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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: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 [email protected]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