viral_seq 1.10.2 → 1.10.4

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Files changed (10) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +13 -2
  3. data/bin/locator +38 -1
  4. data/bin/tcs_sdrm +6 -6
  5. data/lib/viral_seq/hivdr.rb +1 -1
  6. data/lib/viral_seq/recency_report.rb +1 -1
  7. data/lib/viral_seq/seq_hash_pair.rb +1 -1
  8. data/lib/viral_seq/util/drm_list.json +427 -682
  9. data/lib/viral_seq/version.rb +2 -2
  10. metadata +1 -1
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data/README.md CHANGED
@@ -128,14 +128,20 @@ Output data in a new dir as 'libs_dir_SDRM'
128
128
 
129
129
  ---
130
130
 
131
- ### `locator`
131
+ ### `locator` version >= 1.10.3
132
132
 
133
133
  Use executable `locator` to get the coordinates of the sequences on HIV/SIV reference genome from a FASTA file through a terminal
134
134
 
135
135
  ```bash
136
- $ locator -i sequence.fasta -o sequence.fasta.csv
136
+ $ locator -i sequence.fasta
137
137
  ```
138
138
 
139
+ Locator output defaults to a csv file with results and a new file in the same directory named {input}.direction.fasta
140
+
141
+ ### `locator` version < 1.10.3
142
+
143
+ Only has the the results csv file.
144
+
139
145
  ---
140
146
 
141
147
  ## Some Examples
@@ -191,6 +197,11 @@ qc_seqhash.sdrm_hiv_pr(cut_off)
191
197
 
192
198
  ## Updates
193
199
 
200
+ ### Version-1.10.3-12112025
201
+
202
+ 1. Bug fix for SDRM pipeline.
203
+ 2. Add a function in `locator` tool to export sequences in positive sense direction.
204
+
194
205
  ### Version-1.10.2-07210225
195
206
 
196
207
  1. Fixed a bug processing parameters for HIV sequence QC.
data/bin/locator CHANGED
@@ -56,6 +56,26 @@ def myparser
56
56
  return options
57
57
  end
58
58
 
59
+ module ViralSeq
60
+ class SeqHash
61
+ def validate_nt_sequences
62
+ new_dna_hash = {}
63
+ self.dna_hash.each do |title, seq|
64
+ if seq.length < 10
65
+ print "[Warning] ".red.bold + "Sequence '#{title}' is too short (less than 10 nt), please check your input sequence.\n"
66
+ else
67
+ unless seq =~ /\A[ACGTURYSWKMBDHVN\-\s]+\z/i
68
+ print "[Warning] ".red.bold + "Sequence '#{title}' contains invalid characters (not A, C, G, T, U, R, Y, S, W, K, M, B, D, H, V, N, '-', or space), please check your input sequence.\n"
69
+ else
70
+ new_dna_hash[title] = seq
71
+ end
72
+ end
73
+ end
74
+ self.dna_hash = new_dna_hash
75
+ end
76
+ end
77
+ end
78
+
59
79
  puts "\n" + "Sequence Locator (RubyGem::ViralSeq Version #{ViralSeq::VERSION})".red.bold + " by " + "Shuntai Zhou".blue.bold
60
80
  puts "See details at " + "https://github.com/ViralSeq/viral_seq\n".blue
61
81
  puts "Resembling" + " Sequence Locator ".magenta.bold + "from LANL" + " (https://www.hiv.lanl.gov/content/sequence/LOCATE/locate.html)\n".blue
@@ -76,12 +96,19 @@ begin
76
96
  else
77
97
  csv_file = seq_file + ".csv"
78
98
  end
99
+
100
+ fasta_file = csv_file.sub(/\.csv$/i, '.direction.fasta')
101
+
102
+ fasta_handle = File.open(fasta_file, 'w')
79
103
 
80
104
  unless File.exist?(seq_file)
81
105
  raise StandardError.new("Input file sequence file not found".red.bold)
82
106
  end
83
107
 
84
108
  seqs = ViralSeq::SeqHash.fa(seq_file)
109
+
110
+ puts "Only sequences greater than 10 nt and containing valid nt chars will be processed.".blue.bold
111
+ seqs.validate_nt_sequences
85
112
  opt = options[:ref_option] ? options[:ref_option] : :HXB2
86
113
 
