@sjcrh/proteinpaint-server 2.16.0 → 2.17.0

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 (21) hide show
  1. package/dataset/clinvar.hg19.js +53 -51
  2. package/dataset/clinvar.hg38.js +60 -58
  3. package/dataset/clinvar.js +49 -55
  4. package/genome/CriGri.js +23 -1853
  5. package/genome/danRer10.js +48 -1108
  6. package/genome/dm3.js +47 -60
  7. package/genome/dm6.js +48 -1916
  8. package/genome/galGal5.js +48 -23522
  9. package/genome/galGal6.js +48 -512
  10. package/genome/hg19.js +210 -304
  11. package/genome/hg38.js +108 -474
  12. package/genome/hg38.test.js +42 -409
  13. package/genome/hgvirus.js +21 -43
  14. package/genome/mm10.js +70 -135
  15. package/genome/mm9.js +82 -118
  16. package/genome/rn6.js +49 -1000
  17. package/package.json +9 -6
  18. package/server.js +1 -1
  19. package/shared/common.js +4 -0
  20. package/src/serverconfig.js +10 -2
  21. package/genome/genome.sql +0 -54
package/genome/hg19.js CHANGED
@@ -1,304 +1,210 @@
1
- const clinvar = require('../dataset/clinvar')
2
- module.exports = {
3
- species: 'human',
4
- genomefile: 'genomes/hg19.gz',
5
- genedb: {
6
- dbfile: 'anno/genes.hg19.db'
7
- },
8
- proteindomain: {
9
- dbfile: 'anno/db/proteindomain.db',
10
- statement: 'select data from domain where isoform=? collate nocase'
11
- },
12
- repeatmasker: {
13
- dbfile: 'anno/rmsk.hg19.gz',
14
- statement: 'RepeatMasker database'
15
- },
16
- snp: {
17
- bigbedfile: 'anno/dbsnp.hg19.bb'
18
- },
19
- fimo_motif: {
20
- db: 'utils/meme/motif_databases/HUMAN/HOCOMOCOv11_full_HUMAN_mono_meme_format.meme',
21
- annotationfile: 'utils/meme/motif_databases/HUMAN/HOCOMOCOv11_full_annotation_HUMAN_mono.tsv'
22
- },
23
- clinvarVCF: {
24
- file: 'hg19/clinvar.hg19.hgvs_short.vep.bcf.gz',
25
- infokey: 'CLNSIG',
26
- categories: clinvar.clinsig
27
- },
28
- tracks: [
29
- {
30
- __isgene: true, // only for initialization
31
- translatecoding: true, // instructs to translate coding:[]
32
- file: 'anno/refGene.hg19.gz',
33
- type: 'bedj',
34
- name: 'RefGene',
35
- stackheight: 16,
36
- stackspace: 1,
37
- vpad: 4,
38
- color: '#1D591D'
39
- },
40
- {
41
- __isgene: true,
42
- translatecoding: true,
43
- file: 'anno/gencode.v40.hg19.gz',
44
- type: 'bedj',
45
- name: 'GENCODE v40',
46
- stackheight: 16,
47
- stackspace: 1,
48
- vpad: 4,
49
- categories: {
50
- coding: { color: '#004D99', label: 'Coding gene' },
51
- nonCoding: { color: '#009933', label: 'Noncoding gene' },
52
- problem: { color: '#FF3300', label: 'Problem' },
53
- pseudo: { color: '#FF00CC', label: 'Pseudogene' }
54
- }
55
- },
56
- {
57
- type: 'bedj',
58
- name: 'RepeatMasker',
59
- stackheight: 14,
60
- file: 'anno/rmsk.hg19.gz',
61
- onerow: true,
62
- categories: {
63
- SINE: { color: '#ED8C8E', label: 'SINE' },
64
- LINE: { color: '#EDCB8C', label: 'LINE' },
