaris /usr/local/lib/perl5/5.6.1 /usr/local/lib/perl5/site_perl/5.6.1/sun4-solaris /usr/local/lib/perl5/site_perl/5.6.1 /usr/local/lib/perl5/site_perl . ============ end of perl -V output for old 5.6.1 compiler =========== From tex at biosysadmin.com Tue Sep 14 02:04:34 2004 From: tex at biosysadmin.com (James Thompson) Date: Tue Sep 14 18:16:09 2004 Subject: [Bioperl-l] PSI-BLAST Matrix Parser? In-Reply-To: <413F4A59.1040409@utk.edu> Message-ID: Stefan, That does make sense, I'll get started on it this weekend. I think I'll try my hand at adding Bio::Matrix::PSM::ProtMatrix, a lot of the DNA stuff seems hardcoded into the SiteMatrix object. Thanks a lot for the help. :) James Thompson On Wed, 8 Sep 2004, Stefan Kirov wrote: > This seems reasonable to me. The one thing you need to consider is the > structure that should contain the matrix. The current design of > > Bio::Matrix::PSM::Psm and Bio::Matrix::PSM::SiteMatrix does not allow this as SiteMatrix is a DNA only object. > There are two ways to go: > Either change SiteMatrix to accept protein matrix data or add a protein matrix class to Bio::Matrix::PSM (say Bio::Matrix::PSM::ProtMatrix), which will hold the data and make Bio::Matrix::PSM::Psm inherit from the class and be able to contain the object (as it is actually a container right now). > So you will have something like: > my $psmIO= new Bio::Matrix::PSM::IO(-file=>$file, -format=>'psi-blast'); #this will call the actual parser (Bio::Matrix::PSM::IO::psiblast) > my $header=$psmIO->.... #I guess there will be some header data > > while (my $psm=$psmIO->next_psm) { > my $psimatrix=$psm->protmatrix; #This will be Bio::Matrix::PSM::ProtMatrix object > $psimatrix->.....; #Now process the data parsed into this object through its methods... > } > > If you do this maybe you should get an account and commit it yourself? > Does this make sense to you? > Stefan > > James Thompson wrote: > > >Stefan, > > > >Thanks for the response. For reading in the actual alignment I would use > >Bio::AlignIO to read the PSI-BLAST output as it's just another alignment file, > >but the matrix file that I'm talking about is slightly different. Now that > >I've perused CVS more and learned more about how the Bio::Matrix::PSM modules > >work, I think I have a more clear picture of what I'd like to do. > > > >If you run PSI-BLAST with the -Q option, will take the matrix that it > >used for the position-specific search and output it to a file. I've put up a > >link to one of my matrix files up here if you'd like to look at it: > > > >http://bioinformatics.rit.edu/~tex/atp1.matrix > > > >Basically I'd like to make some Bio::Matrix::PSM::Psm objects (or at least > >a PsmI-compliant object), and I think that the correct way to do this would > >be to add a file format parser to Bio::Matrix::PSM::IO. Currently in Bioperl > >there are three format parsers: > > - mast > > - meme > > - transfac > > > >None of these work with the PSI-BLAST matrix files. I'd like to write a new > >matrix file parser (perhaps called psi-blast?) in the spirit of the three other > >parsers. > > > >If I were to write this, could someone commit it for me? > > > >James Thompson > > > >On Tue, 7 Sep 2004, Stefan A Kirov wrote: > > > > > > > >>I am not sure what object you are going to store your data in... Are you > >>going to develop your own class to hold the data or use an existing one? > >>Also is there any reason not to use Bio::AlignIO (it reads PSI-Blast as > >>far as I know)? > >>Stefan > >> > >> > >>On Tue, 7 Sep 2004, James Thompson wrote: > >> > >> > >> > >>>Dear Bioperl-ers, > >>> > >>>I'd like to parse the output of a PSI-BLAST matrix, and I was wondering if > >>>there was a Bioperl way of parsing these files. If not, I'd like to make my > >>>code general enough to be committed, and I'd like some advice on where exactly > >>>to put such a module. From my cursory knowledge of Bioperl, I think that adding > >>>another format parser to Bio::Matrix::PSM::IO would be a good way to go. > >>> > >>>I have a couple of questions: > >>>- Does anyone know what the PSI-BLAST matrix format is called? > >>>- Is this the correct place in which to put code for parsing this type of files? > >>> > >>>The file format represents a position-specific scoring matrix with some added > >>>statistical information, here's a general overview of the information available > >>> > >>> > >>>from the matrix file: > >> > >> > >>>Last position-specific scoring matrix computed, weighted observed percentages > >>>rounded down, information per position, and relative weight of gapless real > >>>matches to p seudocounts. > >>> > >>>Any help is greatly appreciated. > >>> > >>>James Thompson > >>> > >>>_______________________________________________ > >>>Bioperl-l mailing list > >>>Bioperl-l@portal.open-bio.org > >>>http://portal.open-bio.org/mailman/listinfo/bioperl-l > >>> > >>> > >>> > > > > > > > > > > From popgen23 at mac.com Tue Sep 14 23:54:59 2004 From: popgen23 at mac.com (Michael S. Robeson II) Date: Tue Sep 14 23:55:02 2004 Subject: [Bioperl-l] help with remote blast Message-ID: <037AD3E9-06CB-11D9-9D35-000A956C4C82@mac.com> I have been using perl for a while and have become somewhat comfortable with the language, though i have much to learn. However, I have been reading all of the bioperl documentation on remote BLAST in particular and... all I have to say is, "for the first time I have no idea what ya'll are talking about!" :-) I am new to the bioperl community and I have been trying my best, but the documentation is quit confusing to me. All, I am trying to do is set up a way in which I can automatically BLAST a set of sequences in a multi-sequence FASTA file. I have seen the "Read_all_Sequences" commands but every time I use them I get an error saying that nucleotide data is being submitted for protein data when in fact i am sending nucleotide data and the fact that the tutorial states that the default setting should be "nr"! I can not find any clear documentation or examples on the bioperl web site, tutorial, or perldocs that can even help me get started. I have setup and run all the tutorial scripts just fine. Problem is I have no idea how to modify the perl scripts w/o breaking them unlearning what I have learned from them. Are there any other external bioperl references or suggestions from the community? I do not want the answer, I really want to figure this out on my own. I think I just need a little nudge in the write direction to get me started. It's just that, from my limited experience reading the bioperl documentation, it is a world different from reading generic perl documentation. So, any help with the "Rules of Engagement" when reading this documentation would be a life saver! - Thanks for any help! - A totally lost bioperl newbie! - Mike From barry.moore at genetics.utah.edu Wed Sep 15 00:22:12 2004 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Wed Sep 15 00:22:16 2004 Subject: [Bioperl-l] help with remote blast In-Reply-To: <037AD3E9-06CB-11D9-9D35-000A956C4C82@mac.com> References: <037AD3E9-06CB-11D9-9D35-000A956C4C82@mac.com> Message-ID: <4147C374.4050202@genetics.utah.edu> Mike- A couple of suggestions for figuring it out yourself - both of which you may have already done. First, on a module new to me I'll usually look at the synopsis, description and methods to try to figure out what can be done with this module. For instance on your problem with reading in a fasta file. You'll want to use Bio::SeqIO (found here http://doc.bioperl.org/releases/bioperl-1.4/Bio/SeqIO.html). Looking at the doc page for that one the synopsis a description give a good idea of what it does, and some example script of how to do it. But they don't cover all that is possible. You had a problem with the module "guessing" incorrectly that your sequence was protein. In the methods you see that there is an method to set the alphabet. Accompanying that is usage, a one line example, returns, args, throws etc. From that you can deduce that if you add a line $seqio->alphabet('dna') to the synopsis script you will force the parser to interpret you seq as DNA. The second suggestion is to check out script that are kept in the examples and scripts directories of the bioperl-live CVS (found here http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/?cvsroot=bioperl). You can glean alot about usage from seeing how people use even seemingly unrelated scripts. If you want to discuss this more, write back to the list or write me directly. Barry Michael S. Robeson II wrote: > I have been using perl for a while and have become somewhat > comfortable with the language, though i have much to learn. However, I > have been reading all of the bioperl documentation on remote BLAST in > particular and... all I have to say is, "for the first time I have no > idea what ya'll are talking about!" :-) > > I am new to the bioperl community and I have been trying my best, but > the documentation is quit confusing to me. > > All, I am trying to do is set up a way in which I can automatically > BLAST a set of sequences in a multi-sequence FASTA file. I have seen > the "Read_all_Sequences" commands but every time I use them I get an > error saying that nucleotide data is being submitted for protein data > when in fact i am sending nucleotide data and the fact that the > tutorial states that the default setting should be "nr"! I can not > find any clear documentation or examples on the bioperl web site, > tutorial, or perldocs that can even help me get started. > > I have setup and run all the tutorial scripts just fine. Problem is I > have no idea how to modify the perl scripts w/o breaking them > unlearning what I have learned from them. Are there any other external > bioperl references or suggestions from the community? > > I do not want the answer, I really want to figure this out on my own. > I think I just need a little nudge in the write direction to get me > started. It's just that, from my limited experience reading the > bioperl documentation, it is a world different from reading generic > perl documentation. So, any help with the "Rules of Engagement" when > reading this documentation would be a life saver! > > > - Thanks for any help! > - A totally lost bioperl newbie! > - Mike > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Barry Moore Dept. of Human Genetics University of Utah Salt Lake City, UT From simon.mcgowan at molecular-medicine.oxford.ac.uk Wed Sep 15 04:37:31 2004 From: simon.mcgowan at molecular-medicine.oxford.ac.uk (Simon McGowan) Date: Wed Sep 15 04:37:47 2004 Subject: [Bioperl-l] pad individual tracks using panel Message-ID: Hi, Following some feedback here, I should also say that this is for illustrative purposes only and not to produce a meaningful alignment of any kind. Its needed by the users here who want some figures for papers. Would I have to alter all the coordinates for the features in the track, or is there a shortcut involving -add_track? Thanks, Simon -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org] On Behalf Of Simon McGowan Sent: 14 September 2004 09:31 To: Subject: [Bioperl-l] pad individual tracks using panel Hi, After reading in the features of two GenBank files using Bio::SeqIO, I am attempting to render them as a single image using Bio::Graphics::Panel. My question is, is there a way to pad all the coordinates of a single track by a given amount? This would allow me to produce a very basic alignment by lining up the contents of two tracks at a common feature within both files. I can pad the entire panel using '-offset', and I guess I need a similar option for '-add_track'. Could someone please let me know if this is possible? Thanks, Simon ------------------------------------ Simon McGowan Computational Biology Research Group University of Oxford OX1 3RE www.compbio.ox.ac.uk _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From pankaj at nii.res.in Wed Sep 15 04:40:58 2004 From: pankaj at nii.res.in (Pankaj) Date: Wed Sep 15 05:38:34 2004 Subject: [Bioperl-l] (no subject) Message-ID: Hi all, I have a pdb file of 2 superimposed structures. I want to know the rmsd of a part of 1 structure to a part of the 2 structure. For this rmsd calculation I dont want to disturb the superimposition. how do I do that? thanking all in advance Pankaj Kamra Research Scholar From pankaj at nii.res.in Wed Sep 15 04:57:29 2004 From: pankaj at nii.res.in (Pankaj) Date: Wed Sep 15 05:54:50 2004 Subject: [Bioperl-l] rmsd calculation Message-ID: Hi all, I have a pdb file of 2 superimposed structures. I want to know the rmsd of a part of 1 structure to a part of the 2 structure. For this rmsd calculation I dont want to disturb the superimposition. how do I do that? thanking all in advance Pankaj Kamra Research Scholar From pvh at egenetics.com Wed Sep 15 06:11:50 2004 From: pvh at egenetics.com (Peter van Heusden) Date: Wed Sep 15 06:12:13 2004 Subject: [Bioperl-l] 'Nightly build' tracking for Bioperl Message-ID: <41481566.1080104@egenetics.com> Some kind of 'nightly build' system for Bioperl - which automatically builds the current Bioperl distribution from CVS, runs the tests and reports problems - was mentioned as a good idea at the BOF at BOSC 2004. I've spent a bit of time looking at open source build monitoring tools, and I'm pretty frustrated. Everything out there seems to be either really hard to install (e.g. Mozilla Tinderbox) or incomplete (Test::AutoBuild). Has anyone worked on something like this before? Does anyone have recommendations? Thanks, Peter From sdavis2 at mail.nih.gov Wed Sep 15 06:50:54 2004 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Wed Sep 15 06:48:53 2004 Subject: [Bioperl-l] IMAGE clones Message-ID: <1E0D4F76-0705-11D9-A552-000A95D7BA10@mail.nih.gov> Just a quick (not entirely bioperl-related) question... I have a microarray design that is described in terms of IMAGE clones. I am interested in getting the sequences for these clones. However, I can't seem to find a resource for doing so directly (is there one?). I do see that several genbank accessions can be associated with the same IMAGE clone, so I could get all such genbanks associated with each clone and use those as surrogates, ultimately for use in blast analyses. How can I construct a query (or can I) that pulls these genbanks by clone id, or is someone aware of a reliable mapping from image clone to genbank accession? Thanks, Sean From Annie.Law at nrc-cnrc.gc.ca Wed Sep 15 09:38:32 2004 From: Annie.Law at nrc-cnrc.gc.ca (Law, Annie) Date: Wed Sep 15 09:38:29 2004 Subject: [Bioperl-l] IMAGE clones Message-ID: <10C94843061E094A98C02EB77CFC328722FE8F@nrcmrdex1d.imsb.nrc.ca> Hi Sean, I don't know if this is what you are looking for but there are files from the image consortium Ftp site. You can load the file into a table in your database and get the info you want. Here is the link. It should be in this directory but if it's not there it will be in a directory near by. ftp://image.llnl.gov/image/outgoing/arrayed_plate_data/cumulative/ hth, Annie. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org] On Behalf Of Sean Davis Sent: Wednesday, September 15, 2004 6:51 AM To: Bioperl Subject: [Bioperl-l] IMAGE clones Just a quick (not entirely bioperl-related) question... I have a microarray design that is described in terms of IMAGE clones. I am interested in getting the sequences for these clones. However, I can't seem to find a resource for doing so directly (is there one?). I do see that several genbank accessions can be associated with the same IMAGE clone, so I could get all such genbanks associated with each clone and use those as surrogates, ultimately for use in blast analyses. How can I construct a query (or can I) that pulls these genbanks by clone id, or is someone aware of a reliable mapping from image clone to genbank accession? Thanks, Sean _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From heikki at ebi.ac.uk Wed Sep 15 09:41:32 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Wed Sep 15 09:46:42 2004 Subject: [Bioperl-l] Re: [Bioperl-announce-l] bioperl mailing list In-Reply-To: <490D0AFAF3D2D3119F6C00508B6FDF150662CC22@ex.mshri.on.ca> References: <490D0AFAF3D2D3119F6C00508B6FDF150662CC22@ex.mshri.on.ca> Message-ID: <200409151441.32910.heikki@ebi.ac.uk> Rong, Please see http://bio.perl.org/MailList.shtml for information about mailing lists and their intended usage. The mailing list you'll want to join is bioperl-l. Others, This is SeqHound project htttp://seqhound.blueprint.org was given a talk at the ISMB by Ian Donaldson. I've been talking with him about further bioperl integration. Yours, -Heikki On Tuesday 14 Sep 2004 18:19, Rong Yao wrote: > Dear BioPerl staffs, > > I am a software developer in the Blueprint Initiative. Currently, our group > is working on integrating existing Bioperl SeqHound module into cvs tree at > your organization. I would like to join in the mailing list and get > information of events in the bioperl community. > > Best regards, > > Rong Yao > > -- > Software Developer > The Blueprint Initiative - North America > 522 University Ave. > Toronto, Ontario, Canada > M5G 1W7 > http://www.blueprint.org > ryao@blueprint.org > phone: 416-596-8505 ext 6316 > > > > _______________________________________________ > Bioperl-announce-l mailing list > Bioperl-announce-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-announce-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki@ebi.ac.uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From jsun at utdallas.edu Wed Sep 15 15:44:32 2004 From: jsun at utdallas.edu (Sun, Jian) Date: Wed Sep 15 15:44:27 2004 Subject: [Bioperl-l] Error message. Message-ID: Dear all: Could anybody tell me what's the problem of the below perl codes, why I always get the Syntax Error message when I run the command:> perl -c file.name? ********************************************** .............. my $in = new Bio::AlignIO ( -file => $ARGV[0], -format => 'clustalw' ); my $out = newFh Bio::AlignIO ( -fh => \*STDOUT, -format => 'clustalw' ); my $aln = $in->next_aln(); *************************************************** ________________________________ From: bioperl-l-bounces@portal.open-bio.org on behalf of Pankaj Sent: Wed 9/15/2004 3:40 AM To: bio_bulletin_board@bioinformatics.org Cc: bioperl-l@portal.open-bio.org Subject: [Bioperl-l] (no subject) Hi all, I have a pdb file of 2 superimposed structures. I want to know the rmsd of a part of 1 structure to a part of the 2 structure. For this rmsd calculation I dont want to disturb the superimposition. how do I do that? thanking all in advance Pankaj Kamra Research Scholar _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From jsun at utdallas.edu Wed Sep 15 15:44:32 2004 From: jsun at utdallas.edu (Sun, Jian) Date: Wed Sep 15 15:44:28 2004 Subject: [Bioperl-l] Error message. Message-ID: Dear all: Could anybody tell me what's the problem of the below perl codes, why I always get the Syntax Error message when I run the command:> perl -c file.name? ********************************************** .............. my $in = new Bio::AlignIO ( -file => $ARGV[0], -format => 'clustalw' ); my $out = newFh Bio::AlignIO ( -fh => \*STDOUT, -format => 'clustalw' ); my $aln = $in->next_aln(); *************************************************** ________________________________ From: bioperl-l-bounces@portal.open-bio.org on behalf of Pankaj Sent: Wed 9/15/2004 3:40 AM To: bio_bulletin_board@bioinformatics.org Cc: bioperl-l@portal.open-bio.org Subject: [Bioperl-l] (no subject) Hi all, I have a pdb file of 2 superimposed structures. I want to know the rmsd of a part of 1 structure to a part of the 2 structure. For this rmsd calculation I dont want to disturb the superimposition. how do I do that? thanking all in advance Pankaj Kamra Research Scholar _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From dburdick at systemsbiology.org Wed Sep 15 11:37:25 2004 From: dburdick at systemsbiology.org (David Burdick) Date: Wed Sep 15 17:05:46 2004 Subject: [Bioperl-l] (no subject) Message-ID: Gabriel- At the ISB, we've created a software tool called ?Connect the Dots? that can make translations between databases that share identifiers. There is an example web interface at: http://t1dbase.org/cgi-bin/dotHome.cgi though the software is primarily developed for use programatically where you parse only the databases you need. We currently have parsers for 26 databases that collect mostly identifiers (as opposed to major content), and new parsers are easy to write. To use Connect the Dots to translate identifiers, a small query language is used to join databases on identifier and extract the desired columns from each database into a relational table. There are a variety of options for output including flat files and XML. The software is built on the PostgreSQL database, and can be found at sorceforge: http://cvs.sourceforge.net/viewcvs.py/isbiology/connectDots_postgres/ We should have CPAN release soon, though for now you can download the software and read the documentation in the ConnectDots.pm file. It is written in Perl. If you have questions, feel free to email me at dburdick@systemsbiology.org Dave > From: "Gabriel Berriz" > Subject: [Bioperl-l] Gene/protein ID synonyms > > One recurrent headache for much of our bioinformatics development comes from > the fact that for most model organisms any one gene or protein can be > identified by several different IDs (e.g. for yeast genes one has common > names, ORF names, SGD IDs, etc.). We want to give users the option to refer > to genes and proteins according to as many standards as possible, which > means that our software has to be able to translate between all these > standards and its own internal representation. Moreover, this translation > facility has to keep pace with updates to the source databases. > > Are there Bioperl modules to deal with this problem? If not, what would be > a better mailing list or forum to enquire about available solutions to this > problem? I am aware of SRS, which some people find very useful for this > kind of translation, but I'd like to learn more about what else is out > there. > > Many thanks, > > Gabriel From pvh at wfeet.za.net Wed Sep 15 10:42:11 2004 From: pvh at wfeet.za.net (Peter van Heusden) Date: Wed Sep 15 17:06:18 2004 Subject: [Bioperl-l] Bioperl tests Message-ID: <414854C3.2000609@wfeet.za.net> Does anyone run the Bioperl test suite regularly to see what tests fail? I've just fixed a bug in WebDBSeqI.pm which looks to me like it could never have worked. The reason I found the bug is that it triggered a test failed in the tests for Bio::DB::BioFetch, which led to the original question - are these tests only run around 'release' time? Peter From birney at ebi.ac.uk Wed Sep 15 17:19:02 2004 From: birney at ebi.ac.uk (Ewan Birney) Date: Wed Sep 15 17:19:00 2004 Subject: [Bioperl-l] Bioperl tests In-Reply-To: <414854C3.2000609@wfeet.za.net> Message-ID: On Wed, 15 Sep 2004, Peter van Heusden wrote: > Does anyone run the Bioperl test suite regularly to see what tests fail? > I've just fixed a bug in WebDBSeqI.pm which looks to me like it could > never have worked. The reason I found the bug is that it triggered a > test failed in the tests for Bio::DB::BioFetch, which led to the > original question - are these tests only run around 'release' time? > I think they are run at intermittenly by people working on the main trunk. It is as we push towards a new release series and branches where watching the tests becomes more serious (ie, tests failing down a branch is far more serious); What was the bug? Was this main trunk or branch? > Peter > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From jason.stajich at duke.edu Wed Sep 15 17:24:23 2004 From: jason.stajich at duke.edu (Jason Stajich) Date: Wed Sep 15 17:24:29 2004 Subject: [Bioperl-l] Bioperl tests In-Reply-To: <414854C3.2000609@wfeet.za.net> References: <414854C3.2000609@wfeet.za.net> Message-ID: <9CEB8E76-075D-11D9-8B70-000393C44276@duke.edu> It is all a function of how much time core developers have and how many other people are helping out by running tests, fixing bugs, and reporting the problems. I can only speak for myself, but I have much less time for Bioperl than I did a year ago. I don't run the whole test suite very frequently except for the modules that I am changing before doing CVS commits and when helping out in a release. But I am just one developer so I don't know what other people are doing. I have generally ignored BioFetch failing because things have worked off and on wrt network connectivity and the local DB tests are tied together with the network based ones unfortunately. I don't think I paid attention to those failing tests very much because I've lost track of how it is even supposed to work now. Your ideas about tinder-box, etc are well received, it is something that we have talked about off and on for many years but it boils down the open-source principal -- s/he who does it first can claim the glory of, well, being the first person who did it. =) Chris can get you setup with an account on the appropriate box if you want to do it on OBF systems. Would be great for someone to do it - even if it just mean reporting the results of make test in an email to the guts list. Seems to work for the biojava crowd. -jason On Sep 15, 2004, at 10:42 AM, Peter van Heusden wrote: > Does anyone run the Bioperl test suite regularly to see what tests > fail? I've just fixed a bug in WebDBSeqI.pm which looks to me like it > could never have worked. The reason I found the bug is that it > triggered a test failed in the tests for Bio::DB::BioFetch, which led > to the original question - are these tests only run around 'release' > time? > > Peter > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Jason Stajich jason.stajich at duke.edu http://www.duke.edu/~jes12/ From dhoworth at mrc-lmb.cam.ac.uk Thu Sep 16 04:59:53 2004 From: dhoworth at mrc-lmb.cam.ac.uk (Dave Howorth) Date: Thu Sep 16 04:59:50 2004 Subject: [Bioperl-l] 'Nightly build' tracking for Bioperl In-Reply-To: <41481566.1080104@egenetics.com> References: <41481566.1080104@egenetics.com> Message-ID: <41495609.9010907@mrc-lmb.cam.ac.uk> Peter van Heusden wrote: > I've spent a bit of time looking at open source build monitoring tools, > and I'm pretty frustrated. Everything out there seems to be either > really hard to install (e.g. Mozilla Tinderbox) or incomplete > (Test::AutoBuild). > > Has anyone worked on something like this before? Does anyone have > recommendations? I just came across a pointer to The Linux Test Project , who look like they might be a good crowd to ask. There's a link to (STAF) Software Testing Automation Framework on their homepage, for example. HTH, Dave -- Dave Howorth MRC Centre for Protein Engineering Hills Road, Cambridge, CB2 2QH 01223 252960 From pvh at egenetics.com Thu Sep 16 05:22:16 2004 From: pvh at egenetics.com (Peter van Heusden) Date: Thu Sep 16 05:22:24 2004 Subject: [Bioperl-l] Bioperl tests In-Reply-To: <9CEB8E76-075D-11D9-8B70-000393C44276@duke.edu> References: <414854C3.2000609@wfeet.za.net> <9CEB8E76-075D-11D9-8B70-000393C44276@duke.edu> Message-ID: <41495B48.1030606@egenetics.com> Jason Stajich wrote: > > > Your ideas about tinder-box, etc are well received, it is something > that we have talked about off and on for many years but it boils down > the open-source principal -- s/he who does it first can claim the > glory of, well, being the first person who did it. =) Chris can get > you setup with an account on the appropriate box if you want to do it > on OBF systems. Would be great for someone to do it - even if it just > mean reporting the results of make test in an email to the guts list. > Seems to work for the biojava crowd. > Well, we (Electric Genetics) need something like this for our ongoing validation efforts, so it shouldn't be much trouble getting this working with the existing test suite at the same time. I'll keep the list posted with regards to progress. Peter From brian_osborne at cognia.com Thu Sep 16 07:20:25 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Thu Sep 16 07:20:27 2004 Subject: [Bioperl-l] Error message. In-Reply-To: Message-ID: Jian, You could try: my $in = Bio::AlignIO->new( -file => $ARGV[0], -format => 'clustalw' ); my $out = Bio::AlignIO->new( -fh => \*STDOUT, -format => 'clustalw' ); my $aln = $in->next_aln(); I know this is not an answer to your question... Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Sun, Jian Sent: Wednesday, September 15, 2004 3:45 PM To: Bioperl Mailing List Cc: bioperl-l@portal.open-bio.org Subject: [Bioperl-l] Error message. Dear all: Could anybody tell me what's the problem of the below perl codes, why I always get the Syntax Error message when I run the command:> perl -c file.name? ********************************************** .............. my $in = new Bio::AlignIO ( -file => $ARGV[0], -format => 'clustalw' ); my $out = newFh Bio::AlignIO ( -fh => \*STDOUT, -format => 'clustalw' ); my $aln = $in->next_aln(); *************************************************** ________________________________ From: bioperl-l-bounces@portal.open-bio.org on behalf of Pankaj Sent: Wed 9/15/2004 3:40 AM To: bio_bulletin_board@bioinformatics.org Cc: bioperl-l@portal.open-bio.org Subject: [Bioperl-l] (no subject) Hi all, I have a pdb file of 2 superimposed structures. I want to know the rmsd of a part of 1 structure to a part of the 2 structure. For this rmsd calculation I dont want to disturb the superimposition. how do I do that? thanking all in advance Pankaj Kamra Research Scholar _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From jason.stajich at duke.edu Thu Sep 16 07:59:14 2004 From: jason.stajich at duke.edu (Jason Stajich) Date: Thu Sep 16 07:59:08 2004 Subject: [Bioperl-l] Error message. In-Reply-To: References: Message-ID: This works fine for me. You're not telling us what your actual syntax errors are. #!/usr/bin/perl -w use Bio::AlignIO; use strict; my $in = new Bio::AlignIO ( -file => $ARGV[0], -format => 'clustalw' ); my $out = newFh Bio::AlignIO ( -fh => \*STDOUT, -format => 'clustalw' ); my $aln = $in->next_aln(); On Sep 15, 2004, at 3:44 PM, Sun, Jian wrote: > Dear all: > > Could anybody tell me what's the problem of the below perl codes, > why I always get the Syntax Error message when I run the command:> > perl -c file.name? > > ********************************************** > > .............. > > my $in = new Bio::AlignIO ( -file => $ARGV[0], -format => > 'clustalw' ); > > my $out = newFh Bio::AlignIO ( -fh => \*STDOUT, -format => > 'clustalw' ); > > my $aln = $in->next_aln(); > > *************************************************** > > > > ________________________________ > > From: bioperl-l-bounces@portal.open-bio.org on behalf of Pankaj > Sent: Wed 9/15/2004 3:40 AM > To: bio_bulletin_board@bioinformatics.org > Cc: bioperl-l@portal.open-bio.org > Subject: [Bioperl-l] (no subject) > > > > Hi all, > I have a pdb file of 2 superimposed structures. I want to know the > rmsd of a part of 1 structure to a part of the 2 structure. For this > rmsd calculation I dont want to disturb the superimposition. how do I > do that? > thanking all in advance > Pankaj Kamra > Research Scholar > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Jason Stajich jason.stajich at duke.edu http://www.duke.edu/~jes12/ From khufaz83 at yahoo.com Thu Sep 16 07:59:48 2004 From: khufaz83 at yahoo.com (hafiz hafiz) Date: Thu Sep 16 07:59:41 2004 Subject: [Bioperl-l] Build new Swiss-Prot Seq Message-ID: <20040916115948.36209.qmail@web52503.mail.yahoo.com> Hello , everybody can help me, i want to buid a new sequence in swissprot and i have used 3 modul such as Bio::SeqFeature, Bio::Seq, Bio::Annotation::Comments, Bio::Annotation::Simplevalue, Bio::Annotation Bio::Annotation::references and Bio::Annotation::Dblink, so it?s true or not. This is my souces code; $feat = new Bio::SeqFeature::Generic ( -start => 10, -end => 100, -strand => -1, -primary => 'repeat', -source_tag => 'repeatmasker', -display_name => 'alu family', -score => 1000, -tag => { new => 1, author => 'someone', sillytag => 'this is silly!' } ); #my $feat = new Bio::SeqFeature::Generic(-start =>10,-end => 22, -strand =>1, # -tag =>{ author => 'john',note =>'TATA box'}); $feat->add_tag_value("match1","PF000123 e-7.2"); $feat->add_tag_value("match2","PF002534 e-7.2"); my @arr = $feat->get_all_tags; for my $tag (@arr){ print $tag,":",$feat->get_tag_values($tag)," "; } my $seq_obj =Bio::Seq ->new(-seq=>"attcccccchjkhjkhkjh", -display_id=>"BIO52" ); $seq_obj->add_SeqFeature($feat); my $comment =Bio::Annotation::Comment->new; $comment->text("this looks like a good TATA box"); my $coll =new Bio::Annotation::Collection; $coll->add_Annotation('comment',$comment); $seq_obj->annotation($coll); my $col = new Bio::Annotation::Collection; my $sv = new Bio::Annotation::SimpleValue(-value => 'someval'); $col->add_Annotation('tagname', $sv); $reg = Bio::Annotation::Reference->new( -title => 'title line', -location => 'location line', -authors => 'author line', -medline => 998122 ); $link1 = new Bio::Annotation::DBLink(-database => 'TSC', -primary_id => 'TSC0000030' ); #or $link2 = new Bio::Annotation::DBLink(); $link2->database('dbSNP'); $link2->primary_id('2367'); # DBLink is-a Bio::AnnotationI object, can be added to annotation # collections, e.g. the one on features or seqs $feat->annotation->add_Annotation('dblink', $link2); $file3="/home/database/Bioperl/test.gb"; my $io= Bio::SeqIO ->new(-format =>"swiss",-file => ">$file3"); $io ->write_seq($seq_obj); ________________________________________________________________________ Yahoo! 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Download Messenger Now http://uk.messenger.yahoo.com/download/index.html From scannedr at tcd.ie Thu Sep 16 06:53:04 2004 From: scannedr at tcd.ie (Devin Scannell) Date: Thu Sep 16 08:04:43 2004 Subject: [Bioperl-l] Bugz in Consense Message-ID: <95EC4518-07CE-11D9-B344-000393B293CE@tcd.ie> Hi, was having some trouble setting the outgroup when drawing trees with phylip and tracked the problem down to here (changes marked with ###) : Consense.pm sub _set_names_from_tree { my ($self,$tree) = @_; my $newick; my $ios = IO::String->new($newick); my $tio = Bio::TreeIO->new(-fh=>$ios,-format=>'newick'); $tio->write_tree($tree); ### changed \w to [\w\._] ### newick allows at least these and I think a few other symbols my @names = $newick=~/([\w\._]+):\d+/g; my %names; ### changed < to <= for(my $i=0; $i <= $#names; $i++){ $names{$names[$i]} = $i+1; } $self->names(\%names); return; } apologies if there is a better way of submitting fixes than mailing the the whole list... but better to err on the side of caution, right? regards, Devin From brian_osborne at cognia.com Thu Sep 16 08:16:59 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Thu Sep 16 08:16:59 2004 Subject: [Bioperl-l] Build new Swiss-Prot Seq In-Reply-To: <20040916115948.36209.qmail@web52503.mail.yahoo.com> Message-ID: Hafiz, I'm not sure I understand. Are you seeing errors when you run your code? Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of hafiz hafiz Sent: Thursday, September 16, 2004 8:00 AM To: bioperl-l@portal.open-bio.org Subject: [Bioperl-l] Build new Swiss-Prot Seq Hello , everybody can help me, i want to buid a new sequence in swissprot and i have used 3 modul such as Bio::SeqFeature, Bio::Seq, Bio::Annotation::Comments, Bio::Annotation::Simplevalue, Bio::Annotation Bio::Annotation::references and Bio::Annotation::Dblink, so it's true or not. This is my souces code; $feat = new Bio::SeqFeature::Generic ( -start => 10, -end => 100, -strand => -1, -primary => 'repeat', -source_tag => 'repeatmasker', -display_name => 'alu family', -score => 1000, -tag => { new => 1, author => 'someone', sillytag => 'this is silly!' } ); #my $feat = new Bio::SeqFeature::Generic(-start =>10,-end => 22, -strand =>1, # -tag =>{ author => 'john',note =>'TATA box'}); $feat->add_tag_value("match1","PF000123 e-7.2"); $feat->add_tag_value("match2","PF002534 e-7.2"); my @arr = $feat->get_all_tags; for my $tag (@arr){ print $tag,":",$feat->get_tag_values($tag)," "; } my $seq_obj =Bio::Seq ->new(-seq=>"attcccccchjkhjkhkjh", -display_id=>"BIO52" ); $seq_obj->add_SeqFeature($feat); my $comment =Bio::Annotation::Comment->new; $comment->text("this looks like a good TATA box"); my $coll =new Bio::Annotation::Collection; $coll->add_Annotation('comment',$comment); $seq_obj->annotation($coll); my $col = new Bio::Annotation::Collection; my $sv = new Bio::Annotation::SimpleValue(-value => 'someval'); $col->add_Annotation('tagname', $sv); $reg = Bio::Annotation::Reference->new( -title => 'title line', -location => 'location line', -authors => 'author line', -medline => 998122 ); $link1 = new Bio::Annotation::DBLink(-database => 'TSC', -primary_id => 'TSC0000030' ); #or $link2 = new Bio::Annotation::DBLink(); $link2->database('dbSNP'); $link2->primary_id('2367'); # DBLink is-a Bio::AnnotationI object, can be added to annotation # collections, e.g. the one on features or seqs $feat->annotation->add_Annotation('dblink', $link2); $file3="/home/database/Bioperl/test.gb"; my $io= Bio::SeqIO ->new(-format =>"swiss",-file => ">$file3"); $io ->write_seq($seq_obj); ________________________________________________________________________ Yahoo! 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Download Messenger Now http://uk.messenger.yahoo.com/download/index.html _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From khufaz83 at yahoo.com Thu Sep 16 08:27:43 2004 From: khufaz83 at yahoo.com (hafiz hafiz) Date: Thu Sep 16 08:27:36 2004 Subject: [Bioperl-l] Build New SwissProt Seq Message-ID: <20040916122743.40546.qmail@web52507.mail.yahoo.com> yes i am seeing error; my output; ------------- EXCEPTION ------------- MSG: Alphabet not OK for Bio::PrimarySeq=HASH(0x854145c) STACK Bio::Tools::SeqStats::_is_alphabet_strict /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/SeqStats.pm:680 STACK Bio::Tools::SeqStats::get_mol_wt /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/SeqStats.pm:489 STACK Bio::SeqIO::swiss::write_seq /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/swiss.pm:621 STACK main::update_database search10.pl:428 STACK toplevel search10.pl:44 -------------------------------------- author:someone match1:PF000123 e-7.2 match2:PF002534 e-7.2 new:1 sillytag:this is silly! this only my file output; ID BIO52 STANDARD; PRT; 19 AA. AC unknown; DE CC this looks like a good TATA box KW FT repeat 10 100 . ________________________________________________________________________ Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now http://uk.messenger.yahoo.com/download/index.html From brian_osborne at cognia.com Thu Sep 16 08:37:36 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Thu Sep 16 08:37:35 2004 Subject: [Bioperl-l] Build New SwissProt Seq In-Reply-To: <20040916122743.40546.qmail@web52507.mail.yahoo.com> Message-ID: Hafiz, Hmm. Your sequence has a "j" in it, remove that and see if the error goes away. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of hafiz hafiz Sent: Thursday, September 16, 2004 8:28 AM To: bioperl-l@portal.open-bio.org Subject: [Bioperl-l] Build New SwissProt Seq yes i am seeing error; my output; ------------- EXCEPTION ------------- MSG: Alphabet not OK for Bio::PrimarySeq=HASH(0x854145c) STACK Bio::Tools::SeqStats::_is_alphabet_strict /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/SeqStats.pm:680 STACK Bio::Tools::SeqStats::get_mol_wt /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/SeqStats.pm:489 STACK Bio::SeqIO::swiss::write_seq /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/swiss.pm:621 STACK main::update_database search10.pl:428 STACK toplevel search10.pl:44 -------------------------------------- author:someone match1:PF000123 e-7.2 match2:PF002534 e-7.2 new:1 sillytag:this is silly! this only my file output; ID BIO52 STANDARD; PRT; 19 AA. AC unknown; DE CC this looks like a good TATA box KW FT repeat 10 100 . ________________________________________________________________________ Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now http://uk.messenger.yahoo.com/download/index.html _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From brian_osborne at cognia.com Thu Sep 16 08:44:07 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Thu Sep 16 08:44:06 2004 Subject: [Bioperl-l] Bugz in Consense In-Reply-To: <95EC4518-07CE-11D9-B344-000393B293CE@tcd.ie> Message-ID: Devin, >apologies if there is a better way of submitting fixes than mailing the The best way is still http://bugzilla.bioperl.org/ since once it's entered there it will never be forgotten. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Devin Scannell Sent: Thursday, September 16, 2004 6:53 AM To: bioperl-l@bioperl.org Subject: [Bioperl-l] Bugz in Consense Hi, was having some trouble setting the outgroup when drawing trees with phylip and tracked the problem down to here (changes marked with ###) : Consense.pm sub _set_names_from_tree { my ($self,$tree) = @_; my $newick; my $ios = IO::String->new($newick); my $tio = Bio::TreeIO->new(-fh=>$ios,-format=>'newick'); $tio->write_tree($tree); ### changed \w to [\w\._] ### newick allows at least these and I think a few other symbols my @names = $newick=~/([\w\._]+):\d+/g; my %names; ### changed < to <= for(my $i=0; $i <= $#names; $i++){ $names{$names[$i]} = $i+1; } $self->names(\%names); return; } apologies if there is a better way of submitting fixes than mailing the the whole list... but better to err on the side of caution, right? regards, Devin _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From khufaz83 at yahoo.com Thu Sep 16 08:47:54 2004 From: khufaz83 at yahoo.com (hafiz hafiz) Date: Thu Sep 16 08:47:47 2004 Subject: [Bioperl-l] Build new SwissProt Seq Message-ID: <20040916124754.45851.qmail@web52509.mail.yahoo.com> thank you very much :), it don't have error yet. ________________________________________________________________________ Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now http://uk.messenger.yahoo.com/download/index.html From jorvis at gmail.com Thu Sep 16 11:55:01 2004 From: jorvis at gmail.com (Joshua Orvis) Date: Thu Sep 16 11:55:05 2004 Subject: [Bioperl-l] extracting GI number from BLAST hit Message-ID: How can one extract the GI number from hits when doing BLAST against an NCBI-formatted BLAST database? Each entry in the original multi-FASTA file was like this: >gi|30260195|ref|NC_003997.3| Bacillus anthracis str. Ames, complete genome [sequence .....] and formatting was done like: # formatdb -i filename.fna -p F -o T When I BLAST and parse the hit section I cannot see how to get the GI number out of each hit. This code: ## returns a Bio::SearchIO::blast object $report = $fact->blastall($seq); ## returns a Bio::Search::Result::BlastResult object while( my $result = $report->next_result ) { ## returns a Bio::Search::Hit::BlastHit object while( my $hit = $result->next_hit ) { my $acc = $hit->accession || 'NOACC'; my $desc = $hit->description || 'NODESC'; my $name = $hit->name || 'NONAME'; my $locus = $hit->locus || 'NOLOC'; print "$acc - $desc - $name - $locus\n"; ## returns a Bio::Search::HSP::GenericHSP object while( my $hsp = $hit->next_hsp ) { ## TODO, grab the alignments in a bit } } } generates output like this: NC_002940 - Haemophilus ducreyi 35000HP, complete genome - ref|NC_002940.2| - NOLOC NC_004088 - Yersinia pestis KIM, complete genome - ref|NC_004088.1| - NOLOC NC_003143 - Yersinia pestis strain CO92, complete genome - ref|NC_003143.1| - NOLOC NC_002516 - Pseudomonas aeruginosa PA01, complete genome - ref|NC_002516.1| - NOLOC NC_002677 - Mycobacterium leprae strain TN complete genome - ref|NC_002677.1| - NOLOC I expected that I could parse it out of the description line, but that is being done at some stage before. I'm probably just missing a method somewhere in the docs. Any suggestions? Joshua From kellert at ohsu.edu Thu Sep 16 12:00:23 2004 From: kellert at ohsu.edu (Thomas J Keller) Date: Thu Sep 16 12:00:41 2004 Subject: [Bioperl-l] Error message. In-Reply-To: References: Message-ID: <84A924D6-07F9-11D9-A18D-0003930405E2@ohsu.edu> The message I received had html markup (>) within the perl. I don't know if it's present in his program. Obviously if it is, it is a syntax error. >> >> my $in = new Bio::AlignIO ( -file => $ARGV[0], -format => >> 'clustalw' ); >> >> my $out = newFh Bio::AlignIO ( -fh => \*STDOUT, -format => >> 'clustalw' ); >> >> my $aln = $in->next_aln(); >> >> vs > my $in = new Bio::AlignIO ( -file => $ARGV[0], -format => 'clustalw' ); > > my $out = newFh Bio::AlignIO ( -fh => \*STDOUT, -format => 'clustalw' > ); > > my $aln = $in->next_aln(); Could it be that simple? good luck, Tom Keller From kellert at ohsu.edu Thu Sep 16 12:00:23 2004 From: kellert at ohsu.edu (Thomas J Keller) Date: Thu Sep 16 12:00:45 2004 Subject: [Bioperl-l] Error message. In-Reply-To: References: Message-ID: <84A924D6-07F9-11D9-A18D-0003930405E2@ohsu.edu> The message I received had html markup (>) within the perl. I don't know if it's present in his program. Obviously if it is, it is a syntax error. >> >> my $in = new Bio::AlignIO ( -file => $ARGV[0], -format => >> 'clustalw' ); >> >> my $out = newFh Bio::AlignIO ( -fh => \*STDOUT, -format => >> 'clustalw' ); >> >> my $aln = $in->next_aln(); >> >> vs > my $in = new Bio::AlignIO ( -file => $ARGV[0], -format => 'clustalw' ); > > my $out = newFh Bio::AlignIO ( -fh => \*STDOUT, -format => 'clustalw' > ); > > my $aln = $in->next_aln(); Could it be that simple? good luck, Tom Keller From ak at ebi.ac.uk Thu Sep 16 12:18:34 2004 From: ak at ebi.ac.uk (Andreas Kahari) Date: Thu Sep 16 12:18:33 2004 Subject: [Bioperl-l] Error message. In-Reply-To: <84A924D6-07F9-11D9-A18D-0003930405E2@ohsu.edu> References: <84A924D6-07F9-11D9-A18D-0003930405E2@ohsu.edu> Message-ID: <20040916161834.GA11416@ebi.ac.uk> On Thu, Sep 16, 2004 at 09:00:23AM -0700, Thomas J Keller wrote: > The message I received had html markup (>) within the perl. I don't > know if it's present in his program. Obviously if it is, it is a syntax > error. Also, we don't know what the error message actually says, or if the code that was presented to us in fact was the complete code of the program. If it was, is lacks "use Bio::AlignIO;". See the SYNOPSIS section of the documentation of Bio::AlignIO for how to use the newFh() method. Cheers, Andreas > >>my $in = new Bio::AlignIO ( -file => $ARGV[0], -format => > >>'clustalw' ); > >> > >>my $out = newFh Bio::AlignIO ( -fh => \*STDOUT, -format => > >>'clustalw' ); > >> > >>my $aln = $in->next_aln(); > >> > >> > vs > > >my $in = new Bio::AlignIO ( -file => $ARGV[0], -format => 'clustalw' ); > > > >my $out = newFh Bio::AlignIO ( -fh => \*STDOUT, -format => 'clustalw' > >); > > > >my $aln = $in->next_aln(); -- Andreas K?h?ri EMBL-EBI/ensembl GnuPG: 1024D/C2E163CB, F4C4 A41A 665B 448A 3FA9 6AEA 12E3 39DA C2E1 63CB From kellert at ohsu.edu Thu Sep 16 15:22:10 2004 From: kellert at ohsu.edu (Thomas J Keller) Date: Thu Sep 16 15:23:31 2004 Subject: [Bioperl-l] primer3 install on Mac OS 10.3.5 Message-ID: Sorry if this isn't strictly bioperl. I'm installing primer3 but got the following error: $ make primer3_core gcc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -include /usr/include/sys/types.h -O2 -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 primer3_main.c gcc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -include /usr/include/sys/types.h -O2 -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 primer3.c primer3_release.h:3: warning: `pr_release' defined but not used gcc -g -Wall -D__USE_FIXED_PROTOTYPES__ -include /usr/include/sys/types.h -O2 -c -o oligotm.o oligotm.c primer3_release.h:3: warning: `pr_release' defined but not used gcc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -include /usr/include/sys/types.h -O2 -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -o dpal_primer.o dpal.c primer3_release.h:3: warning: `pr_release' defined but not used gcc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -include /usr/include/sys/types.h -O2 -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -o format_output.o format_output.c gcc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -include /usr/include/sys/types.h -O2 -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -o boulder_input.o boulder_input.c primer3_release.h:3: warning: `pr_release' defined but not used gcc -g -o primer3_core primer3_main.o primer3.o oligotm.o dpal_primer.o format_output.o boulder_input.o '-static' -lm ld: can't locate file for: -lcrt0.o make: *** [primer3_core] Error 1 I'm running Mac OS X 10.3.5 Thanks for any suggestions, Tom Keller Tom Keller, Ph.D. http://www.ohsu.edu/research/core kellert@ohsu.edu 503-494-2442 -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1621 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040916/42c124cd/attachment.bin From jason at cgt.duhs.duke.edu Thu Sep 16 15:49:09 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Thu Sep 16 15:54:36 2004 Subject: [Bioperl-l] primer3 install on Mac OS 10.3.5 In-Reply-To: References: Message-ID: <79B9689F-0819-11D9-AFFD-000393C44276@cgt.mc.duke.edu> Remove the -static -jason On Sep 16, 2004, at 3:22 PM, Thomas J Keller wrote: > Sorry if this isn't strictly bioperl. > I'm installing primer3 but got the following error: > > $ make primer3_core > gcc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -include > /usr/include/sys/types.h -O2 -DDPAL_MAX_ALIGN=36 > -DMAX_PRIMER_LENGTH=36 primer3_main.c > gcc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -include > /usr/include/sys/types.h -O2 -DDPAL_MAX_ALIGN=36 > -DMAX_PRIMER_LENGTH=36 primer3.c > primer3_release.h:3: warning: `pr_release' defined but not used > gcc -g -Wall -D__USE_FIXED_PROTOTYPES__ -include > /usr/include/sys/types.h -O2 -c -o oligotm.o oligotm.c > primer3_release.h:3: warning: `pr_release' defined but not used > gcc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -include > /usr/include/sys/types.h -O2 -DDPAL_MAX_ALIGN=36 > -DMAX_PRIMER_LENGTH=36 -o dpal_primer.o dpal.c > primer3_release.h:3: warning: `pr_release' defined but not used > gcc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -include > /usr/include/sys/types.h -O2 -DDPAL_MAX_ALIGN=36 > -DMAX_PRIMER_LENGTH=36 -o format_output.o format_output.c > gcc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -include > /usr/include/sys/types.h -O2 -DDPAL_MAX_ALIGN=36 > -DMAX_PRIMER_LENGTH=36 -o boulder_input.o boulder_input.c > primer3_release.h:3: warning: `pr_release' defined but not used > gcc -g -o primer3_core primer3_main.o primer3.o oligotm.o > dpal_primer.o format_output.o boulder_input.o '-static' -lm > ld: can't locate file for: -lcrt0.o > make: *** [primer3_core] Error 1 > > > I'm running Mac OS X 10.3.5 > > Thanks for any suggestions, > Tom Keller > > Tom Keller, Ph.D. > http://www.ohsu.edu/research/core > kellert@ohsu.edu > 503-494-2442_______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich Duke University jason at cgt.mc.duke.edu -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1944 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040916/f81c450c/attachment-0001.bin From tapo at novozymes.com Fri Sep 17 07:59:08 2004 From: tapo at novozymes.com (TAPO (Thomas Agersten Poulsen)) Date: Fri Sep 17 07:59:01 2004 Subject: [Bioperl-l] Writing embl entry to string Message-ID: <76F96CFE2AA2114C886B028A065A7FC40166081D@exdkba020.novo.dk> Dear List, I am writing a small script to split embl-files into smaller file of a given maximum file size. To this end, I would like to get the output from Bio::SeqIO->write_seq into a string (so I can evaluate length() on it). Would anybody out there know if this is posible???? Best regards Thomas ----------------------------------------------------- Thomas A Poulsen Research Scientist, PhD Novozymes A/S Protein Design / Bioinformatics Brudelysvej 26, 1US.24 Phone: +45 44 42 27 23 DK-2880 Bagsv?rd. Fax: +45 44 98 02 46 From brian_osborne at cognia.com Fri Sep 17 08:07:52 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Fri Sep 17 08:07:54 2004 Subject: [Bioperl-l] Writing embl entry to string In-Reply-To: <76F96CFE2AA2114C886B028A065A7FC40166081D@exdkba020.novo.dk> Message-ID: Thomas, Yes, see question 2.4 in the FAQ (http://bioperl.org/Core/Latest/faq.html). Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of TAPO (Thomas Agersten Poulsen) Sent: Friday, September 17, 2004 7:59 AM To: bioperl-l@bioperl.org Subject: [Bioperl-l] Writing embl entry to string Dear List, I am writing a small script to split embl-files into smaller file of a given maximum file size. To this end, I would like to get the output from Bio::SeqIO->write_seq into a string (so I can evaluate length() on it). Would anybody out there know if this is posible???? Best regards Thomas ----------------------------------------------------- Thomas A Poulsen Research Scientist, PhD Novozymes A/S Protein Design / Bioinformatics Brudelysvej 26, 1US.24 Phone: +45 44 42 27 23 DK-2880 Bagsv?rd. Fax: +45 44 98 02 46 _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From jason.stajich at duke.edu Fri Sep 17 09:35:19 2004 From: jason.stajich at duke.edu (Jason Stajich) Date: Fri Sep 17 09:35:11 2004 Subject: [Bioperl-l] extracting GI number from BLAST hit In-Reply-To: References: Message-ID: <6AE388C3-08AE-11D9-8434-000393C44276@duke.edu> Well is the GI number actually in the Hit in the report or in the description down in the hsp? We only report what is in the report - can you send a sample report which has the gi number in it? You may want to run your blast with -I T -I Show GI's in deflines [T/F] -jason On Sep 16, 2004, at 11:55 AM, Joshua Orvis wrote: > How can one extract the GI number from hits when doing BLAST against > an NCBI-formatted BLAST database? > > Each entry in the original multi-FASTA file was like this: > >> gi|30260195|ref|NC_003997.3| Bacillus anthracis str. Ames, complete >> genome > [sequence .....] > > and formatting was done like: > > # formatdb -i filename.fna -p F -o T > > When I BLAST and parse the hit section I cannot see how to get the GI > number out of each hit. This code: > > ## returns a Bio::SearchIO::blast object > $report = $fact->blastall($seq); > > ## returns a Bio::Search::Result::BlastResult object > while( my $result = $report->next_result ) { > > ## returns a Bio::Search::Hit::BlastHit object > while( my $hit = $result->next_hit ) { > > my $acc = $hit->accession || 'NOACC'; > my $desc = $hit->description || 'NODESC'; > my $name = $hit->name || 'NONAME'; > my $locus = $hit->locus || 'NOLOC'; > > print "$acc - $desc - $name - $locus\n"; > > ## returns a Bio::Search::HSP::GenericHSP object > while( my $hsp = $hit->next_hsp ) { > ## TODO, grab the alignments in a bit > } > } > } > > generates output like this: > > NC_002940 - Haemophilus ducreyi 35000HP, complete genome - > ref|NC_002940.2| - NOLOC > NC_004088 - Yersinia pestis KIM, complete genome - ref|NC_004088.1| - > NOLOC > NC_003143 - Yersinia pestis strain CO92, complete genome - > ref|NC_003143.1| - NOLOC > NC_002516 - Pseudomonas aeruginosa PA01, complete genome - > ref|NC_002516.1| - NOLOC > NC_002677 - Mycobacterium leprae strain TN complete genome - > ref|NC_002677.1| - NOLOC > > > I expected that I could parse it out of the description line, but that > is being done at some stage before. I'm probably just missing a > method somewhere in the docs. Any suggestions? > > Joshua > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Jason Stajich jason.stajich at duke.edu http://www.duke.edu/~jes12/ From sdavis2 at mail.nih.gov Fri Sep 17 09:57:25 2004 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Fri Sep 17 09:55:05 2004 Subject: [Bioperl-l] Re: [BioC] Error in kooperberg procedure In-Reply-To: <8975119BCD0AC5419D61A9CF1A923E951746EA@iahce2knas1.iah.bbsrc.reserved> References: <8975119BCD0AC5419D61A9CF1A923E951746EA@iahce2knas1.iah.bbsrc.reserved> Message-ID: <815D9F0C-08B1-11D9-B5A4-000A95D7BA10@mail.nih.gov> Actually, you can add constants to your matrices. RGmodel$Rb <- RGmodel$Rb + 0.001 I'm not sure this will solve your problem directly, though. Try it and see, but someone with a better understanding of the function may be able to comment in the context of your last post. Sean On Sep 17, 2004, at 9:49 AM, michael watson (IAH-C) wrote: > Hello > > I ran this code and got an error: > >> genepixFiles <- targets$Name >> read.series(genepixFiles, suffix=NULL,skip=26, sep="\t") >> layout <- RG$printer >> RGmodel <- kooperberg(genepixFiles, layout=layout) > Error in integrate(.numeratorBayesianAdjustedFG, ifelse((fg - bg - 4 * > : > a limit is missing > > I guess this may be related to my earlier problem, where I have BG > estimates = zero for one of my arrays, but this is a little trickier to > solve as the data is in data.frames, and I cannot so easily add a small > value to Rb and Gb.... > > Mick > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor From kellert at ohsu.edu Thu Sep 16 19:14:10 2004 From: kellert at ohsu.edu (Thomas J Keller) Date: Fri Sep 17 14:53:01 2004 Subject: [Bioperl-l] passing paramteters to primer3 Message-ID: <1D97BC08-0836-11D9-A18D-0003930405E2@ohsu.edu> Greetings, I'm trying to customize the Primer3 parameters via Bio::Tools::Run::Primer3. I don't understand why my param_string variable is not working (####code####): #### use strict; use warnings; use Bio::Tools::Run::Primer3; use Bio::SeqIO; my $seqio = Bio::SeqIO->new(-file => '/Users/kellert/Documents/Consults/Afentoulis/X03019.fa'); my $seq = $seqio->next_seq; my $primer3 = Bio::Tools::Run::Primer3->new(-seq => $seq, -outfile => '/Users/kellert/Documents/Consults/Afentoulis/temp.out'); unless ($primer3->executable) { print STDERR "primer3 cannot be found.