forked from Ensembl/VEP_plugins
-
Notifications
You must be signed in to change notification settings - Fork 0
/
G2P.pm
1361 lines (1195 loc) · 51.2 KB
/
G2P.pm
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
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2019] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=head1 CONTACT
Ensembl <http://www.ensembl.org/info/about/contact/index.html>
=cut
=head1 NAME
G2P
=head1 SYNOPSIS
mv G2P.pm ~/.vep/Plugins
./vep -i variations.vcf --plugin G2P,file=/path/to/G2P.csv.gz
=head1 DESCRIPTION
A VEP plugin that uses G2P allelic requirements to assess variants in genes
for potential phenotype involvement.
The plugin has multiple configuration options, though minimally requires only
the CSV file of G2P data.
Options are passed to the plugin as key=value pairs, (defaults in parentheses):
file : path to G2P data file, as found at http://www.ebi.ac.uk/gene2phenotype/downloads
af_monoallelic : maximum allele frequency for inclusion for monoallelic genes (0.0001)
af_biallelic : maximum allele frequency for inclusion for biallelic genes (0.005)
all_confidence_levels : set value to 1 to include all confidence levels: confirmed, probable and possible.
Default levels are confirmed and probable.
af_keys : reference populations used for annotating variant alleles with observed
allele frequencies. Allele frequencies are stored in VEP cache files.
Default populations are:
ESP: AA, EA
1000 Genomes: AFR, AMR, EAS, EUR, SAS
gnomAD exomes: gnomAD, gnomAD_AFR, gnomAD_AMR, gnomAD_ASJ, gnomAD_EAS, gnomAD_FIN, gnomAD_NFE, gnomAD_OTH, gnomAD_SAS
Separate multiple values with '&'
af_from_vcf : set value to 1 to include allele frequencies from VCF file.
Specifiy the list of reference populations to include with --af_from_vcf_keys
af_from_vcf_keys : reference populations used for annotating variant alleles with observed
allele frequencies. Allele frequencies are retrieved from VCF files. If
af_from_vcf is set to 1 but no populations specified with --af_from_vcf_keys
all available reference populations are included.
TOPmed: TOPMed
UK10K: ALSPAC, TWINSUK
gnomAD exomes: gnomADe:AFR, gnomADe:ALL, gnomADe:AMR, gnomADe:ASJ, gnomADe:EAS, gnomADe:FIN, gnomADe:NFE, gnomADe:OTH, gnomADe:SAS
gnomAD genomes: gnomADg:AFR, gnomADg:ALL, gnomADg:AMR, gnomADg:ASJ, gnomADg:EAS, gnomADg:FIN, gnomADg:NFE, gnomADg:OTH
Separate multiple values with '&'
default_af : default frequency of the input variant if no frequency data is
found (0). This determines whether such variants are included;
the value of 0 forces variants with no frequency data to be
included as this is considered equivalent to having a frequency
of 0. Set to 1 (or any value higher than af) to exclude them.
types : SO consequence types to include. Separate multiple values with '&'
(splice_donor_variant,splice_acceptor_variant,stop_gained,
frameshift_variant,stop_lost,initiator_codon_variant,
inframe_insertion,inframe_deletion,missense_variant,
coding_sequence_variant,start_lost,transcript_ablation,
transcript_amplification,protein_altering_variant)
log_dir : write stats to log files in log_dir
txt_report : write all G2P complete genes and attributes to txt file
html_report : write all G2P complete genes and attributes to html file
Example:
--plugin G2P,file=G2P.csv,af_monoallelic=0.05,af_keys=AA&gnomAD_ASJ,types=stop_gained&frameshift_variant
--plugin G2P,file=G2P.csv,af_monoallelic=0.05,types=stop_gained&frameshift_variant
--plugin G2P,file=G2P.csv,af_monoallelic=0.05,af_from_vcf=1
--plugin G2P,file=G2P.csv
=cut
package G2P;
use strict;
use warnings;
use Cwd;
use Scalar::Util qw(looks_like_number);
use FileHandle;
use Text::CSV;
use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
our $CAN_USE_HTS_PM;
BEGIN {
if (eval { require Bio::DB::HTS::Tabix; 1 }) {
$CAN_USE_HTS_PM = 1;
}
}
my %DEFAULTS = (
# vars must have a frequency <= to this to pass
af => 0.001,
af_monoallelic => 0.0001,
af_biallelic => 0.005,
af_keys => [qw(AA AFR AMR EA EAS EUR SAS gnomAD gnomAD_AFR gnomAD_AMR gnomAD_ASJ gnomAD_EAS gnomAD_FIN gnomAD_NFE gnomAD_OTH gnomAD_SAS)],
af_from_vcf_keys => [qw(ALSPAC TOPMed TWINSUK gnomADe:AFR gnomADe:ALL gnomADe:AMR gnomADe:ASJ gnomADe:EAS gnomADe:FIN gnomADe:NFE gnomADe:OTH gnomADe:SAS gnomADg:AFR gnomADg:ALL gnomADg:AMR gnomADg:ASJ gnomADg:EAS gnomADg:FIN gnomADg:NFE gnomADg:OTH)],
