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

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