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

Bio::Tools::Prediction::Gene(3pm)			User Contributed Perl Documentation			 Bio::Tools::Prediction::Gene(3pm)

NAME

       Bio::Tools::Prediction::Gene - a predicted gene structure feature

SYNOPSIS

	 #See documentation of methods.

DESCRIPTION

       A feature representing a predicted gene structure. This class actually inherits off Bio::SeqFeature::Gene::Transcript and therefore has all
       that functionality, plus a few methods supporting predicted sequence features, like a predicted CDS and a predicted translation.

       Exons held by an instance of this class will usually be instances of Bio::Tools::Prediction::Exon, although they do not have to be. Refer
       to the documentation of the class that produced the instance.

       Normally, you will not want to create an instance of this class yourself.  Instead, classes representing the results of gene structure
       prediction programs will do that.

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 _

   predicted_cds
	Title	: predicted_cds
	Usage	: $predicted_cds_dna = $gene->predicted_cds();
		  $gene->predicted_cds($predicted_cds_dna);
	Function: Get/Set the CDS (coding sequence) as predicted by a program.

		  This method is independent of an attached_seq. There is no
		  guarantee whatsoever that the returned CDS has anything to do
		  (e.g., matches) with the sequence covered by the exons as annotated
		  through this object.

	Example :
	Returns : A Bio::PrimarySeqI implementing object holding the DNA sequence
		  defined as coding by a prediction of a program.
	Args	: On set, a Bio::PrimarySeqI implementing object holding the DNA
		  sequence defined as coding by a prediction of a program.

   predicted_protein
	Title	: predicted_protein
	Usage	: $predicted_protein_seq = $gene->predicted_protein();
		  $gene->predicted_protein($predicted_protein_seq);
	Function: Get/Set the protein translation as predicted by a program.

		  This method is independent of an attached_seq. There is no
		  guarantee whatsoever that the returned translation has anything to
		  do with the sequence covered by the exons as annotated
		  through this object, or the sequence returned by predicted_cds(),
		  although it should usually be just the standard translation.

	Example :
	Returns : A Bio::PrimarySeqI implementing object holding the protein
		  translation as predicted by a program.
	Args	: On set, a Bio::PrimarySeqI implementing object holding the protein
		  translation as predicted by a program.

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

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)