Bio::Tools::Phylo::GerUser Contributed Perl DocumentBio::Tools::Phylo::Gerp(3)NAMEBio::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:
http://bugzilla.open-bio.org/
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 v5.14.1 2011-07-22 Bio::Tools::Phylo::Gerp(3)