Bio::Tools::Eponine - Results of one Eponine run use Bio::Tools::Eponine; use strict; my $seq = "/data/seq.fa"; my $threshold = "0.999"; my @params = ( -seq => $seq, -threshold => $threshold); my $factory = Bio::Tools::Run::Eponine->new(@params); # run eponine against fasta my $r = $factory->run_eponine($seq); my $parser = Bio::Tools::Eponine->new($r); while (my $feat = $parser->next_prediction){ #$feat contains array of SeqFeature foreach my $orf($feat) { print $orf->seq_id. "\n"; } } Parser for Eponine, a probabilistic transcription start site detector optimized for mammalian genomic sequence. This module inherits off Bio::Tools::AnalysisResult and therefore implements Bio::SeqAnalysisParserI (see Bio::Tools::AnalysisResult and Bio::SeqAnalysisParserI).

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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://bugzilla.bioperl.org/ 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 :

create_feature
Title : create_feature Usage : obj->create_feature($feature) Function: Returns an array of features Returns : Returns an array of features Args : none

_prediction
Title : _prediction() Usage : $gene = $obj->_prediction() Function: internal Example : Returns :

_predictions_parsed
Title : _predictions_parsed Usage : $obj->_predictions_parsed Function: internal Example : Returns : TRUE or FALSE