[Bioperl-l] Help for using Clustalw.pm

[James Wasmuth]

Jane,

Try:

$clustalfound = *Bio::Tools::Run::Alignment::Clustalw*->exists_clustal()

print "$clustalfound";

if '0' then it can't find an executable of clustalw. Does it work from 
the commandline ?

-james


Sun, Jian wrote:

>Dear all:
>     I tried to align multiple sequence through Clustalw.pm, and I used the source code attached below:
>*****************************************************************************************************
>#!C:\Perl\bin\perl.exe
>use lib "C:\Perl\lib";
> 
>use Bio::Perl;
>use Bio::Tools::Run::Alignment::Clustalw;
>use strict;
>use warnings;
> 
>$ENV{CLUSTALDIR} = 'C:/Program Files/Apache Group/Apache2/bin/';
>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
>  my $str = Bio::SeqIO->new(-file=> 'Clustseq.fa', '-format' => 'Fasta');
> my @seq_array =();
> while ( my $seq = $str->next_seq() ) {push (@seq_array, $seq) ;}
>  my $seq_array_ref = \@seq_array;
>      # where @seq_array is an array of Bio::Seq objects
>  my $aln = $factory->align($seq_array_ref);
>**************************************************************************
> 
>and when I run the pl file, I get this error message:
> 
>///////////////////////////////////////////////////////////////////////////////////////////
>Clustalw program not found as clustalw or not executable.
>......  
>'clustalw' is not recognized as an internal or external command, 
>operable program or batch file.
>---------------------EXCEPTION-----------------------------------------
>MSG: Clustalw call <clustal align -infile=C:\...\> crashed:256
> 
>STACK Bio::Tools::Run::Alignment::Clustalw::_run c:/Perl/Site/Lib/Bio/Toold/Run/Alignment/Clustalw.pm:581
>STACK Bio::Tools::Run::Alignment::Clustalw::_run c:/Perl/Site/Lib/Bio/Toold/Run/Alignment/Clustalw.pm:507
>STACK toplevel test726pl.pl:33
>-----------------------------------------------------------------------------------------
>///////////////////////////////////////////////////////////////////////////////////////
> 
>Since I already set the CLUSTALDIR variable, I don't know why the Clustalw is still not execuatable. Did I did the right setting?  Does anyone have this kind of experience? 
> 
>Thanks in advance.
>Jane
> 
>
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