Provided by: libbio-perl-run-perl_1.7.3-9_all bug

NAME

       Bio::Tools::Run::TribeMCL - Markov method for CLustering proteins

SYNOPSIS

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

         # 3 methods to input the blast results

         # straight forward raw blast output (NCBI or WU-BLAST)
         my @params = ('inputtype'=>'blastfile');

         # OR

         # markov program format
         # protein_id1 protein_id2 evalue_magnitude evalue_factor
         # for example:
         # proteins ENSP00000257547  and ENSP00000261659
         # with a blast score evalue of 1e-50
         # and proteins O42187 and ENSP00000257547
         # with a blast score evalue of 1e-119
         # entry would be

         my @array  = [[qw(ENSP00000257547 ENSP00000261659 1 50)],
                       [qw(O42187 ENSP00000257547 1 119)]];
         my @params = ('pairs'=>\@array,I=>'2.0');

         # OR

         # pass in a searchio object
         # slowest of the 3 methods as it does more rigourous parsing
         # than required for us here

         my $sio = Bio::SearchIO->new(-format=>'blast',
                                      -file=>'blast.out');
         my @params=('inputtype'=>'searchio',I=>'2.0');

         # you can specify the path to the executable manually in the following way
         my @params=('inputtype'=>'blastfile',I=>'2.0',
                     'mcl'=>'/home/shawn/software/mcl-02-150/src/shmcl/mcl',
                     'matrix'=>'/home/shawn/software/mcl-02-150/src/contrib/tribe/tribe-matrix');
         my $fact = Bio::Tools::Run::TribeMCL->new(@params);

         # OR

         $fact->matrix_executable('/home/shawn/software/mcl-02-150/src/contrib/tribe/tribe-matrix');
         $fact->mcl_executable('/home/shawn/software/mcl-02-150/src/shmcl/mcl');

         # to run

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

         # Run the program
         # returns an array reference to clusters where members are the ids
         # for example :2 clusters with 3 members per cluster:
         #  $fam = [ [mem1 mem2 mem3],[mem1 mem2 mem3]]

         # pass in either the blastfile path/searchio obj/the array ref to scores
         my $fam = $fact->run($sio);

         # print out your clusters

         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";
           }
         }

DESCRIPTION

       TribeMCL is a method for clustering proteins into related groups, which are termed
       'protein families'. This clustering is achieved by analysing similarity patterns between
       proteins in a given dataset, and using these patterns to assign proteins into related
       groups. In many cases, proteins in the same protein family will have similar functional
       properties.

       TribeMCL uses a novel clustering method (Markov Clustering or MCL) which solves problems
       which normally hinder protein sequence clustering.

       Reference:

         Enright A.J., Van Dongen S., Ouzounis C.A; Nucleic Acids
         Res. 30(7):1575-1584 (2002)

       You will need tribe-matrix (the program used to generate the matrix for input into mcl)
       and mcl (the clustering software) available at:

         http://www.ebi.ac.uk/research/cgg/tribe/ or
         http://micans.org/mcl/.

       Future Work in this module: Port the tribe-matrix program into perl so that we can enable
       have a SearchIO kinda module for reading and writing mcl data format

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to one of the Bioperl mailing lists. Your
       participation is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their
       resolution.  Bug reports can be submitted via the web:

         http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Shawn Hoon

       Email shawnh@fugu-sg.org

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a "_".

   mcl_executable
        Title   : mcl_executable
        Usage   : $self->mcl_executable()
        Function: get set for path to mcl executable
        Returns : String or undef if not installed
        Args    : [optional] string of path to executable
                  [optional] boolean to warn on missing executable status

   matrix_executable
        Title   : matrix_executable
        Usage   : $self->matrix_executable()
        Function: get set for path to tribe-matrix executable
        Returns : String or undef if not installed
        Args    : [optional] string of path to executable
                  [optional] boolean to warn on missing executable status

   run
        Title   : run
        Usage   : $self->run()
        Function: runs the clustering
        Returns : Array Ref of clustered Ids
        Args    :

   _run_mcl
        Title   : _run_mcl
        Usage   : $self->_run_mcl()
        Function: internal function for running the mcl program
        Returns : Array Ref of clustered Ids
        Args    : Index_file name, matrix input file name

   _run_matrix
        Title   : _run_matrix
        Usage   : $self->_run_matrix()
        Function: internal function for running the tribe-matrix program
        Returns : index filepath and matrix file path
        Args    : filepath of parsed ids and scores

   _setup_input
        Title   : _setup_input
        Usage   : $self->_setup_input()
        Function: internal function for running setting up the inputs
                   needed for running mcl
        Returns : filepath of parsed ids and scores
        Args    :

   _get_from_hsp
        Title   : _get_from_hsp
        Usage   : $self->_get_from_hsp()
        Function: internal function for getting blast scores from hsp
        Returns : array ref to ids and score [protein1 protein2 magnitude factor]
        Args    : L<Bio::Search::HSP::GenericHSP>

   _get_from_searchio
        Title   : _get_from_searchio
        Usage   : $self->_get_from_searchio()
        Function: internal function for parsing blast scores from searchio object
        Returns : array ref to ids and score [protein1 protein2 magnitude factor]
        Args    :  L<Bio::Tools::SearchIO>

   _parse_blastfile
        Title   : _parse_blastfile
        Usage   : $self->_parse_blastfile()
        Function: internal function for quickly parsing blast evalue
                  scores from raw blast output file
        Returns : array ref to ids and score [protein1 protein2 magnitude factor]
        Args    :  file path

   _parse_mcl
        Title   : _parse_mcl
        Usage   : $self->_parse_mcl()
        Function: internal function for quickly parsing mcl output and
                  generating the array of clusters
        Returns : Array Ref of clustered Ids
        Args    :  index file path, mcl output file path