1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
|
#!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use lib "$ENV{TRINITY_HOME}/PerlLib";
use Fasta_reader;
use List::Util qw (shuffle);
#use Math::Random;
my $usage = <<__EOUSAGE__;
##################################################################
#
# --fasta <string> fasta filename
#
# --subst_rate <float> rate of single base substitutions
#
# --insert_rate <float> rate of insertion
#
# --insert_size <int> default: 1
#
# --delete_rate <float> rate for deletions
#
# --delete_size <int> default: 1
#
# * note, all rates must be 0 <= x <= 0.25
#
###################################################################
__EOUSAGE__
;
my $fasta_file;
my $subst_rate = 0;
my $insert_rate = 0;
my $insert_size = 1;
my $delete_rate = 0;
my $delete_size = 1;
&GetOptions (
'fasta=s' => \$fasta_file,
'subst_rate=f' => \$subst_rate,
'insert_rate=f' => \$insert_rate,
'insert_size=i' => \$insert_size,
'delete_rate=f' => \$delete_rate,
'delete_size=i' => \$delete_size,
);
unless ($fasta_file) {
die $usage;
}
unless ($subst_rate || $insert_rate || $delete_rate) {
die $usage;
}
foreach my $info_aref ( ['subst_rate', $subst_rate ],
['insert_rate', $insert_rate ],
['delete_rate', $delete_rate ] ) {
my ($rate_type, $val) = @$info_aref;
if ($val > 0.25) {
die "Error, --$rate_type $val exceeds max val of 0.25 ";
}
}
main: {
my $fasta_reader = new Fasta_reader($fasta_file);
my %fasta_seqs = $fasta_reader->retrieve_all_seqs_hash();
foreach my $acc (keys %fasta_seqs) {
my $seq = $fasta_seqs{$acc};
my @seqarray = &convert_to_seqarray($seq);
my %seen;
if ($subst_rate) {
@seqarray = &mutate_seq(\@seqarray, \%seen, $subst_rate, 'substitution');
}
if ($insert_rate) {
@seqarray = &mutate_seq(\@seqarray, \%seen, $insert_rate, 'insertion');
}
if ($delete_rate) {
@seqarray = &mutate_seq(\@seqarray, \%seen, $delete_rate, 'deletion');
}
my $mutated_seq = join("", @seqarray);
print ">$acc mutated\n$mutated_seq\n";
}
exit(0);
}
####
sub convert_to_seqarray {
my ($seq) = @_;
my @chars = split(//, uc $seq);
return(@chars);
}
####
sub mutate_seq {
my ($seqarray_aref, $seen_href, $mut_rate, $mut_type) = @_;
my $seqlen = $#$seqarray_aref + 1;
my $num_mutations = int($mut_rate * $seqlen + 0.5);
for (1..$num_mutations) {
my $pos = -1;
do {
$pos = int(rand($seqlen));
} while ($seen_href->{$pos});
$seen_href->{$pos} = 1;
## Substitutions
if ($mut_type eq 'substitution') {
my $char = $seqarray_aref->[$pos];
my @mut_chars = grep { $_ ne $char } qw(G A T C);
my $mut_base = $mut_chars[ int(rand(3)) ];
$seqarray_aref->[$pos] = lc $mut_base;
}
## Deletions
elsif ($mut_type eq 'deletion') {
for (my $i = $pos; $i < $pos + $delete_size && $i < $seqlen; $i++) {
$seqarray_aref->[$i] = "";
$seen_href->{$i} = 1;
}
}
## Insertions
elsif ($mut_type eq 'insertion') {
## create insertion
my $insertion_seq = "";
my @bases = qw(G A T C);
for (my $i = 0; $i < $insert_size; $i++) {
my $base = $bases[int(rand(4))];
$insertion_seq .= $base;
}
$seqarray_aref->[$pos] .= lc $insertion_seq;
}
else {
confess "Error, do not understand mutation type: $mut_type ";
}
}
return (@$seqarray_aref);
}
|
