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Bio::Tools::Glimmer.3pm
Langue: en
Version: 2008-06-24 (ubuntu - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
NAME
Bio::Tools::Glimmer - parser for GlimmerM/GlimmerHMM eukaryotic gene predictionsSYNOPSIS
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-orgCONTRIBUTORS
Torsten SeemannMark 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
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre