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://github.com/bioperl/bioperl-live/issues

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