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

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

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

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Hilmar Lapp | APPENDIX

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