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) $genscan->close(); The Grail module provides a parser for Grail gene structure prediction output.

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://bio.perl.org/MailList.html - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email jason@bioperl.org Describe contact details here 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