#
# BioPerl module for Bio::Tools::Phylo::Gumby
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Sendu Bala <bix@sendu.me.uk>
#
# Copyright Sendu Bala
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Phylo::Gumby - Parses output from gumby
=head1 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();
=head1 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.
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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
=head1 AUTHOR - Sendu Bala
Email bix@sendu.me.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::Phylo::Gumby;
use strict;
use Bio::SeqFeature::Annotated;
use Bio::Annotation::SimpleValue;
use base qw(Bio::Root::Root Bio::Root::IO);
=head2 new
Title : new
Usage : my $obj = Bio::Tools::Phylo::Gumby->new();
Function: Builds a new Bio::Tools::Phylo::Gumby object
Returns : Bio::Tools::Phylo::Gumby
Args : -file (or -fh) should contain the contents of a gumby .align output
file
=cut
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
$self->_initialize_io(@args);
return $self;
}
=head2 next_result
Title : next_result
Usage : $result = $obj->next_result();
Function: Returns the next set of results available from the input, or undef if
there are no more results.
Returns : list of Bio::SeqFeature::Annotated (one per sequence). Features are
annotated with tags for pvalue and 'kind' (holding 'all', 'exon', or
'nonexon').
NB: Gumby ignores sequence coordinates in input alignments, treating
each sequence as if it started at position 1. If you're running this
manually (ie. not via the Bio::Tools::Run::Phylo::Gumby) you will
have to adjust the coordinates to match up with your input alignment
and sequences.
Args : none
=cut
sub next_result {
my ($self) = @_;
my $line = $self->_readline || return;
while ($line !~ /^start/) {
$line = $self->_readline || return;
if ($line =~ /^(all|exon|nonexon):/) {
$self->{_kind} = $1;
}
}
my ($score, $pvalue) = $line =~ /score (\d+), pvalue (\S+)/;
my @feats;
while ($line = $self->_readline) {
$line =~ /^$/ && last;
$line || last;
my ($seq_id, $start, $end) = split(/\s+/, $line);
my $feature = Bio::SeqFeature::Annotated->new(-seq_id => $seq_id,
-start => $start,
-end => $end,
-score => $score,
-strand => 1,
-source => 'gumby');
my $sv = Bio::Annotation::SimpleValue->new(-tagname => 'pvalue', -value => $pvalue);
$feature->annotation->add_Annotation($sv);
$sv = Bio::Annotation::SimpleValue->new(-tagname => 'kind', -value => $self->{_kind});
$feature->annotation->add_Annotation($sv);
$sv = Bio::Annotation::SimpleValue->new(-tagname => 'predicted', -value => 1);
$feature->annotation->add_Annotation($sv);
push(@feats, $feature);
}
return @feats;
}
1;