87
114
  unless [:HXB2, :SIVmm239].include? opt
@@ -92,9 +119,19 @@ begin
92
119
  locs = seqs.loc(opt)
93
120
  head = ["title", "sequence", "ref", "direction", "start", "end", "similarity", "indel", "aligned_input", "aligned_ref"]
94
121
  locs.unshift(head)
122
+
123
+ directional_fasta = []
95
124
  data = CSV.generate do |csv|
96
- locs.each {|loc| csv << loc}
125
+ locs.each do |loc|
126
+ csv << loc
127
+ directional_fasta << loc[1]
128
+ directional_fasta << loc[8].tr("-", "") # remove gaps for aligned_input
129
+ end
130
+ end
131
+ directional_fasta[2..-1].each do |line|
132
+ fasta_handle.puts line
97
133
  end
134
+ fasta_handle.close
98
135
 
99
136
  File.write(csv_file, data)
100
137
  puts "Output file found at #{csv_file.green.bold}"
data/bin/tcs_sdrm CHANGED
@@ -12,10 +12,10 @@
12
12
  # ├── lib1_IN
13
13
  # ├── lib1_V1V3
14
14
  # ├── lib2
15
- # ├── lib1_RT
16
- # ├── lib1_PR
17
- # ├── lib1_IN
18
- # ├── lib1_V1V3
15
+ # ├── lib2_RT
16
+ # ├── lib2_PR
17
+ # ├── lib2_IN
18
+ # ├── lib2_V1V3
19
19
  # ├── ...
20
20
  #
21
21
  # output data in a new dir as 'libs_dir_SDRM'
@@ -37,7 +37,7 @@ r_version = ViralSeq::R.check_R
37
37
  ViralSeq::R.check_R_packages
38
38
 
39
39
  def abstract_line(data)
40
- return_data = data[3] + data[2] + data[4] + ":" +
40
+ data[3] + data[2] + data[4] + ":" +
41
41
  (data[6].to_f * 100).round(2).to_s + "(" +
42
42
  (data[7].to_f * 100).round(2).to_s + "-" +
43
43
  (data[8].to_f * 100).round(2).to_s + "); "
@@ -143,7 +143,7 @@ libs.each do |lib|
143
143
  seq_basename.gsub!(/\_P17/i, "_CA")
144
144
  region = version_config.query_region(region_name.to_s)
145
145
 
146
- puts "prcessing region: " + region.region
146
+ puts "processing region: " + region.region
147
147
 
148
148
  sh = ViralSeq::SeqHash.fa(path_to_file)
149
149
 
data/lib/viral_seq/hivdr.rb CHANGED
@@ -492,7 +492,7 @@ module ViralSeq
492
492
 
493
493
  self.dna_hash.each do |k,v|
494
494
  r1_seqs[k] = v[0,r1_length]
495
- r2_seqs[k] = v[r1_length, r2_length]
495
+ r2_seqs[k] = v[-r2_length..-1] # to ensure the length from the end. Sometimes the platform will return sequence with one extra base.
496
496
  end
497
497
 
498
498
  r1_sh = ViralSeq::SeqHash.new(r1_seqs)
data/lib/viral_seq/recency_report.rb CHANGED
@@ -106,7 +106,7 @@ module ViralSeq
106
106
  )
107
107
 
108
108
  formatted_text(
109
- text_format2("P17", log[:pi_P17], log[:dist20_P17], log[:tcs_P17])
109
+ text_format2("CA", log[:pi_CA], log[:dist20_CA], log[:tcs_CA])
110
110
  )
111
111
 
112
112
  move_down 30
data/lib/viral_seq/seq_hash_pair.rb CHANGED
@@ -250,7 +250,7 @@ module ViralSeq
250
250
 
