-
Notifications
You must be signed in to change notification settings - Fork 7
/
hapfreq.pl
executable file
·639 lines (541 loc) · 19.6 KB
/
hapfreq.pl
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
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
#!/usr/bin/perl
#
# INGLÊS/ENGLISH
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# http://www.gnu.org/copyleft/gpl.html
#
#
# PORTUGUÊS/PORTUGUESE
# Este programa é distribuído na expectativa de ser útil aos seus
# usuários, porém NÃO TEM NENHUMA GARANTIA, EXPLÍCITAS OU IMPLÍCITAS,
# COMERCIAIS OU DE ATENDIMENTO A UMA DETERMINADA FINALIDADE. Consulte
# a Licença Pública Geral GNU para maiores detalhes.
# http://www.gnu.org/copyleft/gpl.html
#
# Copyright (C) 2012 Universidade de São Paulo
#
# Universidade de São Paulo
# Laboratório de Biologia do Desenvolvimento de Abelhas
# Núcleo de Bioinformática (LBDA-BioInfo)
#
# Daniel Guariz Pinheiro
# http://zulu.fmrp.usp.br/bioinfo
#
# $Id$
=head1 NAME
=head1 SYNOPSIS
=head1 ABSTRACT
=head1 DESCRIPTION
Arguments:
-h/--help Help
-l/--level Log level [Default: FATAL]
OFF
FATAL
ERROR
WARN
INFO
DEBUG
TRACE
ALL
=head1 AUTHOR
Daniel Guariz Pinheiro E<lt>[email protected]<gt>
Copyright (c) 2012 Universidade de São Paulo
=head1 LICENSE
GNU General Public License
http://www.gnu.org/copyleft/gpl.html
=cut
use strict;
use warnings;
use Readonly;
use Getopt::Long;
use Storable;
use vars qw/$LOGGER/;
INIT {
use Log::Log4perl qw/:easy/;
Log::Log4perl->easy_init($FATAL);
$LOGGER = Log::Log4perl->get_logger($0);
}
my ($level, $infile, $freqthreshold, $hetthreshold, $ord, $poplvl, $restlvl);
my %order = ('f'=>'frequency', 'd'=>'data');
my %alllvls = ('one'=>1, 'two'=>2, 'three'=>3);
Usage("Too few arguments") if $#ARGV < 0;
GetOptions( "h|?|help" => sub { &Usage(); },
"l|level=s"=> \$level,
"i|infile=s"=> \$infile,
"t|freqthreshold=s"=>\$freqthreshold,
"h|hetthreshold=s"=>\$hetthreshold,
"e|level=s"=>\$poplvl,
"o|order=s"=>\$ord,
"r|restlevel=s"=>\$restlvl
) or &Usage();
$ord||='d';
$poplvl||='one';
if (defined $hetthreshold) {
$LOGGER->logdie("Heterozygous threshold must be greather than 1") if ($hetthreshold < 2);
}
if (defined $restlvl) {
$LOGGER->logdie("Wrong restrict level ($restlvl). Choose one of: ".join(', ', keys %alllvls)) unless (exists $alllvls{$restlvl});
}
$LOGGER->logdie("Wrong order ($ord). Possible values are: ".join(',', map { $_.' ('.$order{$_}.')' } keys %order ).".") unless (exists $order{$ord});
if ($level) {
my %LEVEL = (
'OFF' =>$OFF,
'FATAL' =>$FATAL,
'ERROR' =>$ERROR,
'WARN' =>$WARN,
'INFO' =>$INFO,
'DEBUG' =>$DEBUG,
'TRACE' =>$TRACE,
'ALL' =>$ALL);
$LOGGER->logdie("Wrong log level ($level). Choose one of: ".join(', ', keys %LEVEL)) unless (exists $LEVEL{$level});
Log::Log4perl->easy_init($LEVEL{$level});
}
$LOGGER->logdie("Missing input file") unless ($infile);
$LOGGER->logdie("Wrong input file ($infile)") unless (-e $infile);
#######################
# FIRST STEP: Load data and split them by number of heterozygous
#######################
$LOGGER->info("FIRST STEP...");
my %DATA;
