bio::tools::mzef(3pm) [debian man page]

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

NAME

       Bio::Tools::MZEF - Results of one MZEF run

SYNOPSIS

	  $mzef = Bio::Tools::MZEF->new(-file => 'result.mzef');
	  # filehandle:
	  $mzef = Bio::Tools::MZEF->new( -fh  => *INPUT );
	  # to indicate that the sequence was reversed prior to feeding it to MZEF
	  # and that you want to have this reflected in the strand() attribute of
	  # the exons, as well have the coordinates translated to the non-reversed
	  # sequence
	  $mzef = Bio::Tools::MZEF->new( -file	 => 'result.mzef',
					 -strand => -1 );

	  # parse the results
	  # note: this class is-a Bio::Tools::AnalysisResult which implements
	  # Bio::SeqAnalysisParserI, i.e., $genscan->next_feature() is the same
	  while($gene = $mzef->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();

	      # internal exons only
	      @intrl_exons = $gene->exons('Internal');
	      # note that presently MZEF predicts only internal exons!
	  }

	  # essential if you gave a filename at initialization (otherwise the file
	  # will stay open)
	  $mzef->close();

DESCRIPTION

       The MZEF module provides a parser for MZEF gene structure prediction output.

       This module inherits off Bio::Tools::AnalysisResult and therefore implements Bio::SeqAnalysisParserI.

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 - Hilmar Lapp
       Email hlapp-at-gmx.net (or hilmar.lapp-at-pharma.novartis.com)

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   analysis_method
	Usage	  : $mzef->analysis_method();
	Purpose   : Inherited method. Overridden to ensure that the name matches
		    /mzef/i.
	Returns   : String
	Argument  : n/a

   next_feature
	Title	: next_feature
	Usage	: while($gene = $mzef->next_feature()) {
			 # do something
		  }
	Function: Returns the next gene structure prediction of the MZEF result
		  file. Call this method repeatedly until FALSE is returned.

		  The returned object is actually a SeqFeatureI implementing object.
		  This method is required for classes implementing the
		  SeqAnalysisParserI interface, and is merely an alias for
		  next_prediction() at present.

		  Note that with the present version of MZEF there will only be one
		  object returned, because MZEF does not predict individual genes
		  but just potential internal exons.
	Example :
	Returns : A Bio::Tools::Prediction::Gene object.
	Args	:

   next_prediction
	Title	: next_prediction
	Usage	: while($gene = $mzef->next_prediction()) {
			 # do something
		  }
	Function: Returns the next gene structure prediction of the MZEF result
		  file. Call this method repeatedly until FALSE is returned.

		  Note that with the present version of MZEF there will only be one
		  object returned, because MZEF does not predict individual genes
		  but just potential internal exons.
	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

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