Re: extracting CDS location from Genbank

Same script as below, but try:

my $file = 'C:\path\to\my\filename.gbk';

-----Original Message-----
From: bioperl-l-bounces@...
[mailto:bioperl-l-bounces@...] On Behalf Of Captainrave
Sent: 04 December 2007 15:42
To: Bioperl-l@...
Subject: Re: [Bioperl-l] extracting CDS location from Genbank


#!/bin/perl

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;

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";            
      }          
   }      
}

exit;

The file is on the same folder.  But how do I tell it to use this file?



michael watson (IAH-C) wrote: example,
> how
> do I tell it which input file to read? I know this might sound stupid,
> but I
> dont understand the Biowiki very well!
>
> --
> View this message in context:
>
http://www.nabble.com/extracting-CDS-location-from-Genbank-tf4942483.htm
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View this message in context:
http://www.nabble.com/extracting-CDS-location-from-Genbank-tf4942483.htm
l#a14152907
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