[Bioperl-l] Retrieving Comments field from GenBank file usin SeqIO?

[Jamie Hatfield]

> [mailto:bioperl-l-admin@bioperl.org] On Behalf Of Dere, Ed
> Is there a method to retrieve the Comments field from a GenBank file?

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use Bio::SeqIO;

my $in     = Bio::SeqIO->new(-file=>"yourfile.gb", -format=>"genbank");
my $seq    = $in->next_seq();
my @values = $seq->annotation()->get_Annotations('comment');
print "Comment = ", $values[0]->as_text(), "\n";
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$seq is a Bio::Seq.  $seq->annotation is a Bio::Annotation::Collection.
Bio::Annotation::Collection->get_Annotations('comment') returns a list
of Bio::Annotation::SimpleValue objects, which have ->as_text() methods.

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Jamie Hatfield                              Room 541H, Marley Building
Systems Programmer                          University of Arizona
Arizona Genomics Computational              Tucson, AZ  85721
  Laboratory (AGCoL)                        (520) 626-9598