Provided by: libbio-perl-perl_1.6.901-2_all bug

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