[Bioperl-l] Clustalw problems!!!

[Chris Fields]

I don't have access to a Windows machine to test this, unfortunately.  I did notice you set CLUSTALWDIR to the actual executable, NOT the directory it is in.  Also, the executable name is 'clustalw.exe', not 'clustalw', so possibly change that prior to instantiation:

$Bio::Tools::Run::Alignment::ClustalW::PROGRAM_NAME = 'clustalw.exe';

Maybe that's a start?

chris

On Apr 29, 2011, at 5:45 PM, duxroq wrote:

> 
> 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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> 
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