[Bioperl-l] Bio::Index::AbstractSeq->fetch() overwrites primary_id with display_id

[Matthew Betts]

Hi,

I was wondering why the fetch method of Bio::Index::AbstractSeq
overwrites primary_id with display_id:

    # 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'));

This means that I lose the GI number from GenBank entries, which doesn't 
happen if I read them directly with SeqIO (i.e. without using an index).

Thanks,

Matthew

-- 
Matthew Betts, mailto:matthew.betts at ii.uib.no
Phone: (+47) 55 58 40 22, Fax: (+47) 55 58 42 95
CBU, BCCS, HiB, UNIFOB / Universitetet i Bergen
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