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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:47:24 +0000
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0:b8b8b52904a5 1:f093e08f21f3
1 package CPT::Bio::ORF;
2 use strict;
3 use warnings;
4 use autodie;
5 use Moose;
6
7 has min_gene_length => (
8 is => 'rw',
9 isa => 'Int',
10 default => sub {
11 0
12 },
13 );
14 has sc_atg => ( is => 'rw', isa => 'Bool', default => sub { 1 } );
15 has sc_ttg => ( is => 'rw', isa => 'Bool', default => sub { 1 } );
16 has sc_ctg => ( is => 'rw', isa => 'Bool', default => sub { 0 } );
17 has sc_gtg => ( is => 'rw', isa => 'Bool', default => sub { 1 } );
18
19 our %code = (
20 "TTT" => "F", "TTC" => "F", "TTA" => "L", "TTG" => "L", "TCT" => "S",
21 "TCC" => "S", "TCA" => "S", "TCG" => "S", "TAT" => "Y", "TAC" => "Y",
22 "TAA" => "*", "TAG" => "*", "TGT" => "C", "TGC" => "C", "TGA" => "*",
23 "TGG" => "W", "CTT" => "L", "CTC" => "L", "CTA" => "L", "CTG" => "L",
24 "CCT" => "P", "CCC" => "P", "CCA" => "P", "CCG" => "P", "CAT" => "H",
25 "CAC" => "H", "CAA" => "Q", "CAG" => "Q", "CGT" => "R", "CGC" => "R",
26 "CGA" => "R", "CGG" => "R", "ATT" => "I", "ATC" => "I", "ATA" => "I",
27 "ATG" => "M", "ACT" => "T", "ACC" => "T", "ACA" => "T", "ACG" => "T",
28 "AAT" => "N", "AAC" => "N", "AAA" => "K", "AAG" => "K", "AGT" => "S",
29 "AGC" => "S", "AGA" => "R", "AGG" => "R", "GTT" => "V", "GTC" => "V",
30 "GTA" => "V", "GTG" => "V", "GCT" => "A", "GCC" => "A", "GCA" => "A",
31 "GCG" => "A", "GAT" => "D", "GAC" => "D", "GAA" => "E", "GAG" => "E",
32 "GGT" => "G", "GGC" => "G", "GGA" => "G", "GGG" => "G",
33 );
34
35
36
37 sub run {
38 my ($self, $sequence) = @_;
39 # Read through forward strand
40 my @putative_starts;
41
42 # 30 seconds with a bioperl object
43 # 5 seconds with string munging. >:|
44 my $dna = uc( $sequence );
45 my $length = length($sequence);
46
47 # Pre-create the regular expressions
48 my ( $regex_forward, $regex_backwards );
49 my $not_statement_f = '^';
50 my $not_statement_r = '^';
51 if ( !$self->sc_atg() ) {
52 $not_statement_f .= 'A';
53 $not_statement_r .= 'T';
54 }
55 if ( !$self->sc_ctg() ) {
56 $not_statement_f .= 'C';
57 $not_statement_r .= 'G';
58 }
59 if ( !$self->sc_ttg() ) {
60 $not_statement_f .= 'T';
61 $not_statement_r .= 'A';
62 }
63 if ( !$self->sc_gtg() ) {
64 $not_statement_f .= 'G';
65 $not_statement_r .= 'C';
66 }
67
68 # If any start is acceptable, we re-add them and remove our ^
69 if($not_statement_r eq '^' && $not_statement_f eq '^'){
70 $not_statement_f = 'ACTG';
71 $not_statement_r = 'ACTG';
72 }
73 $regex_forward = qr/[${not_statement_f}]TG/;
74 $regex_backwards = qr/CA[${not_statement_r}]/;
75
76 # Collect putative starts
77 for ( my $i = 1 ; $i < $length - 1 ; $i++ ) {
78 my $tri_nt = substr( $dna, $i - 1, 3 ); #$seq_obj->subseq($i,$i+2);
79 if ( $tri_nt =~ $regex_forward ) {
80 push( @putative_starts, [ $i, '+' ] );
81 }
82 if ( $tri_nt =~ $regex_backwards ) {
83 push( @putative_starts, [ $i + 2, '-' ] );
84 }
85 }
86 my %ORFs;
87
88 #Loop through all of the starts we have
89 my $fc = 0;
90 my $rc = 0;
91 foreach (@putative_starts) {
92 my @putative_start = @{$_};
93
94 my $final_seq = "";
95
96 my $add;
97 my $tri_nt;
98 if ( $putative_start[1] eq "+" ) {
99 my $end;
100 for ( my $k = $putative_start[0] ; $k < $length ; $k = $k + 3 )
101 {
102 my $tri_nt = substr( $dna, $k, 3 );
103 my $aa = $code{$tri_nt};
104 if ( $aa && $aa ne '*' ) {
105 $end = $k + 3;
106 $final_seq .= $tri_nt;
107 }
108 else {
109 last;
110 }
111 }
112 if ( length($final_seq)/3 > $self->min_gene_length() ) {
113 $ORFs{ 'f_' + $fc++ } = [
114 length($final_seq)/3,
115 $putative_start[0],
116 $end,
117 'F',
118 $final_seq
119 ];
120 }
121 } # - strand
122 else {
123 my $end;
124 for ( my $k = $putative_start[0] ; $k >= 2 ; $k = $k - 3 ) {
125 my $tmp = reverse( substr( $dna, $k - 3, 3 ) );
126
127 $tmp =~ tr/ACTG/qzAC/;
128 $tmp =~ tr/qz/TG/;
129
130 my $aa = $code{$tmp};
131 if ( defined $aa && $aa ne '*' ) {
132 $end = $k - 1;
133 $final_seq .= $tmp;
134 }
135 else {
136 last;
137 }
138
139 }
140 if ( length($final_seq)/3 > $self->min_gene_length() ) {
141 $ORFs{ 'r_' + $rc++ } = [
142 length($final_seq)/3,
143 $end,
144 $putative_start[0],
145 'R',
146 $final_seq
147 ];
148 }
149 }
150 }
151
152 my @orfs;
153
154 for my $orf_key ( sort( keys(%ORFs) ) ) {
155 my @tmp= @{ $ORFs{$orf_key} };
156 my $seqobj = Bio::Seq->new(
157 -display_id => sprintf(
158 'orf%05d_%s',
159 ($orf_key + 1), $tmp[3],
160 ),
161 -desc => sprintf(
162 '[%s-%s; %s aa long]'
163 ,$tmp[1], $tmp[2], $tmp[0]
164 ),
165 -seq => $tmp[4]
166 );
167 push(@orfs, $seqobj);
168 }
169 return @orfs;
170 }
171
172
173
174 no Moose;
175 1;
176
177 __END__
178
179 =pod
180
181 =encoding UTF-8
182
183 =head1 NAME
184
185 CPT::Bio::ORF
186
187 =head1 VERSION
188
189 version 1.99.4
190
191 =function run
192
193 =head1 AUTHOR
194
195 Eric Rasche <rasche.eric@yandex.ru>
196
197 =head1 COPYRIGHT AND LICENSE
198
199 This software is Copyright (c) 2014 by Eric Rasche.
200
201 This is free software, licensed under:
202
203 The GNU General Public License, Version 3, June 2007
204
205 =cut