NAME

       Bio::Tools::Phylo::Gumby - Parses output from gumby

SYNOPSIS

         #!/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();

DESCRIPTION

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

       It works on the .align files produced.

       The result is a list of feature objects.

FEEDBACK

   Mailing Lists
       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
       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 Bugs
       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 Bala

       Email bix@sendu.me.uk

APPENDIX

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

   new
        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
                  file

   next_result
        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
                  'nonexon').

                  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