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Bio::Tools::Phylo::GerUser Contributed Perl DocumentBio::Tools::Phylo::Gerp(3)

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

perl v5.32.1			  2019-12-07	    Bio::Tools::Phylo::Gerp(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Sendu Bala | APPENDIX

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