Bio::Tools::MZEF(3) User Contributed Perl Documentation Bio::Tools::MZEF(3)NAMEBio::Tools::MZEF - Results of one MZEF run
SYNOPSIS
$mzef = Bio::Tools::MZEF->new(-file => 'result.mzef');
# filehandle:
$mzef = Bio::Tools::MZEF->new( -fh => \*INPUT );
# to indicate that the sequence was reversed prior to feeding it to MZEF
# and that you want to have this reflected in the strand() attribute of
# the exons, as well have the coordinates translated to the non-reversed
# sequence
$mzef = Bio::Tools::MZEF->new( -file => 'result.mzef',
-strand => -1 );
# parse the results
# note: this class is-a Bio::Tools::AnalysisResult which implements
# Bio::SeqAnalysisParserI, i.e., $genscan->next_feature() is the same
while($gene = $mzef->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();
# internal exons only
@intrl_exons = $gene->exons('Internal');
# note that presently MZEF predicts only internal exons!
}
# essential if you gave a filename at initialization (otherwise the file
# will stay open)
$mzef->close();
DESCRIPTION
The MZEF module provides a parser for MZEF gene structure prediction
output.
This module inherits off Bio::Tools::AnalysisResult and therefore
implements Bio::SeqAnalysisParserI.
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:
http://bugzilla.open-bio.org/
AUTHOR - Hilmar Lapp
Email hlapp-at-gmx.net (or hilmar.lapp-at-pharma.novartis.com)
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
analysis_method
Usage : $mzef->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/mzef/i.
Returns : String
Argument : n/a
next_feature
Title : next_feature
Usage : while($gene = $mzef->next_feature()) {
# do something
}
Function: Returns the next gene structure prediction of the MZEF result
file. Call this method repeatedly until FALSE is returned.
The returned object is actually a SeqFeatureI implementing object.
This method is required for classes implementing the
SeqAnalysisParserI interface, and is merely an alias for
next_prediction() at present.
Note that with the present version of MZEF there will only be one
object returned, because MZEF does not predict individual genes
but just potential internal exons.
Example :
Returns : A Bio::Tools::Prediction::Gene object.
Args :
next_prediction
Title : next_prediction
Usage : while($gene = $mzef->next_prediction()) {
# do something
}
Function: Returns the next gene structure prediction of the MZEF result
file. Call this method repeatedly until FALSE is returned.
Note that with the present version of MZEF there will only be one
object returned, because MZEF does not predict individual genes
but just potential internal exons.
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
perl v5.14.1 2011-07-22 Bio::Tools::MZEF(3)
