bio::tools::geneid(3pm) [debian man page]
Bio::Tools::Geneid(3pm) User Contributed Perl Documentation Bio::Tools::Geneid(3pm) NAME
Bio::Tools::Geneid - Results of one geneid run SYNOPSIS
use Bio::Tools::Geneid; my $gid = Bio::Tools::Geneid(-file => "geneid.out"); while (my $gene = $gid->next_prediction) { my @transcripts = $gene->transcripts; foreach my $t (@transcripts) { my @exons = $t->exons; foreach my $e (@exons) { printf("Exon %d..%d ", $e->start, $e->end); } } } DESCRIPTION
This is the parser for the output of geneid by Enrique Blanco and Roderic Guigo (IMIM-UPF). See http://www1.imim.es/software/geneid. It relies on native geneid output format internally and will work with geneid versions 1.0 and 1.1. Currently this module supports only the default mode of operation which is to predict exons and assemble an optimal gene prediction. It takes either a file handle or a file name and returns a Bio::SeqFeature::Gene::GeneStructure object. 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 one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Support 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 the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Keith James Email: kdj@sanger.ac.uk APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : $obj->new(-file = "<geneid.out"); $obj->new(-fh => *GI); Function: Constructor for geneid wrapper. Takes either a file : or filehandle Returns : L<Bio::Tools::Geneid> next_prediction Title : next_prediction Usage : while($gene = $geneid->next_prediction) { # do something } Function: Returns the gene structure prediction of the geneid result file. Call this method repeatedly until FALSE is returned. Returns : A Bio::SeqFeature::Gene::GeneStructure object Args : None _add_exon Title : _add_exon Usage : $obj->_add_exon($gene, $transcript, ... exon data ...) Function: Adds a new exon to both gene and transcript from the data : supplied as args Example : Returns : Nothing _set_strand Title : _set_strand Usage : $obj->_set_strand($gene) Function: Sets the overall gene strand to the same strand as all : the exons if they are all on the same strand, or to strand 0 : if the exons are on different strands. Example : Returns : Nothing _target_id Title : _target_id Usage : $obj->_target_id Function: get/set for genomic sequence id Example : Returns : A target ID perl v5.14.2 2012-03-02 Bio::Tools::Geneid(3pm)
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Bio::Tools::MZEF(3pm) User Contributed Perl Documentation Bio::Tools::MZEF(3pm) NAME
Bio::Tools::MZEF - Results of one MZEF run SYNOPSIS
$mzef = Bio::Tools::MZEF->new(-file => 'result.mzef'); # filehandle: $mzef = Bio::Tools::MZEF->new( -fh => *INPUT ); # to indicate that the sequence was reversed prior to feeding it to MZEF # and that you want to have this reflected in the strand() attribute of # the exons, as well have the coordinates translated to the non-reversed # sequence $mzef = Bio::Tools::MZEF->new( -file => 'result.mzef', -strand => -1 ); # parse the results # note: this class is-a Bio::Tools::AnalysisResult which implements # Bio::SeqAnalysisParserI, i.e., $genscan->next_feature() is the same while($gene = $mzef->next_prediction()) { # $gene is an instance of Bio::Tools::Prediction::Gene # $gene->exons() returns an array of # Bio::Tools::Prediction::Exon objects # all exons: @exon_arr = $gene->exons(); # internal exons only @intrl_exons = $gene->exons('Internal'); # note that presently MZEF predicts only internal exons! } # essential if you gave a filename at initialization (otherwise the file # will stay open) $mzef->close(); DESCRIPTION
The MZEF module provides a parser for MZEF gene structure prediction output. This module inherits off Bio::Tools::AnalysisResult and therefore implements Bio::SeqAnalysisParserI. 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 one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Support 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 the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Hilmar Lapp Email hlapp-at-gmx.net (or hilmar.lapp-at-pharma.novartis.com) APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ analysis_method Usage : $mzef->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches /mzef/i. Returns : String Argument : n/a next_feature Title : next_feature Usage : while($gene = $mzef->next_feature()) { # do something } Function: Returns the next gene structure prediction of the MZEF result file. Call this method repeatedly until FALSE is returned. The returned object is actually a SeqFeatureI implementing object. This method is required for classes implementing the SeqAnalysisParserI interface, and is merely an alias for next_prediction() at present. Note that with the present version of MZEF there will only be one object returned, because MZEF does not predict individual genes but just potential internal exons. Example : Returns : A Bio::Tools::Prediction::Gene object. Args : next_prediction Title : next_prediction Usage : while($gene = $mzef->next_prediction()) { # do something } Function: Returns the next gene structure prediction of the MZEF result file. Call this method repeatedly until FALSE is returned. Note that with the present version of MZEF there will only be one object returned, because MZEF does not predict individual genes but just potential internal exons. 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 perl v5.14.2 2012-03-02 Bio::Tools::MZEF(3pm)