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Re: extracting CDS location from Genbank

by Captainrave :: Rate this Message:

#!/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@lists.open-bio.org
[mailto:bioperl-l-bounces@lists.open-bio.org] On Behalf Of Captainrave
Sent: 04 December 2007 15:07
To: Bioperl-l@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!

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