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Summary

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

Package variables

Included modules

Inherit

Bio::Root::IO Bio::Root::Root

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.

Methods

Methods description

 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
           column.

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

Methods code

sub new {

    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    
    $self->_initialize_io(@args);
    
    return $self;

}

sub next_result {

    my ($self) = @_;
    
    my $line = $self->_readline || return;
    
    while ($line !~ /^\d+\s+\d+\s+\d+\s+\S+\s+\S+\s*(?:\S+\s*)?$/) {
        $line = $self->_readline || return;
    }
    
    #start   end     length  RS-score        p-value
    # code elsewhere adds seq_id on the end (not valid GERP), so we capture that
    # if present
    my ($start, $end, undef, $rs_score, $p_value, $seq_id) = split(/\s+/, $line);
    my $feat = Bio::SeqFeature::Annotated->new(
        $seq_id ? (-seq_id => $seq_id) : (),
        -start        => $start, 
        -end          => $end,
        -strand       => 1,
        -score        => $rs_score,
        #-type         => 'conserved_region', ***causes 740x increase in SeqFeatureDB storage requirments!
        -source       => 'GERP');
    
    my $sv = Bio::Annotation::SimpleValue->new(-tagname => 'predicted', -value => 1);
    $feat->annotation->add_Annotation($sv);
    $sv = Bio::Annotation::SimpleValue->new(-tagname => 'pvalue', -value => $p_value);
    $feat->annotation->add_Annotation($sv);
    
    return $feat;
}

1;

}

General documentation

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

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.

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/

Email bix@sendu.me.uk

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