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://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