Bio::Tools::Genemark - Results of one Genemark run $Genemark = Bio::Tools::Genemark->new(-file => 'result.Genemark'); # filehandle: $Genemark = Bio::Tools::Genemark->new( -fh => \*INPUT ); # parse the results # note: this class is-a Bio::Tools::AnalysisResult which implements # Bio::SeqAnalysisParserI, i.e., $Genemark->next_feature() is the same while($gene = $Genemark->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) $Genemark->close(); The Genemark module provides a parser for Genemark gene structure prediction output. It parses one gene prediction into a Bio::SeqFeature::Gene::Transcript- derived object. This module has been developed around genemark.hmm for eukaryots v2.2a and will probably not work with other versions. This module also implements the Bio::SeqAnalysisParserI interface, and thus can be used wherever such an object fits. See 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/ Email hlapp@gmx.net m.w.e.j.fiers@plant.wag-ur.nl The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

analysis_method
Usage : $Genemark->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches /GeneMark.hmm/i. Returns : String Argument : n/a

next_feature
Title : next_feature Usage : while($gene = $Genemark->next_feature()) { # do something } Function: Returns the next gene structure prediction of the Genemark 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 = $Genemark->next_prediction()) { # do something } Function: Returns the next gene structure prediction of the Genemark 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.