NAME¶
Bio::Tools::Fgenesh - parse results of one Fgenesh run
SYNOPSIS¶
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();
DESCRIPTION¶
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.
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 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
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 the bugs
and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
AUTHOR - Chris Dwan¶
Email chris-at-dwan.org
APPENDIX¶
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
analysis_method¶
Usage : $genscan->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/genscan/i.
Returns : String
Argument : n/a
next_feature¶
Title : next_feature
Usage : while($gene = $fgenesh->next_feature()) {
# do something
}
Function: Returns the next gene structure prediction of the Fgenesh result
file. Call this method repeatedly until FALSE is returned.
The returned object is actually a SeqFeatureI implementing object.
This method is required for classes implementing the
SeqAnalysisParserI interface, and is merely an alias for
next_prediction() at present.
Example :
Returns : A Bio::Tools::Prediction::Gene object.
Args :
next_prediction¶
Title : next_prediction
Usage : while($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 :
_parse_predictions¶
Title : _parse_predictions()
Usage : $obj->_parse_predictions()
Function: Parses the prediction section. Automatically called by
next_prediction() if not yet done.
Example :
Returns :
_prediction¶
Title : _prediction()
Usage : $gene = $obj->_prediction()
Function: internal
Example :
Returns :
_add_prediction¶
Title : _add_prediction()
Usage : $obj->_add_prediction($gene)
Function: internal
Example :
Returns :
_predictions_parsed¶
Title : _predictions_parsed
Usage : $obj->_predictions_parsed
Function: internal
Example :
Returns : TRUE or FALSE
_has_cds¶
Title : _has_cds()
Usage : $obj->_has_cds()
Function: Whether or not the result contains the predicted CDSs, too.
Example :
Returns : TRUE or FALSE
_read_fasta_seq¶
Title : _read_fasta_seq()
Usage : ($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