Bio::Tools::Phylo Gerp
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Summary
Bio::Tools::Phylo::Gerp - Parses output from GERP
Package variables
No package variables defined.
Included modules
Bio::Annotation::SimpleValue
Bio::SeqFeature::Annotated
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
newDescriptionCode
next_resultDescriptionCode
Methods description
newcode    nextTop
 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_resultcodeprevnextTop
 Title   : next_result
Usage : $result = $obj->next_result();
Function: Returns the next result available from the input, or undef if there
are no more results.
Returns : Bio::SeqFeature::Annotated object. Features are annotated with a tag
for 'pvalue', and a 'predicted' tag. They have no sequence id unless
the input GERP file is non-standard, with the seq id as the 6th
column.
NB: feature coordinates are alignment columns of the alignment used to create the result file. Args : none
Methods code
newdescriptionprevnextTop
sub new {
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    
    $self->_initialize_io(@args);
    
    return $self;
}
next_resultdescriptionprevnextTop
sub next_result {
    my ($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
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 BalaTop
Email bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _