@platforma-open/milaboratories.mixcr-shm-trees.workflow 3.3.0 → 3.4.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (15) hide show
  1. package/.turbo/turbo-build.log +3 -1
  2. package/CHANGELOG.md +12 -0
  3. package/dist/tengo/lib/export-settings.lib.tengo +534 -92
  4. package/dist/tengo/lib/tablesAggregation.lib.tengo +75 -0
  5. package/dist/tengo/tpl/main.plj.gz +0 -0
  6. package/dist/tengo/tpl/process.plj.gz +0 -0
  7. package/dist/tengo/tpl/reconstruct-shm-trees.plj.gz +0 -0
  8. package/dist/tengo/tpl/soi.plj.gz +0 -0
  9. package/package.json +5 -5
  10. package/src/export-settings.lib.tengo +534 -92
  11. package/src/main.tpl.tengo +1 -0
  12. package/src/process.tpl.tengo +19 -2
  13. package/src/reconstruct-shm-trees.tpl.tengo +16 -39
  14. package/src/soi.tpl.tengo +1 -1
  15. package/src/tablesAggregation.lib.tengo +75 -0
package/src/export-settings.lib.tengo CHANGED
@@ -17,6 +17,7 @@ shmTreeTableOptions := func(dataDescription) {
17
17
  axes := []
18
18
  columns := []
19
19
  cmdArgs := []
20
+ assemblingFeature := dataDescription.assemblingFeature
20
21
 
21
22
  cmdArgs = append(cmdArgs, "-treeId")
22
23
  axes = append(axes, {
@@ -26,7 +27,9 @@ shmTreeTableOptions := func(dataDescription) {
26
27
  type: "Long",
27
28
  domain: { },
28
29
  annotations: {
29
- "pl7.app/label": "Tree id"
30
+ "pl7.app/label": "Tree id",
31
+ "pl7.app/table/visibility": "default",
32
+ "pl7.app/table/orderPriority": "100000"
30
33
  }
31
34
  }
32
35
  })
@@ -40,7 +43,9 @@ shmTreeTableOptions := func(dataDescription) {
40
43
  type: "Long",
41
44
  domain: { },
42
45
  annotations: {
43
- "pl7.app/label": "Subtree id"
46
+ "pl7.app/label": "Chain id",
47
+ "pl7.app/table/visibility": "default",
48
+ "pl7.app/table/orderPriority": "90000"
44
49
  }
45
50
  }
46
51
  })
@@ -56,7 +61,9 @@ shmTreeTableOptions := func(dataDescription) {
56
61
  name: "pl7.app/vdj/uniqueCellCount",
57
62
  valueType: "Long",
58
63
  annotations: {
59
- "pl7.app/label": "Number of cells"
64
+ "pl7.app/label": "Number of cells",
65
+ "pl7.app/table/visibility": "default",
66
+ "pl7.app/table/orderPriority": "70000"
60
67
  }
61
68
  }
62
69
  })
@@ -72,7 +79,9 @@ shmTreeTableOptions := func(dataDescription) {
72
79
  name: "pl7.app/vdj/uniqueMoleculeCount",
73
80
  valueType: "Long",
74
81
  annotations: {
75
- "pl7.app/label": "Number of molecules"
82
+ "pl7.app/label": "Number of molecules",
83
+ "pl7.app/table/visibility": "default",
84
+ "pl7.app/table/orderPriority": "60000"
76
85
  }
77
86
  }
78
87
  })
@@ -87,7 +96,9 @@ shmTreeTableOptions := func(dataDescription) {
87
96
  name: "pl7.app/vdj/numberOfClonesInTree",
88
97
  valueType: "Long",
89
98
  annotations: {
90
- "pl7.app/label": "Number of clones"
99
+ "pl7.app/label": "Number of clones",
100
+ "pl7.app/table/visibility": "default",
101
+ "pl7.app/table/orderPriority": "80000"
91
102
  }
92
103
  }
93
104
  })
@@ -101,7 +112,9 @@ shmTreeTableOptions := func(dataDescription) {
101
112
  name: "pl7.app/vdj/numberOfNodesWithClones",
102
113
  valueType: "Long",
103
114
  annotations: {
104
- "pl7.app/label": "Number of nodes"
115
+ "pl7.app/label": "Number of nodes",
116
+ "pl7.app/table/visibility": "default",
117
+ "pl7.app/table/orderPriority": "90000"
105
118
  }
106
119
  }
107
120
  })
@@ -115,7 +128,9 @@ shmTreeTableOptions := func(dataDescription) {
115
128
  name: "pl7.app/vdj/totalReadsCountInTree",
116
129
  valueType: "Long",
117
130
  annotations: {
118
- "pl7.app/label": "Total reads count"
131
+ "pl7.app/label": "Total reads count",
132
+ "pl7.app/table/visibility": "default",
133
+ "pl7.app/table/orderPriority": "50000"
119
134
  }
120
135
  }
121
136
  })
@@ -133,7 +148,9 @@ shmTreeTableOptions := func(dataDescription) {
133
148
  },
134
149
  annotations: {
135
150
  type: "V gene name",
