Bio::Tools::Run::TribeMCL(3pm)				User Contributed Perl Documentation			    Bio::Tools::Run::TribeMCL(3pm)

NAME

       Bio::Tools::Run::TribeMCL

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 $i 	 ".scalar(@{$fam->[$i]})." members
";
	   foreach my $member (@{$fam->[$i]}){
	     print "	$member
";
	   }
	 }

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

perl v5.12.3							    2011-06-18					    Bio::Tools::Run::TribeMCL(3pm)