bio::tools::phylo::phylip::protdist(3pm) [debian man page]
Bio::Tools::Phylo::Phylip::ProtDist(3pm) User Contributed Perl Documentation Bio::Tools::Phylo::Phylip::ProtDist(3pm) NAME
Bio::Tools::Phylo::Phylip::ProtDist - parser for ProtDist output SYNOPSIS
use Bio::Tools::Phylo::Phylip::ProtDist; my $parser = Bio::Tools::Phylo::Phylip::ProtDist->new(-file => 'outfile'); while( my $result = $parser->next_matrix) { # do something with it } DESCRIPTION
A parser for ProtDist output into a Bio::Matrix::PhylipDist object. See also Bio::Matrix::IO::phylip this module may go away. 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::Phylo::Phylip::ProtDist->new(); Function: Builds a new Bio::Tools::Phylo::Phylip::ProtDist object Returns : Bio::Tools::ProtDist Args : -fh/-file => $val, # for initing input, see Bio::Root::IO -program => 'programname' # name of the program next_matrix Title : next_matrix Usage : my $matrix = $parser->next_matrix Function: Get the next result set from parser data Returns : L<Bio::Matrix::PhylipDist> Args : none perl v5.14.2 2012-03-02 Bio::Tools::Phylo::Phylip::ProtDist(3pm)
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Bio::Tools::Phylo::Gerp(3pm) User Contributed Perl Documentation Bio::Tools::Phylo::Gerp(3pm) NAME
Bio::Tools::Phylo::Gerp - Parses output from GERP SYNOPSIS
use strict; use Bio::Tools::Phylo::Gerp; my $parser = Bio::Tools::Phylo::Gerp->new(-file => "alignment.rates.elems"); while (my $feat = $parser->next_result) { my $start = $feat->start; my $end = $feat->end; my $rs_score = $feat->score; my $p_value = ($feat->annotation->get_Annotations('p-value'))[0]->value; } DESCRIPTION
This module is used to parse the output from 'GERP' (v2) by Eugene Davydov (originally Gregory M. Cooper et al.). You can get details here: http://mendel.stanford.edu/sidowlab/ It works on the .elems files produced by gerpelem. Each result is a Bio::SeqFeature::Annotated representing a single constrained element. 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::Phylo::Gerp->new(); Function: Builds a new Bio::Tools::Phylo::Gerp object Returns : Bio::Tools::Phylo::Gerp Args : -file (or -fh) should contain the contents of a gerpelem .elems file 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 a tag for 'pvalue', and a 'predicted' tag. They have no sequence id unless the input GERP file is non-standard, with the seq id as the 6th column. NB: feature coordinates are alignment columns of the alignment used to create the result file. Args : none perl v5.14.2 2012-03-02 Bio::Tools::Phylo::Gerp(3pm)