#open(POP, "<", 'pop.txt') or $LOGGER->logdie($!);
#while(<POP>) {
while(<DATA>){
chomp;
next if ($_=~/^#/);
my ($lv_one, $lv_two, $hmap, $desc) = split(/\t/, $_);
$DATA{'POPULATION'}->{$hmap} = { 'one' => $lv_one,
'two' => $lv_two,
'three' => $hmap,
'desc' => $desc
};
}
#close(POP);
open(IN, "<", $infile) or $LOGGER->logdie($!);
my %qtd;
my @header;
my @rs;
my %haplotype;
#my @full;
my %view;
my %subject;
## TEST DATA FOR FIRST STEP
#my @in= ( "hmap\tpaciente\tsex\trs1\trs2\trs3\trs4\n",
# "P1\tS1\tMale\tA/A\tC/C\tC/C\tC/N\n",
# "P1\tS2\tMale\tA/T\tG/G\tC/C\tG/C\n",
# "P1\tS3\tMale\tA/A\tG/G\tC/C\tG/G\n",
# "P1\tS4\tFemale\tN/A\tN/N\tC/C\tG/G\n",
# "P2\tS5\tFemale\tT/G\tC/C\tC/C\tG/G\n",
# "P2\tS6\tFemale\tN/T\tC/C\tC/N\tG/G\n",
# "P2\tS7\tFemale\tA/A\tC/C\tC/C\tG/G\n",
# "P2\tS8\tFemale\tG/A\tG/C\tG/C\tG/G\n",
# "P3\tS9\tMale\tA/A\tC/C\tT/C\tG/C\n"
# );
#my $x = 1;
#foreach(@in) {
while(<IN>) {
chomp;
if ($.==1) {
# if ($x==1) {
# $x++;
@header = split(/\t/, $_);
foreach (@header) {
push(@rs, $_) if ($_=~/^rs\d+/);
}
# print join("\t", 'LV1', 'LV2', 'LV3', 'ID', @rs, 'HAPLOTYPE'),"\n";
# print join("\t", 'LV1', 'LV2', 'LV3', 'ID', 'HAPLOTYPE'),"\n";
}
else {
my %v;
@v{@header} = split(/\t/, $_);
@rs = @rs;
for my $m (@rs) {
$v{$m} = [ sort {$a cmp $b} split('/', $v{$m} ) ];
}
$v{'sex'} = 'Unknow' if (($v{'sex'} ne 'Male')&&($v{'sex'} ne 'Female'));
$subject{$v{'paciente'}} = \%v;
my $hap = join(';', (map { (($_->[0] eq $_->[1]) ? $_->[0] : $_->[0].'/'.$_->[1]) } @v{@rs}));
$qtd{ 'one' }->{ $DATA{'POPULATION'}->{ $v{'hmap'} }->{'one'} }++;
$qtd{ 'two' }->{ $DATA{'POPULATION'}->{ $v{'hmap'} }->{'two'} }++;
$qtd{ 'three' }->{ $DATA{'POPULATION'}->{ $v{'hmap'} }->{'three'} }++;
# print join("\t", $DATA{'POPULATION'}->{ $v{'hmap'} }->{'one'},
# $DATA{'POPULATION'}->{ $v{'hmap'} }->{'two'},
# $v{'hmap'},
# $v{'paciente'},
# $hap
# ),"\n";
# push(@full, [ $DATA{'POPULATION'}->{ $v{'hmap'} }->{'one'},
# $DATA{'POPULATION'}->{ $v{'hmap'} }->{'two'},
# $v{'hmap'},
# $v{'paciente'},
# $hap
# ]);
my $nhet=0;
$nhet++ while($hap=~m/\//g);
push(@{ $view{ $DATA{'POPULATION'}->{ $v{'hmap'} }->{$poplvl} }->{ $nhet } }, [$hap, $v{'paciente'}]);
# print join("\t", $DATA{'POPULATION'}->{ $v{'hmap'} }->{'one'},
# $DATA{'POPULATION'}->{ $v{'hmap'} }->{'two'},
# $v{'hmap'},
# $v{'paciente'},
# (map { $_->[0] } @v{@rs}),
# join('', (map { $_->[0] } @v{@rs}))
# ),"\n";
#
# print join("\t", $DATA{'POPULATION'}->{ $v{'hmap'} }->{'one'},
# $DATA{'POPULATION'}->{ $v{'hmap'} }->{'two'},
# $v{'hmap'},
# $v{'paciente'},
# (map { $_->[1] } @v{@rs}),
# join('', (map { $_->[1] } @v{@rs}))
# ),"\n";
}
}
close(IN);
my %general;
my %initial;
foreach my $pel (keys %view) {
my %freq;
#######################
# SECOND STEP: Count frequency for 0 and 1 heterozygous in the haplotype
#######################
$LOGGER->info("Population: $pel # SECOND STEP...");
foreach my $vid (0..1) {
$LOGGER->info("Heterozygosity number: $vid");
foreach my $view_ar ( @{ $view{$pel}->{$vid} } ) {
my ($hap, $sbjct) = @{ $view_ar };
if ($vid == 0) {
my $f = 2;
