Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::Tools::Phylo::Gerp - Parses output from GERP


         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;


       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:

       It works on the .elems files produced by gerpelem.

       Each result is a Bio::SeqFeature::Annotated representing a single constrained element.


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AUTHOR - Sendu Bala



       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

        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

        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

                  NB: feature coordinates are alignment columns of the alignment
                  used to create the result file.
        Args    : none