debian man page for bio::tools::glimmer

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

NAME
       Bio::Tools::Glimmer - parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions

SYNOPSIS
	  use Bio::Tools::Glimmer;

	  # file
	  my $parser = Bio::Tools::Glimmer->new(-file => $file);
	  # filehandle:
	  $parser = Bio::Tools::Glimmer->new( -fh  => *INPUT );
	  # provide a sequence identifier (Glimmer 2.X)
	  my $parser = Bio::Tools::Glimmer->new(-file => $file, -seqname => seqname);
	  # force format (override automatic detection)
	  my $parser = Bio::Tools::Glimmer->new(-file => $file, -format => 'GlimmerM');

	  # parse the results
	  # note: this class is-a Bio::Tools::AnalysisResult which implements
	  # Bio::SeqAnalysisParserI, i.e., $glimmer->next_feature() is the same

	  while(my $gene = $parser->next_prediction()) {
	      # For eukaryotic input (GlimmerM/GlimmerHMM), $gene will be an instance
	      # of Bio::Tools::Prediction::Gene, which inherits off
	      # Bio::SeqFeature::Gene::Transcript, and $gene->exons() will return an
	      # array of Bio::Tools::Prediction::Exon objects.
	      # For prokaryotic input (Glimmer2.X/Glimmer3.X), $gene will be an
	      # instance of Bio::SeqFeature::Generic

	      # all exons (eukaryotic only):
	      @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');
	  }

DESCRIPTION
       This is a module for parsing Glimmer, GlimmerM and GlimmerHMM predictions.  It will create gene objects from the prediction report which
       can be attached to a sequence using Bioperl objects, or output as GFF suitable for loading into Bio::DB::GFF for use with Gbrowse.

       Glimmer is open source and available at <http://www.cbcb.umd.edu/software/glimmer/>.

       GlimmerM is open source and available at <http://www.tigr.org/software/glimmerm/>.

       GlimmerHMM is open source and available at <http://www.cbcb.umd.edu/software/GlimmerHMM/>.

       Note that Glimmer 2.X will only process the first sequence in a fasta file, and the prediction report does not contain any sort of sequence
       identifier

       Note that Glimmer 3.X produces two output files.  This module only parses the .predict file.

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 the
       Bioperl mailing list.  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 of the bugs and their resolution. Bug reports can be submitted via
       email or the web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason-at-bioperl-dot-org

CONTRIBUTORS
       Torsten Seemann

       Mark Johnson

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::Glimmer->new();
	Function: Builds a new Bio::Tools::Glimmer object
	Returns : an instance of Bio::Tools::Glimmer
	Args	: format ('Glimmer', 'GlimmerM', 'GlimmerHMM'), seqname

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

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

   _parse_eukaryotic
	Title	: _parse_eukaryotic()
	Usage	: $obj->_parse_eukaryotic()
	Function: Parses the prediction section. Automatically called by
		  next_prediction() if not yet done.
	Example :
	Returns :

   _parse_prokaryotic
	Title	: _parse_prokaryotic()
	Usage	: $obj->_parse_prokaryotic()
	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

   _seqname
	Title	: _seqname
	Usage	: $obj->_seqname($seqname)
	Function: internal (for Glimmer 2.X)
	Example :
	Returns : String

   _seqlength
	Title	: _seqlength
	Usage	: $obj->_seqlength($seqlength)
	Function: internal (for Glimmer 2.X)
	Example :
	Returns : String

   _format
	Title	: _format
	Usage	: $obj->_format($format)
	Function: internal
	Example :
	Returns : String

   _detail_file
	Title	: _detail_file
	Usage	: $obj->_detail_file($filename)
	Function: internal (for Glimmer 3.X)
	Example :
	Returns : String

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