Bio::Tools::Run::Match.3pm

Langue: en

Autres versions - même langue

Version: 2009-11-04 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Tools::Run::Match - Wrapper for Transfac's match(TM)

SYNOPSIS

   use Bio::Tools::Run::Match;
 
   # Make a Match factory
   $factory = Bio::Tools::Run::Match->new(-mxlib => '/path/to/matrix.dat');
 
   # Run Match on an sequence object
   my @results = $factory->run($bio_seq);
 
   # look at the results
   foreach my $feat (@results) {
     my $seq_id = $feat->seq_id;
     my $start = $feat->start;
     my $end = $feat->end;
     my $score = $feat->score;
     my ($pvalue) = $feat->get_tag_values('pvalue');
   }
 
 

DESCRIPTION

This is a wrapper for running the match(TM) program supplied with Transfac Pro distributions.

You can try supplying normal match command-line arguments to new(), eg. new(-b => 1) or calling arg-named methods (excluding the initial hyphens, eg. $factory->b(1) to set the -b option to true).

Histogram output isn't supported. -p is supported by using -mxprf, see the docs of new() for details.

You will need to enable this match wrapper to find the match executable. This can be done in (at least) three ways:

  1. Make sure match is in your path.
  2. Define an environmental variable MATCHDIR which is a 
     directory which contains the match executable:
     In bash:
 
     export MATCHDIR=/home/username/match/
 
     In csh/tcsh:
 
     setenv MATCHDIR /home/username/match
 
  3. Include a definition of an environmental variable MATCHDIR in
     every script that will use this match wrapper module, e.g.:
 
     BEGIN { $ENV{MATCHDIR} = '/home/username/match/' }
     use Bio::Tools::Run::Match;
 
 

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 the Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Sendu Bala

Email bix@sendu.me.uk

APPENDIX

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

program_name

  Title   : program_name
  Usage   : $factory>program_name()
  Function: holds the program name
  Returns : string
  Args    : None
 
 

program_dir

  Title   : program_dir
  Usage   : $factory->program_dir(@params)
  Function: returns the program directory, obtained from ENV variable.
  Returns : string
  Args    : None
 
 

new

  Title   : new
  Usage   : $factory = Bio::Tools::Run::Match->new()
  Function: creates a new MCS factory
  Returns : Bio::Tools::Run::MCS
  Args    : The following args can either be supplied here or set by calling
            arg-named methods (eg. $factory->imcut(2) ).
 
            -mxlib  => path to the matrix.dat file containing Transfac matricies
            -mxprf  => path to a profile file | [core_thresh, [matrix_thresh]]
                       (defaults to a standard one based on the mxlib provided if
                       file not supplied, using core_thresh and matrix_thresh
                       values if those are supplied instead)
            -imcut  => floating point number, the importance cutoff
            -b | -u => boolean, mutually exclusive
 
 

run

  Title   : run
  Usage   : $result = $factory->run($bio_seqi_object);
  Function: Runs match on a sequence.
  Returns : list of Bio::SeqFeatureI feature objects
  Args    : Bio::SeqI compliant object
 
            NB: mxlib has to have been set prior to calling run(), either as an
            argument to new() or by calling mxlib().
 
 

_setparams

  Title   : _setparams
  Usage   : Internal function, not to be called directly
  Function: Creates a string of params to be used in the command string
  Returns : string of params
  Args    : none