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

[Chris Fields]

The parser no longer has this line; it has been updated to work with  
both old and new format EMBL.  You might want to try updating from  
Subversion or install the nightly build.

http://bioperl.org/DIST/nightly_builds/

chris

On Mar 31, 2008, at 9:35 AM, Damien Pradel wrote:
> 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
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign