[Bioperl-l] Clustalw

[Kevin Brown]

Do you have ClustalW installed and in your path? 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Offord, Victoria
> Sent: Monday, June 22, 2009 9:11 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Clustalw
> 
> Hi,
> 
>  
> 
> Can anyone help and tell me where I am going wrong please J 
> 
> I am getting this error from the following script:
> 
>  
> 
>  
> 
> ------------- EXCEPTION: Bio::Root::Exception -------------
> 
> MSG: ClustalW call (clustalw align  -infile=/tmp/8PVli9JWEa/L_pxrEtzD1
> -output=gcg   -matrix=BLOSUM -ktuple=2
> -outfile=/tmp/8PVli9JWEa/XtAremlqau 2>&1) failed to start: 0 | No such
> file or directory
> 
> STACK: Error::throw
> 
> STACK: Bio::Root::Root::throw
> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
> 
> STACK: Bio::Tools::Run::Alignment::Clustalw::_run
> /usr/lib/perl5/site_perl/5.8.8/Bio/Tools/Run/Alignment/Clustalw.pm:756
> 
> STACK: Bio::Tools::Run::Alignment::Clustalw::align
> /usr/lib/perl5/site_perl/5.8.8/Bio/Tools/Run/Alignment/Clustalw.pm:515
> 
> STACK: tester.pl:25
> 
> -----------------------------------------------------------
> 
>  
> 
>  
> 
>  
> 
>  
> 
> #--------------------------------------------SCRIPT-----------
> ----------
> --------------------------#
> 
> #!/usr/bin/perl -w
> 
> use Bio::Tools::Run::Alignment::Clustalw;
> 
> $ENV{CLUSTALDIR} = '/var/local/clustalw-2.0.9';
> 
> use Bio::Seq;
> 
>  
> 
>  my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
> 
>  my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
> 
>  
> 
> my $a = "NPFECDCSMEWMQRVNNLTARQHPKILDLPNVECIMPHARGTPIRPIISLKPKDFLCK";
> 
> my $b =
> "NPFECDCSMEWLQRINNLTTRQHPHVVDLGNIECLMPHSRSAPLRPLASLSASDFVCKYESHCPP";
> 
> my $seq1 = Bio::Seq->new ( -seq  => $a,
> 
>                            -id   => 'real',
> 
>                            -desc => 'this is a real Seq');
> 
>  my $seq2 = Bio::Seq->new ( -seq  => $b,
> 
>                            -id   => 'test',
> 
>                            -desc => 'this is a test Seq');
> 
> 
>                            
> 
> my @seq_array = ($seq1,$seq2);
> 
>  
> 
> my $seq_array_ref = \@seq_array;
> 
> my $aln = $factory->align($seq_array_ref);
> 
>  
> 
>  
> 
>  
> 
> 
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