@sjcrh/proteinpaint-server 2.44.0 → 2.46.1

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 (82) hide show
  1. package/dataset/clinvar.hg19.js +53 -52
  2. package/dataset/clinvar.hg38.js +74 -73
  3. package/dataset/clinvar.js +164 -47
  4. package/dataset/termdb.test.js +257 -0
  5. package/genome/CriGri.js +1859 -27
  6. package/genome/cgc.js +743 -7
  7. package/genome/danRer10.js +1108 -46
  8. package/genome/dm3.js +71 -44
  9. package/genome/dm6.js +1926 -45
  10. package/genome/galGal5.js +23522 -46
  11. package/genome/galGal6.js +512 -46
  12. package/genome/hg19.js +293 -198
  13. package/genome/hg38.js +472 -105
  14. package/genome/hg38.test.js +406 -40
  15. package/genome/hgvirus.js +45 -20
  16. package/genome/mm10.js +135 -67
  17. package/genome/mm9.js +116 -79
  18. package/genome/rn6.js +1002 -47
  19. package/package.json +31 -35
  20. package/routes/_template_.js +30 -0
  21. package/routes/burden.js +149 -0
  22. package/routes/dataset.js +266 -0
  23. package/routes/dsdata.js +127 -0
  24. package/routes/gdc.maf.js +120 -0
  25. package/routes/gdc.mafBuild.js +106 -0
  26. package/routes/gdc.topMutatedGenes.js +465 -0
  27. package/routes/gene2canonicalisoform.js +41 -0
  28. package/routes/genelookup.js +52 -0
  29. package/routes/genomes.js +144 -0
  30. package/routes/healthcheck.js +30 -0
  31. package/routes/hicdata.js +98 -0
  32. package/routes/hicstat.js +55 -0
  33. package/routes/isoformlst.js +57 -0
  34. package/routes/ntseq.js +43 -0
  35. package/routes/pdomain.js +61 -0
  36. package/routes/snp.js +107 -0
  37. package/routes/termdb.categories.js +209 -0
  38. package/routes/termdb.cluster.js +228 -0
  39. package/routes/termdb.cohort.summary.js +38 -0
  40. package/routes/termdb.cohorts.js +49 -0
  41. package/routes/termdb.config.js +202 -0
  42. package/routes/termdb.getdescrstats.js +102 -0
  43. package/routes/termdb.getnumericcategories.js +92 -0
  44. package/routes/termdb.getpercentile.js +108 -0
  45. package/routes/termdb.getrootterm.js +65 -0
  46. package/routes/termdb.gettermchildren.js +67 -0
  47. package/routes/termdb.singleSampleMutation.js +80 -0
  48. package/routes/termdb.singlecellData.js +46 -0
  49. package/routes/termdb.singlecellSamples.js +160 -0
  50. package/routes/termdb.termsbyids.js +59 -0
  51. package/routes/termdb.topVariablyExpressedGenes.js +171 -0
  52. package/routes/termdb.violin.js +77 -0
  53. package/src/app.js +41500 -0
  54. package/src/serverconfig.js +14 -8
  55. package/start.js +3 -3
  56. package/routes/README.md +0 -84
  57. package/routes/burden.ts +0 -143
  58. package/routes/gdc.maf.ts +0 -195
  59. package/routes/gdc.mafBuild.ts +0 -114
  60. package/routes/gdc.topMutatedGenes.ts +0 -586
  61. package/routes/genelookup.ts +0 -50
  62. package/routes/healthcheck.ts +0 -29
  63. package/routes/hicdata.ts +0 -111
  64. package/routes/hicstat.ts +0 -55
  65. package/routes/termdb.categories.ts +0 -245
  66. package/routes/termdb.cluster.ts +0 -248
  67. package/routes/termdb.getdescrstats.ts +0 -102
  68. package/routes/termdb.getnumericcategories.ts +0 -99
  69. package/routes/termdb.getpercentile.ts +0 -118
  70. package/routes/termdb.getrootterm.ts +0 -73