251
251
  private
252
252
  # determine overlap size from @dna_hash
253
- def determine_overlap_pid_pair(seq_pair_hash, diff = 0.0)
253
+ def determine_overlap_pid_pair(seq_pair_hash, diff = 0.02)
254
254
  overlaps = []
255
255
  seq_pair_hash.each do |_seq_name, seq_pair|
256
256
  overlap_list = []
data/lib/viral_seq/util/drm_list.json CHANGED
@@ -1,684 +1,429 @@
1
1
  {
2
- "HCV_NS5A": [
3
- {
4
- "position": 28,
5
- "wild-type": "M",
6
- "mutations": [
7
- "T"
8
- ]
9
- },
10
- {
11
- "position": 30,
12
- "wild-type": "L",
13
- "mutations": [
14
- "H",
15
- "K",
16
- "R",
17
- "Q",
18
- "A",
19
- "S",
20
- "D"
21
- ]
22
- },
23
- {
24
- "position": 31,
25
- "wild-type": "L",
26
- "mutations": [
27
- "M",
28
- "V",
29
- "F"
30
- ]
31
- },
32
- {
33
- "position": 32,
34
- "wild-type": "P",
35
- "mutations": [
36
- "L"
37
- ]
38
- },
39
- {
40
- "position": 44,
41
- "wild-type": "K",
42
- "mutations": [
43
- "R"
44
- ]
45
- },
46
- {
47
- "position": 58,
48
- "wild-type": "H",
49
- "mutations": [
50
- "D",
51
- "P",
52
- "S"
53
- ]
54
- },
55
- {
56
- "position": 64,
57
- "wild-type": "T",
58
- "mutations": [
59
- "A",
60
- "S"
61
- ]
62
- },
63
- {
64
- "position": 77,
65
- "wild-type": "P",
66
- "mutations": [
67
- "A",
68
- "S"
69
- ]
70
- },
71
- {
72
- "position": 78,
73
- "wild-type": "R",
74
- "mutations": [
75
- "K"
76
- ]
77
- },
78
- {
79
- "position": 79,
80
- "wild-type": "T",
81
- "mutations": [
82
- "A"
83
- ]
84
- },
85
- {
86
- "position": 83,
87
- "wild-type": "T",
88
- "mutations": [
89
- "M"
90
- ]
91
- },
92
- {
93
- "position": 85,
94
- "wild-type": "S",
95
- "mutations": [
96
- "N",
97
- "H",
98
- "Y"
99
- ]
100
- },
101
- {
102
- "position": 92,
103
- "wild-type": "A",
104
- "mutations": [
105
- "P",
106
- "T",
107
- "K",
108
- "E"
109
- ]
110
- },
111
- {
112
- "position": 93,
113
- "wild-type": "Y",
114
- "mutations": [
115
- "C",
116
- "F",
117
- "H",
118
- "N"
119
- ]
120
- },
121
- {
122
- "position": 107,
123
- "wild-type": "K",
124
- "mutations": [
125
- "T",
126
- "S"
127
- ]
128
- },
129
- {
130
- "position": 121,
131
- "wild-type": "I",
132
- "mutations": [
133
- "V"
134
- ]
135
- },
136
- {
137
- "position": 135,
138
- "wild-type": "T",
139
- "mutations": [
140
- "A"
141
- ]
142
- }
143
- ],
144
- "NRTI": [
145
- {
146
- "position": 41,
147
- "wild-type": "M",
148
- "mutations": [
149
- "L"
150
- ]
151
- },
152
- {
153
- "position": 65,
154
- "wild-type": "K",
155
- "mutations": [
156
- "R"
157
- ]
158
- },
159
- {
160
- "position": 67,
161
- "wild-type": "D",
162
- "mutations": [
163
- "N",
164
- "G",
165
- "E"
166
- ]
167
- },
168
- {
169
- "position": 69,
170
- "wild-type": "T",
171
- "mutations": [
172
- "D"
173
- ]
174
- },
175
- {
176
- "position": 70,
177
- "wild-type": "K",
178
- "mutations": [
179
- "R",
180
- "E"
181
- ]
182
- },
183
- {
184
- "position": 74,
185
- "wild-type": "L",
186
- "mutations": [
187
- "V",
188
- "I"
189
- ]
190
- },
191
- {
192
- "position": 75,
193
- "wild-type": "V",
194
- "mutations": [
195
- "M",
196
- "T",
197
- "A",
198
- "S"
199
- ]
200
- },
201
- {
202
- "position": 77,
203
- "wild-type": "F",
204
- "mutations": [
205
- "L"
206
- ]
207
- },
208
- {
209
- "position": 115,
210
- "wild-type": "Y",
211
- "mutations": [
212
- "F"
213
- ]
214
- },
215
- {
216
- "position": 116,
217
- "wild-type": "F",
218
- "mutations": [
219
- "Y"
220
- ]
221
- },
222
- {
223
- "position": 151,
224
- "wild-type": "Q",
225
- "mutations": [
226
- "M"
227
- ]
228
- },
