[Bioperl-l] EMBL Identifier line is incorrect when using SeqIO (1.4)

Bernhard Schmalhofer Bernhard.Schmalhofer at biomax.de
Thu Oct 21 12:49:21 EDT 2004

Hilmar Lapp wrote:

 >> Using bioperl-1.4 on Suse Linux, I find that when writing sequences in
 >> EMBL format using SeqIO, there is no space left after the display_id
 >> e.g.
 >> "J18191-1h03.p1k" becomes "ID   J18191-1h03.p1kstandard; DNA; UNK; 1657
 >> BP.

> If you make the ID shorter, is there still no space? I believe the ID is 
> length-limited in EMBL, but I'd have to check the specs to be sure.
>     -hilmar

I have run into the same problem. For the application I'm currently 
working on, I'm using a wrapper around Bio::SeqIO that does a

   if ( $content =~ m/^ID\s+\S+standard; / )
     # This seems to be a bug in Bio::SeqIO
     $content =~ s/standard; / standard; /;

In the BioPerl-CVS there is a version that truncates the ID to 10 
charactes and leaves a space before the 'standard;'.

CU, Bernhard

Dipl.-Physiker Bernhard Schmalhofer
Senior Developer
Biomax Informatics AG
Lochhamer Str. 11
82152 Martinsried, Germany
Tel: +49 89 895574-839
Fax: +49 89 895574-825
eMail: Bernhard.Schmalhofer at biomax.com
Website: www.biomax.com

More information about the Bioperl-l mailing list