debian man page for bio::tools::grail

Bio::Tools::Grail(3pm)					User Contributed Perl Documentation				    Bio::Tools::Grail(3pm)

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

perl v5.14.2							    2012-03-02						    Bio::Tools::Grail(3pm)