\n"; exit(-1) } my %params = ( PRIMER_TASK => 'pick_pcr_primers_and_hyb_probe', PRIMER_MIN_TM => 48, PRIMER_MAX_TM => 70, PRIMER_OPT_TM => 60, PRIMER_PRODUCT_SIZE_RANGE => '75-150', PRIMER_NUM_RETURN => 10, PRIMER_MAX_POLY_X => 3, ); my $arg_string = join(", ", ( map { "$_ => \'$params{$_}\'" } keys %params)); # set max and min of Tm $primer3->add_targets($arg_string); #### this runs Primer3 but I get the warning: -------------------- WARNING --------------------- MSG: Parameter PRIMER_MIN_TM => '48', PRIMER_MAX_POLY_X => '3', PRIMER_TASK => 'pick_pcr_primers_and_hyb_probe', PRIMER_MAX_TM => '70', PRIMER_NUM_RETURN => '10', PRIMER_PRODUCT_SIZE_RANGE => '75-150', PRIMER_OPT_TM => '60' is not a valid Primer3 parameter --------------------------------------------------- I'm betting I've missed something trivial, but would appreciate your help. Thanks, Tom K Tom Keller, Ph.D. http://www.ohsu.edu/research/core kellert@ohsu.edu 503-494-2442 -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1634 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040916/a07a7352/attachment.bin From kellert at ohsu.edu Fri Sep 17 13:20:18 2004 From: kellert at ohsu.edu (Thomas J Keller) Date: Fri Sep 17 14:53:03 2004 Subject: [Bioperl-l] validation of primer3 for QRT-PCR Message-ID: Before putting all my eggs in one basket: Does anyone know of any studies validating the pcr primers and internal probe picks of primer3 for quantitative real-time PCR? regards, Tom Keller Thomas J. Keller, Ph.D. Director, MMI Core Facility Oregon Health & Science University 3181 SW Sam Jackson Park Rd. Portland, OR, USA, 97239 http://www.ohsu.edu/research/core -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 424 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040917/c2378ab5/attachment.bin From Marc.Logghe at devgen.com Fri Sep 17 15:14:01 2004 From: Marc.Logghe at devgen.com (Marc Logghe) Date: Fri Sep 17 15:14:49 2004 Subject: [Bioperl-l] passing paramteters to primer3 Message-ID: Hi Tom, >my $arg_string = join(", ", ( map { "$_ => \'$params{$_}\'" } keys %params)); > ># set max and min of Tm >$primer3->add_targets($arg_string); This does not work because you are actually passing 1 big string as an argument. The add_targets() methods takes a list. You should adapt your code to this: my @args = map { $_ => $params{$_}} keys %params; $primer3->add_targets(@args); HTH, Marc From kellert at ohsu.edu Fri Sep 17 15:29:54 2004 From: kellert at ohsu.edu (Thomas J Keller) Date: Fri Sep 17 15:30:15 2004 Subject: [Bioperl-l] passing paramteters to primer3 In-Reply-To: References: Message-ID: Thanks! Can I assume this is a general feature of bioperl methods (i.e., list input)? And passing references (I'd first tried passing \%params, which also didn't work) is not generally supported? Thanks again. Tom K. On Sep 17, 2004, at 12:14 PM, Marc Logghe wrote: > Hi Tom, > >> my $arg_string = join(", ", ( map { "$_ => \'$params{$_}\'" } keys >> %params)); >> > >> # set max and min of Tm >> $primer3->add_targets($arg_string); > > This does not work because you are actually passing 1 big string as an > argument. > The add_targets() methods takes a list. You should adapt your code to > this: > > my @args = map { $_ => $params{$_}} keys %params; > $primer3->add_targets(@args); > > HTH, > Marc > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From khufaz83 at yahoo.com Sat Sep 18 02:07:02 2004 From: khufaz83 at yahoo.com (hafiz hafiz) Date: Sat Sep 18 02:07:12 2004 Subject: [Bioperl-l] Bio:;Annotation::Reference; Message-ID: <20040918060702.90292.qmail@web52502.mail.yahoo.com> Hello , everybody can help me, i want to buid a new sequence in swissprot but i have some trouble with my reference. This is my souces code; #for feature my $feat = new Bio::SeqFeature::Generic(-start =>10,-end => 22, -strand =>1, -primary=>?DOMAIN?); #for seq, ID ,AC, alphabet. my $seq_obj =Bio::Seq ->new(-seq=>"attcccccchkhkhkh",-display_id=>"BIO52",-accession_number =>'X78121',-alphabet => 'dna',-is_circular => 1); ); $seq_obj->add_SeqFeature($feat); #for comment my $comment =Bio::Annotation::Comment->new; $comment->text("this looks like a good TATA box"); my $coll =new Bio::Annotation::Collection; $coll->add_Annotation('comment',$comment); $seq_obj->annotation($coll); #reference $reg = Bio::Annotation::Reference->new( -title => 'title line', -location => 'location line', -authors => 'author line', -medline => 998122 ); $seq_obj->annotation($reg); $file3="/home/database/Bioperl/test.gb"; my $io= Bio::SeqIO ->new(-format =>"swiss",-file => ">$file3"); $io ->write_seq($seq_obj); My output; ------------- EXCEPTION ------------- MSG: object of class Bio::Annotation::Reference does not implement Bio::AnnotationCollectionI. Too bad. STACK Bio::Seq::annotation /usr/lib/perl5/site_perl/5.8.0/Bio/Seq.pm:954 STACK main::update_database search10.pl:428 STACK toplevel search10.pl:46 -------------------------------------- ________________________________________________________________________ Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now http://uk.messenger.yahoo.com/download/index.html From hlapp at gmx.net Sat Sep 18 03:59:47 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat Sep 18 03:59:43 2004 Subject: [Bioperl-l] Bio:;Annotation::Reference; In-Reply-To: <20040918060702.90292.qmail@web52502.mail.yahoo.com> Message-ID: On Friday, September 17, 2004, at 11:07 PM, hafiz hafiz wrote: > > $seq_obj->annotation($reg); You're setting the annotation by this (which needs to be a collection, hence the error message). Instead, you want to add to the annotation: $seq_obj->annotation->add_Annotation('', $reg); Hth, -hilmar -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From cldwalker at chwhat.com Sat Sep 18 03:43:26 2004 From: cldwalker at chwhat.com (Gabriel Horner) Date: Sat Sep 18 04:45:38 2004 Subject: [Bioperl-l] shell ideas Message-ID: <20040918074326.GA25539@bigmama.chwhat.com> Hi all, I'm relatively new to the bioinformatics community. Being an avid perl programmer, I'm wondering what ways I could help contribute to this community. I looked around in the scripts/ and examples/ directories and noticed a script bioperl.pl which is a basic shell. Since I specialize in writing shells, I'm wondering what modules/functions would be most helpful in a shell environment. For starters I would think manipulating sequences,creating images and communicating with remote databases would be helpful to have in a shell. I would be basing this on a newer version of Fry::Shell. Thoughts? Thanks, Gabriel -- my looovely website -- http://www.chwhat.com BTW, IF chwhat.com goes down email me at gabriel.horner@cern.ch From khufaz83 at yahoo.com Sat Sep 18 06:03:39 2004 From: khufaz83 at yahoo.com (hafiz hafiz) Date: Sat Sep 18 06:03:33 2004 Subject: [Bioperl-l] Build new Seq in SwissProt Message-ID: <20040918100339.69828.qmail@web52506.mail.yahoo.com> hello, help me, which bioperl modul should we use to insert Date in swiss prot? example; ID GRAA_HUMAN STANDARD; PRT; 262 AA. AC P12544; this date i mean DT 01-OCT-1989 (Rel. 12, Created) DT 01-OCT-1989 (Rel. 12, Last sequence update) DT 28-FEB-2003 (Rel. 41, Last annotation update) my soure code; any suggestion my $feat = new Bio::SeqFeature::Generic(-start =>10,-end => 22, -strand =>1,-primary =>"DOMAIN"); #my @arr = $feat->get_all_tags; #for my $tag (@arr){ # print $tag,":",$feat->get_tag_values($tag)," "; #} my $seq_obj =Bio::Seq ->new(-seq=>"attcccccchkhkhkhaaaaaaaa",-display_id =>"BIO52",-accession_number => 'X78121',-alphabet => 'dna',-is_circular => 1); $seq_obj->add_SeqFeature($feat); my $comment =Bio::Annotation::Comment->new; $comment->text("this looks like a good TATA box"); my $coll =new Bio::Annotation::Collection; $coll->add_Annotation('comment',$comment); $seq_obj->annotation($coll); $species = Bio::Species->new(-classification => [@classification]); # Can also pass classification # array to new as below $species->classification(qw( sapiens Homo Hominidae Catarrhini Primates Eutheria Mammalia Vertebrata Chordata Metazoa Eukaryota )); $genus = $species->genus(); $bi = $species->binomial(); # $bi is now "Homo sapiens" # For storing common name $species->common_name("human"); # For storing subspecies $species->sub_species("accountant"); $seq_obj->species($species); my $reg = Bio::Annotation::Reference->new( -title =>"SwissProt Data", -location => "Gerik" , -authors =>"Muhammad hafiz Mohamed Yusof", -medline => "998122",-comment=>"sdasd",-position=>"sdsadd" ); $seq_obj->annotation->add_Annotation('reference', $reg); $link2 = new Bio::Annotation::DBLink(); $link2->database('dbSNP'); $link2->primary_id('2367'); # DBLink is-a Bio::AnnotationI object, can be added to annotation # collections, e.g. the one on features or seqs $seq_obj->annotation->add_Annotation('dblink', $link2); $file3="/home/database/Bioperl/test.gb"; my $io= Bio::SeqIO ->new(-format =>"swiss",-file => ">$file3"); $io ->write_seq($seq_obj); ________________________________________________________________________ Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now http://uk.messenger.yahoo.com/download/index.html From Marc.Logghe at devgen.com Sat Sep 18 07:53:37 2004 From: Marc.Logghe at devgen.com (Marc Logghe) Date: Sat Sep 18 07:53:53 2004 Subject: [Bioperl-l] Build new Seq in SwissProt Message-ID: Hi, The object you created is a Bio::Seq object. Such object can not deal with dates. You should create a Bio::Seq::RichSeq object instead. There the add_date() method is available.Or you can pass the dates directly to the new() method (-dates => [$date1,$date]) Have a look at the Bio::Seq::RichSeq docs. HTH, Marc > -----Original Message----- > From: hafiz hafiz [mailto:khufaz83@yahoo.com] > Sent: Saturday, September 18, 2004 12:04 PM > To: bioperl-l@portal.open-bio.org > Subject: [Bioperl-l] Build new Seq in SwissProt > > > > hello, help me, which bioperl modul should we use to > insert Date in swiss prot? > > example; > > ID GRAA_HUMAN STANDARD; PRT; 262 AA. > AC P12544; > > this date i mean > DT 01-OCT-1989 (Rel. 12, Created) > DT 01-OCT-1989 (Rel. 12, Last sequence update) > DT 28-FEB-2003 (Rel. 41, Last annotation update) > > my soure code; any suggestion > > my $feat = new Bio::SeqFeature::Generic(-start > =>10,-end => 22, -strand =>1,-primary =>"DOMAIN"); > > > > > #my @arr = $feat->get_all_tags; > #for my $tag (@arr){ > # print $tag,":",$feat->get_tag_values($tag)," > "; > #} > > > my $seq_obj =Bio::Seq > ->new(-seq=>"attcccccchkhkhkhaaaaaaaa",-display_id > =>"BIO52",-accession_number => > 'X78121',-alphabet => 'dna',-is_circular => 1); > > $seq_obj->add_SeqFeature($feat); > > > my $comment =Bio::Annotation::Comment->new; > $comment->text("this looks like a good TATA box"); > my $coll =new Bio::Annotation::Collection; > $coll->add_Annotation('comment',$comment); > $seq_obj->annotation($coll); > > $species = Bio::Species->new(-classification => > [@classification]); > # Can also pass classification > # array to new as below > $species->classification(qw( sapiens Homo Hominidae > Catarrhini Primates > Eutheria > Mammalia Vertebrata > Chordata > Metazoa Eukaryota )); > > $genus = $species->genus(); > > $bi = $species->binomial(); # $bi is now "Homo > sapiens" > > # For storing common name > $species->common_name("human"); > > # For storing subspecies > $species->sub_species("accountant"); > $seq_obj->species($species); > my $reg = Bio::Annotation::Reference->new( -title > =>"SwissProt Data", > -location > => "Gerik" , > -authors > =>"Muhammad hafiz Mohamed Yusof", > -medline > => "998122",-comment=>"sdasd",-position=>"sdsadd" ); > > > > $seq_obj->annotation->add_Annotation('reference', > $reg); > > > $link2 = new Bio::Annotation::DBLink(); > $link2->database('dbSNP'); > $link2->primary_id('2367'); > > # DBLink is-a Bio::AnnotationI object, can be added > to annotation > # collections, e.g. the one on features or seqs > $seq_obj->annotation->add_Annotation('dblink', > $link2); > > > > $file3="/home/database/Bioperl/test.gb"; > > my $io= Bio::SeqIO ->new(-format =>"swiss",-file => > ">$file3"); > > $io ->write_seq($seq_obj); > > > > ______________________________________________________________ > __________ > Yahoo! Messenger - Communicate instantly..."Ping" > your friends today! Download Messenger Now > http://uk.messenger.yahoo.com/download/index.html > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From tomas_marques at hotmail.com Sat Sep 18 03:59:46 2004 From: tomas_marques at hotmail.com (Tomas Marques) Date: Sun Sep 19 09:54:42 2004 Subject: [Bioperl-l] Refseq Ids Message-ID: How can I obtain all RefSeq IDs from Rat genome? (using BioPerl, of course...) I'm using Bio::DB::RefSeq but I have not been able to locate any method(inherit or not)to do it... Thanks. From jrs at farviolet.com Sun Sep 19 17:07:02 2004 From: jrs at farviolet.com (Jeremy Semeiks) Date: Sun Sep 19 17:07:00 2004 Subject: [Bioperl-l] Refseq Ids In-Reply-To: References: Message-ID: <20040919210702.GB15461@farviolet.farviolet.com> On Sat, Sep 18, 2004 at 09:59:46AM +0200, Tomas Marques wrote: > How can I obtain all RefSeq IDs from Rat genome? (using BioPerl, of > course...) > > > > I'm using Bio::DB::RefSeq but I have not been able to locate any > method(inherit or not)to do it... Hi Tomas, The most straightforward way to do this might be to download the rat Refseq files directly. They're at ftp://ftp.ncbi.nlm.nih.gov/refseq/R_norvegicus/ You should be able to use the Bioperl FASTA parser (part of the SeqIO module) to parse these. HTH, Jeremy From sdavis2 at mail.nih.gov Sun Sep 19 19:38:28 2004 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Sun Sep 19 19:38:25 2004 Subject: [Bioperl-l] Refseq Ids References: <20040919210702.GB15461@farviolet.farviolet.com> Message-ID: <000b01c49ea1$c711eae0$04653744@WATSON> I haven't checked rat directly, but I think they are also available at the same place as genbank flat files, in case you need that detail. ----- Original Message ----- From: "Jeremy Semeiks" To: "Tomas Marques" ; Sent: Sunday, September 19, 2004 5:07 PM Subject: Re: [Bioperl-l] Refseq Ids > On Sat, Sep 18, 2004 at 09:59:46AM +0200, Tomas Marques wrote: > > How can I obtain all RefSeq IDs from Rat genome? (using BioPerl, of > > course...) > > > > > > > > I'm using Bio::DB::RefSeq but I have not been able to locate any > > method(inherit or not)to do it... > > Hi Tomas, > > The most straightforward way to do this might be to download the rat > Refseq files directly. They're at > > ftp://ftp.ncbi.nlm.nih.gov/refseq/R_norvegicus/ > > You should be able to use the Bioperl FASTA parser (part of the SeqIO > module) to parse these. > > HTH, > Jeremy > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From jason at cgt.duhs.duke.edu Sun Sep 19 21:56:08 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Sun Sep 19 21:55:55 2004 Subject: [Bioperl-l] Re: bug report Bio::TreeIO::newick In-Reply-To: <8273f6c20409191853644f9eda@mail.gmail.com> References: <8273f6c20409191853644f9eda@mail.gmail.com> Message-ID: <3D9A3764-0AA8-11D9-BDE5-000393C44276@cgt.mc.duke.edu> Jacques - Have fixed the problem of single clade leaves ( the (e)f --> e,f problem). Will also see about getting the root label back. In the future it is best to submit bugs at http://bugzilla.open-bio.org We are slowly updating all the module documentation to this effect. -jason On Sep 19, 2004, at 9:53 PM, Jason Stajich wrote: > ---------- Forwarded message ---------- > From: Jacques van Helden > Date: Wed, 15 Sep 2004 00:59:11 +0200 (MET DST) > Subject: bug report Bio::TreeIO::newick > To: bioperl-bugs@bioperl.org, Jason Stajich > Cc: Jacques van Helden > > > Dear Bioperl developers, > > I started to use your librairy Bio::Tree::TreeIO::newick, which is > very useful for a lot of purposes, and I noticed a bug: when a branch > of a tree has a single leaf, the output is erroneous: the leaf node > appears as a brother of its parent. > > I put hereafter a sample input file, the resulting output, and a small > perl script to demonstrate the bug. The script simply reads a file in > newick format, and exports it in the same format. One would of course > expect to have the same tree, which is not the case. > > Could you please check if this bug could be fixed ? > > Best regards > > Jacques > > ================ Input file ================================== > File in.dnd : > > (((a,b)c)d,(e)f)r; > > ================ Output file ================================== > File out.dnd: > > (e,f,((a,b)c)d); > > Notice the difference at the level of nodes e and f: in the input, e > is a child of f, in the output, they are brothers. Please also note > that the name of the root (r) has disappeared. > > ======== The test script ====================================== > > #!/usr/bin/perl > > ################################################################ > ## A quick test for the Bio::TreeIO library > ## > ## Usage: test-tree.pl in.dnd out.dnd > > use Bio::TreeIO; > > my ($infile, $outfile) = @ARGV; > > unless ($infile) { > die "\tusage: test-tree.pl in.dnd out.dnd\n" > } > > ## read input > my $tree_input = new Bio::TreeIO(-format => "newick", > -file => $infile); > my $tree = $tree_input->next_tree(); > > ## Write output > my $tree_output = new Bio::TreeIO(-format => "newick", > -file => ">".$outfile); > $tree_output->write_tree($tree); > > warn "done\n"; > > > Jacques van Helden > http://www.ucmb.ulb.ac.be/~jvanheld/ > SCMB - Universite Libre de Bruxelles. Campus Plaine. > CP 263. Boulevard du Triomphe. 1050 Bruxelles - Belgium > Tel: +32 2 650 5466 / 650 2013 - Fax: +32 2 650 5425 -- Jason Stajich Duke University jason at cgt.mc.duke.edu From tomas_marques at hotmail.com Mon Sep 20 05:21:53 2004 From: tomas_marques at hotmail.com (Marques Bonet) Date: Mon Sep 20 07:31:11 2004 Subject: [Bioperl-l] Refseq Ids Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040920/43f444a4/attachment.htm From jason.stajich at duke.edu Mon Sep 20 07:36:16 2004 From: jason.stajich at duke.edu (Jason Stajich) Date: Mon Sep 20 07:36:34 2004 Subject: [Bioperl-l] Refseq Ids In-Reply-To: References: Message-ID: <48A891CB-0AF9-11D9-BD7F-000393C44276@duke.edu> On Sep 20, 2004, at 5:21 AM, Marques Bonet wrote: > Thanks for your suggestions, but it's quite strange that there isn't > any method to obtain a simple list of?all refSeq Id's of a genome. > > But, it is possible to obtain a complete list of all genes with > another nomenclature (Locus ID, Accession number, etc...)? Try EnsMart: http://www.ensembl.org > > Thanks. > >From: "Sean Davis" > >To: "Jeremy Semeiks" ,????????"Tomas Marques" > ,???????? > >Subject: Re: [Bioperl-l] Refseq Ids > >Date: Sun, 19 Sep 2004 19:38:28 -0400 > > > >I haven't checked rat directly, but I think they are also available > at the > >same place as genbank flat files, in case you need that detail. > > > > > >----- Original Message ----- > >From: "Jeremy Semeiks" > >To: "Tomas Marques" ; > > > >Sent: Sunday, September 19, 2004 5:07 PM > >Subject: Re: [Bioperl-l] Refseq Ids > > > > > > > On Sat, Sep 18, 2004 at 09:59:46AM +0200, Tomas Marques wrote: > > > > How can I obtain all RefSeq IDs from Rat genome? (using > BioPerl, of > > > > course...) > > > > > > > > > > > > > > > > I'm using Bio::DB::RefSeq but I have not been able to locate any > > > > method(inherit or not)to do it... > > > > > > Hi Tomas, > > > > > > The most straightforward way to do this might be to download the > rat > > > Refseq files directly. They're at > > > > > > ftp://ftp.ncbi.nlm.nih.gov/refseq/R_norvegicus/ > > > > > > You should be able to use the Bioperl FASTA parser (part of the > SeqIO > > > module) to parse these. > > > > > > HTH, > > > Jeremy > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l@portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > Descubre las ventajas de la Barra de Herramientas de MSN Desc?rgatela > gratis aqu? _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich jason.stajich at duke.edu http://www.duke.edu/~jes12/ From brian_osborne at cognia.com Mon Sep 20 09:21:55 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Mon Sep 20 09:26:48 2004 Subject: [Bioperl-l] Build new Seq in SwissProt In-Reply-To: <20040918100339.69828.qmail@web52506.mail.yahoo.com> Message-ID: Hafiz, The DT Annotation is made by constructing a Bio::Annotation::SimpleValue object. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of hafiz hafiz Sent: Saturday, September 18, 2004 6:04 AM To: bioperl-l@portal.open-bio.org Subject: [Bioperl-l] Build new Seq in SwissProt hello, help me, which bioperl modul should we use to insert Date in swiss prot? example; ID GRAA_HUMAN STANDARD; PRT; 262 AA. AC P12544; this date i mean DT 01-OCT-1989 (Rel. 12, Created) DT 01-OCT-1989 (Rel. 12, Last sequence update) DT 28-FEB-2003 (Rel. 41, Last annotation update) my soure code; any suggestion my $feat = new Bio::SeqFeature::Generic(-start =>10,-end => 22, -strand =>1,-primary =>"DOMAIN"); #my @arr = $feat->get_all_tags; #for my $tag (@arr){ # print $tag,":",$feat->get_tag_values($tag)," "; #} my $seq_obj =Bio::Seq ->new(-seq=>"attcccccchkhkhkhaaaaaaaa",-display_id =>"BIO52",-accession_number => 'X78121',-alphabet => 'dna',-is_circular => 1); $seq_obj->add_SeqFeature($feat); my $comment =Bio::Annotation::Comment->new; $comment->text("this looks like a good TATA box"); my $coll =new Bio::Annotation::Collection; $coll->add_Annotation('comment',$comment); $seq_obj->annotation($coll); $species = Bio::Species->new(-classification => [@classification]); # Can also pass classification # array to new as below $species->classification(qw( sapiens Homo Hominidae Catarrhini Primates Eutheria Mammalia Vertebrata Chordata Metazoa Eukaryota )); $genus = $species->genus(); $bi = $species->binomial(); # $bi is now "Homo sapiens" # For storing common name $species->common_name("human"); # For storing subspecies $species->sub_species("accountant"); $seq_obj->species($species); my $reg = Bio::Annotation::Reference->new( -title =>"SwissProt Data", -location => "Gerik" , -authors =>"Muhammad hafiz Mohamed Yusof", -medline => "998122",-comment=>"sdasd",-position=>"sdsadd" ); $seq_obj->annotation->add_Annotation('reference', $reg); $link2 = new Bio::Annotation::DBLink(); $link2->database('dbSNP'); $link2->primary_id('2367'); # DBLink is-a Bio::AnnotationI object, can be added to annotation # collections, e.g. the one on features or seqs $seq_obj->annotation->add_Annotation('dblink', $link2); $file3="/home/database/Bioperl/test.gb"; my $io= Bio::SeqIO ->new(-format =>"swiss",-file => ">$file3"); $io ->write_seq($seq_obj); ________________________________________________________________________ Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now http://uk.messenger.yahoo.com/download/index.html _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From szhan at uoguelph.ca Mon Sep 20 13:55:12 2004 From: szhan at uoguelph.ca (szhan@uoguelph.ca) Date: Mon Sep 20 13:54:59 2004 Subject: [Bioperl-l] how to install clustalw.pm and PAML/* (codeml.pm. yn00..) Message-ID: <1095702912.414f19808e36f@webmail.uoguelph.ca> Hello, Bioperl experts, Can you please tell me how to install clustalw.pm and PAML::* (such as codeml.pm yn00.pl on windows XP? I have run perl5.8 on windows XP and installed bioperl 1.4 using PPM. Now I'd like to do Multiple Sequence Alignment(MSA) and Phylogenetic Analysis using Maximum Likelihood (PAML) analyses from within Bioperl like: use Bio::Tools::Run::Phylo::PAML::Codeml; use Bio::Tools::Run::Alignment::Clustalw; Thank you in advance. Josh From barry.moore at genetics.utah.edu Mon Sep 20 09:52:09 2004 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Mon Sep 20 15:31:11 2004 Subject: [Bioperl-l] Refseq Ids In-Reply-To: References: Message-ID: <414EE089.9060606@genetics.utah.edu> If you just want the IDs, just grep ftp://ftp.ncbi.nih.gov/refseq/release/release-catalog/RefSeq-release7.catalog for the rat taxon id. Barry Marques Bonet wrote: > Thanks for your suggestions, but it's quite strange that there isn't > any method to obtain a simple list of all refSeq Id's of a genome. > > But, it is possible to obtain a complete list of all genes with > another nomenclature (Locus ID, Accession number, etc...)? > > Thanks. > > >From: "Sean Davis" >To: "Jeremy Semeiks" > , "Tomas Marques" > , > >Subject: Re: [Bioperl-l] Refseq Ids >Date: Sun, 19 Sep 2004 19:38:28 > -0400 > >I haven't checked rat directly, but I think they are also > available at the >same place as genbank flat files, in case you need > that detail. > > >----- Original Message ----- >From: "Jeremy Semeiks" > >To: "Tomas Marques" ; > > >Sent: Sunday, September 19, 2004 > 5:07 PM >Subject: Re: [Bioperl-l] Refseq Ids > > > > On Sat, Sep 18, > 2004 at 09:59:46AM +0200, Tomas Marques wrote: > > > How can I obtain > all RefSeq IDs from Rat genome? (using BioPerl, of > > > course...) > > > > > > > > > > > > > I'm using Bio::DB::RefSeq but I have not been > able to locate any > > > method(inherit or not)to do it... > > > > Hi > Tomas, > > > > The most straightforward way to do this might be to > download the rat > > Refseq files directly. They're at > > > > > ftp://ftp.ncbi.nlm.nih.gov/refseq/R_norvegicus/ > > > > You should be > able to use the Bioperl FASTA parser (part of the SeqIO > > module) to > parse these. > > > > HTH, > > Jeremy > > > _______________________________________________ > > Bioperl-l mailing > list > > Bioperl-l@portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > ------------------------------------------------------------------------ > Descubre las ventajas de la Barra de Herramientas de MSN Desc?rgatela > gratis aqu? > >------------------------------------------------------------------------ > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Barry Moore Dept. of Human Genetics University of Utah Salt Lake City, UT From kellert at ohsu.edu Mon Sep 20 13:58:41 2004 From: kellert at ohsu.edu (Thomas J Keller) Date: Mon Sep 20 15:31:39 2004 Subject: [Bioperl-l] Problem installing bioperl-ext Message-ID: Problem installing bioperl-ext Greetings, I can't seem to sort out this error. I was missing the os.h header file from the io_lib dir (long list below). But even after copying that over from io_lib-1.8.12, I still get an error both by hand and the CPAN shell: .. LD_RUN_PATH="" MACOSX_DEPLOYMENT_TARGET=10.3 cc -bundle -undefined dynamic_lookup -L/usr/local/lib Align.o -o ./blib/arch/auto/Bio/Ext/Align/Align.bundle libs/libsw.a -lm ld: archive: libs/libsw.a has no table of contents, add one with ranlib(1) (can't load from it) make[1]: *** [../blib/arch/auto/Bio/Ext/Align/Align.bundle] Error 1 make: *** [subdirs] Error 2 /usr/bin/make -- NOT OK Running make test Can't test without successful make Running make install make had returned bad status, install seems impossible Looks like I'm missing libsw.a Where would I get that? Thanks, Tom Keller Tom Keller, Ph.D. http://www.ohsu.edu/research/core kellert@ohsu.edu 503-494-2442 $ ll /usr/local/include/io_lib/ total 224 drwxr-xr-x 25 root staff 850B 20 Sep 10:24 . drwxr-xr-x 25 root staff 850B 12 Aug 12:10 .. -rw-r--r-- 1 root staff 6K 12 Aug 12:10 Read.h -rw-r--r-- 1 root staff 1K 12 Aug 12:10 abi.h -rw-r--r-- 1 root staff 1K 12 Aug 12:10 alf.h -rw-r--r-- 1 root staff 1K 12 Aug 12:10 array.h -rw-r--r-- 1 root staff 2K 12 Aug 12:10 compress.h -rw-r--r-- 1 root staff 6K 12 Aug 12:10 compression.h -rw-r--r-- 1 root staff 683B 12 Aug 12:10 error.h -rw-r--r-- 1 root staff 6K 12 Aug 12:10 expFileIO.h -rw-r--r-- 1 root staff 645B 12 Aug 12:10 fpoint.h -rw-r--r-- 1 root staff 2K 12 Aug 12:10 mach-io.h -rw-r--r-- 1 root staff 2K 12 Aug 12:10 misc.h -rw-r--r-- 1 root staff 1K 12 Aug 12:10 open_trace_file.h -rw-r--r-- 1 root staff 3K 20 Sep 10:24 os.h -rw-r--r-- 1 root staff 1K 12 Aug 12:10 plain.h -rw-r--r-- 1 root staff 10K 12 Aug 12:10 scf.h -rw-r--r-- 1 root staff 760B 12 Aug 12:10 scf_extras.h -rw-r--r-- 1 root staff 2K 12 Aug 12:10 seqIOABI.h -rw-r--r-- 1 root staff 152B 12 Aug 12:10 seqIOCTF.h -rw-r--r-- 1 root staff 1K 12 Aug 12:10 tar_format.h -rw-r--r-- 1 root staff 1K 12 Aug 12:10 traceType.h -rw-r--r-- 1 root staff 3K 12 Aug 12:10 translate.h -rw-r--r-- 1 root staff 781B 12 Aug 12:10 xalloc.h -rw-r--r-- 1 root staff 3K 12 Aug 12:10 ztr.h -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 2493 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040920/51ded0ad/attachment.bin From sbaird at mgcheo3.med.uottawa.ca Mon Sep 20 10:07:45 2004 From: sbaird at mgcheo3.med.uottawa.ca (Stephen Baird) Date: Mon Sep 20 15:31:56 2004 Subject: [Bioperl-l] Refseq Ids In-Reply-To: <48A891CB-0AF9-11D9-BD7F-000393C44276@duke.edu> Message-ID: Perhaps a Ensembl person could answer.... Is every REFSEQ ID for a genome mapped onto the genomic sequence in ENSEMBL. ...and is every REFSEQ ID for a genome mapped to an Ensembl gene? Stephen On Mon, 20 Sep 2004, Jason Stajich wrote: > > On Sep 20, 2004, at 5:21 AM, Marques Bonet wrote: > > > Thanks for your suggestions, but it's quite strange that there isn't > > any method to obtain a simple list of all refSeq Id's of a genome. > > > > But, it is possible to obtain a complete list of all genes with > > another nomenclature (Locus ID, Accession number, etc...)