  71. package/routes/termdb.gettermchildren.ts +0 -82
  72. package/routes/termdb.singleSampleMutation.ts +0 -87
  73. package/routes/termdb.singlecellData.ts +0 -49
  74. package/routes/termdb.singlecellSamples.ts +0 -175
  75. package/routes/termdb.termsbyids.ts +0 -63
  76. package/routes/termdb.topVariablyExpressedGenes.ts +0 -214
  77. package/routes/termdb.violin.ts +0 -77
  78. package/server.js +0 -2
  79. package/server.js.map +0 -1
  80. package/shared/common.js +0 -1080
  81. package/shared/termdb.initbinconfig.js +0 -96
  82. package/shared/vcf.js +0 -629
package/genome/mm10.js CHANGED
@@ -1,70 +1,138 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.default = {
4
- species: 'mouse',
5
- genomefile: 'genomes/mm10.gz',
6
- genedb: {
7
- dbfile: 'anno/genes.mm10.db'
1
+ var mm10_default = {
2
+ species: "mouse",
3
+ genomefile: "genomes/mm10.gz",
4
+ genedb: {
5
+ dbfile: "anno/genes.mm10.db"
6
+ },
7
+ tracks: [
8
+ {
9
+ __isgene: true,
10
+ // only for initialization
11
+ translatecoding: true,
12
+ file: "anno/refGene.mm10.gz",
13
+ type: "bedj",
14
+ name: "RefGene",
15
+ stackheight: 16,
16
+ stackspace: 1,
17
+ vpad: 4,
18
+ color: "#1D591D"
8
19
  },
9
- tracks: [
10
- {
11
- __isgene: true,
12
- translatecoding: true,
13
- file: 'anno/refGene.mm10.gz',
14
- type: 'bedj',
15
- name: 'RefGene',
16
- stackheight: 16,
17
- stackspace: 1,
18
- vpad: 4,
19
- color: '#1D591D'
20
- },
21
- {
22
- type: 'bedj',
23
- name: 'RepeatMasker',
24
- stackheight: 14,
25
- file: 'anno/rmsk.mm10.gz',
26
- onerow: true,
27
- categories: {
28
- SINE: { color: '#ED8C8E', label: 'SINE' },
29
- LINE: { color: '#EDCB8C', label: 'LINE' },
30
- LTR: { color: '#E38CED', label: 'LTR' },
31
- DNA: { color: '#8C8EED', label: 'DNA transposon' },
32
- simple: { color: '#8EB88C', label: 'Simple repeats' },
33
- low_complexity: { color: '#ACEBA9', label: 'Low complexity' },
34
- satellite: { color: '#B59A84', label: 'Satellite' },
35
- RNA: { color: '#9DE0E0', label: 'RNA repeat' },
36
- other: { color: '#9BADC2', label: 'Other' },
37
- unknown: { color: '#858585', label: 'Unknown' }
38
- }
39
- }
40
- ],
41
- defaultcoord: {
42
- chr: 'chr12',
43
- start: 56694342,
44
- stop: 56713689
20
+ {
21
+ type: "bedj",
22
+ name: "RepeatMasker",
23
+ stackheight: 14,
24
+ file: "anno/rmsk.mm10.gz",
25
+ onerow: true,
26
+ categories: {
27
+ SINE: { color: "#ED8C8E", label: "SINE" },
28
+ LINE: { color: "#EDCB8C", label: "LINE" },
29
+ LTR: { color: "#E38CED", label: "LTR" },
30
+ DNA: { color: "#8C8EED", label: "DNA transposon" },
31
+ simple: { color: "#8EB88C", label: "Simple repeats" },
32
+ low_complexity: { color: "#ACEBA9", label: "Low complexity" },
33
+ satellite: { color: "#B59A84", label: "Satellite" },
34
+ RNA: { color: "#9DE0E0", label: "RNA repeat" },
35
+ other: { color: "#9BADC2", label: "Other" },
36
+ unknown: { color: "#858585", label: "Unknown" }
37
+ }
38
+ }
39
+ ],
40
+ defaultcoord: {
41
+ chr: "chr12",
42
+ start: 56694342,
43
+ stop: 56713689
44
+ },
45
+ hicenzymefragment: [
46
+ {
47
+ enzyme: "DpnII",
48
+ file: "anno/hicFragment/hic.DpnII.mm10.gz"
45
49
  },
46
- hicenzymefragment: [
47
- {
48
- enzyme: 'DpnII',
49
