annotate lib/CPT/Bio/RBS/Algo/Naive.pm @ 1:f093e08f21f3 draft default tip

planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c

1 package CPT::Bio::RBS::Algo::Naive;
2 use Moose;
3 with 'CPT::Bio::RBS::Algo';
4 use CPT::Bio::RBS_Object;
5 
6 my @SDs = (
7 	'aggaggt',
8 	'ggaggt',
9 	'aggagg',
10 	'aggag',
11 	'gaggt',
12 	'ggagg',
13 	'aggt',
14 	'gggt',
15 	'gagg',
16 	'gggg',
17 	'agga',
18 	'ggag',
19 	'gga',
20 	'gag',
21 	'agg',
22 	'ggt',
23 );
24 
25 sub predict {
26 	my ( $self, %params ) = @_;
27 	my $upstream = $params{sequence};
28 	my $only_best = $params{return_best};
29 
30 	my $length = length($upstream);
31 
32 	my @results = ();
33 	foreach my $rbs ( @SDs ){
34 		while ($upstream =~ /$rbs/g) {
35 			# Position of regex match
36 			my $loc = $-[0];
37 			# Seq before RBS
38 			my $before = substr($upstream,0, $loc);
39 			# Seq after RBS
40 			my $after = substr($upstream, $loc + length($rbs));
41 			my $rbs_o = CPT::Bio::RBS_Object->new(
42 				upstream => sprintf('%s %s %s', $before , uc($rbs) , $after),
43 				score => $self->score_match($rbs, length($after)),
44 				rbs_seq => uc($rbs),
45 				separation => length($after),
46 			);
47 			push( @results, $rbs_o );
48 		}
49 	}
50 	@results = sort { $b->score() <=> $a->score() } @results;
51 	if (@results) {
52 		if($only_best){
53 			return ($results[0]);
54 		}else{
55 			return @results;
56 		}
57 	}
58 	else {
59 		return (
60 			CPT::Bio::RBS_Object->new(
61 				upstream =>$upstream,
62 				score => '-1',
63 				rbs_seq => 'None',
64 				separation => -1,
65 			)
66 		);
67 	}
68 }
69 
70 sub score_match {
71 	my ($self, $match, $dist) = @_;
72 	return length($match);
73 }
74 
75 1;
76 
77 __END__
78 
79 =pod
80 
81 =encoding UTF-8
82 
83 =head1 NAME
84 
85 CPT::Bio::RBS::Algo::Naive
86 
87 =head1 VERSION
88 
89 version 1.99.4
90 
91 =head1 AUTHOR
92 
93 Eric Rasche <[e-mail]>
94 
95 =head1 COPYRIGHT AND LICENSE
96 
97 This software is Copyright (c) 2014 by Eric Rasche.
98 
99 This is free software, licensed under:
00 
01   The GNU General Public License, Version 3, June 2007
02 
03 =cut