65
- LTR: { color: '#E38CED', label: 'LTR' },
66
- DNA: { color: '#8C8EED', label: 'DNA transposon' },
67
- simple: { color: '#8EB88C', label: 'Simple repeats' },
68
- low_complexity: { color: '#ACEBA9', label: 'Low complexity' },
69
- satellite: { color: '#B59A84', label: 'Satellite' },
70
- RNA: { color: '#9DE0E0', label: 'RNA repeat' },
71
- other: { color: '#9BADC2', label: 'Other' },
72
- unknown: { color: '#858585', label: 'Unknown' }
73
- }
74
- }
75
- ],
76
- geneset: [
77
- {
78
- name: 'Signaling',
79
- lst: [
80
- { name: 'NRAS' },
81
- { name: 'FLT3' },
82
- { name: 'KRAS' },
83
- { name: 'JAK3' },
84
- { name: 'BRAF' },
85
- { name: 'NF1' },
86
- { name: 'MAPK1' }
87
- ]
88
- },
89
- { name: 'Cell cycle', lst: [{ name: 'TP53' }, { name: 'RB1' }, { name: 'CDKN2A' }, { name: 'CDKN2B' }] },
90
- {
91
- name: 'Epigenetics',
92
- lst: [
93
- { name: 'ATRX' },
94
- { name: 'BCOR' },
95
- { name: 'MYC' },
96
- { name: 'MYCN' },
97
- { name: 'WHSC1' },
98
- { name: 'SUZ12' },
99
- { name: 'EED' },
100
- { name: 'EZH2' },
101
- { name: 'SETD2' },
102
- { name: 'CREBBP' },
103
- { name: 'EHMT2' },
104
- { name: 'PRDM1' },
105
- { name: 'NSD1' },
106
- { name: 'KMT2D' },
107
- { name: 'UBR4' },
108
- { name: 'ARID1A' },
109
- { name: 'EP300' }
110
- ]
111
- },
112
- {
113
- name: 'Development',
114
- lst: [
115
- { name: 'RUNX1' },
116
- { name: 'ETV6' },
117
- { name: 'GATA3' },
118
- { name: 'IKZF1' },
119
- { name: 'EP300' },
120
- { name: 'IKZF2' },
121
- { name: 'IKZF3' },
122
- { name: 'PAX5' },
123
- { name: 'VPREB1' },
124
- { name: 'EBF1' }
125
- ]
126
- }
127
- ],
128
- defaultcoord: {
129
- chr: 'chr17',
130
- start: 7568451,
131
- stop: 7591984,
132
- gene: 'TP53'
133
- },
134
-
135
- hicenzymefragment: [
136
- {
137
- enzyme: 'DpnII',
138
- file: 'anno/hicFragment/hic.DpnII.hg19.gz'
139
- },
140
- {
141
- enzyme: 'EcoRI',
142
- file: 'anno/hicFragment/hic.EcoRI.hg19.gz'
143
- },
144
- {
145
- enzyme: 'HindIII',
146
- file: 'anno/hicFragment/hic.HindIII.hg19.gz'
147
- },
148
- {
149
- enzyme: 'MboI',
150
- file: 'anno/hicFragment/hic.MboI.hg19.gz'
151
- },
152
- {
153
- enzyme: 'NcoI',
154
- file: 'anno/hicFragment/hic.NcoI.hg19.gz'
155
- }
156
- ],
157
-
158
- hicdomain: {
159
- groups: {
160
- RaoCell2014: {
161
- name: 'Rao SS et al, Cell 2014',
162
- reference:
163
- '<a href=https://www.ncbi.nlm.nih.gov/pubmed/25497547 target=_blank>A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping</a>',
164
- sets: {
165
- GM12878: {
166
- name: 'GM12878',
167
- longname: 'Human B-Lymphoblastoid',
168
- file: 'anno/hicTAD/aiden2014/GM12878.domain.hg19.gz'
169
- },
170
- HMEC: {
171
- name: 'HMEC',
172
- longname: 'Human Mammary Epithelial',
173
- file: 'anno/hicTAD/aiden2014/HMEC.domain.hg19.gz'
174
- },
175
- IMR90: {
176
