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Bio::Tools::Match.3pm

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:

   http://bugzilla.open-bio.org/
 
 

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