229
- {
230
- "position": 184,
231
- "wild-type": "M",
232
- "mutations": [
233
- "V",
234
- "I"
235
- ]
236
- },
237
- {
238
- "position": 210,
239
- "wild-type": "L",
240
- "mutations": [
241
- "W"
242
- ]
243
- },
244
- {
245
- "position": 215,
246
- "wild-type": "T",
247
- "mutations": [
248
- "Y",
249
- "F",
250
- "I",
251
- "C",
252
- "D",
253
- "V",
254
- "E"
255
- ]
256
- },
257
- {
258
- "position": 219,
259
- "wild-type": "K",
260
- "mutations": [
261
- "Q",
262
- "E",
263
- "N",
264
- "R"
265
- ]
266
- }
267
- ],
268
- "NNRTI": [
269
- {
270
- "position": 98,
271
- "wild-type": "A",
272
- "mutations": [
273
- "G"
274
- ]
275
- },
276
- {
277
- "position": 100,
278
- "wild-type": "L",
279
- "mutations": [
280
- "I"
281
- ]
282
- },
283
- {
284
- "position": 101,
285
- "wild-type": "K",
286
- "mutations": [
287
- "E",
288
- "P"
289
- ]
290
- },
291
- {
292
- "position": 103,
293
- "wild-type": "K",
294
- "mutations": [
295
- "N",
296
- "S"
297
- ]
298
- },
299
- {
300
- "position": 106,
301
- "wild-type": "V",
302
- "mutations": [
303
- "M",
304
- "A"
305
- ]
306
- },
307
- {
308
- "position": 138,
309
- "wild-type": "E",
310
- "mutations": [
311
- "A",
312
- "K",
313
- "G",
314
- "Q"
315
- ]
316
- },
317
- {
318
- "position": 179,
319
- "wild-type": "V",
320
- "mutations": [
321
- "F",
322
- "D"
323
- ]
324
- },
325
- {
326
- "position": 181,
327
- "wild-type": "Y",
328
- "mutations": [
329
- "C",
330
- "I",
331
- "V"
332
- ]
333
- },
334
- {
335
- "position": 188,
336
- "wild-type": "Y",
337
- "mutations": [
338
- "L",
339
- "H",
340
- "C"
341
- ]
342
- },
343
- {
344
- "position": 190,
345
- "wild-type": "G",
346
- "mutations": [
347
- "A",
348
- "S",
349
- "E",
350
- "C",
351
- "T",
352
- "V"
353
- ]
354
- },
355
- {
356
- "position": 225,
357
- "wild-type": "P",
358
- "mutations": [
359
- "H"
360
- ]
361
- },
362
- {
363
- "position": 230,
364
- "wild-type": "M",
365
- "mutations": [
366
- "L"
367
- ]
368
- }
369
- ],
370
- "PI": [
371
- {
372
- "position": 23,
373
- "wild-type": "L",
374
- "mutations": [
375
- "I"
376
- ]
377
- },
378
- {
379
- "position": 24,
380
- "wild-type": "L",
381
- "mutations": [
382
- "I"
383
- ]
384
- },
385
- {
386
- "position": 30,
387
- "wild-type": "D",
388
- "mutations": [
389
- "N"
390
- ]
391
- },
392
- {
393
- "position": 32,
394
- "wild-type": "V",
395
- "mutations": [
396
- "I"
397
- ]
398
- },
399
- {
400
- "position": 46,
401
- "wild-type": "M",
402
- "mutations": [
403
- "I",
404
- "L"
405
- ]
406
- },
407
- {
408
- "position": 47,
409
- "wild-type": "I",
410
- "mutations": [
411
- "V",
412
- "A"
413
- ]
414
- },
415
- {
416
- "position": 48,
417
- "wild-type": "G",
418
- "mutations": [
419
- "V",
420
- "M"
421
- ]
422
- },
423
- {
424
- "position": 50,
425
- "wild-type": "I",
426
- "mutations": [
427
- "V",
428
- "L"
429
- ]
430
- },
431
- {
432
- "position": 53,
433
- "wild-type": "F",
434
- "mutations": [
435
- "L"
436
- ]
437
- },
438
- {
439
- "position": 54,
440
- "wild-type": "I",
441
- "mutations": [
442
- "V",
443
- "L",
444
- "M",
445
- "T",
446
- "A",
447
- "S"
448
- ]
449
- },
450
- {
451
- "position": 73,
452
- "wild-type": "G",
453
- "mutations": [
454
- "S",
455
- "T",
456
- "C",
457
- "A"
458
- ]
459
- },
460
- {
461
- "position": 76,
462
- "wild-type": "L",
463
- "mutations": [
464
- "V"
465
- ]
466
- },
467
- {
468
- "position": 82,
469
- "wild-type": "V",
470
- "mutations": [
471
- "A",
472
- "T",
473
- "S",
474
- "F",
475
- "L",
476
- "C",
477
- "M"
