| Bio::Tools::Phylo::Gerp(3pm) | User Contributed Perl Documentation | Bio::Tools::Phylo::Gerp(3pm) |
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: 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.
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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
column.
NB: feature coordinates are alignment columns of the alignment
used to create the result file.
Args : none
| 2021-08-15 | perl v5.32.1 |