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

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://github.com/bioperl/bioperl-live/issues

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 v5.24.1			  2017-07-08		  Bio::Tools::Grail(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | APPENDIX

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