# if no MAF data is found, default to 0
# this means absence of MAF data is considered equivalent to MAF=0
# set to 1 to do the "opposite", i.e. exclude variants with no MAF data
default_af => 0,
confidence_levels => [qw(confirmed probable)],
# only include variants with these consequence types
# currently not ontology-resolved, exact term matches only
types => {map {$_ => 1} qw(splice_donor_variant splice_acceptor_variant stop_gained frameshift_variant stop_lost initiator_codon_variant inframe_insertion inframe_deletion missense_variant coding_sequence_variant start_lost transcript_ablation transcript_amplification protein_altering_variant)},
);
my $af_key_2_population_name = {
minor_allele_freq => 'global allele frequency (AF) from 1000 Genomes Phase 3 data',
AFR => '1000GENOMES:phase_3:AFR',
AMR => '1000GENOMES:phase_3:AMR',
EAS => '1000GENOMES:phase_3:EAS',
EUR => '1000GENOMES:phase_3:EUR',
SAS => '1000GENOMES:phase_3:SAS',
AA => 'Exome Sequencing Project 6500:African_American',
EA => 'Exome Sequencing Project 6500:European_American',
gnomAD => 'Genome Aggregation Database:Total',
gnomAD_AFR => 'Genome Aggregation Database exomes:African/African American',
gnomAD_AMR => 'Genome Aggregation Database exomes:Latino',
gnomAD_ASJ => 'Genome Aggregation Database exomes:Ashkenazi Jewish',
gnomAD_EAS => 'Genome Aggregation Database exomes:East Asian',
gnomAD_FIN => 'Genome Aggregation Database exomes:Finnish',
gnomAD_NFE => 'Genome Aggregation Database exomes:Non-Finnish European',
gnomAD_OTH => 'Genome Aggregation Database exomes:Other (population not assigned)',
gnomAD_SAS => 'Genome Aggregation Database exomes:South Asian',
ALSPAC => 'UK10K:ALSPAC cohort',
TOPMed => 'Trans-Omics for Precision Medicine (TOPMed) Program',
TWINSUK => 'UK10K:TWINSUK cohort',
'gnomADe:AFR' => 'Genome Aggregation Database exomes v170228',
'gnomADe:ALL' => 'Genome Aggregation Database exomes v170228',
'gnomADe:AMR' => 'Genome Aggregation Database exomes v170228',
'gnomADe:ASJ' => 'Genome Aggregation Database exomes v170228',
'gnomADe:EAS' => 'Genome Aggregation Database exomes v170228',
'gnomADe:FIN' => 'Genome Aggregation Database exomes v170228',
'gnomADe:NFE' => 'Genome Aggregation Database exomes v170228',
'gnomADe:OTH' => 'Genome Aggregation Database exomes v170228',
'gnomADe:SAS' => 'Genome Aggregation Database exomes v170228',
'gnomADg:AFR' => 'Genome Aggregation Database genomes v170228:African/African American',
'gnomADg:ALL' => 'Genome Aggregation Database genomes v170228:All gnomAD genomes individuals',
'gnomADg:AMR' => 'Genome Aggregation Database genomes v170228:Latino',
'gnomADg:ASJ' => 'Genome Aggregation Database genomes v170228:Ashkenazi Jewish',
'gnomADg:EAS' => 'Genome Aggregation Database genomes v170228:East Asian',
'gnomADg:FIN' => 'Genome Aggregation Database genomes v170228:Finnish',
'gnomADg:NFE' => 'Genome Aggregation Database genomes v170228:Non-Finnish European',
'gnomADg:OTH' => 'Genome Aggregation Database genomes v170228:Other (population not assigned)',
};
my $allelic_requirements = {
'biallelic' => { af => 0.005, rules => {HET => 2, HOM => 1} },
'monoallelic' => { af => 0.0001, rules => {HET => 1, HOM => 1} },
'hemizygous' => { af => 0.0001, rules => {HET => 1, HOM => 1} },
'x-linked dominant' => { af => 0.0001, rules => {HET => 1, HOM => 1} },
'x-linked over-dominance' => { af => 0.0001, rules => {HET => 1, HOM => 1} },
};
my @allelic_requirement_terms = keys %$allelic_requirements;
my @population_wide = qw(minor_allele_freq AA AFR ALSPAC AMR EA EAS EUR SAS TOPMed TWINSUK gnomAD gnomAD_AFR gnomAD_AMR gnomAD_ASJ gnomAD_EAS gnomAD_FIN gnomAD_NFE gnomAD_OTH gnomAD_SAS gnomADe:AFR gnomADe:ALL gnomADe:AMR gnomADe:ASJ gnomADe:EAS gnomADe:FIN gnomADe:NFE gnomADe:OTH gnomADe:SAS gnomADg:AFR gnomADg:ALL gnomADg:AMR gnomADg:ASJ gnomADg:EAS gnomADg:FIN gnomADg:NFE gnomADg:OTH);
sub new {
my $class = shift;
my $self = $class->SUPER::new(@_);
# suppress warnings that the FeatureAdpators spit if using no_slice_cache
Bio::EnsEMBL::Utils::Exception::verbose(1999);
my $supported_af_keys = { map {$_ => 1} @population_wide };
my $params = $self->params_to_hash();
my $file = '';
