Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::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:

         https://redmine.open-bio.org/projects/bioperl/

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