/ 
bioperl-1.5.2_005-RCb
/ Bio::Tools::Glimmer

NAME

Bio::Tools::Glimmer - parser for GlimmerM/GlimmerHMM eukaryotic 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 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.

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/.

BUGS

This module does not parse Glimmer2 or Glimmer3 bacterial gene prediction files. Details on their output formats can be found at http://www.cbcb.umd.edu/software/glimmer/.

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

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.open-bio.org/

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 = 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