# user only supplied file as first param?
if (!keys %$params) {
$file = $self->params->[0];
}
else {
$file = $params->{file};
# process types
if ($params->{types}) {
$params->{types} = {map {$_ => 1} split(/[\;\&\|]/, $params->{types})};
}
# check af
foreach my $af (qw/af_monoallelic af_biallelic/) {
if($params->{$af}) {
die("ERROR: Invalid value for af: ".$params->{$af} . "\n") unless
looks_like_number($params->{$af}) && ($params->{$af} >= 0 && $params->{$af} <= 1)
}
}
my $assembly = $self->{config}->{assembly};
my $af_from_vcf_key_2_collection_id = {
ALSPAC => {GRCh37 => 'uk10k_GRCh37', GRCh38 => 'uk10k_GRCh38'},
TOPMed => {GRCh37 => 'topmed_GRCh37', GRCh38 => 'topmed_GRCh38'},
TWINSUK => {GRCh37 => 'uk10k_GRCh37', GRCh38 => 'uk10k_GRCh38'},
'gnomADe:AFR' => {GRCh37 => 'gnomADe_GRCh37', GRCh38 => 'gnomADe_GRCh38'},
'gnomADe:ALL' => {GRCh37 => 'gnomADe_GRCh37', GRCh38 => 'gnomADe_GRCh38'},
'gnomADe:AMR' => {GRCh37 => 'gnomADe_GRCh37', GRCh38 => 'gnomADe_GRCh38'},
'gnomADe:ASJ' => {GRCh37 => 'gnomADe_GRCh37', GRCh38 => 'gnomADe_GRCh38'},
'gnomADe:EAS' => {GRCh37 => 'gnomADe_GRCh37', GRCh38 => 'gnomADe_GRCh38'},
'gnomADe:FIN' => {GRCh37 => 'gnomADe_GRCh37', GRCh38 => 'gnomADe_GRCh38'},
'gnomADe:NFE' => {GRCh37 => 'gnomADe_GRCh37', GRCh38 => 'gnomADe_GRCh38'},
'gnomADe:OTH' => {GRCh37 => 'gnomADe_GRCh37', GRCh38 => 'gnomADe_GRCh38'},
'gnomADe:SAS' => {GRCh37 => 'gnomADe_GRCh37', GRCh38 => 'gnomADe_GRCh38'},
'gnomADg:AFR' => {GRCh37 => 'gnomADg_GRCh37', GRCh38 => 'gnomADg_GRCh38'},
'gnomADg:ALL' => {GRCh37 => 'gnomADg_GRCh37', GRCh38 => 'gnomADg_GRCh38'},
'gnomADg:AMR' => {GRCh37 => 'gnomADg_GRCh37', GRCh38 => 'gnomADg_GRCh38'},
'gnomADg:ASJ' => {GRCh37 => 'gnomADg_GRCh37', GRCh38 => 'gnomADg_GRCh38'},
'gnomADg:EAS' => {GRCh37 => 'gnomADg_GRCh37', GRCh38 => 'gnomADg_GRCh38'},
'gnomADg:FIN' => {GRCh37 => 'gnomADg_GRCh37', GRCh38 => 'gnomADg_GRCh38'},
'gnomADg:NFE' => {GRCh37 => 'gnomADg_GRCh37', GRCh38 => 'gnomADg_GRCh38'},
'gnomADg:OTH' => {GRCh37 => 'gnomADg_GRCh37', GRCh38 => 'gnomADg_GRCh38'},
};
my @keys = ();
my $vcf_collection_ids = {};
if ($params->{af_keys}) {
push @keys, $params->{af_keys};
} else {
push @keys, @{$DEFAULTS{af_keys}};
}
if ($params->{af_from_vcf}) {
if ($params->{af_from_vcf_keys}) {
push @keys, $params->{af_from_vcf_keys};
} else {
push @keys, @{$DEFAULTS{af_from_vcf_keys}};
}
}
my @af_keys = ();
foreach my $af_key_set (@keys) {
foreach my $af_key (split(/[\;\&\|]/, $af_key_set)) {
die("ERROR: af_key: " . $af_key . " not supported. Check plugin documentation for supported af_keys.\n") unless $supported_af_keys->{$af_key};
push @af_keys, $af_key;
if ($af_from_vcf_key_2_collection_id->{$af_key}) {
$vcf_collection_ids->{$af_from_vcf_key_2_collection_id->{$af_key}->{$assembly}} = 1;
}
}
}
$params->{af_keys} = \@af_keys;
$params->{vcf_collection_ids} = $vcf_collection_ids;
}
my ($sec, $min, $hour, $mday, $mon, $year, $wday, $yday, $isdst) = localtime(time);
$year += 1900;
$mon++;
my $stamp = join('_', ($year, $mon, $mday, $hour, $min));
my $cwd_dir = getcwd;
my $new_log_dir = "$cwd_dir/g2p_log_dir\_$stamp";
my $log_dir = $params->{log_dir} || $new_log_dir;
if (!-d $log_dir) {
mkdir $log_dir, 0755;
$params->{log_dir} = $log_dir;
}
foreach my $report_type (qw/txt_report html_report/) {
if (!$params->{$report_type}) {
my $file_type = ($report_type eq 'txt_report') ? 'txt' : 'html';
$params->{$report_type} = $cwd_dir . "/$report_type\_$stamp.$file_type";
}
}
if ($params->{all_confidence_levels}) {
push @{$params->{confidence_levels}}, 'possible', @{$DEFAULTS{confidence_levels}};
}
# copy in default params
$params->{$_} //= $DEFAULTS{$_} for keys %DEFAULTS;
$self->{user_params} = $params;
if (!defined($self->{config}->{reg})) {
my $reg = 'Bio::EnsEMBL::Registry';
$reg->load_registry_from_db(
-host => $self->config->{host},
-user => $self->config->{user},
-port => $self->config->{port},
-db_version => $self->config->{db_version},
-species => $self->config->{species},
-no_cache => $self->config->{no_slice_cache},
);
$self->{config}->{reg} = $reg;
}
my $vdba = $self->{config}->{reg}->get_DBAdaptor($self->{config}->{species}, 'variation');
$vdba->dbc->reconnect_when_lost(1);
