[Bioperl-l] parsing entrezgene file (lost data)

Carnë Draug carandraug+dev at gmail.com
Mon Jul 4 02:38:36 UTC 2011


I've been trying to get some data from an ASN.1 entrezgene file.
However, I can't seem to access some of the data on the file.  I've
read the Feature-annotations page on the wiki (even fixed a bug in
there) but still nothing. So I used Data::Dumper to look at the Seq
and Annotation objects and couldn't see it in there at all although
it's on the original file (attached).

The data I want from the sequence are the ids "NM_002105" and
"NP_002096" which show up several times on the file. However, when I
do this:

use Data::Dump;
use Bio::SeqIO;
my $file = $ARGV[0];
my $seqio_object = Bio::SeqIO->new(-file => $file, -format => 'entrezgene');
my $seq_object = $seqio_object->next_seq;
print Dumper($seq_object);

I can't find 002105 or 002096 anywhere on the output.

Am I doing something wrong? How can I solve this?

Thanks in advance,
Carnë Draug
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