Cant find Clustalw.exe through Bioperl

Question

[Andrea]

Hello everyone.I m trying to run the script below. but I get the error:

------------- EXCEPTION ------------- MSG: Cannot find executable for clustalw. path="clustalw.exe" STACK Bio::Tools::Run::WrapperBase::executable C:/Perl64/site/lib/Bio/Tools/Run/ WrapperBase.pm:340 STACK Bio::Tools::Run::Alignment::Clustalw::_run C:/Perl64/site/lib/Bio/Tools/Ru n/Alignment/Clustalw.pm:752 STACK Bio::Tools::Run::Alignment::Clustalw::align C:/Perl64/site/lib/Bio/Tools/R un/Alignment/Clustalw.pm:515 STACK toplevel a.pl:29

How to make perl find my clustalw.exe???? I think that already did that by setting at the beginning the environmental variable $ENV{CLUSTALDIR}. Any help will be much appreciated!!!!

    #!/usr/bin/perl
    $ENV{CLUSTALDIR} = 'C:\Program Files (x86)\ClustalW2';
    use warnings;
    use strict;

    use Bio::AlignIO;
    use Bio::SeqIO;
    use Bio::Tools::Run::Alignment::Clustalw;

    my $file = <>; # Get file name from command prompt.
    my $factory = Bio::Tools::Run::Alignment::Clustalw->new(-matrix => 'BLOSUM');
    my $ktuple = 3;
    $factory->ktuple($ktuple);

    my $inseq = Bio::SeqIO->new(
                        -file => "<$file",
                        -format => "fasta"
                       );

    my $seq;
    my @seq_array;
    while ($seq = $inseq->next_seq) {
        push(@seq_array, $seq);
    }

    # Now we do the actual alignment.
    my $seq_array_ref = \@seq_array;
    my $aln = $factory->align($seq_array_ref);

Just a simple fasta file :

>seq0
FQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKF
>seq1
KYRTWEEFTRAAEKLYQADPMKVRVVLKYRHCDGNLCIKVTDDVVCLLYRTDQAQDVKKIEKFHSQLMRLME 
>seq2
EEYQTWEEFARAAEKLYLTDPMKVRVVLKYRHCDGNLCMKVTDDAVCLQYKTDQAQDVKKVEKLHGK
>seq3
MYQVWEEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVCLQYKTDQAQDVK
>seq4
EEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVVSYEMRLFGVQKDNFALEHSLL
>seq5
SWEEFAKAAEVLYLEDPMKCRMCTKYRHVDHKLVVKLTDNHTVLKYVTDMAQDVKKIEKLTTLLMR
>seq6
FTNWEEFAKAAERLHSANPEKCRFVTKYNHTKGELVLKLTDDVVCLQYSTNQLQDVKKLEKLSSTLLRSI
>seq7
SWEEFVERSVQLFRGDPNATRYVMKYRHCEGKLVLKVTDDRECLKFKTDQAQDAKKMEKLNNIFF
>seq8
SWDEFVDRSVQLFRADPESTRYVMKYRHCDGKLVLKVTDNKECLKFKTDQAQEAKKMEKLNNIFFTLM
>seq9
KNWEDFEIAAENMYMANPQNCRYTMKYVHSKGHILLKMSDNVKCVQYRAENMPDLKK
>seq10
FDSWDEFVSKSVELFRNHPDTTRYVVKYRHCEGKLVLKVTDNHECLKFKTDQAQDAKKMEK

Answer 1

[biocyberman]

How about adding 'C:\Program Files (x86)\ClustalW2' to Windows Path variable. Log out and login again. You know the Path works if you can call clustalw.exe from anywhere without the full path.

Check out the last answer in here to see how you can change Path reliably.

[Andrea]

That was one of the first things I did but didn't changed anything. I Just made it work!

Steps to make it work:

1)copy the clustalw2.exe

2)paste it on your e.g. Desktop

3)Rename it to clustalw.exe

4)Give the $ENV{CLUSTALDIR} the new path to clustalw.exe

and it works!

(at first tried to rename the basic clustalw2.exe of 'C:\Program Files (x86)\ClustalW2' but didn't work)

[biocyberman]

I haven't used Bioperl for several years now so i am not familiar with it. However, from your solution it seems that the clustalw module was looking for a different binary name. Maybe you should check if there is clustalw2 module and use that instead of fitting an unexpected binary to the outdated module. Again, it's just general consideration.