| Bio::Tools::Fgenesh(3pm) | User Contributed Perl Documentation | Bio::Tools::Fgenesh(3pm) |
Bio::Tools::Fgenesh - parse results of one Fgenesh run
use Bio::Tools::Fgenesh;
$fgenesh = Bio::Tools::Fgenesh->new(-file => 'result.fgenesh');
# filehandle:
$fgenesh = Bio::Tools::Fgenesh->new( -fh => \*INPUT );
# parse the results
# note: this class is-a Bio::Tools::AnalysisResult which implements
# Bio::SeqAnalysisParserI, i.e., $fgensh->next_feature() is the same
while($gene = $fgenesh->next_prediction()) {
# $gene is an instance of Bio::Tools::Prediction::Gene, which inherits
# off Bio::SeqFeature::Gene::Transcript.
#
# $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 = $gene->exons('Terminal');
# singleton exons:
($single_exon) = $gene->exons();
}
# essential if you gave a filename at initialization (otherwise the file
# will stay open)
$fgenesh->close();
The Fgenesh module provides a parser for Fgenesh (version 2) gene structure prediction output. It parses one gene prediction into a Bio::SeqFeature::Gene::Transcript- derived object.
This module also implements the Bio::SeqAnalysisParserI interface, and thus can be used wherever such an object fits.
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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 _
Usage : $genscan->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/genscan/i.
Returns : String
Argument : n/a
Title : next_feature
Usage : while($gene = $fgenesh->next_feature()) {
# do something
}
Function: Returns the next gene structure prediction of the Fgenesh result
file. Call this method repeatedly until FALSE is returned.
The returned object is actually a SeqFeatureI implementing object.
This method is required for classes implementing the
SeqAnalysisParserI interface, and is merely an alias for
next_prediction() at present.
Example :
Returns : A Bio::Tools::Prediction::Gene object.
Args :
Title : next_prediction
Usage : while($gene = $fgenesh->next_prediction()) { ... }
Function: Returns the next gene structure prediction of the Genscan 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 : $obj->_has_cds() Function: Whether or not the result contains the predicted CDSs, too. Example : Returns : TRUE or FALSE
Title : _read_fasta_seq()
Usage : ($id,$seqstr) = $obj->_read_fasta_seq();
Function: Simple but specialised FASTA format sequence reader. Uses
$self->_readline() to retrieve input, and is able to strip off
the traling description lines.
Example :
Returns : An array of two elements: fasta_id & sequence
| 2021-08-15 | perl v5.32.1 |