[Bioperl-l] ClustalW alignment and Bioperl::Run module

Kevin Brown Kevin.M.Brown at asu.edu
Thu Sep 28 21:48:15 UTC 2006

I've gotten a very simple script to run using bioperl that creates an
alignment using clustalw of two sequences.  I see that clustal outputs
to stdout information like the score, but I don't see any way to store
that or retrieve that from the alignment object that is returned (unless
I'm just blind).  What follows is my very basic script which used code
found in the Wiki.

print $aln->score() spits out an error about using an uninitialized

#!/usr/bin/perl -w

use strict;
use Bio::SeqIO;
use Bio::Perl;
use Bio::AlignIO;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use POSIX;
use Bio::Tools::Run::Alignment::Clustalw;

my $fileName   = "";         # filename(s) to be parsed for information
my $output_dir = "";
my $format     = 'fasta';    # default format for SeqIO module

                   'file=s'   => \$fileName,
                   'output=s' => \$output_dir,

# Parse the input file for the needed information
# SeqIO supports several normal formats including <tab>, <fasta> and

my @files = split(/\|/, $fileName);
my @seq_array;

my $stream_out =
  Bio::AlignIO->new(-file => '>test.msf', -format => 'msf', -flush =>

foreach my $fileName (@files)
        my $file = Bio::SeqIO->new(-format => $format, -file =>
        my $seq;
        while ($seq = $file->next_seq())
                push(@seq_array, $seq);

my @params  = ('ktuple' => 2, 'matrix' => 'BLOSUM');
my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
my $ktuple  = 3;
$factory->ktuple($ktuple);    # change the parameter before executing
    # where @seq_array is an array of {{PM|Bio::Seq}} objects

open my $out, ">seq.txt";

for (my $i = 1 ; $i <= $#seq_array ; $i++)
        my @seq = ($seq_array[0], $seq_array[$i]);
        my $aln = $factory->align(\@seq);
        print $aln->score;
        for my $seq ($aln->each_seq) {
                print $out $seq->display_id() ."\t". $seq->seq()."\n";

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