- file: 'anno/hicFragment/hic.DpnII.mm10.gz'
50
- },
51
- {
52
- enzyme: 'EcoRI',
53
- file: 'anno/hicFragment/hic.EcoRI.mm10.gz'
54
- },
55
- {
56
- enzyme: 'HindIII',
57
- file: 'anno/hicFragment/hic.HindIII.mm10.gz'
58
- },
59
- {
60
- enzyme: 'MboI',
61
- file: 'anno/hicFragment/hic.MboI.mm10.gz'
62
- },
63
- {
64
- enzyme: 'NcoI',
65
- file: 'anno/hicFragment/hic.NcoI.mm10.gz'
66
- }
67
- ],
68
- majorchr: "\nchr1\t195471971\nchr2\t182113224" /* pragma: allowlist secret */ + "\nchrX\t171031299\nchr3\t160039680\nchr4\t156508116\nchr5\t151834684\nchr6\t149736546\nchr7\t145441459\nchr10\t130694993\nchr8\t129401213\nchr14\t124902244\nchr9\t124595110\nchr11\t122082543\nchr13\t120421639\nchr12\t120129022\nchr15\t104043685\nchr16\t98207768\nchr17\t94987271\nchrY\t91744698\nchr18\t90702639\nchr19\t61431566\nchrM\t16299",
69
- minorchr: "\nchr5_JH584299_random\t953012\nchrX_GL456233_random\t336933\nchrY_JH584301_random\t259875\nchr1_GL456211_random\t241735\nchr4_GL456350_random\t227966\nchr4_JH584293_random\t207968\nchr1_GL456221_random\t206961\nchr5_JH584297_random\t205776\nchr5_JH584296_random\t199368\nchr5_GL456354_random\t195993\nchr4_JH584294_random\t191905\nchr5_JH584298_random\t184189\nchrY_JH584300_random\t182347\nchr7_GL456219_random\t175968\nchr1_GL456210_random\t169725\nchrY_JH584303_random\t158099\nchrY_JH584302_random\t155838\nchr1_GL456212_random\t153618\nchrUn_JH584304\t114452\nchrUn_GL456379\t72385\nchr4_GL456216_random\t66673\nchrUn_GL456393\t55711\nchrUn_GL456366\t47073\nchrUn_GL456367\t42057\nchrUn_GL456239\t40056\nchr1_GL456213_random\t39340\nchrUn_GL456383\t38659\nchrUn_GL456385\t35240\nchrUn_GL456360\t31704\nchrUn_GL456378\t31602\nchrUn_GL456389\t28772\nchrUn_GL456372\t28664\nchrUn_GL456370\t26764\nchrUn_GL456381\t25871\nchrUn_GL456387\t24685\nchrUn_GL456390\t24668\nchrUn_GL456394\t24323\nchrUn_GL456392\t23629\nchrUn_GL456382\t23158\nchrUn_GL456359\t22974\nchrUn_GL456396\t21240\nchrUn_GL456368\t20208\nchr4_JH584292_random\t14945\nchr4_JH584295_random\t1976"
50
+ {
51
+ enzyme: "EcoRI",
52
+ file: "anno/hicFragment/hic.EcoRI.mm10.gz"
53
+ },
54
+ {
55
+ enzyme: "HindIII",
56
+ file: "anno/hicFragment/hic.HindIII.mm10.gz"
57
+ },
58
+ {
59
+ enzyme: "MboI",
60
+ file: "anno/hicFragment/hic.MboI.mm10.gz"
61
+ },
62
+ {
63
+ enzyme: "NcoI",
64
+ file: "anno/hicFragment/hic.NcoI.mm10.gz"
65
+ }
66
+ ],
67
+ majorchr: `
68
+ chr1 195471971
69
+ chr2 182113224
70
+ chrX 171031299
71
+ chr3 160039680
72
+ chr4 156508116
73
+ chr5 151834684
74
+ chr6 149736546
75
+ chr7 145441459
76
+ chr10 130694993
77
+ chr8 129401213
78
+ chr14 124902244
79
+ chr9 124595110
80
+ chr11 122082543
81
+ chr13 120421639
82
+ chr12 120129022
83
+ chr15 104043685
84
+ chr16 98207768
85
+ chr17 94987271
86
+ chrY 91744698
87
+ chr18 90702639
88
+ chr19 61431566
89
+ chrM 16299`,
90
+ minorchr: `
91
+ chr5_JH584299_random 953012
92
+ chrX_GL456233_random 336933
93
+ chrY_JH584301_random 259875
94
+ chr1_GL456211_random 241735
95
+ chr4_GL456350_random 227966
96
+ chr4_JH584293_random 207968
97
+ chr1_GL456221_random 206961
98
+ chr5_JH584297_random 205776
99
+ chr5_JH584296_random 199368
100
+ chr5_GL456354_random 195993
101
+ chr4_JH584294_random 191905
