[Bioperl-l] extracting CDS location from Genbank

[michael watson (IAH-C)]

Same script as below, but try:

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

-----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 15:42
To: Bioperl-l at lists.open-bio.org
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:
> 
> Post the script that produces that error, and your file's location 
> 
> -----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 15:07
> To: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] extracting CDS location from Genbank
> 
> 
> Yes but actually implementing it is another story.
> 
> I get an error:
> 
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: file argument provided, but with an undefined value
> STACK: Error::throw
> STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio/Root/Root.pm:359
> STACK: Bio::SeqIO::new C:/Perl/site/lib/Bio/SeqIO.pm:359
> STACK: test3.pl:7
> -----------------------------------------------------------
> 
> Basically because I dont understand the code well enough.  For
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:
>
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> l#a14152264
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> 
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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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