/ 
BioPerl-1.6.901
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Tools::Grail

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://redmine.open-bio.org/projects/bioperl/

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