102
+ chr5_JH584298_random 184189
103
+ chrY_JH584300_random 182347
104
+ chr7_GL456219_random 175968
105
+ chr1_GL456210_random 169725
106
+ chrY_JH584303_random 158099
107
+ chrY_JH584302_random 155838
108
+ chr1_GL456212_random 153618
109
+ chrUn_JH584304 114452
110
+ chrUn_GL456379 72385
111
+ chr4_GL456216_random 66673
112
+ chrUn_GL456393 55711
113
+ chrUn_GL456366 47073
114
+ chrUn_GL456367 42057
115
+ chrUn_GL456239 40056
116
+ chr1_GL456213_random 39340
117
+ chrUn_GL456383 38659
118
+ chrUn_GL456385 35240
119
+ chrUn_GL456360 31704
120
+ chrUn_GL456378 31602
121
+ chrUn_GL456389 28772
122
+ chrUn_GL456372 28664
123
+ chrUn_GL456370 26764
124
+ chrUn_GL456381 25871
125
+ chrUn_GL456387 24685
126
+ chrUn_GL456390 24668
127
+ chrUn_GL456394 24323
128
+ chrUn_GL456392 23629
129
+ chrUn_GL456382 23158
130
+ chrUn_GL456359 22974
131
+ chrUn_GL456396 21240
132
+ chrUn_GL456368 20208
133
+ chr4_JH584292_random 14945
134
+ chr4_JH584295_random 1976`
135
+ };
136
+ export {
137
+ mm10_default as default
70
138
  };
package/genome/mm9.js CHANGED
@@ -1,82 +1,119 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.default = {
4
- species: 'mouse',
5
- genomefile: 'genomes/mm9.gz',
6
- genedb: {
7
- dbfile: 'anno/genes.mm9.db'
1
+ var mm9_default = {
2
+ species: "mouse",
3
+ genomefile: "genomes/mm9.gz",
4
+ genedb: {
5
+ dbfile: "anno/genes.mm9.db"
6
+ },
7
+ tracks: [
8
+ {
9
+ __isgene: true,
10
+ translatecoding: true,
11
+ file: "anno/refGene.mm9.gz",
12
+ type: "bedj",
13
+ name: "RefGene",
14
+ stackheight: 16,
15
+ stackspace: 1,
16
+ vpad: 4,
17
+ color: "#1D591D"
8
18
  },
9
- tracks: [
10
- {
11
- __isgene: true,
12
- translatecoding: true,
13
- file: 'anno/refGene.mm9.gz',
14
- type: 'bedj',
15
- name: 'RefGene',
16
- stackheight: 16,
17
- stackspace: 1,
18
- vpad: 4,
19
- color: '#1D591D'
20
- },
21
- {
22
- __isgene: true,
23
- translatecoding: true,
24
- file: 'anno/gencode.vM9.mm9.gz',
25
- type: 'bedj',
26
- name: 'GENCODE M9',
27
- stackheight: 16,
28
- stackspace: 1,
29
- vpad: 4,
30
- color: '#375E80'
31
- },
32
- {
33
- type: 'bedj',
34
- name: 'RepeatMasker',
35
- stackheight: 14,
36
- file: 'anno/rmsk.mm9.gz',
37
- onerow: true,
38
- categories: {
39
- SINE: { color: '#ED8C8E', label: 'SINE' },
40
- LINE: { color: '#EDCB8C', label: 'LINE' },
41
- LTR: { color: '#E38CED', label: 'LTR' },
42
- DNA: { color: '#8C8EED', label: 'DNA transposon' },
43
- simple: { color: '#8EB88C', label: 'Simple repeats' },
44
- low_complexity: { color: '#ACEBA9', label: 'Low complexity' },
45
- satellite: { color: '#B59A84', label: 'Satellite' },
46
- RNA: { color: '#9DE0E0', label: 'RNA repeat' },
47
- other: { color: '#9BADC2', label: 'Other' },
48
- unknown: { color: '#858585', label: 'Unknown' }
49
- }
50
- }
51
- ],
52
- defaultcoord: {
53
- chr: 'chr12',
54
- start: 57795963,
55
- stop: 57815592,
56
- gene: 'Pax9'
19
+ {
20
+ __isgene: true,
21
+ translatecoding: true,
22
+ file: "anno/gencode.vM9.mm9.gz",
23
+ type: "bedj",
24
+ name: "GENCODE M9",
25
+ stackheight: 16,
26
+ stackspace: 1,
27
+ vpad: 4,
28
+ color: "#375E80"
57
29
  },
58
- hicenzymefragment: [
59
- {
60
- enzyme: 'DpnII',
61
- file: 'anno/hicFragment/hic.DpnII.mm9.gz'