478
- ]
479
- },
480
- {
481
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482
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483
- "mutations": [
484
- "D"
485
- ]
486
- },
487
- {
488
- "position": 84,
489
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490
- "mutations": [
491
- "V",
492
- "A",
493
- "C"
494
- ]
495
- },
496
- {
497
- "position": 88,
498
- "wild-type": "N",
499
- "mutations": [
500
- "D",
501
- "S"
502
- ]
503
- },
504
- {
505
- "position": 90,
506
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507
- "mutations": [
508
- "M"
509
- ]
510
- }
511
- ],
512
- "INSTI": [
513
- {
514
- "position": 66,
515
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516
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517
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518
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519
- "K"
520
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521
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522
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523
- "position": 74,
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525
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526
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527
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528
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529
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530
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531
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532
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533
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534
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535
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536
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537
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538
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539
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540
- "K"
541
- ]
542
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543
- {
544
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545
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546
- "mutations": [
547
- "A"
548
- ]
549
- },
550
- {
551
- "position": 121,
552
- "wild-type": "F",
553
- "mutations": [
554
- "Y"
555
- ]
556
- },
557
- {
558
- "position": 140,
559
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560
- "mutations": [
561
- "A",
562
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563
- "C"
564
- ]
565
- },
566
- {
567
- "position": 143,
568
- "wild-type": "Y",
569
- "mutations": [
570
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571
- "H",
572
- "R"
573
- ]
574
- },
575
- {
576
- "position": 147,
577
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578
- "mutations": [
579
- "G"
580
- ]
581
- },
582
- {
583
- "position": 148,
584
- "wild-type": "Q",
585
- "mutations": [
586
- "H",
587
- "K",
588
- "R"
589
- ]
590
- },
591
- {
592
- "position": 263,
593
- "wild-type": "R",
594
- "mutations": [
595
- "K"
596
- ]
597
- },
598
- {
599
- "position": 155,
600
- "wild-type": [
601
- "N",
602
- [
603
- "S",
604
- "H"
605
- ]
606
- ],
607
- "mutations": [
608
- "R",
609
- [
610
- "K"
611
- ]
612
- ]
613
- }
614
- ],
615
- "CAI": [
616
- {
617
- "position": 56,
618
- "wild-type": "L",
619
- "mutations": [
620
- "I"
621
- ]
622
- },
623
- {
624
- "position": 57,
625
- "wild-type": "N",
626
- "mutations": [
627
- "S"
628
- ]
629
- },
