[Bioperl-l] Clustalw problems!!!

[duxroq]

Hi, I'm not sure whether my program is not finding the clustal w exceutable
or if it is having trouble with the module itself.  Here is my error, in the
image below:

http://old.nabble.com/file/p31509401/Untitled.png Untitled.png 

here is my code:


#!/usr/bin/local/perl -w

use Bio::Perl;
use Bio::AlignIO;
use Bio::Root::IO;
use Bio::Seq;
use Bio::SeqIO;
use Bio::SimpleAlign;
use Bio::TreeIO; 

#--------------------------------------------------------------------------------#

# Main

	unless(($#ARGV + 1) > 1) {
       		print_start_message();
        	exit;
	}

	BEGIN { $ENV{CLUSTALDIR} = 'C:\Program Files\clustalw.exe'}	#-Set
CLUSTALDIR to correct directory
	use Bio::Tools::Run::Alignment::Clustalw;

	my $file_name1 = $ARGV[0];					#-name of file containing all sequences
	my @sequences = read_all_sequences($file_name1,'fasta');

#	alt_revcom(\@sequences);					#-reverse complement of every other seq
#	print_sequences(@sequences);

	my @params = ('outfile' => 'mult_aln.aln');			#-sets parameters for
alignment factory
###################################################
#
#
#
#The error is probably in the next few lines! agh!#
#
#
#
###################################################
	my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
$clustalfound = Bio::Tools::Run::Alignment::Clustalw->exists_clustal(); 
	if ($clustalfound) {
	print "\n we found it!!!\n" }
	my $aln = $factory->align(\@sequences);
	print "\nDevins name is bob. \n";
				#-creates alignment	
	print "\nPercentage Identity:\n",$aln->percentage_identity,"\n\n";

	my $cons_str = $aln->consensus_iupac();				#-configures consensus using
IUPAC codes
	my $cons_name = "Consensus_".save_id(@sequences);
	my $cons_seq = new_sequence($cons_str, $cons_name);

	write_seq_to_file(">cons.fa",$cons_seq);			#-writes consensus to file

	my $file_name2 = $ARGV[1];
	my $lead_seq = read_sequence($file_name2,'fasta');		#-compare consensus
sequence to leader

#	print_sequences($lead_seq);
#	print_sequences($cons_seq);

	my @lead_cons_seqs = ($lead_seq, $cons_seq);			#-forms array for alignment
of leader and consensus
	@params = ('pairgap' => 50);

	print "\n bobisnotmyname\n";

	$factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
	my $aln_lead_cons = $factory->align(\@lead_cons_seqs);
	print "\nPercentage
Identity:\n",$aln_lead_cons->percentage_identity,"\n\n";

	my $seq_len = $aln_lead_cons->length();

	my @aln_seqs = ();						#-array of aligned sequences, including gaps
	my $i = 0;
	foreach $seq ($aln_lead_cons->each_seq() ) {
		$aln_seqs[$i] = $seq;
		$i++;
	}
#	print_sequences(@aln_seqs);

	my $l_aln_str = '';						#-str of leader sequence from alignment
	my $c_aln_str = '';						#-str of consensus sequence from alignment
	$found = 0;
	$i = 1;
	while ($found == 0 && $i < $seq_len) { 		

		$l_aln_str = substr($aln_seqs[0]->seq(),$i,1);		#-gets a substring from
l_aln_str
		if ($l_aln_str !~ m/\./i) {
									#-checks if substring has gap characters
			$cons_slice_str = substr($aln_seqs[1]->seq(),$i,490);
			$found = 1;					#-retrieves 490 characters of consensus where
		}
		$i++;							#-leader begins in alignment
	}

	$cons_slice_seq = new_sequence($cons_slice_str,"Sliced_".$cons_name);
#	print_sequences($cons_slice_seq);
	write_seq_to_file(">cons_slice.fa",$cons_slice_seq);


# End Main

#--------------------------------------------------------------------------------#

# Subroutines

	sub alt_revcom {	
		my @sequences = @_;
		for ( $i=0; $i <= $#sequences; $i++) {
       	 		if ($i%2==1) {
                		$sequences[$i] = reverse_complement($sequences[$i]);
			}
	        }
	}

	sub save_id {
		my @sequences = @_;
		$id = $sequences[0]->display_id;
		return $id;
	}

	sub print_sequences {
		my @sequences = @_;
		for ($i = 0; $i <= $#sequences; $i++) {
			print "Sequence name:",$sequences[$i]->display_id,"\n";
       			print "Sequence acc:",$sequences[$i]->accession_number,"\n";
    			print $sequences[$i]->seq(),"\n";
		}
	}

	sub write_seq_to_file {
		my ($file_name,$seq) = @_;
		write_sequence($file_name,'fasta',$seq);
 		print "\n",$seq->display_id," written to file.\n\n";
	}

	
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