my $va = $vdba->get_VariationAdaptor;
$va->db->use_vcf(1) if ($CAN_USE_HTS_PM);
$va->db->include_failed_variations(1);
$self->{config}->{va} = $va;
my $pa = $vdba->get_PopulationAdaptor;
$self->{config}->{pa} = $pa;
my $vca = $vdba->get_VCFCollectionAdaptor;
$self->{config}->{vca} = $vca;
my $cdba = $self->{config}->{reg}->get_DBAdaptor($self->{config}->{species}, 'core');
$cdba->dbc->reconnect_when_lost(1);
my $ta = $cdba->get_TranscriptAdaptor;
$self->{config}->{ta} = $ta;
# read data from file
$self->{gene_data} = $self->read_gene_data_from_file($file);
$self->synonym_mappings();
# force some config params
$self->{config}->{individual} //= ['all'];
$self->{config}->{symbol} = 1;
$self->{config}->{check_existing} = 1;
$self->{config}->{failed} = 1;
$self->{config}->{af} = 1;
$self->{config}->{af_1kg} = 1;
$self->{config}->{af_esp} = 1;
$self->{config}->{af_gnomad} = 1;
# $self->{config}->{sift} = 'b';
# $self->{config}->{polyphen} = 'b';
# $self->{config}->{hgvsc} = 1;
# $self->{config}->{hgvsp} = 1;
# tell VEP we have a cache so stuff gets shared/merged between forks
$self->{has_cache} = 1;
$self->{cache}->{g2p_in_vcf} = {};
return $self;
}
sub feature_types {
return ['Transcript'];
}
sub get_header_info {
my $self = shift;
return {
G2P_flag => 'Flags zygosity of valid variants for a G2P gene',
G2P_complete => 'Indicates this variant completes the allelic requirements for a G2P gene',
G2P_gene_req => 'MONO or BI depending on the context in which this gene has been explored',
};
}
sub run {
my ($self, $tva, $line) = @_;
# only interested if we know the zygosity
my $zyg = $line->{Extra}->{ZYG} || $line->{ZYG};
return {} unless $zyg;
# only interested in given gene set
my $tr = $tva->transcript;
my $ensembl_gene_id = $tr->{_gene}->stable_id;
my $gene_symbol = $tr->{_gene_symbol} || $tr->{_gene_hgnc};
return {} unless $gene_symbol;
my $gene_data = $self->gene_data($gene_symbol);
if (! defined $gene_data) {
my $ensembl_gene_id = $tr->{_gene}->stable_id;
$gene_data = $self->gene_data($ensembl_gene_id);
}
if (!$self->{cache}->{g2p_in_vcf}->{$gene_symbol}) {
$self->write_report('G2P_in_vcf', $gene_symbol);
$self->{cache}->{g2p_in_vcf}->{$gene_symbol} = 1;
}
return {} unless defined $gene_data;
my @ars = ($gene_data->{'allelic requirement'}) ? @{$gene_data->{'allelic requirement'}} : ();
my %seen;
@ars = grep { !$seen{$_}++ } @ars;
return {} unless (@ars && ( grep { exists($allelic_requirements->{$_}) } @ars));
# limit by type
my @consequence_types = map { $_->SO_term } @{$tva->get_all_OverlapConsequences};
return {} unless grep {$self->{user_params}->{types}->{$_->SO_term}} @{$tva->get_all_OverlapConsequences};
# limit by MAF
my $threshold = 0;
my ($freqs, $existing_variant, $ar_passed) = @{$self->get_freq($tva, \@ars)};
return {} if (!keys %$ar_passed);
my $vf = $tva->base_variation_feature;
my $allele = $tva->variation_feature_seq;
my $start = $vf->{start};
my $end = $vf->{end};
my $individual = $vf->{individual};
my $vf_name = $vf->variation_name;
if ($vf_name || $vf_name eq '.') {
$vf_name = ($vf->{original_chr} || $vf->{chr}) . '_' . $vf->{start} . '_' . ($vf->{allele_string} || $vf->{class_SO_term});
}
my $allele_string = $vf->{allele_string};
my @alleles = split('/', $allele_string);
my $ref = $alleles[0];
my $seq_region_name = $vf->{chr};
my $params = $self->{user_params};
my $refseq = $tr->{_refseq} || 'NA';
my $tr_stable_id = $tr->stable_id;
my $hgvs_t = $tva->hgvs_transcript || 'NA';
my $hgvs_p = $tva->hgvs_protein || 'NA';
my ($clin_sig, $novel, $failed, $frequencies, $existing_name) = ('NA', 'yes', 'NA', 'NA', 'NA');
if ($existing_variant) {
$clin_sig = $existing_variant->{clin_sig} || 'NA';
$failed = ($existing_variant->{failed}) ? 'yes' : 'no';
$existing_name = $existing_variant->{variation_name} || 'NA';
$novel = 'no';
}
my $pph_score = (defined $tva->polyphen_score) ? $tva->polyphen_score : 'NA';
my $pph_pred = (defined $tva->polyphen_prediction) ? $tva->polyphen_prediction : 'NA';
my $sift_score = (defined $tva->sift_score) ? $tva->sift_score : 'NA';
my $sift_pred = (defined $tva->sift_prediction) ? $tva->sift_prediction : 'NA';
if (scalar keys %$freqs > 0) {
