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 listsSupport
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/issuesAUTHOR - 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'), seqnameanalysis_method
Usage : $glimmer->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/glimmer/i.
Returns : String
Argument : n/anext_feature
Title : next_feature
Usage : while($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