| Bio::Tools::Match(3pm) | User Contributed Perl Documentation | Bio::Tools::Match(3pm) |
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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Please direct usage questions or support issues to the mailing list:
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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.
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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
| 2021-08-15 | perl v5.32.1 |