Provided by: libbio-perl-perl_1.7.7-1_all bug


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


          $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)


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


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AUTHOR - Jason Stajich



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

        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    :

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

        Title   : _prediction()
        Usage   : $gene = $obj->_prediction()
        Function: internal
        Example :
        Returns :

        Title   : _add_prediction()
        Usage   : $obj->_add_prediction($gene)
        Function: internal
        Example :
        Returns :

        Title   : _predictions_parsed
        Usage   : $obj->_predictions_parsed
        Function: internal
        Example :
        Returns : TRUE or FALSE

        Title   : _has_cds()
        Usage   : $obj->_has_cds()
        Function: Whether or not the result contains the predicted CDSs, too.
        Example :
        Returns : TRUE or FALSE