[Bioperl-l] Bio::Tools::Run::TribeMCL

[Wenliang Wang]

Hello,

         I’m trying to use TribeMCL to cluster a group of protein sequence
with the following code:

 

use Bio::Tools::Run::TribeMCL;

use Bio::SearchIO;

 

my $usage = "run_tribe.pl blastfile";

my $blastfile = $ARGV[0];

 

my $sio = Bio::SearchIO->new(-format=>'blast',

                        -file=>$blastfile);

 

my @params=('inputtype'=>'searchio',I=>'2.0',

        'mcl'=>'/home/sean/tribemcl/src/shmcl/mcl',

        'matrix'=>'/home/sean/tribemcl/src/contrib/tribe/tribe-matrix');

 

my $fact = Bio::Tools::Run::TribeMCL->new(@params);

 

my $fam = $fact->run($sio);

 

for (my $i = 0; $i <scalar(@{$fam}); $i++){

        print "Cluster $i \t ".scalar(@{$fam->[$i]})." members\n";

        foreach my $member (@{$fam->[$i]}){

                print "\t$member\n";

        }

}

 

But it came out with some wrong message:

 

------------- EXCEPTION: Bio::Root::Exception -------------

MSG: Need inputs for running tribe mcl, nothing provided

STACK: Error::throw

STACK: Bio::Root::Root::throw
/usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:368

STACK: Bio::Tools::Run::TribeMCL::_setup_input /usr/lib/perl5/site_perl/5.8.
8/Bio/Tools/Run/TribeMCL.pm:765

STACK: Bio::Tools::Run::TribeMCL::run
/usr/lib/perl5/site_perl/5.8.8/Bio/Tools/Run/TribeMCL.pm:346

STACK: test.pl:16

 

 

I’m wondering if you can help me with this.

 

Sorry for the long email.

 

 

Best regards！

 

Wenliang Wang

College of Life Science,Wuhan University,Wuhan,Hubei,China.

email:wangwl at mail.whu.edu.cn

MSN:lvxiaopohai at hotmail.com