630
- {
631
- "position": 66,
632
- "wild-type": "M",
633
- "mutations": [
634
- "I"
635
- ]
636
- },
637
- {
638
- "position": 67,
639
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640
- "mutations": [
641
- "H",
642
- "Y",
643
- "N",
644
- "K"
645
- ]
646
- },
647
- {
648
- "position": 70,
649
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650
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651
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652
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653
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654
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655
- ]
656
- },
657
- {
658
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659
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660
- "mutations": [
661
- "D",
662
- "S"
663
- ]
664
- },
665
- {
666
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667
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668
- "mutations": [
669
- "T",
670
- "S",
671
- "E"
672
- ]
673
- },
674
- {
675
- "position": 107,
676
- "wild-type": "T",
677
- "mutations": [
678
- "N",
679
- "S",
680
- "A"
681
- ]
682
- }
683
- ]
2
+ "HCV_NS5A": [
3
+ {
4
+ "position": 28,
5
+ "wild-type": "M",
6
+ "mutations": ["T"]
7
+ },
8
+ {
9
+ "position": 30,
10
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11
+ "mutations": ["H", "K", "R", "Q", "A", "S", "D"]
12
+ },
13
+ {
14
+ "position": 31,
15
+ "wild-type": "L",
16
+ "mutations": ["M", "V", "F"]
17
+ },
18
+ {
19
+ "position": 32,
20
+ "wild-type": "P",
21
+ "mutations": ["L"]
22
+ },
23
+ {
24
+ "position": 44,
25
+ "wild-type": "K",
26
+ "mutations": ["R"]
27
+ },
28
+ {
29
+ "position": 58,
30
+ "wild-type": "H",
31
+ "mutations": ["D", "P", "S"]
32
+ },
33
+ {
34
+ "position": 64,
35
+ "wild-type": "T",
36
+ "mutations": ["A", "S"]
37
+ },
38
+ {
39
+ "position": 77,
40
+ "wild-type": "P",
41
+ "mutations": ["A", "S"]
42
+ },
43
+ {
44
+ "position": 78,
45
+ "wild-type": "R",
46
+ "mutations": ["K"]
47
+ },
48
+ {
49
+ "position": 79,
50
+ "wild-type": "T",
51
+ "mutations": ["A"]
52
+ },
53
+ {
54
+ "position": 83,
55
+ "wild-type": "T",
56
+ "mutations": ["M"]
57
+ },
58
+ {
59
+ "position": 85,
60
+ "wild-type": "S",
61
+ "mutations": ["N", "H", "Y"]
62
+ },
63
+ {
64
+ "position": 92,
65
+ "wild-type": "A",
66
+ "mutations": ["P", "T", "K", "E"]
67
+ },
68
+ {
69
+ "position": 93,
70
+ "wild-type": "Y",
71
+ "mutations": ["C", "F", "H", "N"]
72
+ },
73
+ {
74
+ "position": 107,
75
+ "wild-type": "K",
76
+ "mutations": ["T", "S"]
77
+ },
78
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79
+ "position": 121,
80
+ "wild-type": "I",
81
+ "mutations": ["V"]
82
+ },
83
+ {
84
+ "position": 135,
85
+ "wild-type": "T",
86
+ "mutations": ["A"]
87
+ }
88
+ ],
89
+ "NRTI": [
90
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91
+ "position": 41,
92
+ "wild-type": "M",
93
+ "mutations": ["L"]
94
+ },
95
+ {
96
+ "position": 65,
97
+ "wild-type": "K",
98
+ "mutations": ["R"]
99
+ },
100
+ {
101
+ "position": 67,
102
+ "wild-type": "D",
103
+ "mutations": ["N", "G", "E"]
104
+ },
105
+ {
106
+ "position": 69,
107
+ "wild-type": "T",
108
+ "mutations": ["D"]
109
+ },
110
+ {
111
+ "position": 70,
112
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113
+ "mutations": ["R", "E"]
114
+ },
115
+ {
116
+ "position": 74,
117
+ "wild-type": "L",
118
+ "mutations": ["V", "I"]
119
+ },
120
+ {
121
+ "position": 75,
122
+ "wild-type": "V",
123