- name: 'IRM90',
177
- longname: 'Human Lung Fibroblast',
178
- file: 'anno/hicTAD/aiden2014/IMR90.domain.hg19.gz'
179
- },
180
- KBM7: {
181
- name: 'KBM7',
182
- longname: 'Near Haploid Human Myelogenous Leukemia',
183
- file: 'anno/hicTAD/aiden2014/KBM7.domain.hg19.gz'
184
- },
185
- HeLa: {
186
- name: 'HeLa',
187
- longname: 'Human Cervical Carcinoma',
188
- file: 'anno/hicTAD/aiden2014/HeLa.domain.hg19.gz'
189
- },
190
- HUVEC: {
191
- name: 'HUVEC',
192
- longname: 'Human Umbilical Vein Endothelial',
193
- file: 'anno/hicTAD/aiden2014/HUVEC.domain.hg19.gz'
194
- },
195
- K562: {
196
- name: 'K562',
197
- longname: 'Human Erythroleukemia',
198
- file: 'anno/hicTAD/aiden2014/K562.domain.hg19.gz'
199
- },
200
- NHEK: {
201
- name: 'NHEK',
202
- longname: 'Normal Human Epidermal Keratinocytes',
203
- file: 'anno/hicTAD/aiden2014/NHEK.domain.hg19.gz'
204
- }
205
- }
206
- }
207
- }
208
- },
209
-
210
- majorchr: `chr1 249250621
211
- chr2 243199373
212
- chr3 198022430
213
- chr4 191154276
214
- chr5 180915260
215
- chr6 171115067
216
- chr7 159138663
217
- chr8 146364022
218
- chr9 141213431
219
- chr10 135534747
220
- chr11 135006516
221
- chr12 133851895
222
- chr13 115169878
223
- chr14 107349540
224
- chr15 102531392
225
- chr16 90354753
226
- chr17 81195210
227
- chr18 78077248
228
- chr19 59128983
229
- chr20 63025520
230
- chr21 48129895
231
- chr22 51304566
232
- chrX 155270560
233
- chrY 59373566
234
- chrM 16571`,
235
- minorchr: `
236
- chr6_ssto_hap7 4928567
237
- chr6_mcf_hap5 4833398
238
- chr6_cox_hap2 4795371
239
- chr6_mann_hap4 4683263
240
- chr6_apd_hap1 4622290
241
- chr6_qbl_hap6 4611984
242
- chr6_dbb_hap3 4610396
243
- chr17_ctg5_hap1 1680828
244
- chr4_ctg9_hap1 590426
245
- chr1_gl000192_random 547496
246
- chrUn_gl000225 211173
247
- chr4_gl000194_random 191469
248
- chr4_gl000193_random 189789
249
- chr9_gl000200_random 187035
250
- chrUn_gl000222 186861
251
- chrUn_gl000212 186858
252
- chr7_gl000195_random 182896
253
- chrUn_gl000223 180455
254
- chrUn_gl000224 179693
255
- chrUn_gl000219 179198
256
- chr17_gl000205_random 174588
257
- chrUn_gl000215 172545
258
- chrUn_gl000216 172294
259
- chrUn_gl000217 172149
260
- chr9_gl000199_random 169874
261
- chrUn_gl000211 166566
262
- chrUn_gl000213 164239
263
- chrUn_gl000220 161802
264
- chrUn_gl000218 161147
265
- chr19_gl000209_random 159169
266
- chrUn_gl000221 155397
267
- chrUn_gl000214 137718
268
- chrUn_gl000228 129120
269
- chrUn_gl000227 128374
270
- chr1_gl000191_random 106433
271
- chr19_gl000208_random 92689
272
- chr9_gl000198_random 90085
273
- chr17_gl000204_random 81310
274
- chrUn_gl000233 45941
275
- chrUn_gl000237 45867
276
- chrUn_gl000230 43691
277
- chrUn_gl000242 43523
278
- chrUn_gl000243 43341
279
- chrUn_gl000241 42152
280
- chrUn_gl000236 41934
281
