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


  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;


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.


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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   : 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


 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