@sjcrh/proteinpaint-server 2.16.0 → 2.18.0

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 (22) 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 +110 -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 +11 -7
  18. package/server.js +1 -1
  19. package/shared/common.js +4 -0
  20. package/src/serverconfig.js +10 -2
  21. package/utils/fastclust.R +16 -6
  22. package/genome/genome.sql +0 -54
package/genome/mm10.js CHANGED
@@ -1,135 +1,70 @@
1
- module.exports = {
2
- species: 'mouse',
3
- genomefile: 'genomes/mm10.gz',
4
- genedb: {
5
- dbfile: 'anno/genes.mm10.db'
6
- },
7
- tracks: [
8
- {
9
- __isgene: true, // only for initialization
10
- translatecoding: true,
11
- file: 'anno/refGene.mm10.gz',
12
- type: 'bedj',
13
- name: 'RefGene',
14
- stackheight: 16,
15
- stackspace: 1,
16
- vpad: 4,
17
- color: '#1D591D'
18
- },
19
- {
20
- type: 'bedj',
21
- name: 'RepeatMasker',
22
- stackheight: 14,
23
- file: 'anno/rmsk.mm10.gz',
24
- onerow: true,
25
- categories: {
26
- SINE: { color: '#ED8C8E', label: 'SINE' },
27
- LINE: { color: '#EDCB8C', label: 'LINE' },
28
- LTR: { color: '#E38CED', label: 'LTR' },
29
- DNA: { color: '#8C8EED', label: 'DNA transposon' },
30
- simple: { color: '#8EB88C', label: 'Simple repeats' },
31
- low_complexity: { color: '#ACEBA9', label: 'Low complexity' },
32
- satellite: { color: '#B59A84', label: 'Satellite' },
33
- RNA: { color: '#9DE0E0', label: 'RNA repeat' },
34
- other: { color: '#9BADC2', label: 'Other' },
35
- unknown: { color: '#858585', label: 'Unknown' }
36
- }
37
- }
38
- ],
39
- defaultcoord: {
40
- chr: 'chr12',
41
- start: 56694342,
42
- stop: 56713689
43
- },
44
- hicenzymefragment: [
45
- {
46
- enzyme: 'DpnII',
47
- file: 'anno/hicFragment/hic.DpnII.mm10.gz'
48
- },
49
- {
50
- enzyme: 'EcoRI',
51
- file: 'anno/hicFragment/hic.EcoRI.mm10.gz'
52
- },
53
- {
54
- enzyme: 'HindIII',
55
- file: 'anno/hicFragment/hic.HindIII.mm10.gz'
56
- },
57
- {
58
- enzyme: 'MboI',
59
- file: 'anno/hicFragment/hic.MboI.mm10.gz'
60
- },
61
- {
62
- enzyme: 'NcoI',
63
- file: 'anno/hicFragment/hic.NcoI.mm10.gz'
64
- }
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
- }
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'
8
+ },
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
45
+ },
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"
70
+ };
package/genome/mm9.js CHANGED
@@ -1,118 +1,82 @@
1
- module.exports = {
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'
18
- },
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'
29
- },
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
-
57
- hicenzymefragment: [
58
- {
59
- enzyme: 'DpnII',
60
- file: 'anno/hicFragment/hic.DpnII.mm9.gz'
61
- },
62
- {
63
- enzyme: 'EcoRI',
64
- file: 'anno/hicFragment/hic.EcoRI.mm9.gz'
65
- },
66
- {
67
- enzyme: 'HindIII',
68
- file: 'anno/hicFragment/hic.HindIII.mm9.gz'
69
- },
70
- {
71
- enzyme: 'MboI',
72
- file: 'anno/hicFragment/hic.MboI.mm9.gz'
73
- },
74
- {
75
- enzyme: 'NcoI',
76
- file: 'anno/hicFragment/hic.NcoI.mm9.gz'
77
- }
78
- ],
79
-
80
- majorchr: `
81
- chr1 197195432
82
- chr2 181748087
83
- chr3 159599783
84
- chr4 155630120
85
- chr5 152537259
86
- chr6 149517037
87
- chr7 152524553
88
- chr8 131738871
89
- chr9 124076172
90
- chr10 129993255
91
- chr11 121843856
92
- chr12 121257530
93
- chr13 120284312
94
- chr14 125194864
95
- chr15 103494974
96
- chr16 98319150
97
- chr17 95272651
98
- chr18 90772031
99
- chr19 61342430
100
- chrX 166650296
101
- chrY 15902555
102
- chrM 16299`,
103
- minorchr: `
104
- chr13_random 400311
105
- chr16_random 3994
106
- chr17_random 628739
107
- chr1_random 1231697
108
- chr3_random 41899
109
- chr4_random 160594
110
- chr5_random 357350
111
- chr7_random 362490
112
- chr8_random 849593
113
- chr9_random 449403
114
- chrUn_random 5900358
115
- chrX_random 1785075
116
- chrY_random 58682461
117
- `
118
- }
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'
8
+ },
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'
57
+ },
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"
82
+ };