Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

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

SYNOPSIS

          $grail = Bio::Tools::Grail->new(-file => 'result.grail');
          # filehandle:
          $grail = Bio::Tools::Grail->new( -fh  => \*INPUT );

          # parse the results
          while($gene = $grail->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();

              # 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 only -- should be same as $gene->exons() because
              # there are no other exons supposed to exist in this structure
              @single_exons = $gene->exons('Single');
          }

          # essential if you gave a filename at initialization (otherwise the file
          # will stay open)
          $genscan->close();

DESCRIPTION

       The Grail module provides a parser for Grail gene structure prediction output.

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

AUTHOR - Jason Stajich

       Email jason-at-bioperl.org

APPENDIX

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

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