bio::tools::repeatmasker(3pm) [debian man page]
Bio::Tools::RepeatMasker(3pm) User Contributed Perl Documentation Bio::Tools::RepeatMasker(3pm) NAME
Bio::Tools::RepeatMasker - a parser for RepeatMasker output SYNOPSIS
use Bio::Tools::RepeatMasker; my $parser = Bio::Tools::RepeatMasker->new(-file => 'seq.fa.out'); while( my $result = $parser->next_result ) { # get some value } DESCRIPTION
A parser for RepeatMasker output 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 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 of the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Shawn Hoon Email shawnh@fugu-sg.org 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::RepeatMasker->new(); Function: Builds a new Bio::Tools::RepeatMasker object Returns : Bio::Tools::RepeatMasker Args : -fh/-file => $val, for initing input, see Bio::Root::IO next_result Title : next_result Usage : my $r = $rpt_masker->next_result Function: Get the next result set from parser data Returns : Bio::SeqFeature::FeaturePair Feature1 is the Query coordinates and Feature2 is the Hit Args : none perl v5.14.2 2012-03-02 Bio::Tools::RepeatMasker(3pm)
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Bio::Tools::Match(3pm) User Contributed Perl Documentation Bio::Tools::Match(3pm) NAME
Bio::Tools::Match - Parses output from Transfac's match(TM) SYNOPSIS
use strict; use Bio::Tools::Match; my $parser = Bio::Tools::Match->new(-file => "match.out"); while (my $feat = $parser->next_result) { my $start = $feat->start; my $end = $feat->end; my $core_score = $feat->score; my $matrix_score = ($feat->annotation->get_Annotations('matrix_score'))[0]->value; my $matrix_id = ($feat->annotation->get_Annotations('matrix_id'))[0]->value; } DESCRIPTION
This module is used to parse the output from Transfac's match(TM) program. It doesn't support the histogram output of match. Each result is a Bio::SeqFeature::Annotated representing a single matrix match. 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 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 of the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Sendu Bala Email bix@sendu.me.uk 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::Match->new(); Function: Builds a new Bio::Tools::Match object Returns : Bio::Tools::Match Args : -file (or -fh) should contain the contents of a standard match output next_result Title : next_result Usage : $result = $obj->next_result(); Function: Returns the next result available from the input, or undef if there are no more results. Returns : Bio::SeqFeature::Annotated object. Features are annotated with tags for 'matrix_score', 'matrix_id' and a 'predicted' tag. Args : none perl v5.14.2 2012-03-02 Bio::Tools::Match(3pm)