? > > Try EnsMart: http://www.ensembl.org > > > > > Thanks. > > >From: "Sean Davis" > > >To: "Jeremy Semeiks" ,        "Tomas Marques" > > ,         > > >Subject: Re: [Bioperl-l] Refseq Ids > > >Date: Sun, 19 Sep 2004 19:38:28 -0400 > > > > > >I haven't checked rat directly, but I think they are also available > > at the > > >same place as genbank flat files, in case you need that detail. > > > > > > > > >----- Original Message ----- > > >From: "Jeremy Semeiks" > > >To: "Tomas Marques" ; > > > > > >Sent: Sunday, September 19, 2004 5:07 PM > > >Subject: Re: [Bioperl-l] Refseq Ids > > > > > > > > > > On Sat, Sep 18, 2004 at 09:59:46AM +0200, Tomas Marques wrote: > > > > > How can I obtain all RefSeq IDs from Rat genome? (using > > BioPerl, of > > > > > course...) > > > > > > > > > > > > > > > > > > > > I'm using Bio::DB::RefSeq but I have not been able to locate any > > > > > method(inherit or not)to do it... > > > > > > > > Hi Tomas, > > > > > > > > The most straightforward way to do this might be to download the > > rat > > > > Refseq files directly. They're at > > > > > > > > ftp://ftp.ncbi.nlm.nih.gov/refseq/R_norvegicus/ > > > > > > > > You should be able to use the Bioperl FASTA parser (part of the > > SeqIO > > > > module) to parse these. > > > > > > > > HTH, > > > > Jeremy > > > > _______________________________________________ > > > > Bioperl-l mailing list > > > > Bioperl-l@portal.open-bio.org > > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > > > > > Descubre las ventajas de la Barra de Herramientas de MSN Descárgatela > > gratis aquí _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- > Jason Stajich > jason.stajich at duke.edu > http://www.duke.edu/~jes12/ > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From jason.stajich at duke.edu Mon Sep 20 15:45:30 2004 From: jason.stajich at duke.edu (Jason Stajich) Date: Mon Sep 20 15:48:06 2004 Subject: [Bioperl-l] Problem installing bioperl-ext In-Reply-To: References: Message-ID: Be warned that the bioperl-ext that is on CPAN is not as up-to-date with all the alignment stuff that is in the CVS version. libsw.a is being built as part of this package. You need to run ranlib as the error message is saying. Try: ranlib Bio/Ext/Align/libs/libsw.a -jason On Sep 20, 2004, at 1:58 PM, Thomas J Keller wrote: > Problem installing bioperl-ext > > Greetings, > I can't seem to sort out this error. I was missing the os.h header > file from the io_lib dir (long list below). But even after copying > that over from io_lib-1.8.12, I still get an error both by hand and > the CPAN shell: > .. > LD_RUN_PATH="" MACOSX_DEPLOYMENT_TARGET=10.3 cc -bundle -undefined > dynamic_lookup -L/usr/local/lib Align.o -o > ./blib/arch/auto/Bio/Ext/Align/Align.bundle libs/libsw.a -lm > ld: archive: libs/libsw.a has no table of contents, add one with > ranlib(1) (can't load from it) > make[1]: *** [../blib/arch/auto/Bio/Ext/Align/Align.bundle] Error 1 > make: *** [subdirs] Error 2 > /usr/bin/make -- NOT OK > Running make test > Can't test without successful make > Running make install > make had returned bad status, install seems impossible > > Looks like I'm missing libsw.a > Where would I get that? > > Thanks, > Tom Keller > > Tom Keller, Ph.D. > http://www.ohsu.edu/research/core > kellert@ohsu.edu > 503-494-2442 > > $ ll /usr/local/include/io_lib/ > total 224 > drwxr-xr-x 25 root staff 850B 20 Sep 10:24 . > drwxr-xr-x 25 root staff 850B 12 Aug 12:10 .. > -rw-r--r-- 1 root staff 6K 12 Aug 12:10 Read.h > -rw-r--r-- 1 root staff 1K 12 Aug 12:10 abi.h > -rw-r--r-- 1 root staff 1K 12 Aug 12:10 alf.h > -rw-r--r-- 1 root staff 1K 12 Aug 12:10 array.h > -rw-r--r-- 1 root staff 2K 12 Aug 12:10 compress.h > -rw-r--r-- 1 root staff 6K 12 Aug 12:10 compression.h > -rw-r--r-- 1 root staff 683B 12 Aug 12:10 error.h > -rw-r--r-- 1 root staff 6K 12 Aug 12:10 expFileIO.h > -rw-r--r-- 1 root staff 645B 12 Aug 12:10 fpoint.h > -rw-r--r-- 1 root staff 2K 12 Aug 12:10 mach-io.h > -rw-r--r-- 1 root staff 2K 12 Aug 12:10 misc.h > -rw-r--r-- 1 root staff 1K 12 Aug 12:10 open_trace_file.h > -rw-r--r-- 1 root staff 3K 20 Sep 10:24 os.h > -rw-r--r-- 1 root staff 1K 12 Aug 12:10 plain.h > -rw-r--r-- 1 root staff 10K 12 Aug 12:10 scf.h > -rw-r--r-- 1 root staff 760B 12 Aug 12:10 scf_extras.h > -rw-r--r-- 1 root staff 2K 12 Aug 12:10 seqIOABI.h > -rw-r--r-- 1 root staff 152B 12 Aug 12:10 seqIOCTF.h > -rw-r--r-- 1 root staff 1K 12 Aug 12:10 tar_format.h > -rw-r--r-- 1 root staff 1K 12 Aug 12:10 traceType.h > -rw-r--r-- 1 root staff 3K 12 Aug 12:10 translate.h > -rw-r--r-- 1 root staff 781B 12 Aug 12:10 xalloc.h > -rw-r--r-- 1 root staff 3K 12 Aug 12:10 ztr.h > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich jason.stajich at duke.edu http://www.duke.edu/~jes12/ -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 3086 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040920/e29effb5/attachment.bin From kellert at ohsu.edu Mon Sep 20 20:29:34 2004 From: kellert at ohsu.edu (Thomas J Keller) Date: Mon Sep 20 20:29:48 2004 Subject: [Bioperl-l] torturing newbies are we? SeqIO HowTo question Message-ID: <50153938-0B65-11D9-8EAD-0003930405E2@ohsu.edu> Greetings, in the Bio::SeqIO HOWTO examples: the first example (getaccs) while (my $seq = $inseq->next_seq) { print $seq->accession_no, "\n"; ###<- wrong method name } should read: while (my $seq = $inseq->next_seq) { print $seq->accession_number, "\n"; } Also, in a later example from this HOWTO (in2out.pl) there's a typo: while (my $inseq = $seqin->next_seq) { $outseq->write_seq($inseq); ### should be $seqout->write_seq($inseq); } But what I really want to know is why, when I run this example (in2out.pl), while it gives the correctly formatted output, it gives the warnings: Argument "*main::STDOUT" isn't numeric in numeric eq (==) at /Library/Perl/5.8.1/Bio/Root/IO.pm line 483. .. repeated 6 times for a single genbank input file. I may be slow, but I catch on eventually, you meanies ;-) I hope it's clear that while the typos are real, I'm kidding about the torture. I really appreciate the help I've gotten from the gurus who monitor this list. Thanks, Tom Keller From szhan at uoguelph.ca Mon Sep 20 21:26:57 2004 From: szhan at uoguelph.ca (szhan@uoguelph.ca) Date: Mon Sep 20 21:26:43 2004 Subject: [Bioperl-l] Missing base argument at C:/Perl/site/lib/PPM/Repository.pm ? Message-ID: <1095730017.414f8361162f1@webmail.uoguelph.ca> Hello, Why I can not install bioperl-1.4 successfully using PPM on windows XP? I am using activeState for perl 5.8.0. At first I can issue ppm> search bioperl and receive 28 different bioperl versions and then issue ppm> install 25 but after installing some packages and I got a message said some module can not be found in PPM and ppm stoped. I wonder if I install it successfully. I tried it again: ppm> repository add bioperl http://bioperl.org/DIST Repositories: [ 1] ActiveState PPM2 Repository [ 2] ActiveState Package Repository [ 3] bioperl [ 4] bioperl [ 5] bioperl [ 6] bioperl [ 7] bioperl [ 8] bioperl [ 9] Kobes [10] bioperl [11] bioperl [12] bioperl ppm> search bioperl Searching in Active Repositories Missing base argument at C:/Perl/site/lib/PPM/Repository.pm line 174 Why this time I can not search bioperl? I checked the directory: C:/Perl/site/lib/PPM/Repository in PC and found there are 4 modules which are: Local.pm, PPMServer.pm, PPM3Server.pm and WWW.pm. So what "Missing base argument at C:/Perl/site/lib/PPM/Repository.pm line 174" means? Josh From diriano at rz.uni-potsdam.de Tue Sep 21 06:36:02 2004 From: diriano at rz.uni-potsdam.de (Diego Riano) Date: Tue Sep 21 06:39:33 2004 Subject: [Bioperl-l] problem parsing MEME file Message-ID: <1095762962.3637.6.camel@molbio21.bio.uni-potsdam.de> Hi all I have written a small script to parse MEME results, but I am getting and error. I am using Bioperl 1.4 and MEME 3.0.10, it should work but if does not. could anyone help me? Here is the script: #!/usr/bin/perl use strict; use warnings; use Bio::AlignIO; my $inputf = "$ARGV[0]"; my $in = Bio::AlignIO->new(-file => $inputf, -format => 'meme'); while ( my $aln = $in->next_aln() ) { print "X\n"; } This is the error i got: -------------------- WARNING --------------------- MSG: Unrecognized format: 6_04024 163 5.87e-128 DYSCGGDDSG TEEEQAAFMKELERFYREKLMEFKPPKFYGEGLNCLKLWRQVTGLGGYDQVTSCKLWRQVGESFKPPKTCTTVSWTFRNFYEKALLEYEKHKIETGEFQV AASNLTERIT --------------------------------------------------- thanks Diego Riano -- _____________________________________ Diego Mauricio Riano Pachon Biologist Institute of Biology and Biochemistry Potsdam University Karl-Liebknecht-Str. 24-25 Haus 20 14476 Golm Germany Tel:0331/977-2809 http://bioinf.ibun.unal.edu.co/~gotem http://www.geocities.com/dmrp.geo/ From skirov at utk.edu Tue Sep 21 07:08:06 2004 From: skirov at utk.edu (Stefan Kirov) Date: Tue Sep 21 07:08:06 2004 Subject: [Bioperl-l] problem parsing MEME file In-Reply-To: <1095762962.3637.6.camel@molbio21.bio.uni-potsdam.de> References: <1095762962.3637.6.camel@molbio21.bio.uni-potsdam.de> Message-ID: <41500B96.4050104@utk.edu> I had a similar problem in the past and never got an answer from the guy who wrote the parser. There is also Bio::Matrix::PSM::IO::meme, but it works only on DNA. James Thompson has offered to write a psi-blast parser and will create objects that will also be useful for a protein meme parser. Then it will be easy to add this functionality to Bio::Matrix::PSM::IO::meme. Stefan Diego Riano wrote: >Hi all > >I have written a small script to parse MEME results, but I am getting >and error. I am using Bioperl 1.4 and MEME 3.0.10, it should work but >if does not. could anyone help me? > >Here is the script: > >#!/usr/bin/perl > >use strict; >use warnings; > >use Bio::AlignIO; > >my $inputf = "$ARGV[0]"; >my $in = Bio::AlignIO->new(-file => $inputf, > -format => 'meme'); > > >while ( my $aln = $in->next_aln() ) { > print "X\n"; > } > >This is the error i got: > >-------------------- WARNING --------------------- >MSG: Unrecognized format: >6_04024 163 5.87e-128 DYSCGGDDSG >TEEEQAAFMKELERFYREKLMEFKPPKFYGEGLNCLKLWRQVTGLGGYDQVTSCKLWRQVGESFKPPKTCTTVSWTFRNFYEKALLEYEKHKIETGEFQV AASNLTERIT > >--------------------------------------------------- > >thanks > >Diego Riano > > From pvh at egenetics.com Tue Sep 21 09:23:34 2004 From: pvh at egenetics.com (Peter van Heusden) Date: Tue Sep 21 09:23:36 2004 Subject: [Bioperl-l] Writing embl entry to string In-Reply-To: <76F96CFE2AA2114C886B028A065A7FC40166081D@exdkba020.novo.dk> References: <76F96CFE2AA2114C886B028A065A7FC40166081D@exdkba020.novo.dk> Message-ID: <41502B56.8010302@egenetics.com> TAPO (Thomas Agersten Poulsen) wrote: >Dear List, > > I am writing a small script to split embl-files into smaller file of a given maximum file size. > >To this end, I would like to get the output from Bio::SeqIO->write_seq into a string (so I can evaluate length() on it). Would anybody out there know if this is posible???? > > > There's an example describing how to do this in the SeqIO howto at http://bioperl.org/HOWTOs/SeqIO/string.html: use IO::String; use Bio::SeqIO; my $str; my $io = IO::String->new(\$str); my $seqOut = Bio::SeqIO->new(-format => 'swiss', -fh => $io ); $seqOut->write_seq($seq_obj); print $str; Peter From Bernhard.Schmalhofer at biomax.de Tue Sep 21 09:45:36 2004 From: Bernhard.Schmalhofer at biomax.de (Bernhard Schmalhofer) Date: Tue Sep 21 09:45:32 2004 Subject: [Bioperl-l] Writing embl entry to string In-Reply-To: <41502B56.8010302@egenetics.com> References: <76F96CFE2AA2114C886B028A065A7FC40166081D@exdkba020.novo.dk> <41502B56.8010302@egenetics.com> Message-ID: <41503080.70503@biomax.de> Peter van Heusden wrote: > TAPO (Thomas Agersten Poulsen) wrote: > >> Dear List, >> >> I am writing a small script to split embl-files into smaller file >> of a given maximum file size. >> To this end, I would like to get the output from Bio::SeqIO->write_seq >> into a string (so I can evaluate length() on it). Would anybody out >> there know if this is posible???? >> >> >> > There's an example describing how to do this in the SeqIO howto at > http://bioperl.org/HOWTOs/SeqIO/string.html: > > use IO::String; > use Bio::SeqIO; > my $str; > my $io = IO::String->new(\$str); > my $seqOut = Bio::SeqIO->new(-format => 'swiss', > -fh => $io ); > $seqOut->write_seq($seq_obj); > print $str; > As of Perl 5.6.0 following is also possible, and maybe nicer: use Bio::SeqIO; my $str; open( my $str_fh, '>', \$str ); my $seq_out = Bio::SeqIO->new( -format => 'swiss', -fh => $str_fh ); $seq_out->write_seq( $seq_obj ); print $str; CU, Bernhard -- ************************************************** Dipl.-Physiker Bernhard Schmalhofer Senior Developer Biomax Informatics AG Lochhamer Str. 11 82152 Martinsried, Germany Tel: +49 89 895574-839 Fax: +49 89 895574-825 eMail: Bernhard.Schmalhofer@biomax.com Website: www.biomax.com ************************************************** From jason.stajich at duke.edu Tue Sep 21 11:04:16 2004 From: jason.stajich at duke.edu (Jason Stajich) Date: Tue Sep 21 11:04:00 2004 Subject: [Bioperl-l] torturing newbies are we? SeqIO HowTo question In-Reply-To: <50153938-0B65-11D9-8EAD-0003930405E2@ohsu.edu> References: <50153938-0B65-11D9-8EAD-0003930405E2@ohsu.edu> Message-ID: <81774FFC-0BDF-11D9-97EE-000393C44276@duke.edu> Hmm - Where are you getting the HOWTO from? The website versions of them don't seem to have these bugs. What version of bioperl? I don't get that error for bioperl 1.4 branch CVS code or main trunk CVS code but haven't tried it with the 1.4 release that is on CPAN. You said you are using genbank as input format, but what output format? It may be that you should be passing in the STDOUT like this -fh => \*STDOUT not -fh =>*STDOUT Although I don't think it make much of a difference. But this is all guessing since I can't really make it happen on my machine right now. -j On Sep 20, 2004, at 8:29 PM, Thomas J Keller wrote: > Greetings, > > in the Bio::SeqIO HOWTO examples: > > the first example (getaccs) > while (my $seq = $inseq->next_seq) { > print $seq->accession_no, "\n"; ###<- wrong method name > } > > should read: > while (my $seq = $inseq->next_seq) { > print $seq->accession_number, "\n"; > } > > Also, > in a later example from this HOWTO (in2out.pl) there's a typo: > while (my $inseq = $seqin->next_seq) { > $outseq->write_seq($inseq); ### should be > $seqout->write_seq($inseq); > } > > But what I really want to know is why, when I run this example > (in2out.pl), while it gives the correctly formatted output, it gives > the warnings: > Argument "*main::STDOUT" isn't numeric in numeric eq (==) at > /Library/Perl/5.8.1/Bio/Root/IO.pm line 483. > .. repeated 6 times for a single genbank input file. > I may be slow, but I catch on eventually, you meanies ;-) > > I hope it's clear that while the typos are real, I'm kidding about the > torture. I really appreciate the help I've gotten from the gurus who > monitor this list. > > Thanks, > Tom Keller > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Jason Stajich jason.stajich at duke.edu http://www.duke.edu/~jes12/ From jason.stajich at duke.edu Tue Sep 21 11:05:27 2004 From: jason.stajich at duke.edu (Jason Stajich) Date: Tue Sep 21 11:05:13 2004 Subject: [Bioperl-l] shell ideas In-Reply-To: <20040918074326.GA25539@bigmama.chwhat.com> References: <20040918074326.GA25539@bigmama.chwhat.com> Message-ID: I guess some of the functions in Bio::Perl as examples of starters. -jason On Sep 18, 2004, at 3:43 AM, Gabriel Horner wrote: > Hi all, > I'm relatively new to the bioinformatics community. Being an avid > perl programmer, I'm wondering what ways I could help contribute to > this community. I looked around in the scripts/ and examples/ > directories and > noticed a script bioperl.pl which is a basic shell. Since I specialize > in writing shells, I'm > wondering what modules/functions would be most helpful in a shell > environment. > For starters I would think manipulating sequences,creating images and > communicating with remote > databases would be helpful to have in a shell. > I would be basing this on a newer version of Fry::Shell. > Thoughts? > > Thanks, > Gabriel > -- > my looovely website -- http://www.chwhat.com > BTW, IF chwhat.com goes down email me at gabriel.horner@cern.ch > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Jason Stajich jason.stajich at duke.edu http://www.duke.edu/~jes12/ From jason.stajich at duke.edu Tue Sep 21 11:34:28 2004 From: jason.stajich at duke.edu (Jason Stajich) Date: Tue Sep 21 11:34:13 2004 Subject: [Bioperl-l] Re: how to install clustalw.pm and PAML::* (such as codeml.pm, baseml and yn00.pl on windows XP In-Reply-To: <1095780401.415048311c60a@webmail.uoguelph.ca> References: <1095780401.415048311c60a@webmail.uoguelph.ca> Message-ID: Basically get bioperl-run from http://bioperl.org/DIST. Install this like you would any other perl module. I'm not sure how to do it with PPM since no one has made a bioperl-run PPM - you'd have to roll your own PPM which isn't that hard. Perhaps other ActiveState perl users could help out. -jason On Sep 21, 2004, at 11:26 AM, szhan@uoguelph.ca wrote: > Hello, Jason, > Can you please tell me how to install clustalw.pm and PAML::* (such as > codeml.pm, baseml and yn00.pl) on windows XP? > I have run perl-5.8 on windows XP and installed bioperl 1.4 using > active state > PPM. Now I'd like to do Multiple Sequence Alignment(MSA) and > Phylogenetic > Analysis using Maximum Likelihood (PAML) analyses from within Bioperl > as you > showed in Bio::Tools::Phylo::PAML HOWTO of Bioperl: > use Bio::Tools::Run::Phylo::PAML::Codeml; > use Bio::Tools::Run::Alignment::Clustalw; > Thank you in advance. > Josh > > -- Jason Stajich jason.stajich at duke.edu http://www.duke.edu/~jes12/ From szhan at uoguelph.ca Tue Sep 21 12:46:29 2004 From: szhan at uoguelph.ca (szhan@uoguelph.ca) Date: Tue Sep 21 12:46:15 2004 Subject: [Bioperl-l] how to install bioperl-run on window XP? Message-ID: <1095785189.41505ae52df62@webmail.uoguelph.ca> Hello, Has anybody installed bioperl-run on Window XP using activeState PPM? Would you please share me with your experience? I want to use modules in this package to some analysis. I find this package in the site: http://www.bioperl.org/Pdoc-mirror/bioperl-run/all_packages.html I added this site as repository in PPM but I could not install some module by issuing: ppm> install Bio::Tools::Run::Alignment::Clustalw given message: Searching for 'Bio::Tools::Run::Alignment::Clustalw' returned no results. Try a broader search first. It seems that this site can not be downloaded as a repository. Thank you in advance. Josh From tapo at novozymes.com Wed Sep 22 03:12:03 2004 From: tapo at novozymes.com (TAPO (Thomas Agersten Poulsen)) Date: Wed Sep 22 03:12:05 2004 Subject: [Bioperl-l] Writing embl entry to string Message-ID: <76F96CFE2AA2114C886B028A065A7FC402074F10@exdkba020.novo.dk> Dear Bernhard and Peter, Thank you for the help. I did the IO::String and it works, but the other solution looks better :-) Unfortunately I couldn't use in large scale, as it turned out to be too slow and too many entries were skipped because they did not conform to the format somehow, so I ended up writing a very simple splitter from scratch. Sincerely Thomas -----Original Message----- From: Bernhard Schmalhofer [mailto:Bernhard.Schmalhofer@biomax.de] Sent: 21. september 2004 15:46 To: Peter van Heusden Cc: TAPO (Thomas Agersten Poulsen); bioperl-l@bioperl.org Subject: Re: [Bioperl-l] Writing embl entry to string Peter van Heusden wrote: > TAPO (Thomas Agersten Poulsen) wrote: > >> Dear List, >> >> I am writing a small script to split embl-files into smaller file >> of a given maximum file size. >> To this end, I would like to get the output from Bio::SeqIO->write_seq >> into a string (so I can evaluate length() on it). Would anybody out >> there know if this is posible???? >> >> >> > There's an example describing how to do this in the SeqIO howto at > http://bioperl.org/HOWTOs/SeqIO/string.html: > > use IO::String; > use Bio::SeqIO; > my $str; > my $io = IO::String->new(\$str); > my $seqOut = Bio::SeqIO->new(-format => 'swiss', > -fh => $io ); > $seqOut->write_seq($seq_obj); > print $str; > As of Perl 5.6.0 following is also possible, and maybe nicer: use Bio::SeqIO; my $str; open( my $str_fh, '>', \$str ); my $seq_out = Bio::SeqIO->new( -format => 'swiss', -fh => $str_fh ); $seq_out->write_seq( $seq_obj ); print $str; CU, Bernhard -- ************************************************** Dipl.-Physiker Bernhard Schmalhofer Senior Developer Biomax Informatics AG Lochhamer Str. 11 82152 Martinsried, Germany Tel: +49 89 895574-839 Fax: +49 89 895574-825 eMail: Bernhard.Schmalhofer@biomax.com Website: www.biomax.com ************************************************** From jesus.sanchez01 at campus.upf.es Wed Sep 22 16:38:28 2004 From: jesus.sanchez01 at campus.upf.es (jesus sanchez ruiz) Date: Wed Sep 22 10:38:12 2004 Subject: [Bioperl-l] Has anybody got the clustalw.pm for Windows? Message-ID: <1095863908.12952@mail.infomail.es> I'm looking for it, the clustaw.pm works only on Unix platforms and I would like to use it on Windows... Could somebody send it to me? Thanks a lot ________________________________________________________________________________________ Este mensaje ha sido analizado y protegido por la tecnologia antivirus www.trendmicro.es From jesus.sanchez01 at campus.upf.es Wed Sep 22 16:42:18 2004 From: jesus.sanchez01 at campus.upf.es (jesus sanchez ruiz) Date: Wed Sep 22 10:42:01 2004 Subject: [Bioperl-l] How can I get all the info of a Database object? Message-ID: <1095864138.13737@mail.infomail.es> I'm quite new at Bioperl, and I don't even know if it would be even possible, but I want to have acces to all the information of a database object, without necessarily knowing what's exactly in it. Somebody could give me a clue? Thank you. ________________________________________________________________________________________ Este mensaje ha sido analizado y protegido por la tecnologia antivirus www.trendmicro.es From george.magklaras at biotek.uio.no Wed Sep 22 11:52:47 2004 From: george.magklaras at biotek.uio.no (George Magklaras) Date: Wed Sep 22 11:52:38 2004 Subject: [Bioperl-l] Nexus tree format and nexus.pm version 1.8 Message-ID: <41519FCF.3090102@biotek.uio.no> Hi, ===The Question=== With regards to Bio::TreeIO, are there still issues with writing nexus format trees by means of calling write_tree on BioPerl 1.4? Or in the case below, what am I doing wrong? ==THE background:== A small script that tries to convert newick to nexus format goes: ######### use Bio::TreeIO; ($NEWICKFILE, $NEXUSFILE) = @ARGV; print "newickfile=$NEWICKFILE, nexusfile=$NEXUSFILE\n"; my $treeio = new Bio::TreeIO(-format => 'newick', -file => "$NEWICKFILE"); my $treeout = new Bio::TreeIO(-format => 'nexus', -file => ">$NEXUSFILE"); while(my $tree = $treeio->next_tree) { $treeout->write_tree($treeout); } exit 0; ##### Initially, running this script with the nexus.pm module that comes with the default BioPerl 1.4 (version 1.2) produces the exception ------------- EXCEPTION ------------- MSG: Cannot call method write_tree on Bio::TreeIO object must use a subclass That prompted me to upgrade to version 1.8 of the nexus.pm , according to Jason's suggestions to Csaba Ortutay on the 3rd of August 2004. Re-running the script with the latest module produces a different exception: Can't locate object method "get_nodes" via package "Bio::TreeIO::nexus" at /usr/lib/perl5/site_perl/5.8.0/Bio/TreeIO/nexus.pm line 212, line 1. My PERL details: Summary of my perl5 (revision 5.0 version 8 subversion 0) configuration: Platform: osname=linux, osvers=2.4.20-8smp, archname=i386-linux uname='linux storeslem.uio.no 2.4.20-8smp #1 smp thu mar 13 17:45:54 est 2003 i686 unknown unknown gnulinux ' config_args='-Darchname='i386-linux' -Dperladmin=unix-drift@usit.uio.no -Dcc=cc-wrapper -Dlocincpth=/local/include -Dloclibpth=/local/lib -Uinstallusrbinperl -Dprefix=/local -Dsiteprefix=/local -Dinstallprefix=/local -Darchlib=/local/lib/perl5/5.8.0 -Dprivlib=/local/share/perl5/5.8.0 -Dsitearch=/local/lib/perl5/site_perl/5.8.0 -Dsitelib=/local/share/perl5/site_perl/5.8.0 -Dotherlibdirs=/site/lib/perl5/site_perl/5.8.0:/site/share/perl5/site_perl/5.8.0:/site/lib/perl5/site_perl -Dman1dir=/local/share/man/man1 -Dman3dir=/local/share/man/man3 -de' hint=recommended, useposix=true, d_sigaction=define usethreads=undef use5005threads=undef useithreads=undef usemultiplicity=undef useperlio=define d_sfio=undef uselargefiles=define usesocks=undef use64bitint=undef use64bitall=undef uselongdouble=undef usemymalloc=n, bincompat5005=undef Compiler: cc='cc-wrapper', ccflags ='-fno-strict-aliasing -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm', optimize='-O3', cppflags='-fno-strict-aliasing -I/usr/include/gdbm' ccversion='', gccversion='3.2.2 20030222 (Red Hat Linux 3.2.2-5)', gccosandvers='' intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=1234 d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=12 ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8 alignbytes=4, prototype=define Linker and Libraries: ld='cc-wrapper', ldflags =' -L/local/lib' libpth=/local/lib /lib /usr/lib /usr/local/lib libs=-lnsl -lgdbm -ldb -ldl -lm -lc -lcrypt -lutil perllibs=-lnsl -ldl -lm -lc -lcrypt -lutil libc=/lib/libc-2.3.2.so, so=so, useshrplib=false, libperl=libperl.a gnulibc_version='2.3.2' Dynamic Linking: dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-rdynamic' cccdlflags='-fpic', lddlflags='-shared -L/local/lib' Thanks. -- -- George From jason.stajich at duke.edu Wed Sep 22 13:11:10 2004 From: jason.stajich at duke.edu (Jason Stajich) Date: Wed Sep 22 13:10:58 2004 Subject: [Bioperl-l] Nexus tree format and nexus.pm version 1.8 In-Reply-To: <41519FCF.3090102@biotek.uio.no> References: <41519FCF.3090102@biotek.uio.no> Message-ID: <668FD5FA-0CBA-11D9-AFEE-000393C44276@duke.edu> Well you are almost there, but you are calling it wrong. The error message gives a hint. > Can't locate object method "get_nodes" via package > "Bio::TreeIO::nexus" at > /usr/lib/perl5/site_perl/5.8.0/Bio/TreeIO/nexus.pm line 212, > line 1. Now look at your code > my $treeout = new Bio::TreeIO(-format => 'nexus', -file => > ">$NEXUSFILE"); > > while(my $tree = $treeio->next_tree) { > > $treeout->write_tree($treeout); > > } What type of object are you passing to $treeout->write_tree method. Look like $treeout which is Bio::TreeIO::nexus object. Should be $tree instead as you want a Bio::Tree::Tree object passed in. So the fixed code should be: while( my $tree = $treeio->next_tree ) { $treeout->write_tree($tree); } -jason On Sep 22, 2004, at 11:52 AM, George Magklaras wrote: > Hi, > > ===The Question=== > With regards to Bio::TreeIO, are there still issues with writing nexus > format trees by means of calling write_tree on BioPerl 1.4? Or in the > case below, what am I doing wrong? > > ==THE background:== > > A small script that tries to convert newick to nexus format goes: > ######### > use Bio::TreeIO; > > ($NEWICKFILE, $NEXUSFILE) = @ARGV; > print "newickfile=$NEWICKFILE, nexusfile=$NEXUSFILE\n"; > > my $treeio = new Bio::TreeIO(-format => 'newick', -file => > "$NEWICKFILE"); > > my $treeout = new Bio::TreeIO(-format => 'nexus', -file => > ">$NEXUSFILE"); > > while(my $tree = $treeio->next_tree) { > > $treeout->write_tree($treeout); > > } > > exit 0; > > > ##### > > Initially, running this script with the nexus.pm module that comes > with the default BioPerl 1.4 (version 1.2) produces the exception > > ------------- EXCEPTION ------------- > MSG: Cannot call method write_tree on Bio::TreeIO object must use a > subclass > > That prompted me to upgrade to version 1.8 of the nexus.pm , according > to Jason's suggestions to Csaba Ortutay on the 3rd of August 2004. > Re-running the script with the latest module produces a different > exception: > > Can't locate object method "get_nodes" via package > "Bio::TreeIO::nexus" at > /usr/lib/perl5/site_perl/5.8.0/Bio/TreeIO/nexus.pm line 212, > line 1. > > My PERL details: > > Summary of my perl5 (revision 5.0 version 8 subversion 0) > configuration: > Platform: > osname=linux, osvers=2.4.20-8smp, archname=i386-linux > uname='linux storeslem.uio.no 2.4.20-8smp #1 smp thu mar 13 > 17:45:54 est 2003 i686 unknown unknown gnulinux ' > config_args='-Darchname='i386-linux' > -Dperladmin=unix-drift@usit.uio.no -Dcc=cc-wrapper > -Dlocincpth=/local/include -Dloclibpth=/local/lib -Uinstallusrbinperl > -Dprefix=/local -Dsiteprefix=/local -Dinstallprefix=/local > -Darchlib=/local/lib/perl5/5.8.0 -Dprivlib=/local/share/perl5/5.8.0 > -Dsitearch=/local/lib/perl5/site_perl/5.8.0 > -Dsitelib=/local/share/perl5/site_perl/5.8.0 > -Dotherlibdirs=/site/lib/perl5/site_perl/5.8.0:/site/share/perl5/ > site_perl/5.8.0:/site/lib/perl5/site_perl > -Dman1dir=/local/share/man/man1 -Dman3dir=/local/share/man/man3 -de' > hint=recommended, useposix=true, d_sigaction=define > usethreads=undef use5005threads=undef useithreads=undef > usemultiplicity=undef > useperlio=define d_sfio=undef uselargefiles=define usesocks=undef > use64bitint=undef use64bitall=undef uselongdouble=undef > usemymalloc=n, bincompat5005=undef > Compiler: > cc='cc-wrapper', ccflags ='-fno-strict-aliasing > -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm', > optimize='-O3', > cppflags='-fno-strict-aliasing -I/usr/include/gdbm' > ccversion='', gccversion='3.2.2 20030222 (Red Hat Linux 3.2.2-5)', > gccosandvers='' > intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=1234 > d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=12 > ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='off_t', > lseeksize=8 > alignbytes=4, prototype=define > Linker and Libraries: > ld='cc-wrapper', ldflags =' -L/local/lib' > libpth=/local/lib /lib /usr/lib /usr/local/lib > libs=-lnsl -lgdbm -ldb -ldl -lm -lc -lcrypt -lutil > perllibs=-lnsl -ldl -lm -lc -lcrypt -lutil > libc=/lib/libc-2.3.2.so, so=so, useshrplib=false, libperl=libperl.a > gnulibc_version='2.3.2' > Dynamic Linking: > dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, > ccdlflags='-rdynamic' > cccdlflags='-fpic', lddlflags='-shared -L/local/lib' > > > > Thanks. > > > -- > -- > George > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Jason Stajich jason.stajich at duke.edu http://www.duke.edu/~jes12/ From jsun at utdallas.edu Wed Sep 22 15:21:55 2004 From: jsun at utdallas.edu (Sun, Jian) Date: Wed Sep 22 15:23:36 2004 Subject: [Bioperl-l] About reverse translation using CodonUsage table ? Message-ID: Dear all; I am trying to write a perl script that can reverse tranlate a amino acid sequence to oligos based on specifed genetic code table and Codon Usage table. I have some idea that I can use the Bio::CodonUsage::Table, Bio::Tools::CodonTable etc. while I have some problems in how to make them work yet? Could anybody give me suggestions or references on this issue? Thanks in advance Jian Sun University of Texas at Dallas From tex at biosysadmin.com Tue Sep 21 23:37:46 2004 From: tex at biosysadmin.com (James Thompson) Date: Wed Sep 22 15:48:45 2004 Subject: [Bioperl-l] problem parsing MEME file In-Reply-To: <41500B96.4050104@utk.edu> Message-ID: Stefan, > >That does make sense, I'll get started on it this weekend. I think I'll try > >my hand at adding Bio::Matrix::PSM::ProtMatrix, a lot of the DNA stuff seems > >hardcoded into the SiteMatrix object. > Indeed, it is my fault, but you know everyone does what he is really > interested in.... That makes sense. There's a lot of clever stuff in SiteMatrix.pm, so this might take me a bit of time to generalize to amino acid alphabets. Bio::Matrix::PSM::ProtMatrix is under development as we speak, should I talk to Chris about getting CVS access to upload what I've done thus far? Right now I've got the constructor and should I talk to Chris about getting CVS access to upload what I've done thus far? Right now I've got the constructor finished and tested, and I'll probably ask for input on how to finish out a few of the methods (especially calculating the IUPAC consensus for amino acids and returning regular expressions for matrices). You can view what I've done so far here: http://bioinformatics.rit.edu/~tex/bioperl/ I've basically ripped off SiteMatrix.pm and I'm translating it subroutine by subroutine. I'll keep you and the list posted as I keep working on this. :) James Thompson On Tue, 21 Sep 2004, Stefan Kirov wrote: > I had a similar problem in the past and never got an answer from the guy > who wrote the parser. There is also Bio::Matrix::PSM::IO::meme, but it > works only on DNA. > James Thompson has offered to write a psi-blast parser and will create > objects that will also be useful for a protein meme parser. Then it will > be easy to add this functionality to Bio::Matrix::PSM::IO::meme. > Stefan > > Diego Riano wrote: > > >Hi all > > > >I have written a small script to parse MEME results, but I am getting > >and error. I am using Bioperl 1.4 and MEME 3.0.10, it should work but > >if does not. could anyone help me? > > > >Here is the script: > > > >#!