136
- "pl7.app/label": "V gene"
151
+ "pl7.app/label": "V gene",
152
+ "pl7.app/table/visibility": "default",
153
+ "pl7.app/table/orderPriority": "30000"
137
154
  }
138
155
  }
139
156
  })
@@ -151,7 +168,9 @@ shmTreeTableOptions := func(dataDescription) {
151
168
  },
152
169
  annotations: {
153
170
  type: "J gene name",
154
- "pl7.app/label": "J gene"
171
+ "pl7.app/label": "J gene",
172
+ "pl7.app/table/visibility": "default",
173
+ "pl7.app/table/orderPriority": "29000"
155
174
  }
156
175
  }
157
176
  })
@@ -165,51 +184,107 @@ shmTreeTableOptions := func(dataDescription) {
165
184
  valueType: "String",
166
185
  name: "pl7.app/vdj/chain",
167
186
  annotations: {
168
- "pl7.app/label": "Chain"
187
+ "pl7.app/label": "Chain",
188
+ "pl7.app/table/visibility": "default",
189
+ "pl7.app/table/orderPriority": "40000"
169
190
  }
170
191
  }
171
192
  })
172
-
193
+ orderPriority := 20000
194
+ visibility := undefined
173
195
  for feature in dataDescription.coveredFeatures {
174
- cmdArgs = append(cmdArgs, "-aaFeature", feature, "mrca")
196
+ cmdArgs = append(cmdArgs, "-nFeature", feature, "mrca")
197
+ if feature == "CDR3" {
198
+ visibility = "default"
199
+ } else {
200
+ visibility = "optional"
201
+ }
175
202
  columns = append(columns, {
176
- column: "aaSeq" + feature + "OfMrca",
177
- id: "aa-seq-" + feature + "-mrca",
203
+ column: "nSeq" + feature + "OfMrca",
204
+ id: "n-seq-" + feature + "-mrca",
178
205
  allowNA: allowNA,
179
206
  spec: {
180
207
  name: "pl7.app/vdj/sequence",
181
208
  valueType: "String",
182
209
  domain: {
183
210
  "pl7.app/vdj/feature": feature,
184
- "pl7.app/alphabet": "aminoacid"
211
+ "pl7.app/alphabet": "nucleotide"
185
212
  },
186
213
  annotations: {
187
214
  "pl7.app/type": "sequence",
188
- "pl7.app/label": feature + " of MRCA aa"
215
+ "pl7.app/label": feature + " of MRCA nt",
216
+ "pl7.app/table/visibility": visibility,
217
+ "pl7.app/table/orderPriority": string(orderPriority)
189
218
  }
190
219
  }
191
220
  })
221
+ orderPriority -= 100
192
222
 
193
- cmdArgs = append(cmdArgs, "-nFeature", feature, "mrca")
223
+ cmdArgs = append(cmdArgs, "-aaFeature", feature, "mrca")
194
224
  columns = append(columns, {
195
- column: "nSeq" + feature + "OfMrca",
196
- id: "n-seq-" + feature + "-mrca",
225
+ column: "aaSeq" + feature + "OfMrca",
226
+ id: "aa-seq-" + feature + "-mrca",
197
227
  allowNA: allowNA,
198
228
  spec: {
199
229
  name: "pl7.app/vdj/sequence",
200
230
  valueType: "String",
201
231
  domain: {
202
232
  "pl7.app/vdj/feature": feature,
203
- "pl7.app/alphabet": "nucleotide"
233
+ "pl7.app/alphabet": "aminoacid"
204
234
  },
205
235
  annotations: {
206
236
  "pl7.app/type": "sequence",
207
- "pl7.app/label": feature + " of MRCA nt"
237
+ "pl7.app/label": feature + " of MRCA aa",
238
+ "pl7.app/table/visibility": visibility,
239
+ "pl7.app/table/orderPriority": string(orderPriority)
208
240
  }
209
241
  }
210
242
  })
243
+ orderPriority -= 100
211
244
  }
212
245
 
246
+ cmdArgs = append(cmdArgs, "-nFeature", assemblingFeature, "mrca")
247
+ columns = append(columns, {
248
+ column: "nSeq" + assemblingFeature + "OfMrca",
249
+ id: "n-seq-" + assemblingFeature + "-mrca",
250
+ allowNA: allowNA,
251
+ spec: {
252
+ name: "pl7.app/vdj/sequence",
253
+ valueType: "String",
254
+ domain: {
255
+ "pl7.app/vdj/feature": assemblingFeature,
256
+ "pl7.app/alphabet": "nucleotide"
257
+ },
258
+ annotations: {
259
+ "pl7.app/type": "sequence",
260
+ "pl7.app/label": assemblingFeature + " of MRCA nt",
261
+ "pl7.app/table/visibility": "default",
262
+ "pl7.app/table/orderPriority": "10000"
263
+ }
264
+ }
265
+ })
266
+
267
+ cmdArgs = append(cmdArgs, "-aaFeature", assemblingFeature, "mrca")
268
+ columns = append(columns, {
269
+ column: "aaSeq" + assemblingFeature + "OfMrca",
