[Bioperl-l] Bio::SeqIO - Error in ID value collection

[Damien Pradel]

Hello,

I use the SeqIO module in order to  parse EMBL files.
Unfortunately I got a problem: the ID was not recognised because instead of
the ID value  I get the answer "unknown_id" ...

So to solve this problem I have modified the file embl.pm located in
directory SeqIO at the line 189 as follow :

if( $line =~ /^ID\s+(\S+)\s+\S+\;\s+([^;]+)\;\s+(\S+)\;/ ) {
       ($name,$mol,$div) = ($1,$2,$3);
   }
   unless( defined $name && length($name) ) {
       $name = "unknown_id";
   }

in :
if( $line =~ /^ID\s+(.+?)\;\s+([^;]+)\;\s+(\S+)\;/ ) {
       ($name,$mol,$div) = ($1,$2,$3);
   }
   unless( defined $name && length($name) ) {
       $name = "unknown_id";
   }

With this modification, the ID value is correctly collected.

Hope it will help.

Damien