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Christopher Fields
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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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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