270
+ id: "aa-seq-" + assemblingFeature + "-mrca",
271
+ allowNA: allowNA,
272
+ spec: {
273
+ name: "pl7.app/vdj/sequence",
274
+ valueType: "String",
275
+ domain: {
276
+ "pl7.app/vdj/feature": assemblingFeature,
277
+ "pl7.app/alphabet": "aminoacid"
278
+ },
279
+ annotations: {
280
+ "pl7.app/type": "sequence",
281
+ "pl7.app/label": assemblingFeature + " of MRCA aa",
282
+ "pl7.app/table/visibility": "default",
283
+ "pl7.app/table/orderPriority": "9000"
284
+ }
285
+ }
286
+ })
287
+
213
288
  return {
214
289
  pfconvParams: {
215
290
  axes: axes,
@@ -226,6 +301,7 @@ shmTreeNodesTableOptions := func(dataDescription) {
226
301
  axes := []
227
302
  columns := []
228
303
  cmdArgs := []
304
+ assemblingFeature := dataDescription.assemblingFeature
229
305
 
230
306
  cmdArgs = append(cmdArgs, "-treeId")
231
307
  axes = append(axes, {
@@ -235,7 +311,9 @@ shmTreeNodesTableOptions := func(dataDescription) {
235
311
  type: "Long",
236
312
  domain: { },
237
313
  annotations: {
238
- "pl7.app/label": "Tree id"
314
+ "pl7.app/label": "Tree id",
315
+ "pl7.app/table/visibility": "default",
316
+ "pl7.app/table/orderPriority": "100000"
239
317
  }
240
318
  }
241
319
  })
@@ -249,7 +327,9 @@ shmTreeNodesTableOptions := func(dataDescription) {
249
327
  type: "Long",
250
328
  domain: { },
251
329
  annotations: {
252
- "pl7.app/label": "Subtree id"
330
+ "pl7.app/label": "Chain id",
331
+ "pl7.app/table/visibility": "default",
332
+ "pl7.app/table/orderPriority": "90000"
253
333
  }
254
334
  }
255
335
  })
@@ -263,7 +343,9 @@ shmTreeNodesTableOptions := func(dataDescription) {
263
343
  type: "Long",
264
344
  domain: { },
265
345
  annotations: {
266
- "pl7.app/label": "Node id"
346
+ "pl7.app/label": "Node id",
347
+ "pl7.app/table/visibility": "default",
348
+ "pl7.app/table/orderPriority": "80000"
267
349
  }
268
350
  }
269
351
  })
@@ -278,7 +360,9 @@ shmTreeNodesTableOptions := func(dataDescription) {
278
360
  // TODO change to Boolean when it will be supported
279
361
  valueType: "String",
280
362
  annotations: {
281
- "pl7.app/label": "Is observed in data"
363
+ "pl7.app/label": "Is observed in data",
364
+ "pl7.app/table/visibility": "default",
365
+ "pl7.app/table/orderPriority": "85000"
282
366
  }
283
367
  }
284
368
  })
@@ -293,7 +377,9 @@ shmTreeNodesTableOptions := func(dataDescription) {
293
377
  valueType: "Long",
294
378
  annotations: {
295
379
  "pl7.app/label": "Parent node id",
296
- "pl7.app/dendrogram/isTopology": "true"
380
+ "pl7.app/dendrogram/isTopology": "true",
381
+ "pl7.app/table/visibility": "optional",
382
+ "pl7.app/table/orderPriority": "10000"
297
383
  }
298
384
  }
299
385
  })
@@ -312,7 +398,9 @@ shmTreeNodesTableOptions := func(dataDescription) {
312
398
  annotations: {
313
399
  "pl7.app/label": "Distanse from germline",
314
400
  "pl7.app/dendrogram/distance/from": "germline", // change to domain only, once can be selected in graphmaker
315
- "pl7.app/dendrogram/isDistance": "true"
401
+ "pl7.app/dendrogram/isDistance": "true",
402
+ "pl7.app/table/visibility": "optional",
403
+ "pl7.app/table/orderPriority": "9000"
316
404
  }
317
405
  }
318
406
  })
@@ -331,7 +419,9 @@ shmTreeNodesTableOptions := func(dataDescription) {
331
419
  annotations: {
332
420
  "pl7.app/label": "Distanse from parent",
333
421
  "pl7.app/dendrogram/distance/from": "parent", // change to domain only, once can be selected in graphmaker
334
- "pl7.app/dendrogram/isDistance": "true"
422
+ "pl7.app/dendrogram/isDistance": "true",
423
+ "pl7.app/table/visibility": "optional",
424
+ "pl7.app/table/orderPriority": "8900"
335
425
  }
336
426
  }
337
427
  })
@@ -349,7 +439,221 @@ shmTreeNodesTableOptions := func(dataDescription) {
349
439
  "pl7.app/alphabet": "nucleotide"
350
440
  },
351
441
  annotations: {
352
