Bio::Tools::Grail(3pm) User Contributed Perl Documentation Bio::Tools::Grail(3pm)NAME
Bio::Tools::Grail - Results of one Grail run
SYNOPSIS
$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)
$genscan->close();
DESCRIPTION
The Grail module provides a parser for Grail gene structure prediction output.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich
Email jason-at-bioperl.org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
next_prediction
Title : next_prediction
Usage : while($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 :
_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
perl v5.14.2 2012-03-02 Bio::Tools::Grail(3pm)
Check Out this Related Man Page
Bio::Tools::Fgenesh(3pm) User Contributed Perl Documentation Bio::Tools::Fgenesh(3pm)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://redmine.open-bio.org/projects/bioperl/
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
perl v5.14.2 2012-03-02 Bio::Tools::Fgenesh(3pm)