+ "mutations": ["M", "T", "A", "S"]
124
+ },
125
+ {
126
+ "position": 77,
127
+ "wild-type": "F",
128
+ "mutations": ["L"]
129
+ },
130
+ {
131
+ "position": 115,
132
+ "wild-type": "Y",
133
+ "mutations": ["F"]
134
+ },
135
+ {
136
+ "position": 116,
137
+ "wild-type": "F",
138
+ "mutations": ["Y"]
139
+ },
140
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141
+ "position": 151,
142
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143
+ "mutations": ["M"]
144
+ },
145
+ {
146
+ "position": 184,
147
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148
+ "mutations": ["V", "I"]
149
+ },
150
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151
+ "position": 210,
152
+ "wild-type": "L",
153
+ "mutations": ["W"]
154
+ },
155
+ {
156
+ "position": 215,
157
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158
+ "mutations": ["Y", "F", "I", "C", "D", "V", "E"]
159
+ },
160
+ {
161
+ "position": 219,
162
+ "wild-type": "K",
163
+ "mutations": ["Q", "E", "N", "R"]
164
+ }
165
+ ],
166
+ "NNRTI": [
167
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168
+ "position": 98,
169
+ "wild-type": "A",
170
+ "mutations": ["G"]
171
+ },
172
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173
+ "position": 100,
174
+ "wild-type": "L",
175
+ "mutations": ["I"]
176
+ },
177
+ {
178
+ "position": 101,
179
+ "wild-type": "K",
180
+ "mutations": ["E", "P"]
181
+ },
182
+ {
183
+ "position": 103,
184
+ "wild-type": "K",
185
+ "mutations": ["N", "S"]
186
+ },
187
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188
+ "position": 106,
189
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190
+ "mutations": ["M", "A"]
191
+ },
192
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193
+ "position": 138,
194
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195
+ "mutations": ["A", "K", "G", "Q"]
196
+ },
197
+ {
198
+ "position": 179,
199
+ "wild-type": "V",
200
+ "mutations": ["F", "D"]
201
+ },
202
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203
+ "position": 181,
204
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205
+ "mutations": ["C", "I", "V"]
206
+ },
207
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208
+ "position": 188,
209
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210
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211
+ },
212
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213
+ "position": 190,
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215
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216
+ },
217
+ {
218
+ "position": 225,
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220
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221
+ },
222
+ {
223
+ "position": 230,
224
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225
+ "mutations": ["L"]
226
+ }
227
+ ],
228
+ "PI": [
229
+ {
230
+ "position": 23,
231
+ "wild-type": "L",
232
+ "mutations": ["I"]
233
+ },
234
+ {
235
+ "position": 24,
236
+ "wild-type": "L",
237
+ "mutations": ["I"]
238
+ },
239
+ {
240
+ "position": 30,
241
+ "wild-type": "D",
242
+ "mutations": ["N"]
243
+ },
244
+ {
245
+ "position": 32,
246
+ "wild-type": "V",
247
+ "mutations": ["I"]
248
+ },
249
+ {
250
+ "position": 46,
251
+ "wild-type": "M",
252
+ "mutations": ["I", "L"]
253
+ },
254
+ {
255
+ "position": 47,
256
+ "wild-type": "I",
257
+ "mutations": ["V", "A"]
258
+ },
259
+ {
260
+ "position": 48,
261
+ "wild-type": "G",
262
+ "mutations": ["V", "M"]
263
+ },
264
+ {
265
+ "position": 50,
266
