| Bio::Tools::Glimmer(3pm) | User Contributed Perl Documentation | Bio::Tools::Glimmer(3pm) |
Bio::Tools::Glimmer - parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions
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');
}
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.
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
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.
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
Email jason-at-bioperl-dot-org
Torsten Seemann
Mark Johnson
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
Usage : $glimmer->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/glimmer/i.
Returns : String
Argument : n/a
Title : next_feature
Usage : while($gene = $glimmer->next_feature()) {
# do something
}
Function: Returns the next gene structure prediction of the Glimmer result
file. Call this method repeatedly until FALSE is returned.
The returned object is actually a SeqFeatureI implementing object.
This method is required for classes implementing the
SeqAnalysisParserI interface, and is merely an alias for
next_prediction() at present.
Example :
Returns : A Bio::Tools::Prediction::Gene object.
Args :
Title : next_prediction
Usage : while($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 :
Title : _parse_predictions()
Usage : $obj->_parse_predictions()
Function: Parses the prediction section. Automatically called by
next_prediction() if not yet done.
Example :
Returns :
Title : _parse_eukaryotic()
Usage : $obj->_parse_eukaryotic()
Function: Parses the prediction section. Automatically called by
next_prediction() if not yet done.
Example :
Returns :
Title : _parse_prokaryotic()
Usage : $obj->_parse_prokaryotic()
Function: Parses the prediction section. Automatically called by
next_prediction() if not yet done.
Example :
Returns :
Title : _prediction() Usage : $gene = $obj->_prediction() Function: internal Example : Returns :
Title : _add_prediction() Usage : $obj->_add_prediction($gene) Function: internal Example : Returns :
Title : _predictions_parsed Usage : $obj->_predictions_parsed Function: internal Example : Returns : TRUE or FALSE
Title : _seqname Usage : $obj->_seqname($seqname) Function: internal (for Glimmer 2.X) Example : Returns : String
Title : _seqlength Usage : $obj->_seqlength($seqlength) Function: internal (for Glimmer 2.X) Example : Returns : String
Title : _format Usage : $obj->_format($format) Function: internal Example : Returns : String
Title : _detail_file Usage : $obj->_detail_file($filename) Function: internal (for Glimmer 3.X) Example : Returns : String
| 2020-10-28 | perl v5.30.3 |