[Bioperl-l] Parsing ClustalW reports

Rhazes Spell rus1@duke.edu
Sat, 29 Jun 2002 15:15:08 -0400 (EDT)

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',
my $aln = $stream->next_aln();

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

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