NAME

Bio::Tools::Glimmer - A parser for GLIMMER gene predictions

SYNOPSIS

   use Bio::Tools::Glimmer;
   my $parser = new Bio::Tools::Glimmer(-file => $file);
     # filehandle:
   $parser = Bio::Tools::Glimmer->new( -fh  => \*INPUT );

   # 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()) {
       # $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');
   }

DESCRIPTION

This is a module for parsing Glimmer predictions (currently GlimmerM 3.0 is all that has been tested). 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.

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

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/MailList.shtml  - About the mailing lists

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:

  http://bugzilla.bioperl.org/

AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org

Describe contact details here

CONTRIBUTORS

Additional contributors names and emails here

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 = new Bio::Tools::Glimmer();
 Function: Builds a new Bio::Tools::Glimmer object 
 Returns : an instance of Bio::Tools::Glimmer
 Args    :

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 : 

_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

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq