Provided by: libbio-perl-perl_1.7.2-3_all bug


       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