62
- },
63
- {
64
- enzyme: 'EcoRI',
65
- file: 'anno/hicFragment/hic.EcoRI.mm9.gz'
66
- },
67
- {
68
- enzyme: 'HindIII',
69
- file: 'anno/hicFragment/hic.HindIII.mm9.gz'
70
- },
71
- {
72
- enzyme: 'MboI',
73
- file: 'anno/hicFragment/hic.MboI.mm9.gz'
74
- },
75
- {
76
- enzyme: 'NcoI',
77
- file: 'anno/hicFragment/hic.NcoI.mm9.gz'
78
- }
79
- ],
80
- majorchr: "\nchr1\t197195432\nchr2\t181748087\nchr3\t159599783\nchr4\t155630120\nchr5\t152537259\nchr6\t149517037\nchr7\t152524553\nchr8\t131738871\nchr9\t124076172\nchr10\t129993255\nchr11\t121843856\nchr12\t121257530\nchr13\t120284312\nchr14\t125194864\nchr15\t103494974\nchr16\t98319150\nchr17\t95272651\nchr18\t90772031\nchr19\t61342430\nchrX\t166650296\nchrY\t15902555\nchrM\t16299",
81
- minorchr: "\nchr13_random\t400311\nchr16_random\t3994\nchr17_random\t628739\nchr1_random\t1231697\nchr3_random\t41899\nchr4_random\t160594\nchr5_random\t357350\nchr7_random\t362490\nchr8_random\t849593\nchr9_random\t449403\nchrUn_random\t5900358\nchrX_random\t1785075\nchrY_random\t58682461\n"
30
+ {
31
+ type: "bedj",
32
+ name: "RepeatMasker",
33
+ stackheight: 14,
34
+ file: "anno/rmsk.mm9.gz",
35
+ onerow: true,
36
+ categories: {
37
+ SINE: { color: "#ED8C8E", label: "SINE" },
38
+ LINE: { color: "#EDCB8C", label: "LINE" },
39
+ LTR: { color: "#E38CED", label: "LTR" },
40
+ DNA: { color: "#8C8EED", label: "DNA transposon" },
41
+ simple: { color: "#8EB88C", label: "Simple repeats" },
42
+ low_complexity: { color: "#ACEBA9", label: "Low complexity" },
43
+ satellite: { color: "#B59A84", label: "Satellite" },
44
+ RNA: { color: "#9DE0E0", label: "RNA repeat" },
45
+ other: { color: "#9BADC2", label: "Other" },
46
+ unknown: { color: "#858585", label: "Unknown" }
47
+ }
48
+ }
49
+ ],
50
+ defaultcoord: {
51
+ chr: "chr12",
52
+ start: 57795963,
53
+ stop: 57815592,
54
+ gene: "Pax9"
55
+ },
56
+ hicenzymefragment: [
57
+ {
58
+ enzyme: "DpnII",
59
+ file: "anno/hicFragment/hic.DpnII.mm9.gz"
60
+ },
61
+ {
62
+ enzyme: "EcoRI",
63
+ file: "anno/hicFragment/hic.EcoRI.mm9.gz"
64
+ },
65
+ {
66
+ enzyme: "HindIII",
67
+ file: "anno/hicFragment/hic.HindIII.mm9.gz"
68
+ },
69
+ {
70
+ enzyme: "MboI",
71
+ file: "anno/hicFragment/hic.MboI.mm9.gz"
72
+ },
73
+ {
74
+ enzyme: "NcoI",
75
+ file: "anno/hicFragment/hic.NcoI.mm9.gz"
76
+ }
77
+ ],
78
+ majorchr: `
79
+ chr1 197195432
80
+ chr2 181748087
81
+ chr3 159599783
82
+ chr4 155630120
83
+ chr5 152537259
84
+ chr6 149517037
85
+ chr7 152524553
86
+ chr8 131738871
87
+ chr9 124076172
88
+ chr10 129993255
89
+ chr11 121843856
90
+ chr12 121257530
91
+ chr13 120284312
92
+ chr14 125194864
93
+ chr15 103494974
94
+ chr16 98319150
95
+ chr17 95272651
96
+ chr18 90772031
97
+ chr19 61342430
98
+ chrX 166650296
99
+ chrY 15902555
100
+ chrM 16299`,
101
+ minorchr: `
102
+ chr13_random 400311
103
+ chr16_random 3994
104
+ chr17_random 628739
105
+ chr1_random 1231697
106
+ chr3_random 41899
107
+ chr4_random 160594
108
+ chr5_random 357350
109
+ chr7_random 362490
110
+ chr8_random 849593
111
+ chr9_random 449403
112
+ chrUn_random 5900358
113
+ chrX_random 1785075
114
+ chrY_random 58682461
115
+ `
116
+ };
117
+ export {
118
+ mm9_default as default
82
119
  };