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

NAME

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

SYNOPSIS

	  $Genemark = Bio::Tools::Genemark->new(-file => 'result.Genemark');
	  # filehandle:
	  $Genemark = Bio::Tools::Genemark->new( -fh  => *INPUT );

	  # parse the results
	  # note: this class is-a Bio::Tools::AnalysisResult which implements
	  # Bio::SeqAnalysisParserI, i.e., $Genemark->next_feature() is the same
	  while($gene = $Genemark->next_prediction()) {
	      # $gene is an instance of Bio::Tools::Prediction::Gene, which inherits
	      # off Bio::SeqFeature::Gene::Transcript.
	      #
	      # $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 = $gene->exons('Terminal');
	      # singleton exons:
	      ($single_exon) = $gene->exons();
	  }

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

DESCRIPTION

       The Genemark module provides a parser for Genemark gene structure prediction output. It parses one gene prediction into a
       Bio::SeqFeature::Gene::Transcript- derived object.

       This module has been developed around genemark.hmm for eukaryots v2.2a and will probably not work with other versions.

       This module also implements the Bio::SeqAnalysisParserI interface, and thus can be used wherever such an object fits. See
       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, Mark Fiers
       Email hlapp@gmx.net
	     m.w.e.j.fiers@plant.wag-ur.nl

APPENDIX

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

   new
	Title	: new
	Usage	: my $obj = Bio::Tools::Genemark->new();
	Function: Builds a new Bio::Tools::Genemark object
	Returns : an instance of Bio::Tools::Genemark
	Args	: seqname

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

   next_feature
	Title	: next_feature
	Usage	: while($gene = $Genemark->next_feature()) {
			 # do something
		  }
	Function: Returns the next gene structure prediction of the Genemark 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.

	Example :
	Returns : A Bio::Tools::Prediction::Gene object.
	Args	:

   next_prediction
	Title	: next_prediction
	Usage	: while($gene = $Genemark->next_prediction()) {
			 # do something
		  }
	Function: Returns the next gene structure prediction of the Genemark 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

   _read_fasta_seq
	Title	: _read_fasta_seq()
	Usage	: ($id,$seqstr) = $obj->_read_fasta_seq();
	Function: Simple but specialised FASTA format sequence reader. Uses
		  $self->_readline() to retrieve input, and is able to strip off
		  the traling description lines.
	Example :
	Returns : An array of two elements.

   _seqname
	Title	: _seqname
	Usage	: $obj->_seqname($seqname)
	Function: internal
	Example :
	Returns : String

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