[Bioperl-l] Help for using Clustalw.pm

[James Wasmuth]

Ooops,

I seem to have errant asterisks

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


James Wasmuth wrote:

> 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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>>  
>>
>

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