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

[Chris Fields]

Not sure of it's status , but I don't think TribeMCL is maintained anymore (maybe we should deprecate it?).  You should really look at other tools besides TribeMCL, in particular OrthoMCL, which is essentially a more up-to-date TribeMCL.  Also, a recent set of posts mentioned other tools such as blastclust (comes with NCBI's BLAST tools).

chris

On Feb 28, 2011, at 8:57 AM, Wenliang Wang wrote:

> 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
> 
> 
> 
> 
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