$frequencies = join(',', map {"$_=$freqs->{$_}"} keys %$freqs);
}
my $ar = join(',', sort keys %$ar_passed);
my $ar_in_g2pdb = join(',', sort @ars);
my $g2p_data = {
'zyg' => $zyg,
'allele_requirement' => $ar,
'ar_in_g2pdb' => $ar_in_g2pdb,
'frequencies' => $frequencies,
'consequence_types' => join(',', @consequence_types),
'refseq' => $refseq,
'failed' => $failed,
'clin_sig' => $clin_sig,
'novel' => $novel,
'existing_name' => $existing_name,
'hgvs_t' => $hgvs_t,
'hgvs_p' => $hgvs_p,
'vf_location' => "$seq_region_name:$start-$end $ref/$allele",
'sift_score' => "$sift_score",
'sift_prediction' => $sift_pred,
'polyphen_score' => "$pph_score",
'polyphen_prediction' => $pph_pred,
};
my %return = (
G2P_flag => $zyg
);
$self->write_report('G2P_flag', $gene_symbol, $tr_stable_id, $individual, $vf_name, $g2p_data);
$self->write_report('G2P_complete', $gene_symbol, $tr_stable_id, $individual, $vf_name, $ar, $zyg);
my $cache = $self->{cache}->{$individual}->{$tr->stable_id} ||= {};
delete $cache->{$vf_name} if exists($cache->{$vf_name});
# biallelic genes require >=1 hom or >=2 hets
my $gene_reqs = {};
foreach my $ar (keys %$ar_passed) {
if($ar eq 'biallelic') {
# homozygous, report complete
if(uc($zyg) eq 'HOM') {
$return{G2P_complete} = 1;
$gene_reqs->{BI} = 1;
}
# heterozygous
# we need to cache that we've observed one
elsif(uc($zyg) eq 'HET') {
if(scalar keys %$cache) {
$return{G2P_complete} = 1;
}
$cache->{$vf_name} = 1;
}
}
# monoallelic genes require only one allele
elsif($ar eq 'monoallelic' || $ar eq 'x-linked dominant' || $ar eq 'hemizygous' || $ar eq 'x-linked over-dominance') {
$return{G2P_complete} = 1;
$gene_reqs->{MONO} = 1;
}
else {
return {};
}
}
if ($return{G2P_complete}) {
$return{G2P_gene_req} = join(',', sort keys %$gene_reqs);
}
return \%return;
}
# read G2P CSV dump
# as from http://www.ebi.ac.uk/gene2phenotype/downloads
sub read_gene_data_from_file {
my $self = shift;
my $file = shift;
my $delimiter = shift;
my (@headers, %gene_data);
my $assembly = $self->{config}->{assembly};
die("ERROR: No file specified or could not read from file ".($file || '')."\n") unless $file && -e $file;
my @confidence_levels = @{$self->{user_params}->{confidence_levels}};
# determine file type
my $file_type;
my $fh = FileHandle->new($file, 'r');
while (<$fh>) {
chomp;
if (/Model_Of_Inheritance/) {
$file_type = 'panelapp';
} elsif (/"allelic requirement"/) {
$file_type = 'g2p';
} else {
$file_type = 'unknown';
}
last;
}
$fh->close();
if ($file_type eq 'unknown') {
if ($file =~ /gz$/) {
die("ERROR: G2P plugin can only read uncompressed data");
} else {
die("ERROR: Could not recognize input file format. Format must be one of panelapp, g2p or custom. Check website for details: https://www.ebi.ac.uk/gene2phenotype/g2p_vep_plugin");
}
}
if ($file_type eq 'panelapp') {
my @headers = ();
my $csv = Text::CSV->new ({ sep_char => "\t" });
open my $fh, "<:encoding(utf8)", "$file" or die "$file: $!";
while ( my $row = $csv->getline( $fh ) ) {
unless (@headers) {
@headers = @$row;
} else {
my %tmp = map {$headers[$_] => $row->[$_]} (0..$#headers);
my $gene_symbol = $tmp{"Gene Entity Symbol"};
my $ensembl_gene_id = "";
if ($assembly eq 'GRCh37') {
$ensembl_gene_id = $tmp{"EnsemblId(GRch37)"};
} else { # GRCh38
$ensembl_gene_id = $tmp{"EnsemblId(GRch38)"};
}
if ($ensembl_gene_id) {
my @ars = ();
my $allelic_requirement_panel_app = $tmp{"Model_Of_Inheritance"};
if ($allelic_requirement_panel_app =~ m/MONOALLELIC|BOTH/) {
push @ars, 'monoallelic';
} elsif ($allelic_requirement_panel_app =~ m/BIALLELIC|BOTH/) {
push @ars, 'biallelic';
} elsif ($allelic_requirement_panel_app eq 'X-LINKED: hemizygous mutation in males, biallelic mutations in females') {
push @ars, 'hemizygous';
} elsif ($allelic_requirement_panel_app eq 'X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)') {
push @ars, 'x-linked dominant';
} else {
$self->write_report('log', "no allelelic_requirement for $ensembl_gene_id");
}
foreach my $ar (@ars) {
push @{$gene_data{$ensembl_gene_id}->{"allelic requirement"}}, $ar;
}
} else {
$self->write_report('log', "no ensembl gene id for " . join(' ', @$row));
}
}
}
$csv->eof or $csv->error_diag();
close $fh;
