[Bioperl-l] extracting CDS location from Genbank

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Tue Dec 4 09:48:27 EST 2007

>From the SeqIO howto:


use strict;
use Bio::SeqIO;

my $file = shift; # get the file name, somehow
my $seqio_object = Bio::SeqIO->new(-file => $file);
my $seq_object = $seqio_object->next_seq;

>From the Feature HOWTO:

for my $feat_object ($seq_object->get_SeqFeatures) {          
   print "primary tag: ", $feat_object->primary_tag, "\n";          
   for my $tag ($feat_object->get_all_tags) {             
      print "  tag: ", $tag, "\n";             
      for my $value ($feat_object->get_tag_values($tag)) {

         print "    value: ", $value, "\n";             

Surely you could have fouind that yourself? ;0 

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Captainrave
Sent: 04 December 2007 11:05
To: Bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] extracting CDS location from Genbank

Help.  I'm very new to perl and bioperl.  Basically I need to extract
location of each CDS in a genbank entry e.g.103...120 and export them to
output file as a list.  How would I do this?

Your help would be much appreciated!
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