Bio::Tools::Phylo::GumUser)Contributed Perl DocumenBio::Tools::Phylo::Gumby(3)NAMEBio::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
perl v5.14.1 2011-07-22 Bio::Tools::Phylo::Gumby(3)