- chrUn_gl000240 41933
282
- chr17_gl000206_random 41001
283
- chrUn_gl000232 40652
284
- chrUn_gl000234 40531
285
- chr11_gl000202_random 40103
286
- chrUn_gl000238 39939
287
- chrUn_gl000244 39929
288
- chrUn_gl000248 39786
289
- chr8_gl000196_random 38914
290
- chrUn_gl000249 38502
291
- chrUn_gl000246 38154
292
- chr17_gl000203_random 37498
293
- chr8_gl000197_random 37175
294
- chrUn_gl000245 36651
295
- chrUn_gl000247 36422
296
- chr9_gl000201_random 36148
297
- chrUn_gl000235 34474
298
- chrUn_gl000239 33824
299
- chr21_gl000210_random 27682
300
- chrUn_gl000231 27386
301
- chrUn_gl000229 19913
302
- chrUn_gl000226 15008
303
- chr18_gl000207_random 4262`
304
- }
1
+ "use strict";
2
+ Object.defineProperty(exports, "__esModule", { value: true });
3
+ var clinvar_1 = require("../dataset/clinvar");
4
+ exports.default = {
5
+ species: 'human',
6
+ genomefile: 'genomes/hg19.gz',
7
+ genedb: {
8
+ dbfile: 'anno/genes.hg19.db'
9
+ },
10
+ proteindomain: {
11
+ dbfile: 'anno/db/proteindomain.db',
12
+ statement: 'select data from domain where isoform=? collate nocase'
13
+ },
14
+ repeatmasker: {
15
+ dbfile: 'anno/rmsk.hg19.gz',
16
+ statement: 'RepeatMasker database'
17
+ },
18
+ snp: {
19
+ bigbedfile: 'anno/dbsnp.hg19.bb'
20
+ },
21
+ fimo_motif: {
22
+ db: 'utils/meme/motif_databases/HUMAN/HOCOMOCOv11_full_HUMAN_mono_meme_format.meme',
23
+ annotationfile: 'utils/meme/motif_databases/HUMAN/HOCOMOCOv11_full_annotation_HUMAN_mono.tsv'
24
+ },
25
+ clinvarVCF: {
26
+ file: 'hg19/clinvar.hg19.hgvs_short.vep.bcf.gz',
27
+ infokey: 'CLNSIG',
28
+ categories: clinvar_1.clinsig
29
+ },
30
+ tracks: [
31
+ {
32
+ __isgene: true,
33
+ translatecoding: true,
34
+ file: 'anno/refGene.hg19.gz',
35
+ type: 'bedj',
36
+ name: 'RefGene',
37
+ stackheight: 16,
38
+ stackspace: 1,
39
+ vpad: 4,
40
+ color: '#1D591D'
41
+ },
42
+ {
43
+ __isgene: true,
44
+ translatecoding: true,
45
+ file: 'anno/gencode.v40.hg19.gz',
46
+ type: 'bedj',
47
+ name: 'GENCODE v40',
48
+ stackheight: 16,
49
+ stackspace: 1,
50
+ vpad: 4,
51
+ categories: {
52
+ coding: { color: '#004D99', label: 'Coding gene' },
53
+ nonCoding: { color: '#009933', label: 'Noncoding gene' },
54
+ problem: { color: '#FF3300', label: 'Problem' },
55
+ pseudo: { color: '#FF00CC', label: 'Pseudogene' }
56
+ }
57
+ },
58
+ {
59
+ type: 'bedj',
60
+ name: 'RepeatMasker',
61
+ stackheight: 14,
62
+ file: 'anno/rmsk.hg19.gz',
63
+ onerow: true,
64
+ categories: {
65
+ SINE: { color: '#ED8C8E', label: 'SINE' },
66
+ LINE: { color: '#EDCB8C', label: 'LINE' },
67
+ LTR: { color: '#E38CED', label: 'LTR' },
68
+ DNA: { color: '#8C8EED', label: 'DNA transposon' },
69
+ simple: { color: '#8EB88C', label: 'Simple repeats' },
70
+ low_complexity: { color: '#ACEBA9', label: 'Low complexity' },
71
+ satellite: { color: '#B59A84', label: 'Satellite' },
