| Bio::Tools::Genemark(3pm) | User Contributed Perl Documentation | Bio::Tools::Genemark(3pm) |
Bio::Tools::Genemark - Results of one Genemark run
$Genemark = Bio::Tools::Genemark->new(-file => 'result.Genemark');
# filehandle:
$Genemark = Bio::Tools::Genemark->new( -fh => \*INPUT );
# parse the results
# note: this class is-a Bio::Tools::AnalysisResult which implements
# Bio::SeqAnalysisParserI, i.e., $Genemark->next_feature() is the same
while($gene = $Genemark->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)
$Genemark->close();
The Genemark module provides a parser for Genemark gene structure prediction output. It parses one gene prediction into a Bio::SeqFeature::Gene::Transcript- derived object.
This module has been developed around genemark.hmm for eukaryots v2.2a and will probably not work with other versions.
This module also implements the Bio::SeqAnalysisParserI interface, and thus can be used wherever such an object fits. See Bio::SeqAnalysisParserI.
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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.
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
Email hlapp@gmx.net
m.w.e.j.fiers@plant.wag-ur.nl
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::Genemark->new(); Function: Builds a new Bio::Tools::Genemark object Returns : an instance of Bio::Tools::Genemark Args : seqname
Usage : $Genemark->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/GeneMark.hmm/i.
Returns : String
Argument : n/a
Title : next_feature
Usage : while($gene = $Genemark->next_feature()) {
# do something
}
Function: Returns the next gene structure prediction of the Genemark result
file. Call this method repeatedly until FALSE is returned.
The returned object is actually a SeqFeatureI implementing object.
This method is required for classes implementing the
SeqAnalysisParserI interface, and is merely an alias for
next_prediction() at present.
Example :
Returns : A Bio::Tools::Prediction::Gene object.
Args :
Title : next_prediction
Usage : while($gene = $Genemark->next_prediction()) {
# do something
}
Function: Returns the next gene structure prediction of the Genemark 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.
Title : _seqname Usage : $obj->_seqname($seqname) Function: internal Example : Returns : String
| 2020-10-28 | perl v5.30.3 |