/usr/bin/perl > > > >use strict; > >use warnings; > > > >use Bio::AlignIO; > > > >my $inputf = "$ARGV[0]"; > >my $in = Bio::AlignIO->new(-file => $inputf, > > -format => 'meme'); > > > > > >while ( my $aln = $in->next_aln() ) { > > print "X\n"; > > } > > > >This is the error i got: > > > >-------------------- WARNING --------------------- > >MSG: Unrecognized format: > >6_04024 163 5.87e-128 DYSCGGDDSG > >TEEEQAAFMKELERFYREKLMEFKPPKFYGEGLNCLKLWRQVTGLGGYDQVTSCKLWRQVGESFKPPKTCTTVSWTFRNFYEKALLEYEKHKIETGEFQV AASNLTERIT > > > >--------------------------------------------------- > > > >thanks > > > >Diego Riano > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From skirov at utk.edu Wed Sep 22 16:22:07 2004 From: skirov at utk.edu (Stefan Kirov) Date: Wed Sep 22 16:22:08 2004 Subject: [Bioperl-l] problem parsing MEME file In-Reply-To: References: Message-ID: <4151DEEF.7090706@utk.edu> James, Seems great to me so far. Jason, I think it is reasonable to create an account for James. I am not sure who is handling this, can you help? I know the e-mail, but I don't know the person. Stefan James Thompson wrote: >Stefan, > > > >>>That does make sense, I'll get started on it this weekend. I think I'll try >>>my hand at adding Bio::Matrix::PSM::ProtMatrix, a lot of the DNA stuff seems >>>hardcoded into the SiteMatrix object. >>> >>> > > > >>Indeed, it is my fault, but you know everyone does what he is really >>interested in.... >> >> > >That makes sense. There's a lot of clever stuff in SiteMatrix.pm, so this might >take me a bit of time to generalize to amino acid alphabets. >Bio::Matrix::PSM::ProtMatrix is under development as we speak, should I talk to >Chris about getting CVS access to upload what I've done thus far? Right now >I've got the constructor and should I talk to Chris about getting CVS access to >upload what I've done thus far? Right now I've got the constructor finished and >tested, and I'll probably ask for input on how to finish out a few of the >methods (especially calculating the IUPAC consensus for amino acids and >returning regular expressions for matrices). > >You can view what I've done so far here: > >http://bioinformatics.rit.edu/~tex/bioperl/ > >I've basically ripped off SiteMatrix.pm and I'm translating it subroutine by >subroutine. I'll keep you and the list posted as I keep working on this. :) > >James Thompson > >On Tue, 21 Sep 2004, Stefan Kirov wrote: > > > >>I had a similar problem in the past and never got an answer from the guy >>who wrote the parser. There is also Bio::Matrix::PSM::IO::meme, but it >>works only on DNA. >>James Thompson has offered to write a psi-blast parser and will create >>objects that will also be useful for a protein meme parser. Then it will >>be easy to add this functionality to Bio::Matrix::PSM::IO::meme. >>Stefan >> >>Diego Riano wrote: >> >> >> >>>Hi all >>> >>>I have written a small script to parse MEME results, but I am getting >>>and error. I am using Bioperl 1.4 and MEME 3.0.10, it should work but >>>if does not. could anyone help me? >>> >>>Here is the script: >>> >>>#!/usr/bin/perl >>> >>>use strict; >>>use warnings; >>> >>>use Bio::AlignIO; >>> >>>my $inputf = "$ARGV[0]"; >>>my $in = Bio::AlignIO->new(-file => $inputf, >>> -format => 'meme'); >>> >>> >>>while ( my $aln = $in->next_aln() ) { >>> print "X\n"; >>> } >>> >>>This is the error i got: >>> >>>-------------------- WARNING --------------------- >>>MSG: Unrecognized format: >>>6_04024 163 5.87e-128 DYSCGGDDSG >>>TEEEQAAFMKELERFYREKLMEFKPPKFYGEGLNCLKLWRQVTGLGGYDQVTSCKLWRQVGESFKPPKTCTTVSWTFRNFYEKALLEYEKHKIETGEFQV AASNLTERIT >>> >>>--------------------------------------------------- >>> >>>thanks >>> >>>Diego Riano >>> >>> >>> >>> >>_______________________________________________ >>Bioperl-l mailing list >>Bioperl-l@portal.open-bio.org >>http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> >> > > > -- Stefan Kirov, Ph.D. University of Tennessee/Oak Ridge National Laboratory 1060 Commerce Park, Oak Ridge TN 37830-8026 USA tel +865 576 5120 fax +865 241 1965 e-mail: skirov@utk.edu sao@ornl.gov From tarowas at gmx.de Wed Sep 22 22:29:49 2004 From: tarowas at gmx.de (Marco Landwehr) Date: Wed Sep 22 22:29:31 2004 Subject: [Bioperl-l] names/id in multi-alignment files Message-ID: <30955.1095906589@www70.gmx.net> Hi, when reading in s multi alignment file of the fasta format: #read in alignment $str = Bio::AlignIO->new('-file' => $filename); $aln = $str->next_aln(); I cannot extract the "header" name or id with: foreach $seq ($aln->id()){ print $seq,"\n"; } Is there a way to do this? When using: #alternative way to read all sequences from multi fasta file @seq_object_array = read_all_sequences($filename,'fasta'); I can get the name of a specific sequence with: $seq_object_array[$i] but I dont want to read in the sequences both ways... Thanks for you help... Marco From jesus.sanchez01 at campus.upf.es Thu Sep 23 12:24:40 2004 From: jesus.sanchez01 at campus.upf.es (jesus sanchez ruiz) Date: Thu Sep 23 06:24:43 2004 Subject: [Bioperl-l] Has anybody got the clustalw.pm for Windows? Message-ID: <1095935080.17899@mail.infomail.es> Which version of Bioperl are you using? Maybe I have an old one, I will check it now. Thank you! ________________________________________________________________________________________ Este mensaje ha sido analizado y protegido por la tecnologia antivirus www.trendmicro.es From jason.stajich at duke.edu Thu Sep 23 07:27:45 2004 From: jason.stajich at duke.edu (Jason Stajich) Date: Thu Sep 23 07:27:28 2004 Subject: [Bioperl-l] names/id in multi-alignment files In-Reply-To: <30955.1095906589@www70.gmx.net> References: <30955.1095906589@www70.gmx.net> Message-ID: <975A4F9E-0D53-11D9-8E53-000393C44276@duke.edu> On Sep 22, 2004, at 10:29 PM, Marco Landwehr wrote: > Hi, > when reading in s multi alignment file of the fasta format: > > #read in alignment > $str = Bio::AlignIO->new('-file' => $filename); > $aln = $str->next_aln(); > > I cannot extract the "header" name or id with: > See the API doc for help on what methods you could do, perldoc Bio::SimpleAlign to see what you can do with the $aln object. foreach my $seq ($aln->each_seq ) { print $seq->display_id, "\n"; } > foreach $seq ($aln->id()){ > print $seq,"\n"; > } > > Is there a way to do this? > When using: > > #alternative way to read all sequences from multi fasta file > @seq_object_array = read_all_sequences($filename,'fasta'); > > I can get the name of a specific sequence with: > $seq_object_array[$i] > > but I dont want to read in the sequences both ways... > > Thanks for you help... > > Marco > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Jason Stajich jason.stajich at duke.edu http://www.duke.edu/~jes12/ From mnhwang at kisti.re.kr Thu Sep 23 04:25:22 2004 From: mnhwang at kisti.re.kr (=?ks_c_5601-1987?B?yLK5zLPn?=) Date: Thu Sep 23 10:01:13 2004 Subject: [Bioperl-l] Cannot make test on bioperl-db Message-ID: <000f01c4a146$de9313e0$78ebb796@danji> I have installed the Oracle version of BioSQL and bioperl-db, and they compile and install fine However, make test on bioperl-db fails miserably with hundreds of messages similar to the following on virtually every module: PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/cluster.......driver not set at t/DBTestHarness.pm line 106 DBTestHarness::driver('DBTestHarness=HASH(0x871cccc)') called at t/DBTestHarness.pm line 204 DBTestHarness::create_db('DBTestHarness=HASH(0x871cccc)') called at t/DBTestHarness.pm line 94 DBTestHarness::new('DBTestHarness','biosql') called at t/cluster.t line 19 t/cluster.......dubious Test returned status 255 (wstat 65280, 0xff00) Scalar found where operator expected at (eval 154) line 1, near "'int' $__val" (Missing operator before $__val?) DIED. FAILED tests 1-160 Failed 160/160 tests, 0.00% okay t/comment.......driver not set at t/DBTestHarness.pm line 106 DBTestHarness::driver('DBTestHarness=HASH(0x863fccc)') called at t/DBTestHarness.pm line 204 DBTestHarness::create_db('DBTestHarness=HASH(0x863fccc)') called at t/DBTestHarness.pm line 94 DBTestHarness::new('DBTestHarness','biosql') called at t/comment.t line 20 t/comment.......dubious Test returned status 255 (wstat 65280, 0xff00) .............. I am wary of wasting time trying to load real data if the test fails like this - is it a 'fatal' problem or can I ignore it and load real data anyway? Any idea what's going on here? I can't figure it out. cheers, mnhwang From s9904982 at sms.ed.ac.uk Thu Sep 23 04:24:32 2004 From: s9904982 at sms.ed.ac.uk (martin) Date: Thu Sep 23 10:01:19 2004 Subject: [Bioperl-l] names/id in multi-alignment files In-Reply-To: <30955.1095906589@www70.gmx.net> References: <30955.1095906589@www70.gmx.net> Message-ID: <1095927872.30842.20.camel@mylonchulus.cap.ed.ac.uk> Hi, In your code, you're treating $seq as a string; actually its a Bio::Seq object. Something like this should work: $str = Bio::AlignIO->new('-file' => $filename); $aln = $str->next_aln; foreach $seq ($aln->each_seq){ print $seq->display_id, "\n"; } calling the display_id method on a Bio::Seq object returns the name/ Hope this helps Martin On Thu, 2004-09-23 at 03:29, Marco Landwehr wrote: > Hi, > when reading in s multi alignment file of the fasta format: > > #read in alignment > $str = Bio::AlignIO->new('-file' => $filename); > $aln = $str->next_aln(); > > I cannot extract the "header" name or id with: > > foreach $seq ($aln->id()){ > print $seq,"\n"; > } > > Is there a way to do this? > When using: > > #alternative way to read all sequences from multi fasta file > @seq_object_array = read_all_sequences($filename,'fasta'); > > I can get the name of a specific sequence with: > $seq_object_array[$i] > > but I dont want to read in the sequences both ways... > > Thanks for you help... > > Marco > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Martin Jones Blaxter Nematode Genomics Group School of Biological Sciences Ashworth Laboratories University of Edinburgh Edinburgh EH9 3JT UK tel: +44 131 650 7403 web: www.nematodes.org From hlapp at gnf.org Thu Sep 23 14:20:22 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Thu Sep 23 14:20:59 2004 Subject: [Bioperl-l] Cannot make test on bioperl-db In-Reply-To: <000f01c4a146$de9313e0$78ebb796@danji> Message-ID: <3B5A06C8-0D8D-11D9-B16C-000A959EB4C4@gnf.org> Looks like you forgot to copy t/DBHarness.conf.example to t/DBHarness.biosql.conf and edit to set your driver, and login credentials etc. Let me know if you did do that and you get the error nonetheless. In that case, also provide the versions of OS, perl, DBI, DBD::Oracle, and Oracle. -hilmar On Thursday, September 23, 2004, at 01:25 AM, ??? wrote: > > I have installed the Oracle version of BioSQL and bioperl-db, > and they compile and install fine > > However, make > test on bioperl-db fails miserably with hundreds of messages similar to > the following on virtually every module: > > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/cluster.......driver not set at t/DBTestHarness.pm line 106 > DBTestHarness::driver('DBTestHarness=HASH(0x871cccc)') called > at t/DBTestHarness.pm line 204 > DBTestHarness::create_db('DBTestHarness=HASH(0x871cccc)') > called at t/DBTestHarness.pm line 94 > DBTestHarness::new('DBTestHarness','biosql') called at > t/cluster.t line 19 > t/cluster.......dubious > Test returned status 255 (wstat 65280, 0xff00) > Scalar found where operator expected at (eval 154) line 1, near "'int' > $__val" > (Missing operator before $__val?) > DIED. FAILED tests 1-160 > Failed 160/160 tests, 0.00% okay > t/comment.......driver not set at t/DBTestHarness.pm line 106 > DBTestHarness::driver('DBTestHarness=HASH(0x863fccc)') called > at t/DBTestHarness.pm line 204 > DBTestHarness::create_db('DBTestHarness=HASH(0x863fccc)') > called at t/DBTestHarness.pm line 94 > DBTestHarness::new('DBTestHarness','biosql') called at > t/comment.t line 20 > t/comment.......dubious > Test returned status 255 (wstat 65280, 0xff00) > .............. > > > I am wary of wasting time trying to load real data if the test fails > like this - is it a 'fatal' problem or can I ignore it and load real > data anyway? > > Any idea what's going on here? I can't figure it out. > > cheers, > mnhwang_______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From brian_osborne at cognia.com Thu Sep 23 19:10:33 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Thu Sep 23 19:10:26 2004 Subject: [Bioperl-l] torturing newbies are we? SeqIO HowTo question In-Reply-To: <50153938-0B65-11D9-8EAD-0003930405E2@ohsu.edu> Message-ID: Tom, Thanks for pointing these out. The typos were corrected in the *sgml files (and online) a while back but the HTML files in bioperl-live are not correct. I'll take a look at that other error... Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Thomas J Keller Sent: Monday, September 20, 2004 8:30 PM To: BioPerl-List Subject: [Bioperl-l] torturing newbies are we? SeqIO HowTo question Greetings, in the Bio::SeqIO HOWTO examples: the first example (getaccs) while (my $seq = $inseq->next_seq) { print $seq->accession_no, "\n"; ###<- wrong method name } should read: while (my $seq = $inseq->next_seq) { print $seq->accession_number, "\n"; } Also, in a later example from this HOWTO (in2out.pl) there's a typo: while (my $inseq = $seqin->next_seq) { $outseq->write_seq($inseq); ### should be $seqout->write_seq($inseq); } But what I really want to know is why, when I run this example (in2out.pl), while it gives the correctly formatted output, it gives the warnings: Argument "*main::STDOUT" isn't numeric in numeric eq (==) at /Library/Perl/5.8.1/Bio/Root/IO.pm line 483. .. repeated 6 times for a single genbank input file. I may be slow, but I catch on eventually, you meanies ;-) I hope it's clear that while the typos are real, I'm kidding about the torture. I really appreciate the help I've gotten from the gurus who monitor this list. Thanks, Tom Keller _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From brian_osborne at cognia.com Thu Sep 23 19:10:33 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Thu Sep 23 19:10:28 2004 Subject: [Bioperl-l] torturing newbies are we? SeqIO HowTo question In-Reply-To: <81774FFC-0BDF-11D9-97EE-000393C44276@duke.edu> Message-ID: Jason, Tom must have been talking about the HTML files in the distribution, but they're updated now. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Jason Stajich Sent: Tuesday, September 21, 2004 11:04 AM To: Thomas J Keller Cc: BioPerl-List List Subject: Re: [Bioperl-l] torturing newbies are we? SeqIO HowTo question Hmm - Where are you getting the HOWTO from? The website versions of them don't seem to have these bugs. What version of bioperl? I don't get that error for bioperl 1.4 branch CVS code or main trunk CVS code but haven't tried it with the 1.4 release that is on CPAN. You said you are using genbank as input format, but what output format? It may be that you should be passing in the STDOUT like this -fh => \*STDOUT not -fh =>*STDOUT Although I don't think it make much of a difference. But this is all guessing since I can't really make it happen on my machine right now. -j On Sep 20, 2004, at 8:29 PM, Thomas J Keller wrote: > Greetings, > > in the Bio::SeqIO HOWTO examples: > > the first example (getaccs) > while (my $seq = $inseq->next_seq) { > print $seq->accession_no, "\n"; ###<- wrong method name > } > > should read: > while (my $seq = $inseq->next_seq) { > print $seq->accession_number, "\n"; > } > > Also, > in a later example from this HOWTO (in2out.pl) there's a typo: > while (my $inseq = $seqin->next_seq) { > $outseq->write_seq($inseq); ### should be > $seqout->write_seq($inseq); > } > > But what I really want to know is why, when I run this example > (in2out.pl), while it gives the correctly formatted output, it gives > the warnings: > Argument "*main::STDOUT" isn't numeric in numeric eq (==) at > /Library/Perl/5.8.1/Bio/Root/IO.pm line 483. > .. repeated 6 times for a single genbank input file. > I may be slow, but I catch on eventually, you meanies ;-) > > I hope it's clear that while the typos are real, I'm kidding about the > torture. I really appreciate the help I've gotten from the gurus who > monitor this list. > > Thanks, > Tom Keller > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Jason Stajich jason.stajich at duke.edu http://www.duke.edu/~jes12/ _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From gongwuming at gmail.com Fri Sep 24 03:15:12 2004 From: gongwuming at gmail.com (Wuming Gong) Date: Fri Sep 24 03:15:06 2004 Subject: [Bioperl-l] What's wrong with openBQS service? Message-ID: <24d6fd0504092400156d0fb471@mail.gmail.com> Hi list, It seems that there is something the soap service of openBQS. I tried the the one line command in the Bio::Biblio documents , perl -MBio::Biblio -e 'print new Bio::Biblio->get_by_id ("94033980")' but it throws the following exception just like my other scripts: ------------ EXCEPTION: Bio::Root::Exception ------------- MSG: --- SOAP FAULT --- SOAP-ENV:Server.Exception: java.lang.OutOfMemoryError STACK: Error::throw STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm:328 STACK: try{} block /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Biblio/soap.pm:119 STACK: SOAP::Lite::call /usr/lib/perl5/site_perl/5.8.0/SOAP/Lite.pm:3006 STACK: try{} block /usr/lib/perl5/site_perl/5.8.0/SOAP/Lite.pm:2950 STACK: Bio::DB::Biblio::soap::get_by_id /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Biblio/soap.pm:368 STACK: -e:1 ----------------------------------------------------------- Regards, Wuming From Richard.Adams at ed.ac.uk Fri Sep 24 06:10:12 2004 From: Richard.Adams at ed.ac.uk (Richard Adams) Date: Fri Sep 24 06:10:04 2004 Subject: [Bioperl-l] About reverse translation using CodonUsage table ? Message-ID: <4153F284.4070605@ed.ac.uk> Hi Jian, I've added a new method in the CVS to Bio::Tools::CodonTable. To get a reverse translation of a protein sequence in IUPAC nucleotide sequence my $cttable = Bio::Tools::CodonTable->new(-id=>1); my $str = "DFGTRF" ; my $seq = Bio::Seq->new(-seq=>$str); my $iu = $cttable->reverse_translate_all($seq); ##takes a sequence object as argument) print $iu; HTH, Richard -- Dr Richard Adams Psychiatric Genetics Group, Medical Genetics, Molecular Medicine Centre, Western General Hospital, Crewe Rd West, Edinburgh UK EH4 2XU Tel: 44 131 651 1084 richard.adams@ed.ac.uk From hlapp at gnf.org Fri Sep 24 12:53:44 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Fri Sep 24 12:53:31 2004 Subject: [Bioperl-l] Cannot make test on bioperl-db In-Reply-To: <000a01c4a1d1$c04a0610$78ebb796@danji> References: <3B5A06C8-0D8D-11D9-B16C-000A959EB4C4@gnf.org> <000a01c4a1d1$c04a0610$78ebb796@danji> Message-ID: <4BDEE09D-0E4A-11D9-B1CA-000A95AE92B0@gnf.org> I'm not convinced that you can successfully load the DBD::Oracle driver. Try setting the environment variable HARNESS_VERBOSE to 1 before you run the tests. This will produce lots of output, send the transcript for just one test, not all of them. Note that your settings below mean that you should be able to successfully login using $ sqlplus sgowner/sgbio@biosql If that doesn't log you in you need to correct your settings. Also, I'd comment out the port; it's not needed if it's the default, and you would usually set this up in the service description in tnsnames.ora. I'm assuming that you do have a properly set up tnsnames.ora on your machine at an expected location? -hilmar On Sep 23, 2004, at 5:59 PM, ??? wrote: > Thanks your comment ^^ > > > I copyed t/DBHarness.conf.example to t/DBHarness.biosql.conf. > --------------------t/DBHarness.biosql.conf------------------------ > { > # DBD driver to use - mandatory > 'driver' => 'Oracle', > # machine to connect to - mandatory > 'host' => '127.0.0.1', > # user to connect to server as - mandatory > 'user' => 'sgowner', > # port the server is running on - optional > 'port' => '1521', > # Password if needed > 'password' => 'sgbio', > # uncomment if no Biosql database exists. This is the Mysql > version. > #'schema_sql' => [ '../biosql-schema/sql/biosqldb-mysql.sql'], > # or for the marker database: > #'schema_sql' => [ './sql/markerdb-mysql.sql'], > # Set to the name of your existing Biosql database. If this is not > # set the test scripts will build a temporary database from scratch > # at the beginning and destroy it at the end. Note that if you set > # this the database must exist, or else the tests will fail. > 'dbname' => 'biosql', > # The name of the database within bioperl-db (biosql or map) > 'database' => 'biosql', > } > ---------------------------------------------------------------- > version > Oracle: 10.1.0 > DBD::Oracle : 1.15 > perl :: 5.8.5 > DBI - latetest version > OS : redhat 9.1 > ---------------------------------------------------------------- > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/cluster.......ok 5/160 > ------------- EXCEPTION ------------- > MSG: failed to load adaptor driver for class > Bio::DB::BioSQL::BioNamespaceAdaptor as well as parents > Bio::DB::BioSQL::BasePersistenceAdaptor > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_get_driver_class > /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:1569 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::dbd > /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:1518 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key > /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:928 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key > /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:856 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create > /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:183 > STACK Bio::DB::Persistent::PersistentObject::create > /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/Persistent/ > PersistentObject.pm:243 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create > /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:170 > STACK Bio::DB::Persistent::PersistentObject::create > /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/Persistent/ > PersistentObject.pm:243 > STACK toplevel t/cluster.t:35 > > -------------------------------------- > t/cluster.......dubious > Test returned status 2 (wstat 512, 0x200) > Scalar found where operator expected at (eval 154) line 1, near "'int' > $__val" > (Missing operator before $__val?) > DIED. FAILED tests 6-160 > Failed 155/160 tests, 3.12% okay > t/comment.......ok 2/11 > ------------- EXCEPTION ------------- > MSG: failed to load adaptor driver for class > Bio::DB::BioSQL::BioNamespaceAdaptor as well as parents > Bio::DB::BioSQL::BasePersistenceAdaptor > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_get_driver_class > /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:1569 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::dbd > /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:1518 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key > /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:928 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key > /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:856 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create > /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:183 > STACK Bio::DB::Persistent::PersistentObject::create > /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/Persistent/ > PersistentObject.pm:243 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create > /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:170 > STACK Bio::DB::Persistent::PersistentObject::create > /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/Persistent/ > PersistentObject.pm:243 > STACK toplevel t/comment.t:32 > ......... > > Test returned status 2 (wstat 512, 0x200) > DIED. FAILED tests 6-52 > Failed 47/52 tests, 9.62% okay > Failed Test Stat Wstat Total Fail Failed List of Failed > ----------------------------------------------------------------------- > -------- > t/cluster.t 2 512 160 310 193.75% 6-160 > t/comment.t 2 512 11 18 163.64% 3-11 > t/dbadaptor.t 255 65280 6 4 66.67% 5-6 > t/dblink.t 2 512 18 32 177.78% 3-18 > t/ensembl.t 2 512 15 26 173.33% 3-15 > t/fuzzy2.t 2 512 21 38 180.95% 3-21 > t/genbank.t 2 512 18 32 177.78% 3-18 > t/locuslink.t 2 512 110 212 192.73% 5-110 > t/ontology.t 2 512 302 596 197.35% 5-302 > t/remove.t 2 512 59 116 196.61% 2-59 > t/seqfeature.t 2 512 48 90 187.50% 4-48 > t/simpleseq.t 2 512 59 108 183.05% 6-59 > t/species.t 255 65280 65 120 184.62% 6-65 > t/swiss.t 2 512 52 94 180.77% 6-52 > Failed 14/15 test scripts, 6.67% okay. 898/962 subtests failed, 6.65% > okay. > > ============================================ > > What am I doing wrong? > > mnhwang > > > > ----- Original Message ----- > From: "Hilmar Lapp" > To: "H29L3g" > Cc: > Sent: Friday, September 24, 2004 3:20 AM > Subject: Re: [Bioperl-l] Cannot make test on bioperl-db > > > Looks like you forgot to copy t/DBHarness.conf.example to > t/DBHarness.biosql.conf and edit to set your driver, and login > credentials etc. > > Let me know if you did do that and you get the error nonetheless. In > that case, also provide the versions of OS, perl, DBI, DBD::Oracle, and > Oracle. > > -hilmar > > On Thursday, September 23, 2004, at 01:25 AM, ??? wrote: > >> >> I have installed the Oracle version of BioSQL and bioperl-db, >> and they compile and install fine >> >> However, make >> test on bioperl-db fails miserably with hundreds of messages similar >> to >> the following on virtually every module: >> >> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" >> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t >> t/cluster.......driver not set at t/DBTestHarness.pm line 106 >> DBTestHarness::driver('DBTestHarness=HASH(0x871cccc)') called >> at t/DBTestHarness.pm line 204 >> DBTestHarness::create_db('DBTestHarness=HASH(0x871cccc)') >> called at t/DBTestHarness.pm line 94 >> DBTestHarness::new('DBTestHarness','biosql') called at >> t/cluster.t line 19 >> t/cluster.......dubious >> Test returned status 255 (wstat 65280, 0xff00) >> Scalar found where operator expected at (eval 154) line 1, near "'int' >> $__val" >> (Missing operator before $__val?) >> DIED. FAILED tests 1-160 >> Failed 160/160 tests, 0.00% okay >> t/comment.......driver not set at t/DBTestHarness.pm line 106 >> DBTestHarness::driver('DBTestHarness=HASH(0x863fccc)') called >> at t/DBTestHarness.pm line 204 >> DBTestHarness::create_db('DBTestHarness=HASH(0x863fccc)') >> called at t/DBTestHarness.pm line 94 >> DBTestHarness::new('DBTestHarness','biosql') called at >> t/comment.t line 20 >> t/comment.......dubious >> Test returned status 255 (wstat 65280, 0xff00) >> .............. >> >> >> I am wary of wasting time trying to load real data if the test fails >> like this - is it a 'fatal' problem or can I ignore it and load real >> data anyway? >> >> Any idea what's going on here? I can't figure it out. >> >> cheers, >> mnhwang_______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- > ------------------------------------------------------------- > Hilmar Lapp email: lapp at gnf.org > GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 > ------------------------------------------------------------- > > > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From cporter at ohri.ca Fri Sep 24 16:39:29 2004 From: cporter at ohri.ca (Christopher Porter) Date: Fri Sep 24 16:39:10 2004 Subject: [Bioperl-l] Retrieving from an indexed fasta file into a LargeSeq object Message-ID: I have a fasta file containing large contig sequences, which I have indexed using Bio::Index::Fasta. Is there a way to use the index to retrieve sequences into a Bio::Seq::LargeSeq object rather than Bio::Seq? What I'm currently doing is essentially: #!