$freq{$hap}->{'data'}->{$sbjct} = $f;
$freq{$hap}->{'f'}+=$f;
$LOGGER->debug("$pel:$sbjct:$hap=$f");
}
else {
my $orig = $hap;
my @alter;
&recpossibleshet($hap, \@alter, 0);
$LOGGER->logdie("Wrong number of alleles: ".scalar(@alter)) if (scalar(@alter)!=2);
foreach my $alt (@alter) {
my $f = 2/scalar(@alter);
$freq{$alt}->{'data'}->{$sbjct} = $f;
$freq{$alt}->{'f'}+=$f;
$LOGGER->debug("$pel:$sbjct:$alt=$f");
}
}
}
}
## TEST DATA FOR THIRD STEP
#%freq = ( 'A;C;G;N;T;N' => { 'data' => [ ['S1',2], ['S2',2] ] ,
# 'f' => 4
# },
# 'A;C;G;T;T;T' => { 'data' => [ ['S3',2] ],
# 'f' => 2
# },
# 'A;C;G;T;T;N' => { 'data' => [ ['S4',2] ],
# 'f' => 2
# },
# 'A;A;T;A;A;A' => { 'data' => [ ['S5',2] ],
# 'f' => 2
# }
#);
#######################
# THIRD STEP: Count Ns
#######################
$LOGGER->info("Population: $pel # THIRD STEP...");
my @tmp = keys %freq;
foreach my $h ( @tmp ) {
if ($h =~/N/) {
my $orig = $h;
#print ">",$orig,"\t",scalar(@{$freq{$orig}}),"\n";
my @alter;
&recpossibles($h, \@alter, 0);
my %aux;
my $qglobal = 0;
# SE EXISTE GANHA UMA PROBABILIDADE MAIOR
foreach my $alt (@alter) {
if ( exists $freq{$alt} ) {
$aux{$alt} = 1+$freq{$alt}->{'f'};
$qglobal+=$aux{$alt};
}
else {
$aux{$alt}=1;
$qglobal+=1;
}
}
foreach my $alt (@alter) {
#print "\t",$alt,"\n";
foreach my $sbjct (keys %{ $freq{ $orig }->{'data'} }) {
my $f = ($freq{ $orig }->{'data'}->{ $sbjct }*$aux{$alt})/$qglobal;
$freq{$alt}->{'data'}->{$sbjct} = $f;
$freq{$alt}->{'f'}+=$f;
$LOGGER->debug("$pel:$sbjct:$alt=$f");
}
}
delete($freq{$orig});
}
}
foreach my $h ( keys %freq ) {
foreach my $sbjct(keys %{ $freq{ $h }->{'data'} } ) {
$initial{ $h }->{'data'}->{ $sbjct }=$freq{ $h }->{'data'}->{ $sbjct };
$initial{ $h }->{'f'}+=$initial{ $h }->{'data'}->{ $sbjct };
}
}
}
# copy initial data to general
foreach my $h (keys %initial) {
my $f = 0;
foreach my $s (keys %{$initial{$h}->{'data'}}) {
$general{$h}->{ 'data' }->{ $s } = $initial{ $h }->{'data'}->{ $s };
$f+=$initial{ $h }->{'data'}->{ $s };
}
$general{$h}->{ 'f' } = $f;
}
foreach my $pel (keys %view) {
my %freq;
# copy initial data to freq
foreach my $h (keys %initial) {
my $f = 0;
foreach my $s (keys %{$initial{$h}->{'data'}}) {
$freq{$h}->{ 'data' }->{ $s } = $initial{ $h }->{'data'}->{ $s };
$f+=$initial{ $h }->{'data'}->{ $s };
}
$freq{$h}->{ 'f' } = $f;
}
#######################
# FOURTH STEP: Count frequency for 2 or more heterozygous in the haplotype
#######################
$LOGGER->info("Population: $pel # FOURTH STEP...");
foreach my $vid (2..($hetthreshold||scalar(@rs))) {
$LOGGER->info("Heterozygosity number: $vid");
foreach my $view_ar ( @{ $view{$pel}->{$vid} } ) {
my ($hap, $sbjct) = @{ $view_ar };
my @haps = split(/\;/, $hap);
my %tmp;
foreach my $h (keys %freq) {
my @hs = split(/\;/, $h);
my $match = 0;
for (my $i=0; $i<=$#hs; $i++) {
if ($haps[$i]=~/$hs[$i]|N/) {
$match++;
}
else {
last;
}
}
if ($match==scalar(@hs)) {
$tmp{ $h } = undef;
}
}
my @alter = keys %tmp;
my @betteralter;
if (scalar(@alter) == 0 ) {
$LOGGER->logwarn("Not found an aproximate haplotype for $hap. Trying to found all possibles...");
