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

Fernan Aguero fernan at iib.unsam.edu.ar
Mon Jun 13 12:22:07 EDT 2005


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been replaced by pubmed, but this is not the case.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 ...


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