/usr/bin/perl use strict; use Bio::SeqIO; use Bio::Index::Fasta; my $idx = Bio::Index::Fasta->new('-filename'=>$hcindex); foreach my $acc(keys %$foo){ my $seqobj = $idx->fetch($acc); ... } How can I force $seqobj to be a LargeSeq? (At another point in the script I'm using SeqIO to read short sequences from a non-indexed fasta file - I don't really want to use LargeSeq for that part.) Thanks, Chris From cain at cshl.edu Sat Sep 25 08:53:16 2004 From: cain at cshl.edu (Scott Cain) Date: Sat Sep 25 08:52:56 2004 Subject: [Bioperl-l] Bioperl OBO format parser Message-ID: <1096116796.1970.5.camel@localhost.localdomain> Hi Chris, I found out yesterday that the version of SO that I am using in chado is actually several months old, because the dagedit formatted file is no longer maintained. So I am in search of an OBO parser for bioperl. I was just googling around to make sure that my perception that there isn't a OBO format parser in bioperl was correct, and I found an email where you indicated that you have an OBO parser as part of go-dev. I was wondering if I could beseech you to add a OBO parser to Bio::OntologyIO? Thanks much, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain@cshl.org GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory From qfdong at iastate.edu Sun Sep 26 11:13:48 2004 From: qfdong at iastate.edu (Qunfeng) Date: Sun Sep 26 11:13:25 2004 Subject: [Bioperl-l] skip "exception" Message-ID: <5.2.0.9.2.20040926100620.00bbfa80@qfdong.mail.iastate.edu> Hi, When I try to use Bioperl to parse genbank sequence file downloaded from NCBI, I am getting the following "exception" with sequence (acc# AJ635582). It seems to be the format problem in this genbank file. My question is: is there any way in bioperl for users to test if there is any format problem in the sequence object and then decide by the users if they want to throw an exception or simply skips to the next object? Thanks! Qunfeng -------------------- WARNING --------------------- MSG: exception while parsing location line [1163^1163] in reading EMBL/GenBank/SwissProt, ignoring feature variation (seqid=AJ6355 82): ------------- EXCEPTION ------------- MSG: Only adjacent residues when location type is IN-BETWEEN. Not [1163] and [1163] STACK Bio::Location::Simple::location_type /usr/lib/perl5/site_perl/5.8.0/Bio/Location/Simple.pm:280 STACK Bio::Location::Simple::new /usr/lib/perl5/site_perl/5.8.0/Bio/Location/Simple.pm:95 STACK Bio::Factory::FTLocationFactory::_parse_location /usr/lib/perl5/site_perl/5.8.0/Bio/Factory/FTLocationFactory.pm:218 STACK Bio::Factory::FTLocationFactory::from_string /usr/lib/perl5/site_perl/5.8.0/Bio/Factory/FTLocationFactory.pm:157 STACK (eval) /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/FTHelper.pm:124 STACK Bio::SeqIO::FTHelper::_generic_seqfeature /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/FTHelper.pm:123 STACK Bio::SeqIO::genbank::next_seq /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/genbank.pm:501 From skirov at utk.edu Sun Sep 26 13:18:23 2004 From: skirov at utk.edu (Stefan Kirov) Date: Sun Sep 26 13:18:24 2004 Subject: [Bioperl-l] skip "exception" In-Reply-To: <5.2.0.9.2.20040926100620.00bbfa80@qfdong.mail.iastate.edu> References: <5.2.0.9.2.20040926100620.00bbfa80@qfdong.mail.iastate.edu> Message-ID: <4156F9DF.3070203@utk.edu> Sometimes it is not reasonable to continue after an error, but Qunfeng has a point. Maybe we can add to at least some parsers an option like -ignore=>{number of allowed exceptions}, warn if the parser generates less errors than tne number requested by the user, die if the number becomes greater. Any thoughts on this? Stefan Qunfeng wrote: > Hi, > > When I try to use Bioperl to parse genbank sequence file downloaded > from NCBI, I am getting the following "exception" with sequence (acc# > AJ635582). It seems to be the format problem in this genbank file. > > My question is: is there any way in bioperl for users to test if there > is any format problem in the sequence object and then decide by the > users if they want to throw an exception or simply skips to the next > object? Thanks! > > Qunfeng > > -------------------- WARNING --------------------- > MSG: exception while parsing location line [1163^1163] in reading > EMBL/GenBank/SwissProt, ignoring feature variation (seqid=AJ6355 > 82): > ------------- EXCEPTION ------------- > MSG: Only adjacent residues when location type is IN-BETWEEN. Not > [1163] and [1163] > STACK Bio::Location::Simple::location_type > /usr/lib/perl5/site_perl/5.8.0/Bio/Location/Simple.pm:280 > STACK Bio::Location::Simple::new > /usr/lib/perl5/site_perl/5.8.0/Bio/Location/Simple.pm:95 > STACK Bio::Factory::FTLocationFactory::_parse_location > /usr/lib/perl5/site_perl/5.8.0/Bio/Factory/FTLocationFactory.pm:218 > STACK Bio::Factory::FTLocationFactory::from_string > /usr/lib/perl5/site_perl/5.8.0/Bio/Factory/FTLocationFactory.pm:157 > STACK (eval) /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/FTHelper.pm:124 > STACK Bio::SeqIO::FTHelper::_generic_seqfeature > /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/FTHelper.pm:123 > STACK Bio::SeqIO::genbank::next_seq > /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/genbank.pm:501 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Stefan Kirov, Ph.D. University of Tennessee/Oak Ridge National Laboratory 1060 Commerce Park, Oak Ridge TN 37830-8026 USA tel +865 576 5120 fax +865 241 1965 e-mail: skirov@utk.edu sao@ornl.gov From qfdong at iastate.edu Sun Sep 26 16:26:35 2004 From: qfdong at iastate.edu (Qunfeng) Date: Sun Sep 26 16:26:22 2004 Subject: [Bioperl-l] skip "exception" In-Reply-To: <4156F9DF.3070203@utk.edu> References: <5.2.0.9.2.20040926100620.00bbfa80@qfdong.mail.iastate.edu> <5.2.0.9.2.20040926100620.00bbfa80@qfdong.mail.iastate.edu> Message-ID: <5.2.0.9.2.20040926152423.00bbfb88@qfdong.mail.iastate.edu> In my case, if I simply want to ignore the exception and proceed with the next seq object in my input file, the following code seems to be working for me: ---------------------------------------------------------------------------------------------------------------- eval{ $seq_object = $seqio_object->next_seq; }; if($@){ print STDERR "EXCEPTION FOUND; SKIP THIS OBJECT\n"; next; } --------------------------------------------------------------------------------------------------------------- However, it might be nice if I can still work on the bad object and parse out the good part out of it. Qunfeng At 01:18 PM 9/26/2004 -0400, Stefan Kirov wrote: >Sometimes it is not reasonable to continue after an error, but Qunfeng has >a point. Maybe we can add to at least some parsers an option like >-ignore=>{number of allowed exceptions}, warn if the parser generates less >errors than tne number requested by the user, die if the number becomes >greater. >Any thoughts on this? >Stefan > >Qunfeng wrote: > >>Hi, >> >>When I try to use Bioperl to parse genbank sequence file downloaded from >>NCBI, I am getting the following "exception" with sequence (acc# >>AJ635582). It seems to be the format problem in this genbank file. >> >>My question is: is there any way in bioperl for users to test if there is >>any format problem in the sequence object and then decide by the users if >>they want to throw an exception or simply skips to the next object? Thanks! >> >>Qunfeng >> >>-------------------- WARNING --------------------- >>MSG: exception while parsing location line [1163^1163] in reading >>EMBL/GenBank/SwissProt, ignoring feature variation (seqid=AJ6355 >>82): >>------------- EXCEPTION ------------- >>MSG: Only adjacent residues when location type is IN-BETWEEN. Not [1163] >>and [1163] >>STACK Bio::Location::Simple::location_type >>/usr/lib/perl5/site_perl/5.8.0/Bio/Location/Simple.pm:280 >>STACK Bio::Location::Simple::new >>/usr/lib/perl5/site_perl/5.8.0/Bio/Location/Simple.pm:95 >>STACK Bio::Factory::FTLocationFactory::_parse_location >>/usr/lib/perl5/site_perl/5.8.0/Bio/Factory/FTLocationFactory.pm:218 >>STACK Bio::Factory::FTLocationFactory::from_string >>/usr/lib/perl5/site_perl/5.8.0/Bio/Factory/FTLocationFactory.pm:157 >>STACK (eval) /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/FTHelper.pm:124 >>STACK Bio::SeqIO::FTHelper::_generic_seqfeature >>/usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/FTHelper.pm:123 >>STACK Bio::SeqIO::genbank::next_seq >>/usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/genbank.pm:501 >> >>_______________________________________________ >>Bioperl-l mailing list >>Bioperl-l@portal.open-bio.org >>http://portal.open-bio.org/mailman/listinfo/bioperl-l > > >-- >Stefan Kirov, Ph.D. >University of Tennessee/Oak Ridge National Laboratory >1060 Commerce Park, Oak Ridge >TN 37830-8026 >USA >tel +865 576 5120 >fax +865 241 1965 >e-mail: skirov@utk.edu >sao@ornl.gov From hlapp at gmx.net Sun Sep 26 20:15:55 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Sun Sep 26 20:29:11 2004 Subject: [Bioperl-l] skip "exception" In-Reply-To: <4156F9DF.3070203@utk.edu> Message-ID: <66268420-101A-11D9-91FB-000A959EB4C4@gmx.net> Note that this is a warning, not an exception. Or so it should be. I.e., you won't have that feature in your feature array and have a nasty looking message printed on your terminal, but otherwise the program/script should run just fine and return a perfectly legal Bio::SeqI object. -hilmar On Sunday, September 26, 2004, at 10:18 AM, Stefan Kirov wrote: > Sometimes it is not reasonable to continue after an error, but Qunfeng > has a point. Maybe we can add to at least some parsers an option like > -ignore=>{number of allowed exceptions}, warn if the parser generates > less errors than tne number requested by the user, die if the number > becomes greater. > Any thoughts on this? > Stefan > > Qunfeng wrote: > >> Hi, >> >> When I try to use Bioperl to parse genbank sequence file downloaded >> from NCBI, I am getting the following "exception" with sequence (acc# >> AJ635582). It seems to be the format problem in this genbank file. >> >> My question is: is there any way in bioperl for users to test if >> there is any format problem in the sequence object and then decide by >> the users if they want to throw an exception or simply skips to the >> next object? Thanks! >> >> Qunfeng >> >> -------------------- WARNING --------------------- >> MSG: exception while parsing location line [1163^1163] in reading >> EMBL/GenBank/SwissProt, ignoring feature variation (seqid=AJ6355 >> 82): >> ------------- EXCEPTION ------------- >> MSG: Only adjacent residues when location type is IN-BETWEEN. Not >> [1163] and [1163] >> STACK Bio::Location::Simple::location_type >> /usr/lib/perl5/site_perl/5.8.0/Bio/Location/Simple.pm:280 >> STACK Bio::Location::Simple::new >> /usr/lib/perl5/site_perl/5.8.0/Bio/Location/Simple.pm:95 >> STACK Bio::Factory::FTLocationFactory::_parse_location >> /usr/lib/perl5/site_perl/5.8.0/Bio/Factory/FTLocationFactory.pm:218 >> STACK Bio::Factory::FTLocationFactory::from_string >> /usr/lib/perl5/site_perl/5.8.0/Bio/Factory/FTLocationFactory.pm:157 >> STACK (eval) /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/FTHelper.pm:124 >> STACK Bio::SeqIO::FTHelper::_generic_seqfeature >> /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/FTHelper.pm:123 >> STACK Bio::SeqIO::genbank::next_seq >> /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/genbank.pm:501 >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > -- > Stefan Kirov, Ph.D. > University of Tennessee/Oak Ridge National Laboratory > 1060 Commerce Park, Oak Ridge > TN 37830-8026 > USA > tel +865 576 5120 > fax +865 241 1965 > e-mail: skirov@utk.edu > sao@ornl.gov > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From allenday at ucla.edu Sun Sep 26 23:41:50 2004 From: allenday at ucla.edu (Allen Day) Date: Sun Sep 26 23:41:27 2004 Subject: [Bioperl-l] Re: [Gmod-schema] Bioperl OBO format parser In-Reply-To: <1096116796.1970.5.camel@localhost.localdomain> References: <1096116796.1970.5.camel@localhost.localdomain> Message-ID: correct, there is not one in bioperl. there have been a few short threads about wanting one, but no-one has broken down and written (or in chris' case committed) it yet. i'd really like to see it appear though, even if outside bioperl! bugfixing and extending the current bioperl GO-format parser is... less than easy. my impression is this is largely due to (1) the GO file format, and (2) unnecessary layers of abstraction in Bio::Ontology* -allen On Sat, 25 Sep 2004, Scott Cain wrote: > Hi Chris, > > I found out yesterday that the version of SO that I am using in chado is > actually several months old, because the dagedit formatted file is no > longer maintained. So I am in search of an OBO parser for bioperl. > > I was just googling around to make sure that my perception that there > isn't a OBO format parser in bioperl was correct, and I found an email > where you indicated that you have an OBO parser as part of go-dev. I > was wondering if I could beseech you to add a OBO parser to > Bio::OntologyIO? > > Thanks much, > Scott > > From ram at i122server.vu-wien.ac.at Mon Sep 27 07:04:28 2004 From: ram at i122server.vu-wien.ac.at (Rambabu Gudavalli) Date: Mon Sep 27 07:04:25 2004 Subject: [Bioperl-l] Unable to retrieve genebank file with GI number In-Reply-To: <200409161956.i8GJtaKu022095@portal.open-bio.org> References: <200409161956.i8GJtaKu022095@portal.open-bio.org> Message-ID: <007F6856-1075-11D9-ADA6-000A95EBF744@i122server.vu-wien.ac.at> Dear Sirs, i am trying to connect the genbank remotely with GI number using the bioperl in this link, they are telling we can connect genbank remotely using GI numbers http://doc.bioperl.org/releases/bioperl-1.4/Bio/DB/GenBank.html i am retrieving the data using the Accession numbers but not with GI numbers. with GI number, is not connecting and it is giving warning like this -------------------- WARNING --------------------- MSG: acc (gb|24585102) does not exist --------------------------------------------------- Use of uninitialized value in length at /Library/Perl/5.8.1/Bio/Perl.pm line 271. Use of uninitialized value in concatenation (.) or string at /Library/Perl/5.8.1/Bio/Perl.pm line 283. You have a non object [] passed to write_sequence. It maybe that you want to use new_sequence to make this string into a sequence object? at /Library/Perl/5.8.1/Bio/Perl.pm line 283 Bio::Perl::write_sequence('>x.fasta','fasta','undef') called at ConnectGenbak1.pl line 14 any help, thanks, Ram From brian_osborne at cognia.com Mon Sep 27 07:52:24 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Mon Sep 27 07:52:00 2004 Subject: [Bioperl-l] Unable to retrieve genebank file with GI number In-Reply-To: <007F6856-1075-11D9-ADA6-000A95EBF744@i122server.vu-wien.ac.at> Message-ID: Ram, If you're using GI numbers you want to do something like this: my $db = new Bio::DB::GenBank; my $seqobj = $db->get_Seq_by_id(24585102); Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Rambabu Gudavalli Sent: Monday, September 27, 2004 7:04 AM To: bioperl-l@portal.open-bio.org Subject: [Bioperl-l] Unable to retrieve genebank file with GI number Dear Sirs, i am trying to connect the genbank remotely with GI number using the bioperl in this link, they are telling we can connect genbank remotely using GI numbers http://doc.bioperl.org/releases/bioperl-1.4/Bio/DB/GenBank.html i am retrieving the data using the Accession numbers but not with GI numbers. with GI number, is not connecting and it is giving warning like this -------------------- WARNING --------------------- MSG: acc (gb|24585102) does not exist --------------------------------------------------- Use of uninitialized value in length at /Library/Perl/5.8.1/Bio/Perl.pm line 271. Use of uninitialized value in concatenation (.) or string at /Library/Perl/5.8.1/Bio/Perl.pm line 283. You have a non object [] passed to write_sequence. It maybe that you want to use new_sequence to make this string into a sequence object? at /Library/Perl/5.8.1/Bio/Perl.pm line 283 Bio::Perl::write_sequence('>x.fasta','fasta','undef') called at ConnectGenbak1.pl line 14 any help, thanks, Ram _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From mnhwang at kisti.re.kr Thu Sep 23 20:59:31 2004 From: mnhwang at kisti.re.kr (=?ks_c_5601-1987?B?yLK5zLPn?=) Date: Mon Sep 27 09:19:37 2004 Subject: [Bioperl-l] Cannot make test on bioperl-db References: <3B5A06C8-0D8D-11D9-B16C-000A959EB4C4@gnf.org> Message-ID: <000a01c4a1d1$c04a0610$78ebb796@danji> Thanks your comment ^^ I copyed t/DBHarness.conf.example to t/DBHarness.biosql.conf. --------------------t/DBHarness.biosql.conf------------------------ { # DBD driver to use - mandatory 'driver' => 'Oracle', # machine to connect to - mandatory 'host' => '127.0.0.1', # user to connect to server as - mandatory 'user' => 'sgowner', # port the server is running on - optional 'port' => '1521', # Password if needed 'password' => 'sgbio', # uncomment if no Biosql database exists. This is the Mysql version. #'schema_sql' => [ '../biosql-schema/sql/biosqldb-mysql.sql'], # or for the marker database: #'schema_sql' => [ './sql/markerdb-mysql.sql'], # Set to the name of your existing Biosql database. If this is not # set the test scripts will build a temporary database from scratch # at the beginning and destroy it at the end. Note that if you set # this the database must exist, or else the tests will fail. 'dbname' => 'biosql', # The name of the database within bioperl-db (biosql or map) 'database' => 'biosql', } ---------------------------------------------------------------- version Oracle: 10.1.0 DBD::Oracle : 1.15 perl :: 5.8.5 DBI - latetest version OS : redhat 9.1 ---------------------------------------------------------------- PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/cluster.......ok 5/160 ------------- EXCEPTION ------------- MSG: failed to load adaptor driver for class Bio::DB::BioSQL::BioNamespaceAdaptor as well as parents Bio::DB::BioSQL::BasePersistenceAdaptor STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_get_driver_class /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1569 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::dbd /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1518 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:928 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:856 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:183 STACK Bio::DB::Persistent::PersistentObject::create /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:243 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:170 STACK Bio::DB::Persistent::PersistentObject::create /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:243 STACK toplevel t/cluster.t:35 -------------------------------------- t/cluster.......dubious Test returned status 2 (wstat 512, 0x200) Scalar found where operator expected at (eval 154) line 1, near "'int' $__val" (Missing operator before $__val?) DIED. FAILED tests 6-160 Failed 155/160 tests, 3.12% okay t/comment.......ok 2/11 ------------- EXCEPTION ------------- MSG: failed to load adaptor driver for class Bio::DB::BioSQL::BioNamespaceAdaptor as well as parents Bio::DB::BioSQL::BasePersistenceAdaptor STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_get_driver_class /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1569 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::dbd /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1518 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:928 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:856 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:183 STACK Bio::DB::Persistent::PersistentObject::create /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:243 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:170 STACK Bio::DB::Persistent::PersistentObject::create /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:243 STACK toplevel t/comment.t:32 ......... Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 6-52 Failed 47/52 tests, 9.62% okay Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/cluster.t 2 512 160 310 193.75% 6-160 t/comment.t 2 512 11 18 163.64% 3-11 t/dbadaptor.t 255 65280 6 4 66.67% 5-6 t/dblink.t 2 512 18 32 177.78% 3-18 t/ensembl.t 2 512 15 26 173.33% 3-15 t/fuzzy2.t 2 512 21 38 180.95% 3-21 t/genbank.t 2 512 18 32 177.78% 3-18 t/locuslink.t 2 512 110 212 192.73% 5-110 t/ontology.t 2 512 302 596 197.35% 5-302 t/remove.t 2 512 59 116 196.61% 2-59 t/seqfeature.t 2 512 48 90 187.50% 4-48 t/simpleseq.t 2 512 59 108 183.05% 6-59 t/species.t 255 65280 65 120 184.62% 6-65 t/swiss.t 2 512 52 94 180.77% 6-52 Failed 14/15 test scripts, 6.67% okay. 898/962 subtests failed, 6.65% okay. ============================================ What am I doing wrong? mnhwang ----- Original Message ----- From: "Hilmar Lapp" To: "H29L3g" Cc: Sent: Friday, September 24, 2004 3:20 AM Subject: Re: [Bioperl-l] Cannot make test on bioperl-db Looks like you forgot to copy t/DBHarness.conf.example to t/DBHarness.biosql.conf and edit to set your driver, and login credentials etc. Let me know if you did do that and you get the error nonetheless. In that case, also provide the versions of OS, perl, DBI, DBD::Oracle, and Oracle. -hilmar On Thursday, September 23, 2004, at 01:25 AM, ??? wrote: > > I have installed the Oracle version of BioSQL and bioperl-db, > and they compile and install fine > > However, make > test on bioperl-db fails miserably with hundreds of messages similar to > the following on virtually every module: > > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/cluster.......driver not set at t/DBTestHarness.pm line 106 > DBTestHarness::driver('DBTestHarness=HASH(0x871cccc)') called > at t/DBTestHarness.pm line 204 > DBTestHarness::create_db('DBTestHarness=HASH(0x871cccc)') > called at t/DBTestHarness.pm line 94 > DBTestHarness::new('DBTestHarness','biosql') called at > t/cluster.t line 19 > t/cluster.......dubious > Test returned status 255 (wstat 65280, 0xff00) > Scalar found where operator expected at (eval 154) line 1, near "'int' > $__val" > (Missing operator before $__val?) > DIED. FAILED tests 1-160 > Failed 160/160 tests, 0.00% okay > t/comment.......driver not set at t/DBTestHarness.pm line 106 > DBTestHarness::driver('DBTestHarness=HASH(0x863fccc)') called > at t/DBTestHarness.pm line 204 > DBTestHarness::create_db('DBTestHarness=HASH(0x863fccc)') > called at t/DBTestHarness.pm line 94 > DBTestHarness::new('DBTestHarness','biosql') called at > t/comment.t line 20 > t/comment.......dubious > Test returned status 255 (wstat 65280, 0xff00) > .............. > > > I am wary of wasting time trying to load real data if the test fails > like this - is it a 'fatal' problem or can I ignore it and load real > data anyway? > > Any idea what's going on here? I can't figure it out. > > cheers, > mnhwang_______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From Richard.Adams at ed.ac.uk Fri Sep 24 04:20:23 2004 From: Richard.Adams at ed.ac.uk (Richard Adams) Date: Mon Sep 27 09:19:39 2004 Subject: [Bioperl-l] About reverse translation using CodonUsage table ? Message-ID: <4153D8C7.7060300@ed.ac.uk> Hi, You can use Bio::Tools::CodonTable::revtranslate to reverse translate e.g., use Bio::Tools::CodonTable; my $seq = 'DFGTR'; #get your codon table of choice my $CodonTable2 = Bio::Tools::CodonTable -> new ( -id => 3 ); my @dna_seq; my @seq = split '', $seq; for my $aa (@seq) { my @codons = $codonTable2->revtranslate($aa); push @dna_seq, \@codons; } ## now you have an array of arrays where each sequence position has a reference to a list of possible codons. I don't think there's a way to translate alternative codons back to IUPAC ids at the moment, it would be worth doing. I'll look into it. Richard -- Dr Richard Adams Psychiatric Genetics Group, Medical Genetics, Molecular Medicine Centre, Western General Hospital, Crewe Rd West, Edinburgh UK EH4 2XU Tel: 44 131 651 1084 richard.adams@ed.ac.uk From tan10 at psu.edu Fri Sep 24 15:52:02 2004 From: tan10 at psu.edu (Todd Naumann) Date: Mon Sep 27 09:19:41 2004 Subject: [Bioperl-l] Re:About reverse translation using..... Message-ID: <3475F56C-0E63-11D9-BDFC-000D9336B8C8@psu.edu> Jian, The following program takes a species, genetic code i.d., and peptide sequence as input. It then retrieves data from the web using Bio::DB::CUTG to create a Bio::CodonUsage::Table object. (Check out www.kazusa.or.jp./codon/ to find correct species name to use, for E. coli there are several). I then use Bio::Tools::CodonTable to do the reverse translation and Bio::CodonUsage to determine which of the codons is most frequent. The output is then the oligo sequence matching the given peptide using the most frequent codons. I think this or something similar is what you are trying to do. If not maybe it will help put you on the right track. -Todd #!/usr/bin/perl use strict; use warnings; #use lib "/Users/todd/.cpan/build/bioperl-1.4"; use Bio::CodonUsage::Table; use Bio::DB::CUTG; my $organism = "Escherichia coli K12"; my $gc = "11"; my $amino_acids = "AKLMG"; my @peptide = split //, $amino_acids; my $oligo; # get a codon usage table from web database my $db = Bio::DB::CUTG->new(-sp => $organism, -gc => $gc); my $CUT = $db->get_request(); # This is Bio::CondonUsage::Table object # use Bio::Tools::CodonTable to do the reverse translation # with a specified table my $CodonTable = Bio::Tools::CodonTable->new(-id => $gc); # Loop throught the amino acids and pick most frequent # codon foreach (@peptide) { my @possible_codons = $CodonTable->revtranslate($_); my $most_frequent = shift @possible_codons; foreach my $next_codon (@possible_codons) { if ($CUT->codon_rel_frequency($next_codon) > $CUT->codon_rel_frequency($most_frequent)) { $most_frequent = $next_codon; } } $oligo .= $most_frequent; } print "The DNA sequence is: $oligo.