- "pl7.app/label": "Mutations rate nt"
442
+ "pl7.app/label": "Mutations rate nt",
443
+ "pl7.app/table/visibility": "optional",
444
+ "pl7.app/table/orderPriority": "8800"
445
+ }
446
+ }
447
+ })
448
+
449
+ cmdArgs = append(cmdArgs, "-aaMutationsRate")
450
+ columns = append(columns, {
451
+ column: "aaMutationsRate",
452
+ id: "aa-mutations-rate",
453
+ allowNA: allowNA,
454
+ spec: {
455
+ name: "pl7.app/vdj/mutationsRate",
456
+ valueType: "Double",
457
+ domain: {
458
+ "pl7.app/vdj/features": assemblingFeature,
459
+ "pl7.app/alphabet": "aminoacid"
460
+ },
461
+ annotations: {
462
+ "pl7.app/label": "Mutations rate aa",
463
+ "pl7.app/table/visibility": "optional",
464
+ "pl7.app/table/orderPriority": "8700"
465
+ }
466
+ }
467
+ })
468
+
469
+ cmdArgs = append(cmdArgs, "-vBestIdentityPercent")
470
+ columns = append(columns, {
471
+ column: "vBestIdentityPercent",
472
+ id: "v-best-identity-percent",
473
+ allowNA: allowNA,
474
+ spec: {
475
+ name: "pl7.app/vdj/vIdentityPercent",
476
+ valueType: "Double",
477
+ annotations: {
478
+ "pl7.app/label": "V gene identity",
479
+ "pl7.app/table/visibility": "optional",
480
+ "pl7.app/table/orderPriority": "8600"
481
+ }
482
+ }
483
+ })
484
+
485
+ cmdArgs = append(cmdArgs, "-jBestIdentityPercent")
486
+ columns = append(columns, {
487
+ column: "jBestIdentityPercent",
488
+ id: "j-best-identity-percent",
489
+ allowNA: allowNA,
490
+ spec: {
491
+ name: "pl7.app/vdj/jIdentityPercent",
492
+ valueType: "Double",
493
+ annotations: {
494
+ "pl7.app/label": "J gene identity",
495
+ "pl7.app/table/visibility": "optional",
496
+ "pl7.app/table/orderPriority": "8500"
497
+ }
498
+ }
499
+ })
500
+
501
+ cmdArgs = append(cmdArgs, "-nMutations", assemblingFeature, "mrca")
502
+ columns = append(columns, {
503
+ column: "nMutations"+assemblingFeature+"BasedOnMrca",
504
+ id: "n-mutations-" + assemblingFeature+"-mrca",
505
+ allowNA: allowNA,
506
+ spec: {
507
+ name: "pl7.app/vdj/mutations",
508
+ valueType: "String",
509
+ domain: {
510
+ "pl7.app/vdj/features": assemblingFeature,
511
+ "pl7.app/alphabet": "nucleotide"
512
+ },
513
+ annotations: {
514
+ "pl7.app/label": assemblingFeature+" nt mutations based on MRCA",
515
+ "pl7.app/table/visibility": "optional",
516
+ "pl7.app/table/orderPriority": "8400"
517
+ }
518
+ }
519
+ })
520
+
521
+ cmdArgs = append(cmdArgs, "-aaMutations", assemblingFeature, "mrca")
522
+ columns = append(columns, {
523
+ column: "aaMutations"+assemblingFeature+"BasedOnMrca",
524
+ id: "aa-mutations"+assemblingFeature+"-mrca",
525
+ allowNA: allowNA,
526
+ spec: {
527
+ name: "pl7.app/vdj/mutations",
528
+ valueType: "String",
529
+ domain: {
530
+ "pl7.app/vdj/features": assemblingFeature,
531
+ "pl7.app/alphabet": "aminoacid"
532
+ },
533
+ annotations: {
534
+ "pl7.app/label": assemblingFeature+" aa mutations based on MRCA",
535
+ "pl7.app/table/visibility": "optional",
536
+ "pl7.app/table/orderPriority": "8300"
537
+ }
538
+ }
539
+ })
540
+
541
+ cmdArgs = append(cmdArgs, "-nMutations", assemblingFeature, "germline")
542
+ columns = append(columns, {
543
+ column: "nMutations"+assemblingFeature+"BasedOnGermline",
544
+ id: "n-mutations-" + assemblingFeature+"-germline",
545
+ allowNA: allowNA,
546
+ spec: {
547
+ name: "pl7.app/vdj/mutations",
548
+ valueType: "String",
549
+ domain: {
550
+ "pl7.app/vdj/features": assemblingFeature,
551
+ "pl7.app/alphabet": "nucleotide"
552
+ },
553
+ annotations: {
554
+ "pl7.app/label": assemblingFeature+" nt mutations based on germline",
555
+ "pl7.app/table/visibility": "optional",
556
+ "pl7.app/table/orderPriority": "8200"
557
+ }
558
+ }
559
+ })
560
+
561
+ cmdArgs = append(cmdArgs, "-aaMutations", assemblingFeature, "germline")
562
+ columns = append(columns, {
563
+ column: "aaMutations"+assemblingFeature+"BasedOnGermline",
