Provided by: libbio-perl-perl_1.7.6-3_all bug

NAME

       Bio::Tools::Match - Parses output from Transfac's match(TM)

SYNOPSIS

         use strict;

         use Bio::Tools::Match;

         my $parser = Bio::Tools::Match->new(-file => "match.out");

         while (my $feat = $parser->next_result) {
           my $start = $feat->start;
           my $end = $feat->end;
           my $core_score = $feat->score;
           my $matrix_score = ($feat->annotation->get_Annotations('matrix_score'))[0]->value;
           my $matrix_id = ($feat->annotation->get_Annotations('matrix_id'))[0]->value;
         }

DESCRIPTION

       This module is used to parse the output from Transfac's match(TM) program. It doesn't
       support the histogram output of match.

       Each result is a Bio::SeqFeature::Annotated representing a single matrix 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:

         https://github.com/bioperl/bioperl-live/issues

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 _

   new
        Title   : new
        Usage   : my $obj = Bio::Tools::Match->new();
        Function: Builds a new Bio::Tools::Match object
        Returns : Bio::Tools::Match
        Args    : -file (or -fh) should contain the contents of a standard match output

   next_result
        Title   : next_result
        Usage   : $result = $obj->next_result();
        Function: Returns the next result available from the input, or undef if there
                  are no more results.
        Returns : Bio::SeqFeature::Annotated object. Features are annotated with tags
                  for 'matrix_score', 'matrix_id' and a 'predicted' tag.
        Args    : none