[Bioperl-l] Parsing ClustalW reports

[Brian Osborne]

Rhazes,

Your code looks right. What version of bioperl are you using and how did you
get a hold of the file act1.aln? My first suspicion is that something's
wrong with that input file.

Also, bear in mind that no sequence descriptions can be obtained from a
clustalw output file, a better test might be to print $seq->seq or $seq->id,
for example.

Brian O.


-----Original Message-----
From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]On
Behalf Of Rhazes Spell
Sent: Saturday, June 29, 2002 3:15 PM
To: bioperl-l@bioperl.org
Subject: [Bioperl-l] Parsing ClustalW reports

I am having trouble parsing a ClustalW report.  After creating the stream
I call the next_aln method, but I don't get an alignment object.  I
assume that I making a simple newbie mistake.  If anyone could be of
assistance I would
appreciate it.

Here is a simple script and the output generated:

use strict;
use Bio::AlignIO;

my $stream  = Bio::AlignIO->new(-format =>'clustalw',
                                -file=>'act1.aln');
my $aln = $stream->next_aln();

foreach my $seq ( $aln->each_seq() ) {
    print $seq->desc();
}

OUTPUT:
perl clustalParse.pl
Can't call method "each_seq" on an undefined value at clustalParse.pl line
21, <GEN0> line 44.



Thanks in advance
Rhazes Spell

**************************************
Duke University
Department of Biomedical Engineering
Duke University Medical Center,
 Center for Genome Technology

rhazes.spell@duke.edu
919.684.2720
***************************************

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