[Bioperl-l] Extracting gi no from refseq record

[Siddhartha Basu]

Hi,

That worked like a charm, thanks a lot hilamar.
Now i am facing another new problem. I wonder whether bioperl is able to 
deal with the swissprot entries having multiple id lines and of course 
multiple taxon ids. Because the Bio::Index::Swissprot module is stopping 
on those ids having mulitple lines. Any idea how to deal with these ids.
And why the entries have such multiple lines.

bye
siddhartha

Hilmar Lapp wrote:
> The problem is not in SeqIO. The offending statement is in the method  
> fetch() in Bio::Index::AbstractSeq, which is the method that does the  
> actual retrieval work. The chunk of input is handed off to  
> SeqIO::genbank, which I'm sure does the right job, only to be  
> overwritten after it returns the parsed sequence object to fetch():
> 
>     # we essentially assumme that the primary_id for the database
>     # is the display_id
>     $seq->primary_id($seq->display_id()) if( defined $seq && ref($seq)  &&
>                          $seq->isa('Bio::PrimarySeqI') );
> 
> Can anyone explain the usefulness of this statement? Otherwise we just  
> delete it and the bug is fixed. (Siddharta, as an immediate fix you  
> might just want to do this.)
> 
>     -hilmar