NAME

       Bio::Tools::Glimmer - parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM
       eukaryotic gene predictions

SYNOPSIS

          use Bio::Tools::Glimmer;

          # file
          my $parser = Bio::Tools::Glimmer->new(-file => $file);
          # filehandle:
          $parser = Bio::Tools::Glimmer->new( -fh  => \*INPUT );
          # provide a sequence identifier (Glimmer 2.X)
          my $parser = Bio::Tools::Glimmer->new(-file => $file, -seqname => seqname);
          # force format (override automatic detection)
          my $parser = Bio::Tools::Glimmer->new(-file => $file, -format => 'GlimmerM');

          # parse the results
          # note: this class is-a Bio::Tools::AnalysisResult which implements
          # Bio::SeqAnalysisParserI, i.e., $glimmer->next_feature() is the same

          while(my $gene = $parser->next_prediction()) {
              # For eukaryotic input (GlimmerM/GlimmerHMM), $gene will be an instance
              # of Bio::Tools::Prediction::Gene, which inherits off
              # Bio::SeqFeature::Gene::Transcript, and $gene->exons() will return an
              # array of Bio::Tools::Prediction::Exon objects.
              # For prokaryotic input (Glimmer2.X/Glimmer3.X), $gene will be an
              # instance of Bio::SeqFeature::Generic

              # all exons (eukaryotic only):
              @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');
          }

DESCRIPTION

       This is a module for parsing Glimmer, GlimmerM and GlimmerHMM predictions.  It will create
       gene objects from the prediction report which can be attached to a sequence using Bioperl
       objects, or output as GFF suitable for loading into Bio::DB::GFF for use with Gbrowse.

       Glimmer is open source and available at <http://www.cbcb.umd.edu/software/glimmer/>.

       GlimmerM is open source and available at <http://www.tigr.org/software/glimmerm/>.

       GlimmerHMM is open source and available at <http://www.cbcb.umd.edu/software/GlimmerHMM/>.

       Note that Glimmer 2.X will only process the first sequence in a fasta file, and the
       prediction report does not contain any sort of sequence identifier

       Note that Glimmer 3.X produces two output files.  This module only parses the .predict
       file.

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 the Bioperl mailing list.  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 of the bugs and their
       resolution. Bug reports can be submitted via email or the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

       Email jason-at-bioperl-dot-org

CONTRIBUTORS

       Torsten Seemann

       Mark Johnson

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::Glimmer->new();
        Function: Builds a new Bio::Tools::Glimmer object
        Returns : an instance of Bio::Tools::Glimmer
        Args    : format ('Glimmer', 'GlimmerM', 'GlimmerHMM'), seqname

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

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

   _parse_eukaryotic
        Title   : _parse_eukaryotic()
        Usage   : $obj->_parse_eukaryotic()
        Function: Parses the prediction section. Automatically called by
                  next_prediction() if not yet done.
        Example :
        Returns :

   _parse_prokaryotic
        Title   : _parse_prokaryotic()
        Usage   : $obj->_parse_prokaryotic()
        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

   _seqname
        Title   : _seqname
        Usage   : $obj->_seqname($seqname)
        Function: internal (for Glimmer 2.X)
        Example :
        Returns : String

   _seqlength
        Title   : _seqlength
        Usage   : $obj->_seqlength($seqlength)
        Function: internal (for Glimmer 2.X)
        Example :
        Returns : String

   _format
        Title   : _format
        Usage   : $obj->_format($format)
        Function: internal
        Example :
        Returns : String

   _detail_file
        Title   : _detail_file
        Usage   : $obj->_detail_file($filename)
        Function: internal (for Glimmer 3.X)
        Example :
        Returns : String