@sjcrh/proteinpaint-server 2.43.3-0 → 2.46.0

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 (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 +32 -36
  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 +201 -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 +41498 -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/dm3.js CHANGED
@@ -1,47 +1,74 @@
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- "use strict";
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- Object.defineProperty(exports, "__esModule", { value: true });
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- exports.default = {
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- species: 'fruit fly',
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- genomefile: 'genomes/dm3.gz',
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- genedb: {
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- dbfile: 'anno/genes.dm3.db',
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+ var dm3_default = {
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+ species: "fruit fly",
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+ genomefile: "genomes/dm3.gz",
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+ genedb: {
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+ dbfile: "anno/genes.dm3.db"
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+ },
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+ tracks: [
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+ {
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+ __isgene: true,
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+ // only for initialization
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+ translatecoding: true,
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+ file: "anno/refGene.dm3.gz",
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+ type: "bedj",
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+ name: "RefGene",
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+ stackheight: 16,
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+ stackspace: 1,
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+ vpad: 4,
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+ color: "#1D591D"
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  },
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- tracks: [
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- {
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- __isgene: true,
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- translatecoding: true,
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- file: 'anno/refGene.dm3.gz',
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- type: 'bedj',
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- name: 'RefGene',
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- stackheight: 16,
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- stackspace: 1,
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- vpad: 4,
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- color: '#1D591D',
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- },
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- {
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- __isgene: true,
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- translatecoding: true,
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- file: 'anno/ensGene.dm3.gz',
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- type: 'bedj',
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- name: 'Ensembl genes',
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- stackheight: 16,
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- stackspace: 1,
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- vpad: 4,
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- color: '#004D99'
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- },
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- {
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- "type": "bedj",
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- "name": "RepeatMasker",
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- "stackheight": 14,
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- "file": "anno/rmsk.dm3.gz",
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- "onerow": true,
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- categories: { "LINE": { "color": "#EDCB8C", "label": "LINE" }, "LTR": { "color": "#E38CED", "label": "LTR" }, "DNA": { "color": "#8C8EED", "label": "DNA transposon" }, "simple": { "color": "#8EB88C", "label": "Simple repeats" }, "low_complexity": { "color": "#ACEBA9", "label": "Low complexity" }, "satellite": { "color": "#B59A84", "label": "Satellite" }, "RNA": { "color": "#9DE0E0", "label": "RNA repeat" }, "other": { "color": "#9BADC2", "label": "Other" }, "unknown": { "color": "#858585", "label": "Unknown" } }
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- }
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- ],
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- defaultcoord: {
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- chr: 'chr2L',
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- start: 6718954,
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- stop: 6723802,
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+ {
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+ __isgene: true,
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+ // only for initialization
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+ translatecoding: true,
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+ file: "anno/ensGene.dm3.gz",
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+ type: "bedj",
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+ name: "Ensembl genes",
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+ stackheight: 16,
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+ stackspace: 1,
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+ vpad: 4,
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+ color: "#004D99"
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  },
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- majorchr: "chr2L\t23011544\nchr2LHet\t368872\nchr2R\t21146708\nchr2RHet\t3288761\nchr3L\t24543557\nchr3LHet\t2555491\nchr3R\t27905053\nchr3RHet\t2517507\nchr4\t1351857\nchrU\t10049037\nchrUextra\t29004656\nchrX\t22422827\nchrXHet\t204112\nchrYHet\t347038\nchrM\t19517",
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+ {
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+ type: "bedj",
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+ name: "RepeatMasker",
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+ stackheight: 14,
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+ file: "anno/rmsk.dm3.gz",
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+ onerow: true,
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+ categories: {
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+ LINE: { color: "#EDCB8C", label: "LINE" },
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+ LTR: { color: "#E38CED", label: "LTR" },
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+ DNA: { color: "#8C8EED", label: "DNA transposon" },
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+ simple: { color: "#8EB88C", label: "Simple repeats" },
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+ low_complexity: { color: "#ACEBA9", label: "Low complexity" },
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+ satellite: { color: "#B59A84", label: "Satellite" },
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+ RNA: { color: "#9DE0E0", label: "RNA repeat" },
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+ other: { color: "#9BADC2", label: "Other" },
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+ unknown: { color: "#858585", label: "Unknown" }
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+ }
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+ }
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+ ],
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+ defaultcoord: {
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+ chr: "chr2L",
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+ start: 6718954,
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+ stop: 6723802
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+ },
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+ majorchr: `chr2L 23011544
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+ chr2LHet 368872
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+ chr2R 21146708
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+ chr2RHet 3288761
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+ chr3L 24543557
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+ chr3LHet 2555491
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+ chr3R 27905053
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+ chr3RHet 2517507
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+ chr4 1351857
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+ chrU 10049037
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+ chrUextra 29004656
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+ chrX 22422827
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+ chrXHet 204112
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+ chrYHet 347038
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+ chrM 19517`
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+ };
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+ export {
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+ dm3_default as default
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  };