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Bio::Tools::Genemark(3User Contributed Perl DocumentatiBio::Tools::Genemark(3)

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

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

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Hilmar Lapp, Mark Fiers | APPENDIX

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