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://github.com/bioperl/bioperl-live/issues
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