564
+ id: "aa-mutations"+assemblingFeature+"-germline",
565
+ allowNA: allowNA,
566
+ spec: {
567
+ name: "pl7.app/vdj/mutations",
568
+ valueType: "String",
569
+ domain: {
570
+ "pl7.app/vdj/features": assemblingFeature,
571
+ "pl7.app/alphabet": "aminoacid"
572
+ },
573
+ annotations: {
574
+ "pl7.app/label": assemblingFeature+" aa mutations based on germline",
575
+ "pl7.app/table/visibility": "optional",
576
+ "pl7.app/table/orderPriority": "8100"
577
+ }
578
+ }
579
+ })
580
+
581
+ cmdArgs = append(cmdArgs, "-nMutationsCount", assemblingFeature, "mrca")
582
+ columns = append(columns, {
583
+ column: "nMutationCount"+assemblingFeature+"BasedOnMrca",
584
+ id: "n-mutation-count-"+assemblingFeature+"-mrca",
585
+ allowNA: allowNA,
586
+ spec: {
587
+ name: "pl7.app/vdj/mutationCount",
588
+ valueType: "Long",
589
+ domain: {
590
+ "pl7.app/vdj/features": assemblingFeature,
591
+ "pl7.app/alphabet": "nucleotide"
592
+ },
593
+ annotations: {
594
+ "pl7.app/label": assemblingFeature+" nt mutations count based on MRCA",
595
+ "pl7.app/table/visibility": "optional",
596
+ "pl7.app/table/orderPriority": "8000"
597
+ }
598
+ }
599
+ })
600
+
601
+ cmdArgs = append(cmdArgs, "-aaMutationsCount", assemblingFeature, "mrca")
602
+ columns = append(columns, {
603
+ column: "aaMutationCount"+assemblingFeature+"BasedOnMrca",
604
+ id: "aa-mutation-count-"+assemblingFeature+"-mrca",
605
+ allowNA: allowNA,
606
+ spec: {
607
+ name: "pl7.app/vdj/mutationCount",
608
+ valueType: "Long",
609
+ domain: {
610
+ "pl7.app/vdj/features": assemblingFeature,
611
+ "pl7.app/alphabet": "aminoacid"
612
+ },
613
+ annotations: {
614
+ "pl7.app/label": assemblingFeature+" aa mutations count based on MRCA",
615
+ "pl7.app/table/visibility": "optional",
616
+ "pl7.app/table/orderPriority": "7900"
617
+ }
618
+ }
619
+ })
620
+
621
+ cmdArgs = append(cmdArgs, "-nMutationsCount", assemblingFeature, "germline")
622
+ columns = append(columns, {
623
+ column: "nMutationCount"+assemblingFeature+"BasedOnGermline",
624
+ id: "n-mutation-count-"+assemblingFeature+"-germline",
625
+ allowNA: allowNA,
626
+ spec: {
627
+ name: "pl7.app/vdj/mutationCount",
628
+ valueType: "Long",
629
+ domain: {
630
+ "pl7.app/vdj/features": assemblingFeature,
631
+ "pl7.app/alphabet": "nucleotide"
632
+ },
633
+ annotations: {
634
+ "pl7.app/label": assemblingFeature+" nt mutations count based on germline",
635
+ "pl7.app/table/visibility": "optional",
636
+ "pl7.app/table/orderPriority": "7800"
637
+ }
638
+ }
639
+ })
640
+
641
+ cmdArgs = append(cmdArgs, "-aaMutationsCount", assemblingFeature, "germline")
642
+ columns = append(columns, {
643
+ column: "aaMutationCount"+assemblingFeature+"BasedOnGermline",
644
+ id: "aa-mutation-count-"+assemblingFeature+"-germline",
645
+ allowNA: allowNA,
646
+ spec: {
647
+ name: "pl7.app/vdj/mutationCount",
648
+ valueType: "Long",
649
+ domain: {
650
+ "pl7.app/vdj/features": assemblingFeature,
651
+ "pl7.app/alphabet": "aminoacid"
652
+ },
653
+ annotations: {
654
+ "pl7.app/label": assemblingFeature+" aa mutations count based on germline",
655
+ "pl7.app/table/visibility": "optional",
656
+ "pl7.app/table/orderPriority": "7700"
353
657
  }
354
658
  }
355
659
  })
@@ -367,7 +671,9 @@ shmTreeNodesTableOptions := func(dataDescription) {
367
671
  },
368
672
  annotations: {
369
673
  type: "V gene name",
370
- "pl7.app/label": "V gene"
674
+ "pl7.app/label": "V gene",
675
+ "pl7.app/table/visibility": "default",
676
+ "pl7.app/table/orderPriority": "49000"
371
677
  }
372
678
  }
373
679
  })
@@ -385,51 +691,107 @@ shmTreeNodesTableOptions := func(dataDescription) {
385
691
  },
386
692
  annotations: {
387
693
  type: "J gene name",
388
- "pl7.app/label": "J gene"
694
+ "pl7.app/label": "J gene",
695
+ "pl7.app/table/visibility": "default",
