[Bioperl-l] Bio/SeqIO/genbank.pm patch

Erik er at xs4all.nl
Thu Nov 16 16:01:12 EST 2006


Hi all,

Using bioperl-live, I noticed a problem with the parsing in
Bio/SeqIO/genbank.pm.

It occurs in the DBSOURCE section, where the 'dblink' annotation gets its
values. I got several values that had a double colon, like
InterPro::IPR011000 etc. Not all 'dblink' values were affected.

Here is a patch which seems to fix it / it works for me:

=======
--- Bio/SeqIO/genbank.pm.orig	2006-11-16 18:33:30.060417520 +0100
+++ Bio/SeqIO/genbank.pm	2006-11-16 20:29:59.014934936 +0100
@@ -504,7 +504,7 @@
 				my $db;
 				# this is because GenBank dropped the spaces!!!
 				# I'm sure we're not going to get this right
-				if( $id =~
s/^(EchoBASE|IntAct|SWISS-2DPAGE|ECO2DBASE|ECOGENE|TIGRFAMs|TIGR|GO|InterPro|Pfam|PROSITE|SGD|GermOnline|HSSP|PhosSite)//i
) {
+				if( $id =~
s/^(EchoBASE|IntAct|SWISS-2DPAGE|ECO2DBASE|ECOGENE|TIGRFAMs|TIGR|GO|InterPro|Pfam|PROSITE|SGD|GermOnline|HSSP|PhosSite)://i
) {
 				    $db = $1;
 				}
 				$annotation->add_Annotation=======


I also wrote a few tests for the problem, which also needed an extra file
in t/data.

I will attach the lot

hth,

Erik


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