[Bioperl-l] clustalw

Luba Pardo lubapardo at gmail.com
Tue Mar 6 05:56:52 EST 2007

I tried to post this question yesterday (sorry if you get the email several
I am trying to run a script for Clustalw based on few examples. I always get
an error:

EXCEPTION: Bio::Root::Exception -------------
MSG: Bad input data (sequences need an id ) or less than 2 sequences in
ARRAY(0x8861280) !
STACK: Error::throw
STACK: Bio::Root::Root::throw
STACK: Bio::Tools::Run::Alignment::Clustalw::align
STACK: clustal1.pl:17

EXCEPTION: Bio::Root::NotImplemented -------------
MSG: Abstract method "Bio::Tools::Run::WrapperBase::run" is not implemented
by package Bio::Tools::Run::Alignment::Clustalw.
This is not your fault - author of Bio::Tools::Run::Alignment::Clustalw
should be blamed!

No matter if I used a scalar  inputfile  or a SeqIO object. I also run the
clustalw.pl script, but I can not run the example number 3.
Is there anything going with the clustalw module? Because clustalw runs OK
with my files if I use it without Bioperl.


BEGIN {$ENV{CLUSTALDIR} = '/home/luba/bin/clustalx1.82.linux/';}

use Bio::SeqIO;
use Bio::Tools::Run::Alignment::Clustalw;
use Bio::SimpleAlign;
use Bio::AlignIO;
#use strict;
use warnings;

my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
  my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);

  my $str = Bio::SeqIO->new(-file=> 'clustalw.fa ', '-format' => 'Fasta');
  my @seq_array =();
  while ( my $seq = $str->next_seq() ) {push (@seq_array, $seq) ;}
  my $seq_array_ref = \@seq_array;

  my $aln = $factory->align($seq_array_ref);

   # Get a tree of the sequences
  $tree = $factory->tree(\@seq_array);

  # Get both an alignment and a tree
  ($aln, $tree) = $factory->run(\@seq_array);

  # Do a footprinting analysis on the supplied sequences, getting back the
  # most conserved sub-alignments
  my @results = $factory->footprint(\@seq_array);
  foreach my $result (@results) {
    print $result->consensus_string, "\n";

Thanks in advance,

L. Pardo

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