696
+ "pl7.app/table/orderPriority": "47000"
389
697
  }
390
698
  }
391
699
  })
392
700
 
701
+ orderPriority := 40000
702
+ visibility := undefined
393
703
  for feature in dataDescription.coveredFeatures {
394
- cmdArgs = append(cmdArgs, "-aaFeature", feature)
704
+ cmdArgs = append(cmdArgs, "-nFeature", feature)
705
+ if feature == "CDR3" {
706
+ visibility = "default"
707
+ } else {
708
+ visibility = "optional"
709
+ }
395
710
  columns = append(columns, {
396
- column: "aaSeq" + feature,
397
- id: "aa-seq-" + feature,
711
+ column: "nSeq" + feature,
712
+ id: "n-seq-" + feature,
398
713
  allowNA: allowNA,
399
714
  spec: {
400
715
  name: "pl7.app/vdj/sequence",
401
716
  valueType: "String",
402
717
  domain: {
403
718
  "pl7.app/vdj/feature": feature,
404
- "pl7.app/alphabet": "aminoacid"
719
+ "pl7.app/alphabet": "nucleotide"
405
720
  },
406
721
  annotations: {
407
722
  "pl7.app/type": "sequence",
408
- "pl7.app/label": feature + " aa"
723
+ "pl7.app/label": feature + " nt",
724
+ "pl7.app/table/visibility": visibility,
725
+ "pl7.app/table/orderPriority": string(orderPriority)
409
726
  }
410
727
  }
411
728
  })
412
-
413
- cmdArgs = append(cmdArgs, "-nFeature", feature)
729
+ orderPriority -= 100
730
+ cmdArgs = append(cmdArgs, "-aaFeature", feature)
414
731
  columns = append(columns, {
415
- column: "nSeq" + feature,
416
- id: "n-seq-" + feature,
732
+ column: "aaSeq" + feature,
733
+ id: "aa-seq-" + feature,
417
734
  allowNA: allowNA,
418
735
  spec: {
419
736
  name: "pl7.app/vdj/sequence",
420
737
  valueType: "String",
421
738
  domain: {
422
739
  "pl7.app/vdj/feature": feature,
423
- "pl7.app/alphabet": "nucleotide"
740
+ "pl7.app/alphabet": "aminoacid"
424
741
  },
425
742
  annotations: {
426
743
  "pl7.app/type": "sequence",
427
- "pl7.app/label": feature + " nt"
744
+ "pl7.app/label": feature + " aa",
745
+ "pl7.app/table/visibility": visibility,
746
+ "pl7.app/table/orderPriority": string(orderPriority)
428
747
  }
429
748
  }
430
749
  })
750
+ orderPriority -= 100
431
751
  }
432
752
 
753
+ cmdArgs = append(cmdArgs, "-nFeature", assemblingFeature)
754
+ columns = append(columns, {
755
+ column: "nSeq" + assemblingFeature,
756
+ id: "n-seq-" + assemblingFeature,
757
+ allowNA: allowNA,
758
+ spec: {
759
+ name: "pl7.app/vdj/sequence",
760
+ valueType: "String",
761
+ domain: {
762
+ "pl7.app/vdj/feature": assemblingFeature,
763
+ "pl7.app/alphabet": "nucleotide"
764
+ },
765
+ annotations: {
766
+ "pl7.app/type": "sequence",
767
+ "pl7.app/label": assemblingFeature + " nt",
768
+ "pl7.app/table/visibility": "default",
769
+ "pl7.app/table/orderPriority": "30000"
770
+ }
771
+ }
772
+ })
773
+
774
+ cmdArgs = append(cmdArgs, "-aaFeature", assemblingFeature)
775
+ columns = append(columns, {
776
+ column: "aaSeq" + assemblingFeature,
777
+ id: "aa-seq-" + assemblingFeature,
778
+ allowNA: allowNA,
779
+ spec: {
780
+ name: "pl7.app/vdj/sequence",
781
+ valueType: "String",
782
+ domain: {
783
+ "pl7.app/vdj/feature": assemblingFeature,
784
+ "pl7.app/alphabet": "aminoacid"
785
+ },
786
+ annotations: {
787
+ "pl7.app/type": "sequence",
788
+ "pl7.app/label": assemblingFeature + " aa",
789
+ "pl7.app/table/visibility": "default",
790
+ "pl7.app/table/orderPriority": "29000"
791
+ }
792
+ }
793
+ })
794
+
433
795
  return {
434
796
  pfconvParams: {
435
797
  axes: axes,
@@ -458,7 +820,9 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
458
820
  type: "Long",
459
821
  domain: { },
460
822
  annotations: {
461
- "pl7.app/label": "Tree id"
823
+ "pl7.app/label": "Tree id",
824
+ "pl7.app/table/visibility": "default",
825
+ "pl7.app/table/orderPriority": "100000"
462
826
  }
463
827
  }
464
828
  })
@@ -472,7 +836,9 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
472
836
  type: "Long",
473
837
  domain: { },
