Provided by: libbio-perl-run-perl_1.6.9-1_all bug


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


         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');


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

       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;


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AUTHOR - Sendu Bala



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

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

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

        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

        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().

        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