Bio::Tools::Run::TribeMCL(3pm)

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

[email protected]

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 [email protected]

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