}
if ($file_type eq 'g2p') {
# this regexp allows for nested ",", e.g.
# item,description
# cheese,"salty,delicious"
my $re = qr/(?: "\( ( [^()""]* ) \)" | \( ( [^()]* ) \) | " ( [^"]* ) " | ( [^,]* ) ) , \s* /x;
my $fh = FileHandle->new($file, 'r');
while(<$fh>) {
chomp;
$_ =~ s/\R//g;
my @split = grep defined, "$_," =~ /$re/g;
unless(@headers) {
if ($file_type eq 'g2p') {
@headers = map {s/\"//g; $_} @split;
} else {
@headers = @split;
}
}
else {
my %tmp = map {$headers[$_] => $split[$_]} (0..$#split);
die("ERROR: Gene symbol column not found\n$_\n") unless $tmp{"gene symbol"};
my $confidence_value = $tmp{"DDD category"};
next if (!grep{$_ eq $confidence_value} @confidence_levels);
my $gene_symbol = $tmp{"gene symbol"};
$gene_data{$gene_symbol}->{"prev symbols"} = $tmp{"prev symbols"};
push @{$gene_data{$gene_symbol}->{"allelic requirement"}}, $tmp{"allelic requirement"} if ($tmp{"allelic requirement"});
$self->write_report('G2P_list', $tmp{"gene symbol"}, $tmp{"DDD category"});
}
}
$fh->close;
}
return \%gene_data;
}
# return either whole gene data hash or one gene's data
# this should allow updates to this plugin to e.g. query a REST server, for example
sub gene_data {
my ($self, $gene_symbol) = @_;
my $gene_data = $self->{gene_data}->{$gene_symbol};
if (!$gene_data) {
my $prev_gene_symbol = $self->{prev_symbol_mappings}->{$gene_symbol};
return $prev_gene_symbol ? $self->{gene_data}->{$prev_gene_symbol} : undef;
}
return $gene_data;
}
sub synonym_mappings {
my $self = shift;
my $gene_data = $self->{gene_data};
my $synonym_mappings = {};
foreach my $gene_symbol (keys %$gene_data) {
my $prev_symbols = $gene_data->{$gene_symbol}->{'prev symbols'};
if ($prev_symbols) {
foreach my $prev_symbol (split(';', $prev_symbols)) {
$synonym_mappings->{$prev_symbol} = $gene_symbol;
}
}
}
$self->{prev_symbol_mappings} = $synonym_mappings;
}
sub get_freq {
my $self = shift;
my $tva = shift;
my $ars = shift;
my $allele = $tva->variation_feature_seq;
my $vf = $tva->base_variation_feature;
reverse_comp(\$allele) if $vf->{strand} < 0;
my $vf_name = $vf->variation_name;
if ($vf_name || $vf_name eq '.') {
$vf_name = ($vf->{original_chr} || $vf->{chr}) . '_' . $vf->{start} . '_' . ($vf->{allele_string} || $vf->{class_SO_term});
}
my $cache = $self->{cache}->{$vf_name}->{_g2p_freqs} ||= {};
if (exists $cache->{$allele}->{failed}) {
return [$cache->{$allele}->{freq}, $cache->{$allele}->{ex_variant}, {}];
}
if (exists $cache->{$allele}->{freq}) {
return [$cache->{$allele}->{freq}, $cache->{$allele}->{ex_variant}, $cache->{$allele}->{passed_ar}];
}
if (!$vf->{existing} || ! scalar @{$vf->{existing}}) {
my $failed_ars = {};
my $freqs = {};
my $passed = $self->frequencies_from_VCF($freqs, $vf, $allele, $ars, $failed_ars);
if (!$passed) {
$cache->{$allele}->{failed} = 1;
return [{}, {}, {}];
} else {
$cache->{$allele}->{freq} = $freqs;
$cache->{$allele}->{ex_variant} = undef;
# if we get to here return all allelic requirements that passed threshold filtering
my $passed_ar = {};
foreach my $ar (@$ars) {
if (!$failed_ars->{$ar}) {
$passed_ar->{$ar} = 1;
}
}
$cache->{$allele}->{passed_ar} = $passed_ar;
return [$cache->{$allele}->{freq}, $cache->{$allele}->{ex_variant}, $cache->{$allele}->{passed_ar}];
}
}
my @existing_variants = @{$vf->{existing}};
# favour dbSNP variants
my @dbSNP_variants = grep {$_->{variation_name} =~ /^rs/} @existing_variants;
if (@dbSNP_variants) {
@existing_variants = @dbSNP_variants;
}
foreach my $ex (@existing_variants) {
my $existing_allele_string = $ex->{allele_string};
my $variation_name = $ex->{variation_name};
my $freqs = {};
my $failed_ars = {};
foreach my $af_key (@{$self->{user_params}->{af_keys}}) {
my $freq = $self->{user_params}->{default_af};
if ($af_key eq 'minor_allele_freq') {
if (defined $ex->{minor_allele_freq}) {
if (($ex->{minor_allele} || '') eq $allele ) {
$freq = $ex->{minor_allele_freq};
} else {
$freq = $self->correct_frequency($tva, $existing_allele_string, $ex->{minor_allele}, $ex->{minor_allele_freq}, $allele, $variation_name, $af_key, $vf_name) || $freq;
}
}
}
else {
my @pairs = split(',', $ex->{$af_key} || '');
my $found = 0;
if (scalar @pairs == 0) {
$found = 1; # no allele frequency for this population/af_key available
}
foreach my $pair (@pairs) {
