Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)


Bio::Tools::Phylo::Gumby - 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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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::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