72
+ RNA: { color: '#9DE0E0', label: 'RNA repeat' },
73
+ other: { color: '#9BADC2', label: 'Other' },
74
+ unknown: { color: '#858585', label: 'Unknown' }
75
+ }
76
+ }
77
+ ],
78
+ geneset: [
79
+ {
80
+ name: 'Signaling',
81
+ lst: [
82
+ { name: 'NRAS' },
83
+ { name: 'FLT3' },
84
+ { name: 'KRAS' },
85
+ { name: 'JAK3' },
86
+ { name: 'BRAF' },
87
+ { name: 'NF1' },
88
+ { name: 'MAPK1' }
89
+ ]
90
+ },
91
+ { name: 'Cell cycle', lst: [{ name: 'TP53' }, { name: 'RB1' }, { name: 'CDKN2A' }, { name: 'CDKN2B' }] },
92
+ {
93
+ name: 'Epigenetics',
94
+ lst: [
95
+ { name: 'ATRX' },
96
+ { name: 'BCOR' },
97
+ { name: 'MYC' },
98
+ { name: 'MYCN' },
99
+ { name: 'WHSC1' },
100
+ { name: 'SUZ12' },
101
+ { name: 'EED' },
102
+ { name: 'EZH2' },
103
+ { name: 'SETD2' },
104
+ { name: 'CREBBP' },
105
+ { name: 'EHMT2' },
106
+ { name: 'PRDM1' },
107
+ { name: 'NSD1' },
108
+ { name: 'KMT2D' },
109
+ { name: 'UBR4' },
110
+ { name: 'ARID1A' },
111
+ { name: 'EP300' }
112
+ ]
113
+ },
114
+ {
115
+ name: 'Development',
116
+ lst: [
117
+ { name: 'RUNX1' },
118
+ { name: 'ETV6' },
119
+ { name: 'GATA3' },
120
+ { name: 'IKZF1' },
121
+ { name: 'EP300' },
122
+ { name: 'IKZF2' },
123
+ { name: 'IKZF3' },
124
+ { name: 'PAX5' },
125
+ { name: 'VPREB1' },
126
+ { name: 'EBF1' }
127
+ ]
128
+ }
129
+ ],
130
+ defaultcoord: {
131
+ chr: 'chr17',
132
+ start: 7568451,
133
+ stop: 7591984,
134
+ gene: 'TP53'
135
+ },
136
+ hicenzymefragment: [
137
+ {
138
+ enzyme: 'DpnII',
139
+ file: 'anno/hicFragment/hic.DpnII.hg19.gz'
140
+ },
141
+ {
142
+ enzyme: 'EcoRI',
143
+ file: 'anno/hicFragment/hic.EcoRI.hg19.gz'
144
+ },
145
+ {
146
+ enzyme: 'HindIII',
147
+ file: 'anno/hicFragment/hic.HindIII.hg19.gz'
148
+ },
149
+ {
150
+ enzyme: 'MboI',
151
+ file: 'anno/hicFragment/hic.MboI.hg19.gz'
152
+ },
153
+ {
154
+ enzyme: 'NcoI',
155
+ file: 'anno/hicFragment/hic.NcoI.hg19.gz'
156
+ }
157
+ ],
158
+ hicdomain: {
159
+ groups: {
160
+ RaoCell2014: {
161
+ name: 'Rao SS et al, Cell 2014',
162
+ reference: '<a href=https://www.ncbi.nlm.nih.gov/pubmed/25497547 target=_blank>A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping</a>',
163
+ sets: {
164
+ GM12878: {
165
+ name: 'GM12878',
166
+ longname: 'Human B-Lymphoblastoid',
167
+ file: 'anno/hicTAD/aiden2014/GM12878.domain.hg19.gz'
168
+ },
169
+ HMEC: {
170
+ name: 'HMEC',
171
+ longname: 'Human Mammary Epithelial',
172
+ file: 'anno/hicTAD/aiden2014/HMEC.domain.hg19.gz'
173
+ },
174
+ IMR90: {
175
+ name: 'IRM90',
176
+ longname: 'Human Lung Fibroblast',
177
+ file: 'anno/hicTAD/aiden2014/IMR90.domain.hg19.gz'
178
+ },
179
+ KBM7: {
180
+ name: 'KBM7',
181
+ longname: 'Near Haploid Human Myelogenous Leukemia',
182
+ file: 'anno/hicTAD/aiden2014/KBM7.domain.hg19.gz'
183
+ },
184
+ HeLa: {
185