474
838
  annotations: {
475
- "pl7.app/label": "Subtree id"
839
+ "pl7.app/label": "Chain id",
840
+ "pl7.app/table/visibility": "default",
841
+ "pl7.app/table/orderPriority": "90000"
476
842
  }
477
843
  }
478
844
  })
@@ -486,7 +852,9 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
486
852
  type: "Long",
487
853
  domain: { },
488
854
  annotations: {
489
- "pl7.app/label": "Node id"
855
+ "pl7.app/label": "Node id",
856
+ "pl7.app/table/visibility": "default",
857
+ "pl7.app/table/orderPriority": "80000"
490
858
  }
491
859
  }
492
860
  })
@@ -503,7 +871,12 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
503
871
  replacement: "$1"
504
872
  }
505
873
  ],
506
- spec: donorColumnSpec.axesSpec[0]
874
+ spec: donorColumnSpec.axesSpec[0],
875
+ annotations: {
876
+ "pl7.app/label": "Sample name",
877
+ "pl7.app/table/visibility": "default",
878
+ "pl7.app/table/orderPriority": "110000"
879
+ }
507
880
  })
508
881
 
509
882
  cmdArgs = append(cmdArgs, "-cloneId")
@@ -518,7 +891,9 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
518
891
  type: "Long",
519
892
  // TODO domain with blockId
520
893
  annotations: {
521
- "pl7.app/label": "Clone id"
894
+ "pl7.app/label": "Clone id",
895
+ "pl7.app/table/visibility": "default",
896
+ "pl7.app/table/orderPriority": "70000"
522
897
  }
523
898
  }
524
899
  })
@@ -533,7 +908,9 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
533
908
  name: "pl7.app/vdj/uniqueCellCount",
534
909
  valueType: "Long",
535
910
  annotations: {
536
- "pl7.app/label": "Number of cells"
911
+ "pl7.app/label": "Number of cells",
912
+ "pl7.app/table/visibility": "default",
913
+ "pl7.app/table/orderPriority": "60000"
537
914
  }
538
915
  }
539
916
  })
@@ -549,7 +926,9 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
549
926
  name: "pl7.app/vdj/uniqueMoleculeCount",
550
927
  valueType: "Long",
551
928
  annotations: {
552
- "pl7.app/label": "Number of molecules"
929
+ "pl7.app/label": "Number of molecules",
930
+ "pl7.app/table/visibility": "default",
931
+ "pl7.app/table/orderPriority": "59000"
553
932
  }
554
933
  }
555
934
  })
@@ -564,7 +943,9 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
564
943
  name: "pl7.app/vdj/readCount",
565
944
  valueType: "Long",
566
945
  annotations: {
567
- "pl7.app/label": "Number of Reads"
946
+ "pl7.app/label": "Number of Reads",
947
+ "pl7.app/table/visibility": "default",
948
+ "pl7.app/table/orderPriority": "58000"
568
949
  }
569
950
  }
570
951
  })
@@ -578,44 +959,9 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
578
959
  name: "pl7.app/vdj/readFraction",
579
960
  valueType: "Double",
580
961
  annotations: {
581
- "pl7.app/label": "Fraction of reads"
582
- }
583
- }
584
- })
585
-
586
- cmdArgs = append(cmdArgs, "-targetSequences")
587
- columns = append(columns, {
588
- column: "targetSequences",
589
- id: "n-seq-clonal-sequences",
590
- allowNA: true,
591
- spec: {
592
- name: "pl7.app/vdj/sequence",
593
- valueType: "String",
594
- domain: {
595
- "pl7.app/vdj/sequence": "clonalSequence",
596
- "pl7.app/alphabet": "nucleotide"
597
- },
598
- annotations: {
599
- "pl7.app/type": "sequence",
600
- "pl7.app/label": "Clonal sequences"
601
- }
602
- }
603
- })
604
-
605
- cmdArgs = append(cmdArgs, "-targetQualities")
606
- columns = append(columns, {
607
- column: "targetQualities",
608
- id: "clonal-qualities",
609
- allowNA: true,
610
- spec: {
611
- name: "pl7.app/vdj/sequenceQuality",
612
- valueType: "String",
613
- domain: {
614
- "pl7.app/vdj/quality": "clonalQuality"
615
- },
616
- annotations: {
617
- type: "quality string",
618
- "pl7.app/label": "Clonal qualities"
962
+ "pl7.app/label": "Fraction of reads",
963
+ "pl7.app/table/visibility": "default",
964
+ "pl7.app/table/orderPriority": "57000"
619
965
  }
620