my ($a, $f) = split(':', $pair);
if(($a || '') eq $allele && defined($f)) {
$freq = $f;
$found = 1;
}
}
if (!$found) {
$freq = $self->correct_frequency($tva, $existing_allele_string, undef, undef, $allele, $variation_name, $af_key, $vf_name) || $freq;
}
}
if (!$self->continue_af_annotation($ars, $failed_ars, $freq)) {
# cache failed results
$cache->{$allele}->{failed} = 1;
return [$cache->{$allele}->{freq}, $cache->{$allele}->{ex_variant}, {}];
}
$freqs->{$af_key} = $freq if ($freq);
}
if ($self->{user_params}->{af_from_vcf}) {
my $passed = $self->frequencies_from_VCF($freqs, $vf, $allele, $ars, $failed_ars);
if (!$passed) {
$cache->{$allele}->{failed} = 1;
return [$cache->{$allele}->{freq}, $cache->{$allele}->{ex_variant}, {}];
}
}
$cache->{$allele}->{freq} = $freqs;
$cache->{$allele}->{ex_variant} = $ex;
# if we get to here return all allelic requirements that passed threshold filtering
my $passed_ar = {};
foreach my $ar (@$ars) {
if (!$failed_ars->{$ar}) {
$passed_ar->{$ar} = 1;
}
}
$cache->{$allele}->{passed_ar} = $passed_ar;
}
return [$cache->{$allele}->{freq}, $cache->{$allele}->{ex_variant}, $cache->{$allele}->{passed_ar}];
}
sub correct_frequency {
my ($self, $tva, $allele_string, $minor_allele, $af, $allele, $variation_name, $af_key, $vf_name) = @_;
my @existing_alleles = split('/', $allele_string);
if (!grep( /^$allele$/, @existing_alleles)) {
return 0.0;
}
if ($af_key eq 'minor_allele_freq' && (scalar @existing_alleles == 2)) {
my $existing_ref_allele = $existing_alleles[0];
my $existing_alt_allele = $existing_alleles[1];
if ( ($minor_allele eq $existing_ref_allele && ($allele eq $existing_alt_allele)) ||
($minor_allele eq $existing_alt_allele && ($allele eq $existing_ref_allele)) ) {
return (1.0 - $af);
}
} else {
my $va = $self->{config}->{va};
my $pa = $self->{config}->{pa};
my $variation = $va->fetch_by_name($variation_name);
my $af_key = $self->{user_params}->{af_keys};
my $population_name = $af_key_2_population_name->{$af_key};
if ($population_name) {
my $population = $self->{config}->{$population_name};
if (!$population) {
$population = $pa->fetch_by_name($population_name);
$self->{config}->{$population_name} = $population;
}
foreach (@{$variation->get_all_Alleles($population)}) {
if ($_->allele eq $allele) {
return $_->frequency;
}
}
}
}
return 0.0;
}
sub frequencies_from_VCF {
my $self = shift;
my $freqs = shift;
my $vf = shift;
my $vf_allele = shift;
my $ars = shift;
my $failed_ars = shift;
return 1 if (!defined $self->{user_params}->{af_from_vcf});
return 1 if (!$CAN_USE_HTS_PM);
my $vca = $self->{config}->{vca};
my $collections = $vca->fetch_all;
foreach my $vc (@$collections) {
next if (! $self->{user_params}->{vcf_collection_ids}->{$vc->id});
my $alleles = $vc->get_all_Alleles_by_VariationFeature($vf);
foreach my $allele (@$alleles) {
if ($allele->allele eq $vf_allele) {
my $af_key = $allele->population->name;
my $freq = $allele->frequency;
return 0 if (!$self->continue_af_annotation($ars, $failed_ars, $freq));
$freqs->{$af_key} = $freq;
}
}
}
return 1;
}
sub continue_af_annotation {
my $self = shift;
my $ars = shift;
my $failed_ars = shift;
my $freq = shift;
foreach my $ar (@$ars) {
if (!$failed_ars->{$ar}) {
if (defined $allelic_requirements->{$ar}) {
my $threshold = $allelic_requirements->{$ar}->{af};
if ($freq > $threshold) {
$failed_ars->{$ar} = 1;
}
}
}
}
return (scalar @$ars != scalar keys %$failed_ars);
}
sub write_report {
my $self = shift;
my $flag = shift;
my $log_dir = $self->{user_params}->{log_dir};
my $log_file = "$log_dir/$$.txt";
open(my $fh, '>>', $log_file) or die "Could not open file '$flag $log_file' $!";
if ($flag eq 'G2P_list') {
my ($gene_symbol, $DDD_category) = @_;
$DDD_category ||= 'Not assigned';
print $fh "$flag\t$gene_symbol\t$DDD_category\n";
} elsif ($flag eq 'G2P_in_vcf') {
my $gene_symbol = shift;
print $fh "$flag\t$gene_symbol\n";
} elsif ($flag eq 'G2P_complete') {
print $fh join("\t", $flag, @_), "\n";
} elsif ($flag eq 'log') {
print $fh join("\t", $flag, @_), "\n";
} else {
my ($gene_symbol, $tr_stable_id, $individual, $vf_name, $data) = @_;
$data = join(';', map {"$_=$data->{$_}"} sort keys %$data);
print $fh join("\t", $flag, $gene_symbol, $tr_stable_id, $individual, $vf_name, $data), "\n";
}
close $fh;
}
sub finish {
