[Bioperl-l] pubmed not used in Bio::Annotation::Reference if medline is present

[Brian Osborne]

Fernan,

What is the $dataFile or id?

Brian O.


On 6/13/05 12:22 PM, "Fernan Aguero" <fernan at iib.unsam.edu.ar> wrote:

> Hi!
> 
> I'm parsing GenBank files using bioperl-1.4:
> 
> my $bpSeqIoObj   = Bio::SeqIO->new
> ( -format => 'GenBank', -file => $dataFile );
> 
> while ( my $bpSeqObj = $bpSeqIoObj->next_seq() ) {
>   my $bpAnnotObj = $bpSeqObj->annotation();
>   my @bpRefObjs = $bpAnnotObj->get_Annotations('reference');
>   my $bpRefObj = shift(@bpRefObjs);
> 
>   my $pubmed = $bpRefObj->{'pubmed'};
>   my $medline= $bpRefObj->{'medline'};
>   
>   ...
> }
> 
> The problem that I'm seeing is that whenever a genbank
> record has both PUBMED and MEDLINE IDs,
> $bpRefObj->{'pubmed'} is empty.
> 
> It would be OK if ->{'medline'} was empty, since MEDLINE has
> been replaced by pubmed, but this is not the case.
> 
> Anyone can confirm this? I haven't found any bugs open
> related to this issue. Perhaps it's already fixed in 1.5 or
> in CVS? I can fix it if I knew who is loading the
> Bio::Annotation object upon parsing the GenBank file ...
> 
> Fernan
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