+ "wild-type": "I",
267
+ "mutations": ["V", "L"]
268
+ },
269
+ {
270
+ "position": 53,
271
+ "wild-type": "F",
272
+ "mutations": ["L"]
273
+ },
274
+ {
275
+ "position": 54,
276
+ "wild-type": "I",
277
+ "mutations": ["V", "L", "M", "T", "A", "S"]
278
+ },
279
+ {
280
+ "position": 73,
281
+ "wild-type": "G",
282
+ "mutations": ["S", "T", "C", "A"]
283
+ },
284
+ {
285
+ "position": 76,
286
+ "wild-type": "L",
287
+ "mutations": ["V"]
288
+ },
289
+ {
290
+ "position": 82,
291
+ "wild-type": "V",
292
+ "mutations": ["A", "T", "S", "F", "L", "C", "M"]
293
+ },
294
+ {
295
+ "position": 83,
296
+ "wild-type": "N",
297
+ "mutations": ["D"]
298
+ },
299
+ {
300
+ "position": 84,
301
+ "wild-type": "I",
302
+ "mutations": ["V", "A", "C"]
303
+ },
304
+ {
305
+ "position": 88,
306
+ "wild-type": "N",
307
+ "mutations": ["D", "S"]
308
+ },
309
+ {
310
+ "position": 90,
311
+ "wild-type": "L",
312
+ "mutations": ["M"]
313
+ }
314
+ ],
315
+ "INSTI": [
316
+ {
317
+ "position": 66,
318
+ "wild-type": "T",
319
+ "mutations": ["A", "I", "K"]
320
+ },
321
+ {
322
+ "position": 74,
323
+ "wild-type": "L",
324
+ "mutations": ["M"]
325
+ },
326
+ {
327
+ "position": 92,
328
+ "wild-type": "E",
329
+ "mutations": ["Q"]
330
+ },
331
+ {
332
+ "position": 95,
333
+ "wild-type": "Q",
334
+ "mutations": ["K"]
335
+ },
336
+ {
337
+ "position": 97,
338
+ "wild-type": "T",
339
+ "mutations": ["A"]
340
+ },
341
+ {
342
+ "position": 121,
343
+ "wild-type": "F",
344
+ "mutations": ["Y"]
345
+ },
346
+ {
347
+ "position": 140,
348
+ "wild-type": "G",
349
+ "mutations": ["A", "S", "C"]
350
+ },
351
+ {
352
+ "position": 143,
353
+ "wild-type": "Y",
354
+ "mutations": ["C", "H", "R"]
355
+ },
356
+ {
357
+ "position": 147,
358
+ "wild-type": "S",
359
+ "mutations": ["G"]
360
+ },
361
+ {
362
+ "position": 148,
363
+ "wild-type": "Q",
364
+ "mutations": ["H", "K", "R"]
365
+ },
366
+ {
367
+ "position": 263,
368
+ "wild-type": "R",
369
+ "mutations": ["K"]
370
+ },
371
+ {
372
+ "position": 155,
373
+ "wild-type": "N",
374
+ "mutations": ["S", "H", "T", "D"]
375
+ },
376
+ {
377
+ "position": 157,
378
+ "wild-type": "E",
379
+ "mutations": ["Q"]
380
+ },
381
+ {
382
+ "position": 163,
383
+ "wild-type": "G",
384
+ "mutations": ["R", "K"]
385
+ }
386
+ ],
387
+ "CAI": [
388
+ {
389
+ "position": 56,
390
+ "wild-type": "L",
391
+ "mutations": ["I"]
392
+ },
393
+ {
394
+ "position": 57,
395
+ "wild-type": "N",
396
+ "mutations": ["S"]
397
+ },
398
+ {
399
+ "position": 66,
400
+ "wild-type": "M",
401
+ "mutations": ["I"]
402
+ },
403
+ {
404
+ "position": 67,
405
+ "wild-type": "Q",
406
+ "mutations": ["H", "Y", "N", "K"]
407
+ },
408
+ {
409
+ "position": 70,
410
+ "wild-type": "K",
411
+ "mutations": ["N", "H", "R", "S"]
412
+ },
413
+ {
414
+ "position": 74,
415
+ "wild-type": "N",
416
+ "mutations": ["D", "S"]
417
+ },
418
+ {
419
+ "position": 105,
420
+ "wild-type": "A",
421
+ "mutations": ["T", "S", "E"]
422
+ },
423
+ {
424
+ "position": 107,
425
+ "wild-type": "T",
426
+ "mutations": ["N", "S", "A"]
427
+ }
428
+ ]
684
429
  }
data/lib/viral_seq/version.rb CHANGED
@@ -2,6 +2,6 @@
2
2
  # version info and histroy
3
3
 
4
4
  module ViralSeq
5
- VERSION = "1.10.2"
6
- TCS_VERSION = "2.7.3"
5
+ VERSION = "1.10.4"
6
+ TCS_VERSION = "2.7.4"
7
7
  end
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: viral_seq
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.10.2
4
+ version: 1.10.4
5
5
  platform: ruby
6
6
  authors:
7
7
  - Shuntai Zhou