| Bio::Tools::Grail(3pm) | User Contributed Perl Documentation | Bio::Tools::Grail(3pm) |
Bio::Tools::Grail - Results of one Grail run
$grail = Bio::Tools::Grail->new(-file => 'result.grail');
# filehandle:
$grail = Bio::Tools::Grail->new( -fh => \*INPUT );
# parse the results
while($gene = $grail->next_prediction()) {
# $gene is an instance of Bio::Tools::Prediction::Gene
# $gene->exons() returns an array of
# Bio::Tools::Prediction::Exon objects
# all exons:
@exon_arr = $gene->exons();
# initial exons only
@init_exons = $gene->exons('Initial');
# internal exons only
@intrl_exons = $gene->exons('Internal');
# terminal exons only
@term_exons = $gene->exons('Terminal');
# singleton exons only -- should be same as $gene->exons() because
# there are no other exons supposed to exist in this structure
@single_exons = $gene->exons('Single');
}
# essential if you gave a filename at initialization (otherwise the file
# will stay open)
$genscan->close();
The Grail module provides a parser for Grail gene structure prediction output.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : next_prediction
Usage : while($gene = $grail->next_prediction()) {
# do something
}
Function: Returns the next gene structure prediction of the Grail result
file. Call this method repeatedly until FALSE is returned.
Example :
Returns : A Bio::Tools::Prediction::Gene object.
Args :
Title : _parse_predictions()
Usage : $obj->_parse_predictions()
Function: Parses the prediction section. Automatically called by
next_prediction() if not yet done.
Example :
Returns :
Title : _prediction() Usage : $gene = $obj->_prediction() Function: internal Example : Returns :
Title : _add_prediction() Usage : $obj->_add_prediction($gene) Function: internal Example : Returns :
Title : _predictions_parsed Usage : $obj->_predictions_parsed Function: internal Example : Returns : TRUE or FALSE
Title : _has_cds() Usage : $obj->_has_cds() Function: Whether or not the result contains the predicted CDSs, too. Example : Returns : TRUE or FALSE
| 2020-10-28 | perl v5.30.3 |