\n\n"; exit; Todd Naumann Post-Doc, Stephen Benkovic lab Dept. of Chemistry Penn State University University Park, PA 16801 -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1905 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040924/e7a9cb82/attachment.bin From yunliu at iupui.edu Sat Sep 25 03:30:13 2004 From: yunliu at iupui.edu (Yunlong Liu) Date: Mon Sep 27 09:19:45 2004 Subject: [Bioperl-l] GFF MySQL sever failure Message-ID: <200409250730.i8P7UG9V029446@anatomy.iupui.edu> Dear all: I am new in both bioperl and database. Can anyone help me to solve this problem? I was trying to retrieve sequences from a specific region on the human genome, for instance, chr2, 1 - 10000. I am using Bio::DB::GFF to solve this. I copied the following script from http://doc.bioperl.org/releases/bioperl-1.4/Bio/DB/GFF.html#SYNOPSIS use Bio::DB::GFF; # Open the sequence database my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysqlopt', -dsn => 'dbi:mysql:elegans', -fasta => '/usr/local/fasta_files' ); # fetch a 1 megabase segment of sequence starting at landmark "ZK909" my $segment = $db->segment('ZK909', 1 => 1000000); However, I got the following error message: DBI connect ('elegans', '',.) failed: Can't connect to MySQL server on 'localhost' <10061> at C:/Perl/site/lib/Bio/DB/GFF/Adaptor/dbi/caching-handle.pm line 139. Can anyone help me to solve this. Thanks, Yunlong Liu From yunliu at iupui.edu Sat Sep 25 17:15:08 2004 From: yunliu at iupui.edu (Yunlong Liu) Date: Mon Sep 27 09:19:47 2004 Subject: [Bioperl-l] Help needed on GFF Message-ID: <001b01c4a344$c008ead0$0100a8c0@baobaoyue> I am new in both bioperl and database. Can anyone help me to solve this problem? I was trying to retrieve sequences from a specific region on the human genome, for instance, chr2, 1 - 10000. I am using Bio::DB::GFF to solve this. I copied the following script from http://doc.bioperl.org/releases/bioperl-1.4/Bio/DB/GFF.html#SYNOPSIS use Bio::DB::GFF; # Open the sequence database my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysqlopt', -dsn => 'dbi:mysql:elegans', -fasta => '/usr/local/fasta_files' ); # fetch a 1 megabase segment of sequence starting at landmark "ZK909" my $segment = $db->segment('ZK909', 1 => 1000000); However, I got the following error message: DBI connect ('elegans', '',.) failed: Can't connect to MySQL server on 'localhost' <10061> at C:/Perl/site/lib/Bio/DB/GFF/Adaptor/dbi/caching-handle.pm line 139. Can anyone help me to solve it? Thanks, Yunlong Liu From jason.stajich at duke.edu Mon Sep 27 09:26:44 2004 From: jason.stajich at duke.edu (Jason Stajich) Date: Mon Sep 27 09:26:21 2004 Subject: [Bioperl-l] Help needed on GFF In-Reply-To: <001b01c4a344$c008ead0$0100a8c0@baobaoyue> References: <001b01c4a344$c008ead0$0100a8c0@baobaoyue> Message-ID: On Sep 25, 2004, at 5:15 PM, Yunlong Liu wrote: > I am new in both bioperl and database. > > Can anyone help me to solve this problem? > > > > I was trying to retrieve sequences from a specific region on the human > genome, for instance, chr2, 1 - 10000. > I am using Bio::DB::GFF to solve this. I copied the following script > from > http://doc.bioperl.org/releases/bioperl-1.4/Bio/DB/GFF.html#SYNOPSIS > > Add -user and -pass options when you initialize the DB::GFF object or have your mysql server accept connections to the elegans database with > > use Bio::DB::GFF; > > # Open the sequence database > my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysqlopt', > -dsn => 'dbi:mysql:elegans', > -fasta => '/usr/local/fasta_files' -user => $username, -pass => $password, > ); > # fetch a 1 megabase segment of sequence starting at landmark "ZK909" > my $segment = $db->segment('ZK909', 1 => 1000000); > > > > > > However, I got the following error message: > > > > DBI connect ('elegans', '',.) failed: Can't connect to MySQL server on > 'localhost' <10061> at > C:/Perl/site/lib/Bio/DB/GFF/Adaptor/dbi/caching-handle.pm line 139. > And of course you have already loaded the celegans data into a database called 'elegans' ? > > > Can anyone help me to solve it? > > > > Thanks, > > > > Yunlong Liu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich jason.stajich at duke.edu http://www.duke.edu/~jes12/ From jason.stajich at duke.edu Mon Sep 27 09:35:22 2004 From: jason.stajich at duke.edu (Jason Stajich) Date: Mon Sep 27 09:34:57 2004 Subject: [Bioperl-l] Retrieving from an indexed fasta file into a LargeSeq object In-Reply-To: References: Message-ID: <150B4FBA-108A-11D9-812C-000393C44276@duke.edu> Depends on how many games you want to play here and why you really want a LargeSeq. i.e. are you still going to call 'seq' on the large seq object to get the sequence as a string? Yes it can be done by changing the factory which SeqIO uses to create the sequence - if you look at the Index::AbstractSeq object. you'd want to call: (not pretty I know) $idx->_get_SeqIO_object->sequence_factory(Bio::Seq::Factory->new(-type => 'Bio::Seq::LargeSeq')); However, Lincoln's Bio::DB::Fasta module is better for handling this sort of thing I think as you can request virtual slices of the sequence data. I bet it will be much faster than how the LargeSeq implementation works although the two use the same idea of using the filesystem instead of memory for the seq storage. Just make sure your Fasta file is consistently formatted (all sequence lines are the same length, a quick 'sreformat fasta fafile > newfafile; mv newfafile fafile;' can take care of that). -jason On Sep 24, 2004, at 4:39 PM, Christopher Porter wrote: > > I have a fasta file containing large contig sequences, which I have > indexed using Bio::Index::Fasta. Is there a way to use the index to > retrieve sequences into a Bio::Seq::LargeSeq object rather than > Bio::Seq? > > What I'm currently doing is essentially: > > #!/usr/bin/perl > > use strict; > use Bio::SeqIO; > use Bio::Index::Fasta; > > my $idx = Bio::Index::Fasta->new('-filename'=>$hcindex); > > foreach my $acc(keys %$foo){ > my $seqobj = $idx->fetch($acc); > ... > } > > How can I force $seqobj to be a LargeSeq? > > (At another point in the script I'm using SeqIO to read short > sequences from a non-indexed fasta file - I don't really want to use > LargeSeq for that part.) > > > Thanks, > > Chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Jason Stajich jason.stajich at duke.edu http://www.duke.edu/~jes12/ From jsun at utdallas.edu Mon Sep 27 10:59:56 2004 From: jsun at utdallas.edu (Sun, Jian) Date: Mon Sep 27 11:00:35 2004 Subject: [Bioperl-l] RE: About reverse translation using..... Message-ID: Thanks a lot. Todd. While accroding to the CodonUsage table, I still have a question. For example, I want to use the Drosophila melanogaster codonUsage table, (its corresponding genetic code table is, id=>5). From the site-www.kazusa.or.jp./codon/, I get the species name for 'Drosophila melanogaster' ($organism = "Drosophila melanogaster") and tried the program. And a warning message shows as below: -------------------------Warning---------------------------------- MSG: too many species - not a unique species id - ....... ------------------------------------------------------------------- The how can get the unique species id? Thanks a lot Jian Sun University of Texas at Dallas ________________________________ From: Todd Naumann [mailto:tan10@psu.edu] Sent: Fri 9/24/2004 2:52 PM To: jsun@utdallas.edu Cc: bioperl-l@portal.open-bio.org Subject: Re:About reverse translation using..... Jian, The following program takes a species, genetic code i.d., and peptide sequence as input. It then retrieves data from the web using Bio::DB::CUTG to create a Bio::CodonUsage::Table object. (Check out www.kazusa.or.jp./codon/ to find correct species name to use, for E. coli there are several). I then use Bio::Tools::CodonTable to do the reverse translation and Bio::CodonUsage to determine which of the codons is most frequent. The output is then the oligo sequence matching the given peptide using the most frequent codons. I think this or something similar is what you are trying to do. If not maybe it will help put you on the right track. -Todd #!/usr/bin/perl use strict; use warnings; #use lib "/Users/todd/.cpan/build/bioperl-1.4"; use Bio::CodonUsage::Table; use Bio::DB::CUTG; my $organism = "Escherichia coli K12"; my $gc = "11"; my $amino_acids = "AKLMG"; my @peptide = split //, $amino_acids; my $oligo; # get a codon usage table from web database my $db = Bio::DB::CUTG->new(-sp => $organism, -gc => $gc); my $CUT = $db->get_request(); # This is Bio::CondonUsage::Table object # use Bio::Tools::CodonTable to do the reverse translation # with a specified table my $CodonTable = Bio::Tools::CodonTable->new(-id => $gc); # Loop throught the amino acids and pick most frequent # codon foreach (@peptide) { my @possible_codons = $CodonTable->revtranslate($_); my $most_frequent = shift @possible_codons; foreach my $next_codon (@possible_codons) { if ($CUT->codon_rel_frequency($next_codon) > $CUT->codon_rel_frequency($most_frequent)) { $most_frequent = $next_codon; } } $oligo .= $most_frequent; } print "The DNA sequence is: $oligo.\n\n"; exit; Todd Naumann Post-Doc, Stephen Benkovic lab Dept. of Chemistry Penn State University University Park, PA 16801 From tan10 at psu.edu Mon Sep 27 11:51:28 2004 From: tan10 at psu.edu (Todd Naumann) Date: Mon Sep 27 11:49:16 2004 Subject: [Bioperl-l] Re: About reverse translation In-Reply-To: References: Message-ID: <1838E79B-109D-11D9-AC1F-000D9336B8C8@psu.edu> Jian, Searching for Drosophila melanogaster at www.kazusa.or.jp/codon gives 4 possible tables. I think that your program is picking the genome usage table by default. If this is what you want I think you are in business. I am not sure how to specify if you want 1 of the others. With Escherichia coli I was able to specify by simply adding the 'K12'. In your case I tried to specify 'mitochondrion Drosophila melanogaster' or 'Drosophila melanogaster mitochondrion' but always get an error and the program defaults to Homo sapiens. -Todd On Sep 27, 2004, at 10:59 AM, Sun, Jian wrote: > Thanks a lot. Todd. While accroding to the CodonUsage table, I still > have a question. For example, I want to use the Drosophila > melanogaster codonUsage table, (its corresponding genetic code table > is, id=>5). From the site-www.kazusa.or.jp./codon/, I get the species > name for 'Drosophila melanogaster' ($organism = "Drosophila > melanogaster") and tried the program. And a warning message shows as > below: > -------------------------Warning---------------------------------- > MSG: too many species - not a unique species id - ....... > ------------------------------------------------------------------- > The how can get the unique species id? > > Thanks a lot > Jian Sun > University of Texas at Dallas > > > ________________________________ > > From: Todd Naumann [mailto:tan10@psu.edu] > Sent: Fri 9/24/2004 2:52 PM > To: jsun@utdallas.edu > Cc: bioperl-l@portal.open-bio.org > Subject: Re:About reverse translation using..... > > > Jian, > > The following program takes a species, genetic code i.d., and peptide > sequence as input. It then retrieves data from the web using > Bio::DB::CUTG to create a Bio::CodonUsage::Table object. (Check out > www.kazusa.or.jp./codon/ to find correct species name to use, for E. > coli there are several). I then use Bio::Tools::CodonTable to do the > reverse translation and Bio::CodonUsage to determine which of the > codons is most frequent. The output is then the oligo sequence > matching the given peptide using the most frequent codons. I think > this or something similar is what you are trying to do. If not maybe > it will help put you on the right track. > > -Todd > > > #!/usr/bin/perl > > use strict; > use warnings; > #use lib "/Users/todd/.cpan/build/bioperl-1.4"; > use Bio::CodonUsage::Table; > use Bio::DB::CUTG; > > my $organism = "Escherichia coli K12"; > my $gc = "11"; > my $amino_acids = "AKLMG"; > my @peptide = split //, $amino_acids; > my $oligo; > > # get a codon usage table from web database > my $db = Bio::DB::CUTG->new(-sp => $organism, > -gc => $gc); > my $CUT = $db->get_request(); # This is Bio::CondonUsage::Table object > > # use Bio::Tools::CodonTable to do the reverse translation > # with a specified table > my $CodonTable = Bio::Tools::CodonTable->new(-id => $gc); > > # Loop throught the amino acids and pick most frequent > # codon > foreach (@peptide) { > my @possible_codons = $CodonTable->revtranslate($_); > my $most_frequent = shift @possible_codons; > foreach my $next_codon (@possible_codons) { > if ($CUT->codon_rel_frequency($next_codon) > > $CUT->codon_rel_frequency($most_frequent)) { > $most_frequent = $next_codon; > } > } > $oligo .= $most_frequent; > } > print "The DNA sequence is: $oligo.\n\n"; > exit; > > > Todd Naumann > Post-Doc, Stephen Benkovic lab > Dept. of Chemistry > Penn State University > University Park, PA 16801 > > From cporter at ohri.ca Mon Sep 27 15:07:31 2004 From: cporter at ohri.ca (Christopher Porter) Date: Mon Sep 27 15:07:08 2004 Subject: [Bioperl-l] Retrieving from an indexed fasta file into a LargeSeq object In-Reply-To: <150B4FBA-108A-11D9-812C-000393C44276@duke.edu> References: <150B4FBA-108A-11D9-812C-000393C44276@duke.edu> Message-ID: <7BA5E501-10B8-11D9-ADE6-000393CD9EA6@ohri.ca> I don't think that I followed how the call to set the factory should be used. After creating the Bio::Index::Fasta object, I called the _get_SeqIO_object method as described. In return my script exited with the exception below (I didn't supply an index to the _get_SeqIO_object call). ------------- EXCEPTION ------------- MSG: Can't get filename for index : STACK Bio::Index::Abstract::_file_handle /Library/Perl/5.8.1/Bio/Index/Abstract.pm:662 STACK Bio::Index::AbstractSeq::_get_SeqIO_object /Library/Perl/5.8.1/Bio/Index/AbstractSeq.pm:171 STACK toplevel ./parseBLAST.pl:172 -------------------------------------- This is somewhat of academic interest; I'm going to try to rewrite using the Bio::DB::Fasta module instead - getting a slice of a large sequence is exactly what I need to do. Chris On 27-Sep-04, at 9:35 AM, Jason Stajich wrote: > Depends on how many games you want to play here and why you really > want a LargeSeq. i.e. are you still going to call 'seq' on the large > seq object to get the sequence as a string? Yes it can be done by > changing the factory which SeqIO uses to create the sequence - if you > look at the Index::AbstractSeq object. > > you'd want to call: > (not pretty I know) > > $idx->_get_SeqIO_object->sequence_factory(Bio::Seq::Factory->new(-type > => 'Bio::Seq::LargeSeq')); > > > However, Lincoln's Bio::DB::Fasta module is better for handling this > sort of thing I think as you can request virtual slices of the > sequence data. I bet it will be much faster than how the LargeSeq > implementation works although the two use the same idea of using the > filesystem instead of memory for the seq storage. Just make sure your > Fasta file is consistently formatted (all sequence lines are the same > length, a quick > 'sreformat fasta fafile > newfafile; mv newfafile fafile;' can take > care of that). > > -jason > On Sep 24, 2004, at 4:39 PM, Christopher Porter wrote: > >> >> I have a fasta file containing large contig sequences, which I have >> indexed using Bio::Index::Fasta. Is there a way to use the index to >> retrieve sequences into a Bio::Seq::LargeSeq object rather than >> Bio::Seq? >> >> What I'm currently doing is essentially: >> >> #!/usr/bin/perl >> >> use strict; >> use Bio::SeqIO; >> use Bio::Index::Fasta; >> >> my $idx = Bio::Index::Fasta->new('-filename'=>$hcindex); >> >> foreach my $acc(keys %$foo){ >> my $seqobj = $idx->fetch($acc); >> ... >> } >> >> How can I force $seqobj to be a LargeSeq? >> >> (At another point in the script I'm using SeqIO to read short >> sequences from a non-indexed fasta file - I don't really want to use >> LargeSeq for that part.) >> >> >> Thanks, >> >> Chris >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> > -- > Jason Stajich > jason.stajich at duke.edu > http://www.duke.edu/~jes12/ > From cjm at fruitfly.org Mon Sep 27 11:34:41 2004 From: cjm at fruitfly.org (Chris Mungall) Date: Mon Sep 27 20:51:48 2004 Subject: [Bioperl-l] Re: [Gmod-schema] Bioperl OBO format parser In-Reply-To: References: <1096116796.1970.5.camel@localhost.localdomain> Message-ID: On Sun, 26 Sep 2004, Allen Day wrote: > correct, there is not one in bioperl. there have been a few short threads > about wanting one, but no-one has broken down and written (or in chris' > case committed) it yet. > > i'd really like to see it appear though, even if outside bioperl! You could always use the go-perl parser - it doesn't use the bioperl object model though http://www.godatabase.org/dev/go-perl/doc/go-perl-doc.html > bugfixing and extending the current bioperl GO-format parser is... less > than easy. my impression is this is largely due to (1) the GO file > format, and (2) unnecessary layers of abstraction in Bio::Ontology* > > -allen > > > On Sat, 25 Sep 2004, Scott Cain wrote: > > > Hi Chris, > > > > I found out yesterday that the version of SO that I am using in chado is > > actually several months old, because the dagedit formatted file is no > > longer maintained. So I am in search of an OBO parser for bioperl. > > > > I was just googling around to make sure that my perception that there > > isn't a OBO format parser in bioperl was correct, and I found an email > > where you indicated that you have an OBO parser as part of go-dev. I > > was wondering if I could beseech you to add a OBO parser to > > Bio::OntologyIO? > > > > Thanks much, > > Scott > > > > > From cromologic at yahoo.com Mon Sep 27 15:53:31 2004 From: cromologic at yahoo.com (BORN II CODE) Date: Mon Sep 27 20:51:53 2004 Subject: [Bioperl-l] XML for Bioinformatics Message-ID: <20040927195331.49614.qmail@web12824.mail.yahoo.com> Hi, I am new to bioinformatics.I just want to know how XML can help in data integration for Bioinformatics applications.Is it only used to translate FASTA files to XML or more than that?pls guide me as i am very much new to this field.thanks alot. cheers, sargunan --------------------------------- Do you Yahoo!? New and Improved Yahoo! Mail - 100MB free storage! From Richard.Adams at ed.ac.uk Tue Sep 28 08:26:42 2004 From: Richard.Adams at ed.ac.uk (Richard Adams) Date: Tue Sep 28 08:26:19 2004 Subject: [Bioperl-l] About reverse translation using CodonUsage table ? Message-ID: <41595882.1060903@ed.ac.uk> Hi Jian I've changed the reverse_translate_all() method in Bio::Tools::CodonTable in CVS so that you can pass it a codon usage table and a threshold. e.g., ## a default codon table my $myCodonTable2 = Bio::Tools::CodonTable -> new ( -id => 1 ); ## a codon usage table my $db = Bio::DB::CUTG->new(); my $cdtable = $db->get_request(-sp =>'Pan troglodytes'); ## get a protein sequence my $seq = Bio::PrimarySeq->new(-seq=> 'LSRTA'); # reverse translates and generates a IUPAC nucleotide string my $str = $myCodonTable2->reverse_translate_all($seq); print "str = $str\n"; ## when passed with a CUT and a threshold returns a IUPAC string made only from codons with a relative frequency higher than the threshold my $str2 = $myCodonTable2->reverse_translate_all($seq, $cdtable, 15); print "st2 = $str2\n"; In this case, for the peptide sequence above, $str = YTNWSNMGNACNGCN whereas $st2 = CTSWSYMGVACHGCN Hope this is of some use. If you want to get hold of the codons above a threshold you can call a method probable_codons() in Bio::CodonUsage::Table which returns a hash reference where keys are single letter amino acids code and values are references to a list of codons above the threshold. e.g., my $ref = $cut->probable_codons(15); Best wishes Richard -- Dr Richard Adams Psychiatric Genetics Group, Medical Genetics, Molecular Medicine Centre, Western General Hospital, Crewe Rd West, Edinburgh UK EH4 2XU Tel: 44 131 651 1084 richard.adams@ed.ac.uk From rmaps005 at cib.csic.es Tue Sep 28 11:07:07 2004 From: rmaps005 at cib.csic.es (rmaps005@cib.csic.es) Date: Tue Sep 28 11:41:49 2004 Subject: [Bioperl-l] genbank to cds Message-ID: <200409281507.i8SF77jr018366@calisto.cib.csic.es> hello, i was using this program to covert genbank file (actually a human chromosome) to cds but even if it does work and generate some cds, always comes out with this error: Argument "*main::STDIN" isn't numeric in numeric eq (==) at /usr/lib/perl5/site_perl/5.8.3/Bio/Root/IO.pm line 483. don't know if it is because runs out of memory or i made a mistake.... can somebody help me with this? Thanks $seqin = Bio::SeqIO->new( '-format' => 'GenBank', -fh => *STDIN); while((my $seqobj = $seqin->next_seq())) { $genomic_id = $seqobj->display_id; foreach $feat ( $seqobj->top_SeqFeatures() ) { $length = $seqobj->length; if ($feat->primary_tag eq "CDS"){ # Check if protein_id tag exists. if (join(" ",$feat->all_tags()) =~ m/db\_xref/){ $protein_id = join("",$feat->each_tag_value('db_xref')); } else { $protein_id = "UNKNOWN"; } $cds = $feat->location->to_FTstring; if ($cds =~ m/complement/){ $strand = "-"; } else { $strand = "+"; } $cds =~ s/\.\.|,|join\(|\)|complement\(|\(/ /g; print ("$genomic_id\_$protein_id $length $strand $cds \n"); } } } IlohaCIB From jason.stajich at duke.edu Tue Sep 28 11:49:14 2004 From: jason.stajich at duke.edu (Jason Stajich) Date: Tue Sep 28 11:48:47 2004 Subject: [Bioperl-l] genbank to cds In-Reply-To: <200409281507.i8SF77jr018366@calisto.cib.csic.es> References: <200409281507.i8SF77jr018366@calisto.cib.csic.es> Message-ID: Escape the STDIN handle $seqin = Bio::SeqIO->new( '-format' => 'GenBank', -fh => \*STDIN); You can also use the special handle ARGV to allow both files to be on the cmdline or from STDIN $seqin = Bio::SeqIO->new( '-format' => 'GenBank', -fh => \*ARGV); This is how you get access to the magic empty diamond (<>) as a filehandle you can pass around. Also if you wanted the protein sequence length for the annotated feature (excluding the potential introns) you can call my $cds_seq = $feat->spliced_seq; my $cds_len = $cdsseq->length; my $pep_len = $cdsseq->translate->length; n.b. there have been some improvements/bugfixes to spliced_seq since the 1.4 release that are only in the CVS tree (http://cvs.open-bio.org) until we get the 1.5 release done. -jason On Sep 28, 2004, at 11:07 AM, rmaps005@cib.csic.es wrote: > hello, > i was using this program to covert genbank file (actually a human > chromosome) to cds but even if it does work and generate some cds, > always comes out with this error: > > Argument "*main::STDIN" isn't numeric in numeric eq (==) at > /usr/lib/perl5/site_perl/5.8.3/Bio/Root/IO.pm line 483. > > don't know if it is because runs out of memory or i made a mistake.... > can somebody help me with this? > > Thanks > > $seqin = Bio::SeqIO->new( '-format' => 'GenBank', -fh => *STDIN); > while((my $seqobj = $seqin->next_seq())) > { > $genomic_id = $seqobj->display_id; > foreach $feat ( $seqobj->top_SeqFeatures() ) { > $length = $seqobj->length; > if ($feat->primary_tag eq "CDS"){ > # Check if protein_id tag exists. > if (join(" ",$feat->all_tags()) =~ m/db\_xref/){ > $protein_id = > join("",$feat->each_tag_value('db_xref')); > } > else { > $protein_id = "UNKNOWN"; > } > $cds = $feat->location->to_FTstring; > if ($cds =~ m/complement/){ > $strand = "-"; > } > else { > $strand = "+"; > } > $cds =~ s/\.\.|,|join\(|\)|complement\(|\(/ /g; > print ("$genomic_id\_$protein_id $length $strand $cds > \n"); > } > } > } > > > IlohaCIB > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Jason Stajich jason.stajich at duke.edu http://www.duke.edu/~jes12/ From lstein at cshl.edu Wed Sep 29 13:55:41 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Wed Sep 29 13:55:30 2004 Subject: [Bioperl-l] Bio::Graphics : Switching Glyph Colors On One Track In-Reply-To: <000d01c48704$3b554740$e200a8c0@apartment.leesam.net> References: <000d01c48704$3b554740$e200a8c0@apartment.leesam.net> Message-ID: <200409291355.41032.lstein@cshl.edu> Once you've added the track you can use the track object's configure() method to change options. You can also use a callback to change options on a feature-by-feature basis. Lincoln On Friday 20 August 2004 06:22 pm, Lee Sam wrote: > Is there a way to change the glyph fillcolor and the bump option > once the track has been added? I'm trying to draw glyphs one top of > other glyphs (HSPs on top of genes in my case). > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From lstein at cshl.edu Wed Sep 29 13:58:14 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Wed Sep 29 13:57:51 2004 Subject: [Bioperl-l] Bio::Graphics::Panel In-Reply-To: <41122D84.8050607@health.nb.ca> References: <41122D84.8050607@health.nb.ca> Message-ID: <200409291358.14111.lstein@cshl.edu> Yes, you can open multiple panels and print out their GIFs (or JPEGs or PNGs). The problem you're seeing is that you're printing them out as a single continuous file, and the image rendering program only recognizes the first image in the file. You should instead open up separate output files and print into them: open OUT,">picture1.gif"; print $panel1->gd->gif; close OUT; open OUT,">picture2.gif"; print $panel2->gd->gif; close OUT: Lincoln On Thursday 05 August 2004 08:52 am, Miroslava Cuperlovic-Culf wrote: > Dear All, > I would like to use Bio::Graphics to present exons mapped to dna > in a gff file. I get nice figure for exact lengths of exons and > introns. But as exons are much shorter than introns it is > impossible to see their lengths. Thus I would like to either > present exons in correct lengths and introns only as "..." or as a > number of bases or alternatively as several figures, one for each > exon. Is either of these possible? From perldoc for Bio::Graphics I > understood that it is possible to open several pictures from one > program so I tried to use: > .. > my $panel = Bio::Graphics::Panel->new( ... > .. > print $panel->gd->gif; > $panel ->finished;... > my $panel1 = Bio::Graphics::Panel->new( ... > .. > print $panel1->gd->gif; > $panel1 ->finished; > > but in this way I only got the first panel opened. > What am I doing wrong? > Thanks very much for the ongoing help > Mira > > - -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From lstein at cshl.edu Wed Sep 29 13:59:56 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Wed Sep 29 13:59:40 2004 Subject: [Bioperl-l] Help needed on GFF In-Reply-To: <001b01c4a344$c008ead0$0100a8c0@baobaoyue> References: <001b01c4a344$c008ead0$0100a8c0@baobaoyue> Message-ID: <200409291359.56718.lstein@cshl.edu> To use this strategy first you need to create a local GFF database containing all the human sequences. This probably isn't what you want to do. You should go to Ensembl and fetch the sequences from there. There is a nice Perl interface that you can script to. Lincoln On Saturday 25 September 2004 05:15 pm, Yunlong Liu wrote: > I am new in both bioperl and database. > > Can anyone help me to solve this problem? > > > > I was trying to retrieve sequences from a specific region on the > human genome, for instance, chr2, 1 - 10000. > > I am using Bio::DB::GFF to solve this. I copied the following > script from > http://doc.bioperl.org/releases/bioperl-1.4/Bio/DB/GFF.html#SYNOPSI >S > > > > use Bio::DB::GFF; > > # Open the sequence database > my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysqlopt', > -dsn => 'dbi:mysql:elegans', > -fasta => > '/usr/local/fasta_files' ); > # fetch a 1 megabase segment of sequence starting at landmark > "ZK909" my $segment = $db->segment('ZK909', 1 => 1000000); > > > > > > However, I got the following error message: > > > > DBI connect ('elegans', '',.) failed: Can't connect to MySQL server > on 'localhost' <10061> at > C:/Perl/site/lib/Bio/DB/GFF/Adaptor/dbi/caching-handle.pm line 139. > > > > Can anyone help me to solve it? > > > > Thanks, > > > > Yunlong Liu -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From lstein at cshl.edu Wed Sep 29 14:00:26 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Wed Sep 29 14:00:23 2004 Subject: [Bioperl-l] Lining Up Glyphs on Bio::Panel In-Reply-To: <004601c47bea$a6a436c0$e200a8c0@apartment.leesam.net> References: <004601c47bea$a6a436c0$e200a8c0@apartment.leesam.net> Message-ID: <200409291400.26316.lstein@cshl.edu> Set the -bump option to 0. Lincoln On Friday 06 August 2004 03:21 pm, Lee Sam wrote: > When I use Bio::Graphics to render a number of adjacent genes, I > can't get them to line up (they always render on two lines). Is > there a way to force them to render on a single line? > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From lstein at cshl.edu Wed Sep 29 14:02:42 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Wed Sep 29 14:02:34 2004 Subject: [Bioperl-l] pad individual tracks using panel In-Reply-To: References: Message-ID: <200409291402.42237.lstein@cshl.edu> This is a little late, but the simplest thing to do is to create two GD images and adjust the starting coordinates so that the features line up at the same place. Then you can merge the two images into a single picture using the GD copy() call. Lincoln On Wednesday 15 September 2004 04:37 am, Simon McGowan wrote: > Hi, > Following some feedback here, I should also say that this is for > illustrative purposes only and not to produce a meaningful > alignment of any kind. Its needed by the users here who want some > figures for papers. Would I have to alter all the coordinates for > the features in the track, or is there a shortcut involving > -add_track? > > Thanks, Simon > > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org > [mailto:bioperl-l-bounces@portal.open-bio.org] On Behalf Of Simon > McGowan Sent: 14 September 2004 09:31 > To: > Subject: [Bioperl-l] pad individual tracks using panel > > Hi, > After reading in the features of two GenBank files using > Bio::SeqIO, I am attempting to render them as a single image using > Bio::Graphics::Panel. My question is, is there a way to pad all the > coordinates of a single track by a given amount? This would allow > me to produce a very basic alignment by lining up the contents of > two tracks at a common feature within both files. I can pad the > entire panel using '-offset', and I guess I need a similar option > for '-add_track'. Could someone please let me know if this is > possible? > > Thanks, Simon > > ------------------------------------ > Simon McGowan > Computational Biology Research Group > University of Oxford OX1 3RE > www.compbio.ox.ac.uk > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From dlyzxl at yahoo.com Wed Sep 29 13:26:25 2004 From: dlyzxl at yahoo.com (Xiangli Zhang) Date: Wed Sep 29 15:27:00 2004 Subject: [Bioperl-l] problem using lagan.pm Message-ID: <20040929172625.85486.qmail@web51106.mail.yahoo.com> Dear all: Error occured : Lagan.pm cannot be found. I am trying to use lagan alignment tool as "my $lagan = new Bio::Tools::Run::Alignment::Lagan(@params)"; And I manually check bioperl installation, I really didnot find this module. Where is the point for this problem? It is on bioperl installation or on using. Can anybody help me figure out this problem? Thanks, Justin Xiangli Zhang (Justin) 306-310 Decaire Street, Coquitlam BC, Canada, V3K 6X1 phone: 604-9399181 __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From jcsanchez at cib.csic.es Wed Sep 29 05:24:08 2004 From: jcsanchez at cib.csic.es (Juan Carlos =?ISO-8859-1?Q?S=E1nchez?