&recpossibleshet($hap,\@betteralter,0);
}
else {
my $c = 0;
my $last_freq = 0;
for my $x (sort { (($freq{$b}) ? $freq{$b}->{'f'} : 0) <=> (($freq{$a}) ? $freq{$a}->{'f'} : 0) } @alter) {
if ($c<1) {
push(@betteralter,$x);
my $f = $freq{$x}->{'f'}||0;
if ($last_freq<$f) {
$c++;
}
$last_freq = $f;
}
}
$betteralter[1] = join(';', &otherhap(\@haps,$betteralter[0]));
}
foreach my $balt (@betteralter) {
my $f = 2/scalar(@betteralter);
# print ">>>>>>>>>>>>>>>>>>$f (".scalar(@betteralter).")\n";
$freq{$balt}->{'data'}->{$sbjct} = $f;
$freq{$balt}->{'f'}+=$f;
$LOGGER->debug("$pel:$sbjct:$balt=$f");
}
}
}
#######################
# FIFTH STEP: Merge haplotypes and frequencies
#######################
$LOGGER->info("Population: $pel # FIFTH STEP...");
foreach my $h ( keys %freq ) {
foreach my $sbjct(keys %{ $freq{ $h }->{'data'} } ) {
my $aux = ($freq{ $h }->{'data'}->{ $sbjct }-($initial{ $h }->{'data'}->{$sbjct}||0));
$general{ $h }->{'data'}->{ $sbjct }+=$aux;
$general{ $h }->{'f'}+=$aux;
}
}
}
# FINAL RESULT
my @arres;
if ($ord eq 'f') {
@arres = (sort { $general{$b}->{'f'} <=> $general{$a}->{'f'} } keys %general);
}
else {
@arres = (sort {$a cmp $b} keys %general);
}
my @sellvls;
if (defined $restlvl) {
@sellvls = $restlvl;
}
else {
@sellvls = sort { $alllvls{$a} <=> $alllvls{$b} } keys %alllvls;
}
print join(';', @rs),"\n";
foreach my $h ( @arres ) {
if ((! defined $freqthreshold) || ($general{$h}->{'f'} >= $freqthreshold)) {
print $h,"\t", sprintf("%.2f",$general{$h}->{'f'}).'/'.(scalar(keys %subject)*2),"\t",
sprintf("%.2f",100*( $general{$h}->{'f'}/(scalar(keys %subject)*2))),"%\n";
# FREQUENCIES
my %r;
foreach my $sbjct (keys %{ $general{ $h }->{'data'} }) {
foreach my $lv ( @sellvls ) {
$r{$lv}->{'data'}->{
$DATA{'POPULATION'}->{ $subject{ $sbjct }->{'hmap'} }->{$lv}
}+= $general{ $h }->{'data'}->{$sbjct};
$r{$lv}->{'f'}+= $general{ $h }->{'data'}->{$sbjct};
}
}
foreach my $lv ( @sellvls ) {
print "\tLEVEL: $lv\t(",sprintf("%.2f", ($r{$lv}->{'f'})),"/",(scalar(keys %subject)*2)," = ",sprintf("%.2f", 100*($r{$lv}->{'f'}/(scalar(keys %subject)*2))),"%)\n";
foreach my $el (keys %{ $r{$lv}->{'data'} }) {
print "\t\t",$el,"\t",sprintf("%.2f",$r{$lv}->{'data'}->{$el}),"/",($qtd{$lv}->{$el}*2),"\t",sprintf("%.2f",100*($r{$lv}->{'data'}->{$el}/($qtd{$lv}->{$el}*2))),"%\n";
}
}
}
}
# Subroutines
sub Usage {
my ($msg) = @_;
Readonly my $USAGE => <<"END_USAGE";
Daniel Guariz Pinheiro (dgpinheiro\@gmail.com)
(c)2012 Universidade de São Paulo
Usage
$0 [-h/--help] [-l/--level <LEVEL>]
Argument(s)
-h --help Help
-l --level Log level [Default: FATAL]
-i --infile Input file
-f --freqthreshold Frequency threshold
-h --hetthreshold Heterozygotes threshold
-o --order Order
-e --level Population level [Default: one]
-r --restlevel Restrict to this level
END_USAGE
print STDERR "\nERR: $msg\n\n" if $msg;
print STDERR qq[$0 ] . q[$Revision$] . qq[\n];
print STDERR $USAGE;
exit(1);
}
#print "\n\n###\n\n";
#my @ar;
#&recpossibles('N;N;N;N;N',\@ar,0);
#foreach my $x (@ar) {
# print $x,"\n";
#}
