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Bio::Tools::Phylo::Gumby.3pm

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:

   http://bugzilla.open-bio.org/
 
 

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