= Ferrero) Date: Wed Sep 29 15:27:21 2004 Subject: [Bioperl-l] genbank to cds In-Reply-To: Message-ID: <200409290924.i8T9O8jr005260@calisto.cib.csic.es> Changing -fh => *STDIN to -fh => *ARGV didn't work and got the same error but the suggestion made by Thomas did work And just a comment actually comparing the resulting files of using each *STDIN and \*STDIN they are the same, even if an error comes out when using *STDIN..... Thanks to all!! Con fecha 28/9/2004, "Thomas J Keller" escribi?: >Hoorah, a question I can help with. (I've gotten so much help from this >list, I want to be able to contribute). > >Try passing a reference to the glob, instead of the glob itself: i.e. >change >> -fh => *STDIN >to > -fh => \*STDIN > >regards, >Tom Keller > >Tom Keller, Ph.D. >http://www.ohsu.edu/research/core >kellert@ohsu.edu >503-494-2442 > >On Sep 28, 2004, at 8:07 AM, rmaps005@cib.csic.es wrote: > >> hello, >> i was using this program to covert genbank file (actually a human >> chromosome) to cds but even if it does work and generate some cds, >> always comes out with this error: >> >> Argument "*main::STDIN" isn't numeric in numeric eq (==) at >> /usr/lib/perl5/site_perl/5.8.3/Bio/Root/IO.pm line 483. >> >> don't know if it is because runs out of memory or i made a mistake.... >> can somebody help me with this? >> >> Thanks >> >> $seqin = Bio::SeqIO->new( '-format' => 'GenBank', -fh => *STDIN); >> while((my $seqobj = $seqin->next_seq())) >> { >> $genomic_id = $seqobj->display_id; >> foreach $feat ( $seqobj->top_SeqFeatures() ) { >> $length = $seqobj->length; >> if ($feat->primary_tag eq "CDS"){ >> # Check if protein_id tag exists. >> if (join(" ",$feat->all_tags()) =~ m/db\_xref/){ >> $protein_id = >> join("",$feat->each_tag_value('db_xref')); >> } >> else { >> $protein_id = "UNKNOWN"; >> } >> $cds = $feat->location->to_FTstring; >> if ($cds =~ m/complement/){ >> $strand = "-"; >> } >> else { >> $strand = "+"; >> } >> $cds =~ s/\.\.|,|join\(|\)|complement\(|\(/ /g; >> print ("$genomic_id\_$protein_id $length $strand $cds >> \n"); >> } >> } >> } >> >> >> IlohaCIB >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l > > IlohaCIB From tomas_marques at hotmail.com Wed Sep 29 10:44:33 2004 From: tomas_marques at hotmail.com (Marques Bonet) Date: Wed Sep 29 15:27:38 2004 Subject: [Bioperl-l] Gene positions Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040929/2181c8e9/attachment.htm From jason.stajich at duke.edu Wed Sep 29 15:30:29 2004 From: jason.stajich at duke.edu (Jason Stajich) Date: Wed Sep 29 15:29:58 2004 Subject: [Bioperl-l] problem using lagan.pm In-Reply-To: <20040929172625.85486.qmail@web51106.mail.yahoo.com> References: <20040929172625.85486.qmail@web51106.mail.yahoo.com> Message-ID: <05AEF449-124E-11D9-861F-000393C44276@duke.edu> install bioperl-run http://www.bioperl.org/Core/Latest/faq.html#6 On Sep 29, 2004, at 1:26 PM, Xiangli Zhang wrote: > > > > Dear all: > > Error occured : Lagan.pm cannot be found. > > I am trying to use lagan alignment tool as "my $lagan = new > Bio::Tools::Run::Alignment::Lagan(@params)"; > > And I manually check bioperl installation, I really didnot find this > module. > > Where is the point for this problem? It is on bioperl installation or > on using. > > Can anybody help me figure out this problem? > > > > Thanks, > > > > Justin > > > > Xiangli Zhang (Justin) > 306-310 Decaire Street, Coquitlam > BC, Canada, V3K 6X1 > phone: 604-9399181 > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich jason.stajich at duke.edu http://www.duke.edu/~jes12/ From jason.stajich at duke.edu Wed Sep 29 15:36:47 2004 From: jason.stajich at duke.edu (Jason Stajich) Date: Wed Sep 29 15:36:20 2004 Subject: [Bioperl-l] genbank to cds In-Reply-To: <200409290924.i8T9O8jr005260@calisto.cib.csic.es> References: <200409290924.i8T9O8jr005260@calisto.cib.csic.es> Message-ID: On Sep 29, 2004, at 5:24 AM, Juan Carlos S?nchez Ferrero wrote: > Changing -fh => *STDIN to -fh => *ARGV didn't work and got the same > error > but the suggestion made by Thomas did work > Of course not, you didn't escape the glob. Pass in \*ARGV or \*STDIN NOT *ARGV or *STDIN. The whole point of this is to make this WARNING go away which is just some code checking to see that you aren't trying to close the STDIN,STDOUT, or STDERR handles. >>> Argument "*main::STDIN" isn't numeric in numeric eq (==) at >>> /usr/lib/perl5/site_perl/5.8.3/Bio/Root/IO.pm line 483. > And just a comment > actually comparing the resulting files of using each > *STDIN > and \*STDIN > they are the same, even if an error comes out when using *STDIN..... > yep - perl is pretty permissive and does the right thing anyways. > Thanks to all!! > > > Con fecha 28/9/2004, "Thomas J Keller" escribi?: > >> Hoorah, a question I can help with. (I've gotten so much help from >> this >> list, I want to be able to contribute). >> >> Try passing a reference to the glob, instead of the glob itself: i.e. >> change >>> -fh => *STDIN >> to >> -fh => \*STDIN >> >> regards, >> Tom Keller >> >> Tom Keller, Ph.D. >> http://www.ohsu.edu/research/core >> kellert@ohsu.edu >> 503-494-2442 >> >> On Sep 28, 2004, at 8:07 AM, rmaps005@cib.csic.es wrote: >> >>> hello, >>> i was using this program to covert genbank file (actually a human >>> chromosome) to cds but even if it does work and generate some cds, >>> always comes out with this error: >>> >>> Argument "*main::STDIN" isn't numeric in numeric eq (==) at >>> /usr/lib/perl5/site_perl/5.8.3/Bio/Root/IO.pm line 483. >>> >>> don't know if it is because runs out of memory or i made a >>> mistake.... >>> can somebody help me with this? >>> >>> Thanks >>> >>> $seqin = Bio::SeqIO->new( '-format' => 'GenBank', -fh => *STDIN); >>> while((my $seqobj = $seqin->next_seq())) >>> { >>> $genomic_id = $seqobj->display_id; >>> foreach $feat ( $seqobj->top_SeqFeatures() ) { >>> $length = $seqobj->length; >>> if ($feat->primary_tag eq "CDS"){ >>> # Check if protein_id tag exists. >>> if (join(" ",$feat->all_tags()) =~ m/db\_xref/){ >>> $protein_id = >>> join("",$feat->each_tag_value('db_xref')); >>> } >>> else { >>> $protein_id = "UNKNOWN"; >>> } >>> $cds = $feat->location->to_FTstring; >>> if ($cds =~ m/complement/){ >>> $strand = "-"; >>> } >>> else { >>> $strand = "+"; >>> } >>> $cds =~ s/\.\.|,|join\(|\)|complement\(|\(/ /g; >>> print ("$genomic_id\_$protein_id $length $strand $cds >>> \n"); >>> } >>> } >>> } >>> >>> >>> IlohaCIB >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l@portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> > > IlohaCIB > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Jason Stajich jason.stajich at duke.edu http://www.duke.edu/~jes12/ From sdavis2 at mail.nih.gov Wed Sep 29 16:03:05 2004 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Wed Sep 29 16:01:26 2004 Subject: [Bioperl-l] Gene positions In-Reply-To: References: Message-ID: <93917E20-1252-11D9-8492-000A95D7BA10@mail.nih.gov> Probably the easiest way to do this with a fixed set of genes is to use the USCS table browser or ensembl mart. If that won't fit your problem, you can set up a local UCSC database, a Bio::DB::GFF database, or use the Ensembl perl API. Sean On Sep 29, 2004, at 10:44 AM, Marques Bonet wrote: > I'm starting with Bioperl, and I would like to know how obtain the > chromosomal position of a list of genes. > ? > I've been trying some classes, but I've not been able to achieve it. > Which will be the easiest way to do it with BIoperl? > ? > Thanks in advance. > > Reparaciones, servicios a domicilio, empresas, profesionales... Todo > en la gu?a telef?nica de QDQ. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From fzhang at vcu.edu Wed Sep 29 16:21:14 2004 From: fzhang at vcu.edu (Fengkai Zhang (Tony)) Date: Wed Sep 29 16:20:47 2004 Subject: [Bioperl-l] Ask help for Bio::Tools::Run::Primer3 Message-ID: <200409292021.QAA13887@despina.vcu.edu> Hi, I am a newbie for bioperl and met the below question. I was trying to use Bio::Tools::Run::Primer3. When I run the example code in the documentation of this module, I got the following error message: -------------------------------- $ perl -I ../primer3_1.0.0/src/ -w primer3run_test.pl Use of uninitialized value in concatenation (.) or string at /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/Primer3.pm line 212, line 1. primer3 can not be found. Is it installed? -------------------------------- I already installed Primer3 according its instruction and it works well to run the test and example. I also noticed that the primer_test.pl in primer3 package calls "primer3_core" rather than "primer3". Does it matter for Bio::Tools::Run::Primer3 module? Thanks ahead for your help. Tony VIPBG@VCU From kellert at ohsu.edu Wed Sep 29 16:45:04 2004 From: kellert at ohsu.edu (Thomas J Keller) Date: Wed Sep 29 16:45:02 2004 Subject: [Bioperl-l] Ask help for Bio::Tools::Run::Primer3 In-Reply-To: <200409292021.QAA13887@despina.vcu.edu> References: <200409292021.QAA13887@despina.vcu.edu> Message-ID: <70A3249A-1258-11D9-A390-0003930405E2@ohsu.edu> Hi Tony, Jason answered this question not too long ago. I happened to have saved his answer (pasted below). Note that he gave the path to primer3_core >> Hello Bioperlers >> I have been trying to use the BioPerl-run Primer3.pm module to run >> primer3. In doing so I think I have found 2 bugs that prevent it from >> working properly (I hope this is the right place to ask this). > > This is exactly the right place to ask this question > >> >> The line >> my $executable = $self->{'program_dir'}.$self->{'program'}; >> I think should be >> my $executable = $self->{'program_dir'}.$self->{'program_name'}; >> otherwise the primer3 executable is never found using the -path option >> in a call to the constructor >> my $primer3 = >> Bio::Tools::Run::Primer3->new(-path=>'/usr/mbin/primer3_core',- >> seq=>$seq, >> -outfile=>"temp.out"); and rob - I think you want to call $self->program_dir and $self->program so they can overriden as well - that's why I set up the Base Class to have these methods. On Sep 29, 2004, at 1:21 PM, Fengkai Zhang (Tony) wrote: > Hi, I am a newbie for bioperl and met the below question. > > I was trying to use Bio::Tools::Run::Primer3. When I run the example > code in the documentation of this module, I got the following error > message: > -------------------------------- > $ perl -I ../primer3_1.0.0/src/ -w primer3run_test.pl > > Use of uninitialized value in concatenation (.) or string at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/Primer3.pm line 212, > line 1. > primer3 can not be found. Is it installed? > -------------------------------- > > I already installed Primer3 according its instruction and it works > well to run the test and example. I also noticed that the > primer_test.pl in primer3 package calls "primer3_core" rather than > "primer3". Does it matter for Bio::Tools::Run::Primer3 module? > > > Thanks ahead for your help. > > > > Tony > > VIPBG@VCU > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From allenday at ucla.edu Wed Sep 29 16:52:39 2004 From: allenday at ucla.edu (Allen Day) Date: Wed Sep 29 16:52:07 2004 Subject: [Bioperl-l] Re: [Bioperl-guts-l] bioperl commit In-Reply-To: <200409251141.i8PBfT03002463@pub.open-bio.org> References: <200409251141.i8PBfT03002463@pub.open-bio.org> Message-ID: Scott, You can't handle Ontology_term as a SimpleValue, that's why I didn't implement it that way. You need to rather create a Bio::Annotation::OntologyTerm. -Allen On Sat, 25 Sep 2004, Scott Cain wrote: > > scain > Sat Sep 25 07:41:29 EDT 2004 > Update of /home/repository/bioperl/bioperl-live/Bio/FeatureIO > In directory pub.open-bio.org:/tmp/cvs-serv2444/Bio/FeatureIO > > Modified Files: > gff.pm > Log Message: > two things: > * adding SOFA as an available ontology to DocumentRegistry.pm > * modifying FeatureIO::gff to use SOFA to validate, and to parse Ontology_term > > bioperl-live/Bio/FeatureIO gff.pm,1.9,1.10 > =================================================================== > RCS file: /home/repository/bioperl/bioperl-live/Bio/FeatureIO/gff.pm,v > retrieving revision 1.9 > retrieving revision 1.10 > diff -u -r1.9 -r1.10 > --- /home/repository/bioperl/bioperl-live/Bio/FeatureIO/gff.pm 2004/09/21 23:15:22 1.9 > +++ /home/repository/bioperl/bioperl-live/Bio/FeatureIO/gff.pm 2004/09/25 11:41:29 1.10 > @@ -91,8 +91,9 @@ > } > $self->_pushback($directive); > > + #need to validate against SOFA, no SO > $self->so( > - Bio::Ontology::OntologyStore->get_ontology('Sequence Ontology') > + Bio::Ontology::OntologyStore->get_ontology('Sequence Ontology Feature Annotation') > ); > } > > @@ -315,9 +316,9 @@ > } > > #Handle Ontology_term attributes > - if($attr{Ontology_term}){ > - $self->warn("Warning for line:\n$feature_string\nOntology_term attribute handling not yet implemented, skipping it"); > - } > +# if($attr{Ontology_term}){ > +# $self->warn("Warning for line:\n$feature_string\nOntology_term attribute handling not yet implemented, skipping it"); > +# } > > #Handle Gap attributes > if($attr{Gap}){ > @@ -351,7 +352,7 @@ > $ac->add_Annotation('Name',$a); > } > > - foreach my $other_canonical (qw(Alias Parent Note)){ > + foreach my $other_canonical (qw(Alias Parent Note Ontology_term)){ > if($attr{$other_canonical}){ > foreach my $value (@{ $attr{$other_canonical} }){ > my $a = Bio::Annotation::SimpleValue->new(); > > _______________________________________________ > Bioperl-guts-l mailing list > Bioperl-guts-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-guts-l > From jesus.sanchez01 at campus.upf.es Thu Sep 30 12:20:03 2004 From: jesus.sanchez01 at campus.upf.es (jesus sanchez ruiz) Date: Thu Sep 30 06:19:40 2004 Subject: [Bioperl-l] Error with PAML: Can't unlink file ... Message-ID: <1096539603.12701@mail.infomail.es> Hi! I'm trying to walk my first steps with PAML using it with the Bioperl modules; I've seen some example scripts, but I always get an error like this when I run mine: ########### Can't unlink file C:\DOCUME~1\U6179\CONFIG~1\Temp\dMekwOzc9l/mlc: Permission denied at c:/Aplic/ActivePerl/site/lib/Bio/Root/IO.pm line 809 Can't remove directory C:\DOCUME~1\U6179\CONFIG~1\Temp\dMekwOzc9l: Directory not empty at c:/Aplic/ActivePerl/site/lib/Bio/Root/IO.pm line 809 ########### I've been looking the IO.pm and well, probably because I'm not a Perl expert, I don't know what to do with it. Another question: in the HOWTO example it's used Bio::Align::Utilities qw(aa_to_dna_aln); it seems quite simple to use, but I always get this error: #### cannot find *sequence ID* at proves PAML.pl line 41 #### Can somebody help me? Thank you! ________________________________________________________________________________________ Este mensaje ha sido analizado y protegido por la tecnologia antivirus www.trendmicro.es From amackey at pcbi.upenn.edu Thu Sep 30 11:54:28 2004 From: amackey at pcbi.upenn.edu (Aaron J. Mackey) Date: Thu Sep 30 11:53:59 2004 Subject: [Bioperl-l] Attention: upcoming BioPerl 1.5 developer's release Message-ID: <028658BC-12F9-11D9-9C32-000A9577009E@pcbi.upenn.edu> With much-appreciated help from Steve Chervitz and Allen Day, there's about to be a real push towards a 1.5 developer's release; as such, I highly encourage all module authors/maintainers to get in those documentation updates and finish any functionalities you've only "stubbed" in place. I'm not yet declaring a freeze, but don't be surprised if I do so soon ... I have a pretty good idea of the new things that have gone in since 1.4, but it wouldn't hurt you to drop me a private line about any significant new functionality, changed API or bug fixes you've done since the 1.4 releases. You should also check the AUTHORS file and make sure your contact and attribution information is listed as you so desire. Now is also the time for you with "odd" systems (for me that means Sun, SGI, and any Windows) to give the bioperl-live CVS checkout a full make test, and to post your results (preferably only the stuff that didn't work). If you can provide a patch, even better! I hope to have a release candidate available by the end of next week, with the real thing following very shortly thereafter (unless there are show-stoppers, of course) Thanks, -Aaron -- Aaron J. Mackey, Ph.D. Dept. of Biology, Goddard 212 University of Pennsylvania email: amackey@pcbi.upenn.edu 415 S. University Avenue office: 215-898-1205 Philadelphia, PA 19104-6017 fax: 215-746-6697 From EwingAD at hiram.edu Wed Sep 29 16:38:18 2004 From: EwingAD at hiram.edu (Ewing, Adam D.) Date: Thu Sep 30 16:02:32 2004 Subject: [Bioperl-l] Ask help for Bio::Tools::Run::Primer3 Message-ID: Yes, it does matter... simply change the name of primer3_core to primer3, put it in your path, and you should be good to go! Adam -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org on behalf of Fengkai Zhang (Tony) Sent: Wed 9/29/2004 4:21 PM To: bioperl-l@bioperl.org Subject: [Bioperl-l] Ask help for Bio::Tools::Run::Primer3 Hi, I am a newbie for bioperl and met the below question. I was trying to use Bio::Tools::Run::Primer3. When I run the example code in the documentation of this module, I got the following error message: -------------------------------- $ perl -I ../primer3_1.0.0/src/ -w primer3run_test.pl Use of uninitialized value in concatenation (.) or string at /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/Primer3.pm line 212, line 1. primer3 can not be found. Is it installed? -------------------------------- I already installed Primer3 according its instruction and it works well to run the test and example. I also noticed that the primer_test.pl in primer3 package calls "primer3_core" rather than "primer3". Does it matter for Bio::Tools::Run::Primer3 module? Thanks ahead for your help. Tony VIPBG@VCU _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From jsun at utdallas.edu Thu Sep 30 18:48:13 2004 From: jsun at utdallas.edu (Sun, Jian) Date: Thu Sep 30 18:48:00 2004 Subject: [Bioperl-l] Existing bioperl module/function? Message-ID: Dear all; I need some help on this problem: Is there any bioperl module or functions available to be used to get the corresponding nucletide sequence of a certain protein ? Then also can retrive the oligo sequence of a specified peptide segment of this protein sequence? At the NCBI site, we can retrieve the both sequences through its protein and nucleotide database seperately and then find the corresponding matches at the certain sequence position. In bioperl, it is possible that I may can use the reverse translation to soluve this, but it leads to the degenerate sequence, not the one to one match of a certain protein. And I am more interested in the retriving the corresponding nucleotide sequence of the peptide fragment of the same protein. So I just wonder if there is a more direct way through using the existing bioperl module. Thanks in advance Jian Sun From jason.stajich at duke.edu Thu Sep 30 20:01:08 2004 From: jason.stajich at duke.edu (Jason Stajich) Date: Thu Sep 30 20:00:58 2004 Subject: [Bioperl-l] Existing bioperl module/function? In-Reply-To: References: Message-ID: See the example HOWTO Feature-Annotation - if the peptide has a has an annotated CDS you can grab that cross-reference from the genbank file and then use the Bio::DB::GenBank to retrieve that CDS record. From my tutorials you can also see example solution. With some background here http://jason.open-bio.org/Bioperl_Tutorials/Duke_2004/ BioperlProjects.pdf and an answer for retrieval from swissprot/EMBL some modification needed to get it from GenPept/GenBank. http://jason.open-bio.org/Bioperl_Tutorials/Duke_2004/problem_sets/ Project1/get_cds_for_protein.pl -jason On Sep 30, 2004, at 6:48 PM, Sun, Jian wrote: > Dear all; > I need some help on this problem: Is there any bioperl module or > functions available to be used to get the corresponding nucletide > sequence of a certain protein ? Then also can retrive the oligo > sequence of a specified peptide segment of this protein sequence? > > At the NCBI site, we can retrieve the both sequences through its > protein and nucleotide database seperately and then find the > corresponding matches at the certain sequence position. In bioperl, it > is possible that I may can use the reverse translation to soluve this, > but it leads to the degenerate sequence, not the one to one match of a > certain protein. And I am more interested in the retriving the > corresponding nucleotide sequence of the peptide fragment of the same > protein. So I just wonder if there is a more direct way through using > the existing bioperl module. > > Thanks in advance > Jian Sun > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Jason Stajich jason.stajich at duke.edu http://www.duke.edu/~jes12/ From tex at biosysadmin.com Thu Sep 30 20:32:55 2004 From: tex at biosysadmin.com (James Thompson) Date: Fri Oct 1 12:44:49 2004 Subject: [Bioperl-l] Attention: upcoming BioPerl 1.5 developer's release In-Reply-To: <028658BC-12F9-11D9-9C32-000A9577009E@pcbi.upenn.edu> Message-ID: I've run the a "make test" on my CVS version of bioperl-live on a Sun E450 running Solaris 8 and Perl 5.8.5, here's the summary output: Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/CodonTable.t 40 4 10.00% 41-44 t/DB.t 78 2 2.56% 34 39 t/ProtMatrix.t 15 4 26.67% 12-15 t/Registry.t 255 65280 6 3 50.00% 5-6 t/RootStorable.t 2 512 34 56 164.71% 7-34 t/SeqIO.t 2 512 270 386 142.96% 78-270 t/SeqStats.t 28 9 32.14% 10-12 21-24 26 28 t/SimpleAlign.t 255 65280 61 16 26.23% 54-61 t/splicedseq.t 9 4 44.44% 3 5-6 9 111 subtests skipped. I have more detailed output if anyone wants it. Cheers, James On Thu, 30 Sep 2004, Aaron J. Mackey wrote: > > With much-appreciated help from Steve Chervitz and Allen Day, there's > about to be a real push towards a 1.5 developer's release; as such, I > highly encourage all module authors/maintainers to get in those > documentation updates and finish any functionalities you've only > "stubbed" in place. I'm not yet declaring a freeze, but don't be > surprised if I do so soon ... > > I have a pretty good idea of the new things that have gone in since > 1.4, but it wouldn't hurt you to drop me a private line about any > significant new functionality, changed API or bug fixes you've done > since the 1.4 releases. You should also check the AUTHORS file and > make sure your contact and attribution information is listed as you so > desire. > > Now is also the time for you with "odd" systems (for me that means Sun, > SGI, and any Windows) to give the bioperl-live CVS checkout a full make > test, and to post your results (preferably only the stuff that didn't > work). If you can provide a patch, even better! > > I hope to have a release candidate available by the end of next week, > with the real thing following very shortly thereafter (unless there are > show-stoppers, of course) > > Thanks, > > -Aaron > > -- > Aaron J. Mackey, Ph.D. > Dept. of Biology, Goddard 212 > University of Pennsylvania email: amackey@pcbi.upenn.edu > 415 S. University Avenue office: 215-898-1205 > Philadelphia, PA 19104-6017 fax: 215-746-6697 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From tex at biosysadmin.com Thu Sep 30 22:00:08 2004 From: tex at biosysadmin.com (James Thompson) Date: Fri Oct 1 14:12:00 2004 Subject: [Bioperl-l] Attention: upcoming BioPerl 1.5 developer's release In-Reply-To: Message-ID: Jason, > Hey James - isn't this your module - you need to implement get_string() > in ProtMatrix. You're right, and I'm working on it. :) I just finished the implementation a while ago, and I'm re-running "make test" right now. Sorry about that, I should have mentioned this in my e-mail this morning. I'm just ironing out a few more methods in ProtMatrix.pm. Should be finished by the end of today. Quick question - would it be more useful to everyone if I set the BIOPERLDEBUG variable before I ran "make test"? If so, let me know and I'll re-run it and e-mail results to the list. James > > t/Registry.t 255 65280 6 3 50.00% 5-6 > > t/RootStorable.t 2 512 34 56 164.71% 7-34 > > t/SeqIO.t 2 512 270 386 142.96% 78-270 > > t/SeqStats.t 28 9 32.14% 10-12 21-24 26 28 > fixed, needed to round > > t/SimpleAlign.t 255 65280 61 16 26.23% 54-61 > > t/splicedseq.t 9 4 44.44% 3 5-6 9 > fixed > > 111 subtests skipped. > > > > I have more detailed output if anyone wants it. > > > > Cheers, > > > > James > > > > On Thu, 30 Sep 2004, Aaron J. Mackey wrote: > > > >> > >> With much-appreciated help from Steve Chervitz and Allen Day, there's > >> about to be a real push towards a 1.5 developer's release; as such, I > >> highly encourage all module authors/maintainers to get in those > >> documentation updates and finish any functionalities you've only > >> "stubbed" in place. I'm not yet declaring a freeze, but don't be > >> surprised if I do so soon ... > >> > >> I have a pretty good idea of the new things that have gone in since > >> 1.4, but it wouldn't hurt you to drop me a private line about any > >> significant new functionality, changed API or bug fixes you've done > >> since the 1.4 releases. You should also check the AUTHORS file and > >> make sure your contact and attribution information is listed as you so > >> desire. > >> > >> Now is also the time for you with "odd" systems (for me that means > >> Sun, > >> SGI, and any Windows) to give the bioperl-live CVS checkout a full > >> make > >> test, and to post your results (preferably only the stuff that didn't > >> work). If you can provide a patch, even better! > >> > >> I hope to have a release candidate available by the end of next week, > >> with the real thing following very shortly thereafter (unless there > >> are > >> show-stoppers, of course) > >> > >> Thanks, > >> > >> -Aaron > >> > >> -- > >> Aaron J. Mackey, Ph.D. > >> Dept. of Biology, Goddard 212 > >> University of Pennsylvania email: amackey@pcbi.upenn.edu > >> 415 S. University Avenue office: 215-898-1205 > >> Philadelphia, PA 19104-6017 fax: 215-746-6697 > >> > >> _______________________________________________ > >> Bioperl-l mailing list > >> Bioperl-l@portal.open-bio.org > >> http://portal.open-bio.org/mailman/listinfo/bioperl-l > >> > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > -- > Jason Stajich > jason.stajich at duke.edu > http://www.duke.edu/~jes12/ > > From tex at biosysadmin.com Thu Sep 30 22:49:40 2004 From: tex at biosysadmin.com (James Thompson) Date: Fri Oct 1 15:01:29 2004 Subject: [Bioperl-l] Questions on Representing Protein Ambiguity In-Reply-To: Message-ID: Bioperl-ers, I'm currently working on an implementation of a protein-specific Position Specific Matrix based of the design in Bio::Matrix::PSM::SiteMatrix and SiteMatrixI. I'm a uncertain about the best way to calculate a consensus sequence based on a protein PSM, and I'd appreciate some input. When dealing with nucleotides in a consensus sequences, it's possible to use IUB ambiguity codes for ambiguous positions (for example, an 'S' maps to an 'A' or 'G'). With protein alphabets it's not possible to represent all of the combinations with a single letter, and I'm not certain exactly how to deal with this. One solution (currently in ProtMatrix.pm) simply takes the most probable amino acid at each position and puts an 'X' in any position below a threshold. This isn't bad, but it loses some information on all of the amino acids that are above the threshold but not the most probable. An alternative would be to borrow an idea from Perl's regex character classes and represent multiple residues at a position inside of a set of brackets, like this: M[ES]N[IAP]S However, this may not be compatible with what people expect out of a consensus sequence. One compromise that I could think of would be to leave the consensus sequence stuff alone and make the regexp method of ProtMatrix take an argument as a threshold. That way consensus sequences have one letter per position, but there's still a way for a user to get at information if desirable. Does this compromise sound reasonable? Any input on the subject is greatly appreciated. :) Thanks, James Thompson