#
#print "\n\n###\n\n";
#my @ar;
#&recpossibleshet('A;T;C/A;G;T/A',\@ar,0);
#foreach my $x (@ar) {
# print $x,"\n";
#}
sub recpossibles {
my ($h,$arr,$lv) = @_;
if ($h=~m/N/g) {
my $p = pos($h);
# print "$lv BEGIN($p): $h\n";
my $tmp = $h;
foreach my $b ('A','C','G','T') {
# print "$lv SUB($b): $h\n";
substr($tmp, $p-1, 1, $b);
# print "$lv SENT: \t\t\t",$h,"\n";
&recpossibles($tmp, $arr, $lv+1);
}
}
else {
# print "$lv STORED: $h\n";
push(@{$arr}, $h);
}
}
sub recpossibleshet {
my ($h,$arr,$lv,$hr_freq) = @_;
# print "HAP: $h\n";
if ($h=~m/\//g) {
# print "FOUND HET: $h\n";
my @allm = split(/\;/, $h);
#print join('-', @allm),"\n";
my $i = 0;
while ( $allm[$i]!~/\// ) {
# print $i,"\t",$allm[$i],"\n";
$i++;
}
my ($left, $right) = split(/\//, $allm[$i]);
my $tmp;
#print ">>>$i\t$allm[$i]\n";
$allm[$i] = $left;
$tmp=join(';', @allm);
&recpossibleshet($tmp, $arr, $lv+1, $hr_freq);
$allm[$i] = $right;
$tmp=join(';', @allm);
&recpossibleshet($tmp, $arr, $lv+1, $hr_freq);
}
else {
# print "$lv STORED: $h\n";
if ((!defined $hr_freq) || (exists $hr_freq->{$h})) {
push(@{$arr}, $h);
}
}
}
sub otherhap {
my ($ar_haps, $h) = @_;
my @r;
my @h = split(';', $h);
for (my $i=0;$i<=$#{$ar_haps};$i++) {
if ($ar_haps->[$i] eq $h[$i]) {
push(@r, $ar_haps->[$i]);
}
else {
foreach my $eb (split(/\//, $ar_haps->[$i])) {
unless ($eb eq $h[$i]) {
push(@r, $eb);
last;
}
}
}
}
return @r;
}
__DATA__
European European CEU Utah residents (CEPH) with Northern and Western European ancestry (CEU)
European European TSI Toscani in Italia (TSI)
European European GBR British from England and Scotland (GBR)
European European FIN Finnish from Finland (FIN)
European European IBS Iberian populations in Spain (IBS)
Asian East-Asian CHB Han Chinese in Beijing, China (CHB)
Asian East-Asian JPT Japanese in Toyko, Japan (JPT)
Asian East-Asian CHS Han Chinese South (CHS)
Asian East-Asian CHD Chinese in Denver, Colorado (CHD) (pilot 3 only)
Asian South-Asian GIH Gujarati Indian in Houston, TX (GIH)
African West-African YRI Yoruba in Ibadan, Nigeria (YRI)
African West-African LWK Luhya in Webuye, Kenya (LWK)
African West-African MKK Maasai in Kinyawa, Kenya (MKK)
African Afro-American ASW African Ancestry in Southwest US (ASW)
American North-American MEX Mexican Ancestry in Los Angeles, CA (MXL)
American North-American PUR Puerto Rican in Puerto Rico (PUR)
American South-American CLM Colombian in Medellin, Colombia (CLM)
#Asian East-Asian CDX Chinese Dai in Xishuangbanna (CDX)
#Asian East-Asian KHV Kinh in Ho Chi Minh City, Vietnam (KHV)
#Asian South-Asian PJL Punjabi in Lahore, Pakistan (PJL)
#Asian South-Asian BEB Bengali in Bangladesh (BEB)
#Asian South-Asian STU Sri Lankan Tamil in the UK (STU)
#Asian South-Asian ITU Indian Telegu in the UK (ITU)
#African West-African GWD Gambian in Western Division, The Gambia (GWD)
#African West-African MSL Mende in Sierra Leono (MSL)
#African West-African ESN Esan in Nigeria (ESN)
#African Afro-American ACB African Caribbean in Barbados (ACB)
#American South-American PEL Peruvian in Lima, Peru (PEL)