parse genebank for gene name/ id
newtoperlprog <[email protected]>
| Newsgroups | gmane.comp.lang.perl.bio.general |
|---|---|
| Message-ID | <[email protected]> |
Dear All,
I am trying to parse a genebank summary files for the following records:
Sequence, description, division, GI number, gene id/name, version and
organism.
I used a script from the bioperl webpage and used to parse the above.
I am getting problem parsing the gene id/name, version and cds information,
organism.
Could you please help with the same.
Below is the code I am using:
#!/usr/bin/perl
use strict;
use warnings;
use Bio::SeqIO;
use Bio::Seq;
my $seqobj;
my $file = "NM_000040.summary";
my $seqio = Bio::SeqIO->new (-format => 'GenBank',
-file => $file);
print ref($seqio);
while ($seqobj = $seqio->next_seq ()) {
printf "Sequence: %s\n",$seqobj->seq;
printf "Display ID: %s\n",$seqobj->display_id;
printf "Description: %s\n",$seqobj->desc;
printf "Division: %s\n",$seqobj->division;
printf "Accession: %s\n",$seqobj->accession_number;
printf "GI number: %s\n",$seqobj->primary_id;
printf "Definition: %s\n",$seqobj->seq_version;
}
Any help is greatly appreciated.
Regards
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