Bio::Tools::Phylo::Gumby(3) Parses output from gumby


#!/usr/bin/perl -Tw
use strict;
use Bio::Tools::Phylo::Gumby;
my $parser = Bio::Tools::Phylo::Gumby->new(-file => "out.align");
my @features = $parser->next_result();


This module is used to parse the output from 'gumby' by Shyam Prabhakar. You can get details here:

It works on the .align files produced.

The result is a list of feature objects.


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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::Gumby->new();
 Function: Builds a new Bio::Tools::Phylo::Gumby object
 Returns : Bio::Tools::Phylo::Gumby
 Args    : -file (or -fh) should contain the contents of a gumby .align output


 Title   : next_result
 Usage   : $result = $obj->next_result();
 Function: Returns the next set of results available from the input, or undef if
           there are no more results.
 Returns : list of Bio::SeqFeature::Annotated (one per sequence). Features are
           annotated with tags for pvalue and 'kind' (holding 'all', 'exon', or
           NB: Gumby ignores sequence coordinates in input alignments, treating
           each sequence as if it started at position 1. If you're running this
           manually (ie. not via the Bio::Tools::Run::Phylo::Gumby) you will
           have to adjust the coordinates to match up with your input alignment
           and sequences.
 Args    : none