/ 
BioPerl-Run-1.007001
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::TribeMCL

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 $i \t ".scalar(@{$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