bio::tools::genomewise(3pm) [debian man page]
Bio::Tools::Genomewise(3pm) User Contributed Perl Documentation Bio::Tools::Genomewise(3pm) NAME
Bio::Tools::Genomewise - Results of one Genomewise run SYNOPSIS
use Bio::Tools::Genomewise; my $gw = Bio::Tools::Genomewise(-file=>"genomewise.out"); while (my $gene = $gw->next_prediction){ my @transcripts = $gene->transcripts; foreach my $t(@transcripts){ my @exons = $t->exons; foreach my $e(@exons){ print $e->start." ".$e->end." "; } } } DESCRIPTION
This is the parser for the output of Genewise. It takes either a file handle or a file name and returns a Bio::SeqFeature::Gene::GeneStructure object. You will need to specify the proper target sequence id on the object with the $feature->seq_id($seqid). 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 - Fugu Team, Jason Stajich Email: fugui-at-worf.fugu-sg.org jason-at-bioperl-dot-org 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=>"genewise.out"); $obj->new(-fh=>*GW); Function: Constructor for genomewise wrapper. Takes either a file or filehandle Example : Returns : L<Bio::Tools::Genomewise> _get_strand Title : _get_strand Usage : $obj->_get_strand Function: takes start and end values, swap them if start>end and returns end Example : Returns :$start,$end,$strand score Title : score Usage : $obj->score Function: get/set for score info Example : Returns : a score value _prot_id Title : _prot_id Usage : $obj->_prot_id Function: get/set for protein id Example : Returns :a protein id _target_id Title : _target_id Usage : $obj->_target_id Function: get/set for genomic sequence id Example : Returns :a target id next_prediction Title : next_prediction Usage : while($gene = $genewise->next_prediction()) { # do something } Function: Returns the gene structure prediction of the Genomewise result file. Call this method repeatedly until FALSE is returned. Example : Returns : a Bio::SeqFeature::Gene::GeneStructure object Args : perl v5.14.2 2012-03-02 Bio::Tools::Genomewise(3pm)
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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)