my $self = shift;
$self->generate_report;
}
sub generate_report {
my $self = shift;
my $result_summary = $self->parse_log_files;
my $chart_txt_data = $self->chart_and_txt_data($result_summary);
my $chart_data = $chart_txt_data->{chart_data};
my $txt_data = $chart_txt_data->{txt_data};
my $canonical_transcripts = $chart_txt_data->{canonical_transcripts};
$self->write_txt_output($txt_data);
$self->write_charts($result_summary, $chart_data, $canonical_transcripts);
}
sub write_txt_output {
my $self = shift;
my $txt_output_data = shift;
my $txt_output_file = $self->{user_params}->{txt_report};
my $fh_txt = FileHandle->new($txt_output_file, 'w');
foreach my $individual (sort keys %$txt_output_data) {
foreach my $gene_symbol (keys %{$txt_output_data->{$individual}}) {
foreach my $ar (keys %{$txt_output_data->{$individual}->{$gene_symbol}}) {
foreach my $tr_stable_id (keys %{$txt_output_data->{$individual}->{$gene_symbol}->{$ar}}) {
my $is_canonical = $txt_output_data->{$individual}->{$gene_symbol}->{$ar}->{$tr_stable_id}->{is_canonical};
my $canonical_tag = ($is_canonical) ? 'is_canonical' : 'not_canonical';
my $req = $txt_output_data->{$individual}->{$gene_symbol}->{$ar}->{$tr_stable_id}->{REQ};
my $variants = join(';', @{$txt_output_data->{$individual}->{$gene_symbol}->{$ar}->{$tr_stable_id}->{variants}});
print $fh_txt join("\t", $individual, $gene_symbol, $tr_stable_id, $canonical_tag, "OBS=$ar", "REQ=$req", $variants), "\n";
}
}
}
}
$fh_txt->close();
}
sub write_charts {
my $self = shift;
my $result_summary = shift;
my $chart_data = shift;
my $canonical_transcripts = shift;
my $count_g2p_genes = keys %{$result_summary->{g2p_list}};
my $count_in_vcf_file = keys %{$result_summary->{in_vcf_file}};
my $count_complete_genes = scalar keys %{$result_summary->{complete_genes}};
my @charts = ();
my @frequencies_header = ();
foreach my $short_name (sort @{$self->{user_params}->{af_keys}}) {
my $text = $af_key_2_population_name->{$short_name};
push @frequencies_header, "<a style=\"cursor: pointer\" data-placement=\"top\" data-toggle=\"tooltip\" data-container=\"body\" title=\"$text\">$short_name</a>";
}
my $count = 1;
my @new_header = (
'Variant location and alleles (REF/ALT)',
'Variant name',
'Existing name',
'Zygosity',
'All allelic requirements from G2P DB',
'Consequence types',
'ClinVar annotation',
'SIFT',
'PolyPhen',
'Novel variant',
'Has been failed by Ensembl',
@frequencies_header,
'HGVS transcript',
'HGVS protein',
'RefSeq IDs',
);
my $html_output_file = $self->{user_params}->{html_report};
my $fh_out = FileHandle->new($html_output_file, 'w');
print $fh_out stats_html_head(\@charts);
print $fh_out "<div class='main_content container'>";
print $fh_out "<h1>G2P report</h1>";
print $fh_out "<p>Input and output files:</p>";
print $fh_out "<dl class='dl-horizontal'>";
print $fh_out "<dt>G2P list</dt>";
print $fh_out "<dd>" . $self->{user_params}->{file} . "</dd>";
print $fh_out "<dt>Log directory</dt>";
print $fh_out "<dd>" . $self->{user_params}->{log_dir} . "</dd>";
print $fh_out "<dt>HTML report</dt>";
print $fh_out "<dd>" . $self->{user_params}->{html_report} . "</dd>";
print $fh_out "<dt>TXT report</dt>";
print $fh_out "<dd>" . $self->{user_params}->{txt_report} . "</dd>";
print $fh_out "</dl>";
print $fh_out "<p>Counts:</p>";
print $fh_out "<dl class='dl-horizontal text-overflow'>";
print $fh_out "<dt>$count_g2p_genes</dt>";
print $fh_out "<dd>G2P genes</dd>";
print $fh_out "<dt>$count_in_vcf_file</dt>";
print $fh_out "<dd>G2P genes in input VCF file</dd>";
print $fh_out "<dt>$count_complete_genes</dt>";
print $fh_out "<dd>G2P complete genes in input VCF file</dd>";
print $fh_out "</dl>";
print $fh_out "<h1>Summary of G2P complete genes per individual</h1>";
print $fh_out "<p>G2P complete gene: A sufficient number of variant hits for the observed allelic requirement in at least one of the gene's transcripts. Variants are filtered by frequency.</p>";
print $fh_out "<p>Frequency thresholds and number of required variant hits for each allelic requirement:</p>";
print $fh_out "<table class='table table-bordered'>";
print $fh_out "<thead>";
print $fh_out "<tr><th>Allelic requirement</th><th>Frequency threshold for filtering</th><th>Variant counts by zygosity</th></tr>";
print $fh_out "</thead>";