+ name: 'HeLa',
186
+ longname: 'Human Cervical Carcinoma',
187
+ file: 'anno/hicTAD/aiden2014/HeLa.domain.hg19.gz'
188
+ },
189
+ HUVEC: {
190
+ name: 'HUVEC',
191
+ longname: 'Human Umbilical Vein Endothelial',
192
+ file: 'anno/hicTAD/aiden2014/HUVEC.domain.hg19.gz'
193
+ },
194
+ K562: {
195
+ name: 'K562',
196
+ longname: 'Human Erythroleukemia',
197
+ file: 'anno/hicTAD/aiden2014/K562.domain.hg19.gz'
198
+ },
199
+ NHEK: {
200
+ name: 'NHEK',
201
+ longname: 'Normal Human Epidermal Keratinocytes',
202
+ file: 'anno/hicTAD/aiden2014/NHEK.domain.hg19.gz'
203
+ }
204
+ }
205
+ }
206
+ }
207
+ },
208
+ majorchr: "chr1\t249250621\nchr2\t243199373\nchr3\t198022430\nchr4\t191154276\nchr5\t180915260\nchr6\t171115067\nchr7\t159138663\nchr8\t146364022\nchr9\t141213431\nchr10\t135534747\nchr11\t135006516\nchr12\t133851895\nchr13\t115169878\nchr14\t107349540\nchr15\t102531392\nchr16\t90354753\nchr17\t81195210\nchr18\t78077248\nchr19\t59128983\nchr20\t63025520\nchr21\t48129895\nchr22\t51304566\nchrX\t155270560\nchrY\t59373566\nchrM\t16571",
209
+ minorchr: "\nchr6_ssto_hap7\t4928567\nchr6_mcf_hap5\t4833398\nchr6_cox_hap2\t4795371\nchr6_mann_hap4\t4683263\nchr6_apd_hap1\t4622290\nchr6_qbl_hap6\t4611984\nchr6_dbb_hap3\t4610396\nchr17_ctg5_hap1\t1680828\nchr4_ctg9_hap1\t590426\nchr1_gl000192_random\t547496\nchrUn_gl000225\t211173\nchr4_gl000194_random\t191469\nchr4_gl000193_random\t189789\nchr9_gl000200_random\t187035\nchrUn_gl000222\t186861\nchrUn_gl000212\t186858\nchr7_gl000195_random\t182896\nchrUn_gl000223\t180455\nchrUn_gl000224\t179693\nchrUn_gl000219\t179198\nchr17_gl000205_random\t174588\nchrUn_gl000215\t172545\nchrUn_gl000216\t172294\nchrUn_gl000217\t172149\nchr9_gl000199_random\t169874\nchrUn_gl000211\t166566\nchrUn_gl000213\t164239\nchrUn_gl000220\t161802\nchrUn_gl000218\t161147\nchr19_gl000209_random\t159169\nchrUn_gl000221\t155397\nchrUn_gl000214\t137718\nchrUn_gl000228\t129120\nchrUn_gl000227\t128374\nchr1_gl000191_random\t106433\nchr19_gl000208_random\t92689\nchr9_gl000198_random\t90085\nchr17_gl000204_random\t81310\nchrUn_gl000233\t45941\nchrUn_gl000237\t45867\nchrUn_gl000230\t43691\nchrUn_gl000242\t43523\nchrUn_gl000243\t43341\nchrUn_gl000241\t42152\nchrUn_gl000236\t41934\nchrUn_gl000240\t41933\nchr17_gl000206_random\t41001\nchrUn_gl000232\t40652\nchrUn_gl000234\t40531\nchr11_gl000202_random\t40103\nchrUn_gl000238\t39939\nchrUn_gl000244\t39929\nchrUn_gl000248\t39786\nchr8_gl000196_random\t38914\nchrUn_gl000249\t38502\nchrUn_gl000246\t38154\nchr17_gl000203_random\t37498\nchr8_gl000197_random\t37175\nchrUn_gl000245\t36651\nchrUn_gl000247\t36422\nchr9_gl000201_random\t36148\nchrUn_gl000235\t34474\nchrUn_gl000239\t33824\nchr21_gl000210_random\t27682\nchrUn_gl000231\t27386\nchrUn_gl000229\t19913\nchrUn_gl000226\t15008\nchr18_gl000207_random\t4262"
210
+ };