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Bio::Tools::Glimmer(3)User Contributed Perl DocumentatioBio::Tools::Glimmer(3)

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

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

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | CONTRIBUTORS | APPENDIX

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