Bio::Tools::MZEF - Results of one MZEF run $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(); The MZEF module provides a parser for MZEF gene structure prediction output. This module inherits off the Bio::Tools::AnalysisResult manpage and therefore implements the Bio::SeqAnalysisParserI manpage.

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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 email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ Email hlapp@gmx.net (or hilmar.lapp@pharma.novartis.com) Describe contact details here 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