debian man page for bio::tools::phylo::gerp

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)