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The Basics
Id: 44536
Status: resolved
Priority: 0/
Queue: bioperl

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Owner: cjfields [...] uiuc.edu
Requestors: gresham [...] cse.msstate.edu
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Subject: BioPerl, NCBI Eutilities genbank format
Date: Tue, 24 Mar 2009 16:02:15 -0500
To: <bug-bioperl [...] rt.cpan.org>
From: "Cathy Gresham" <gresham [...] cse.msstate.edu>
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BioPerl version 1.6.0 Perl version 5.8.8 Linux Suse version 10 sp2 Noticed that the genbank format in BioPerl was not returning all the DBSOURCES. especially the xrefs (non-sequence databases): my @db_links=(); my $collection = $seq->annotation; for my $dblink ( $collection->get_Annotations('dblink')) { # my $temp_link = sprintf("%s:%s",$dblink->database,$dblink->primary_id); my $temp_link = $dblink->database . ":" . $dblink->primary_id; push (@db_links,$temp_link); } Looked in genbank.pm saw where it was only going to return them if the DBSOURCE had an initial line of swissprot: the line I had was UniProtKB: I added the following lines idb:/usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO # diff genbank.pm genbankKEEP.pm 463,465c463 < if (($dbsource =~ s/swissprot:\s+locus\s+(\S+)\,.+\n// ) || < ($dbsource =~ s/UniProtKB:\s+locus\s+(\S+)\,.+\n// ) || < ($dbsource =~ s/UniProt:\s+locus\s+(\S+)\,.+\n// )) { --- Show quoted text
> if( $dbsource =~ s/swissprot:\s+locus\s+(\S+)\,.+\n// ) {
seems to be returning the values now. Cathy
This is now fixed in the BioPerl svn main trunk and will be in the 1.6.1 release. Thanks!


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