[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

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 =~
) {
+				if( $id =~
) {
 				    $db = $1;

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

I will attach the lot



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