966
  }
621
967
  })
@@ -633,7 +979,9 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
633
979
  },
634
980
  annotations: {
635
981
  type: "D gene name",
636
- "pl7.app/label": "Best D hit"
982
+ "pl7.app/label": "Best D hit",
983
+ "pl7.app/table/visibility": "default",
984
+ "pl7.app/table/orderPriority": "48000"
637
985
  }
638
986
  }
639
987
  })
@@ -651,7 +999,9 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
651
999
  },
652
1000
  annotations: {
653
1001
  type: "C gene name",
654
- "pl7.app/label": "Best C hit"
1002
+ "pl7.app/label": "Best C hit",
1003
+ "pl7.app/table/visibility": "default",
1004
+ "pl7.app/table/orderPriority": "46000"
655
1005
  }
656
1006
  }
657
1007
  })
@@ -665,7 +1015,9 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
665
1015
  valueType: "String",
666
1016
  name: "pl7.app/vdj/isotype",
667
1017
  annotations: {
668
- "pl7.app/label": "IG isotype"
1018
+ "pl7.app/label": "IG isotype",
1019
+ "pl7.app/table/visibility": "default",
1020
+ "pl7.app/table/orderPriority": "50000"
669
1021
  }
670
1022
  }
671
1023
  })
@@ -681,9 +1033,99 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
681
1033
  }
682
1034
  }
683
1035
 
1036
+ shmTreeNodesUniqueIsotypeTableOptions := func(dataDescription) {
1037
+
1038
+ axes := []
1039
+ columns := []
1040
+
1041
+ axes = append(axes, {
1042
+ column: "treeId",
1043
+ spec: {
1044
+ name: "pl7.app/dendrogram/treeId",
1045
+ type: "Long",
1046
+ domain: { },
1047
+ annotations: {
1048
+ "pl7.app/label": "Tree id",
1049
+ "pl7.app/table/visibility": "default",
1050
+ "pl7.app/table/orderPriority": "100000"
1051
+ }
1052
+ }
1053
+ })
1054
+
1055
+ if dataDescription.cellsAssembled {
1056
+ axes = append(axes, {
1057
+ column: "subtreeId",
1058
+ spec: {
1059
+ name: "pl7.app/dendrogram/subtreeId",
1060
+ type: "Long",
1061
+ domain: { },
1062
+ annotations: {
1063
+ "pl7.app/label": "Chain id",
1064
+ "pl7.app/table/visibility": "default",
1065
+ "pl7.app/table/orderPriority": "90000"
1066
+ }
1067
+ }
1068
+ })
1069
+ }
1070
+
1071
+ axes = append(axes, {
1072
+ column: "nodeId",
1073
+ spec: {
1074
+ name: "pl7.app/dendrogram/nodeId",
1075
+ type: "Long",
1076
+ domain: { },
1077
+ annotations: {
1078
+ "pl7.app/label": "Node id",
1079
+ "pl7.app/table/visibility": "default",
1080
+ "pl7.app/table/orderPriority": "80000"
1081
+ }
1082
+ }
1083
+ })
1084
+
1085
+ columns = append(columns, {
1086
+ column: "readCount",
1087
+ id: "read-count",
1088
+ allowNA: true,
1089
+ spec: {
1090
+ name: "pl7.app/vdj/readCount",
1091
+ valueType: "Long",
1092
+ annotations: {
1093
+ "pl7.app/label": "Top clone reads number",
1094
+ "pl7.app/table/visibility": "optional",
1095
+ "pl7.app/table/orderPriority": "58000"
1096
+ }
1097
+ }
1098
+ })
1099
+
1100
+ columns = append(columns, {
1101
+ column: "isotype",
1102
+ id: "isotype",
1103
+ allowNA: true,
1104
+ spec: {
1105
+ valueType: "String",
1106
+ name: "pl7.app/vdj/isotype",
1107
+ annotations: {
1108
+ "pl7.app/label": "Top IG isotype",
1109
+ "pl7.app/table/visibility": "optional",
1110
+ "pl7.app/table/orderPriority": "50000"
1111
+ }
1112
+ }
1113
+ })
1114
+
1115
+ return {
1116
+ pfconvParams: {
1117
+ axes: axes,
1118
+ columns: columns,
1119
+ storageFormat: "Binary",
1120
+ partitionKeyLength: 0
1121
+ }
1122
+ }
1123
+ }
1124
+
684
1125
  // to use the file as a library, we should explicitly export functions
685
1126
  export ll.toStrict({
686
1127
  shmTreeTableOptions: shmTreeTableOptions,
687
1128
  shmTreeNodesTableOptions: shmTreeNodesTableOptions,
688
- shmTreeNodesWithClonesTableOptions: shmTreeNodesWithClonesTableOptions
1129
+ shmTreeNodesWithClonesTableOptions: shmTreeNodesWithClonesTableOptions,
1130
+ shmTreeNodesUniqueIsotypeTableOptions: shmTreeNodesUniqueIsotypeTableOptions
689
1131
  })