NAME

       Bio::Tools::Genemark - Results of one Genemark run

SYNOPSIS

          $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();

DESCRIPTION

       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.

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, Mark Fiers

       Email hlapp@gmx.net
             m.w.e.j.fiers@plant.wag-ur.nl

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

   new
        Title   : new
        Usage   : my $obj = Bio::Tools::Genemark->new();
        Function: Builds a new Bio::Tools::Genemark object
        Returns : an instance of Bio::Tools::Genemark
        Args    : seqname

   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.

   _seqname
        Title   : _seqname
        Usage   : $obj->_seqname($seqname)
        Function: internal
        Example :
        Returns : String