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fix: fix gene definition files to make reference allele be first
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- also update expected CFTR reference allele name
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@whaleyr
whaleyr committed Dec 10, 2020
1 parent 1195d4b commit 0951f57
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Showing 4 changed files with 110 additions and 110 deletions.
92 changes: 46 additions & 46 deletions src/main/resources/org/pharmgkb/pharmcat/definition/alleles/CFTR_translation.json
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"formatVersion": 1,
"modificationDate": "2020-12-08T21:17:58.468Z",
"modificationDate": "2020-12-09T23:49:03.918Z",
"gene": "CFTR",
"chromosome": "chr7",
"genomeBuild": "b38",
Expand Down Expand Up @@ -642,6 +642,51 @@
]
],
"namedAlleles": [
{
"name": "ivacaftor non-responsive CFTR sequence",
"id": "261572",
"alleles": [
"G",
"C",
"C",
"G",
"C",
"C",
"G",
"G",
"G",
"A",
"T",
"G",
"G",
"C",
"A",
"G",
"T",
"G",
"G",
"A",
"G",
"G",
"C",
"C",
"A",
"T",
"A",
"G",
"G",
"C",
"G",
"T",
"G",
"C",
"G",
"G",
"T",
"G",
"G"
]
},
{
"name": "2789+5G->A",
"id": "261574",
Expand Down Expand Up @@ -2396,51 +2441,6 @@
null,
null
]
},
{
"name": "ivacaftor non-responsive CFTR sequence",
"id": "261572",
"alleles": [
"G",
"C",
"C",
"G",
"C",
"C",
"G",
"G",
"G",
"A",
"T",
"G",
"G",
"C",
"A",
"G",
"T",
"G",
"G",
"A",
"G",
"G",
"C",
"C",
"A",
"T",
"A",
"G",
"G",
"C",
"G",
"T",
"G",
"C",
"G",
"G",
"T",
"G",
"G"
]
}
]
}
48 changes: 24 additions & 24 deletions src/main/resources/org/pharmgkb/pharmcat/definition/alleles/NUDT15_translation.json
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"formatVersion": 1,
"modificationDate": "2020-12-08T21:17:58.915Z",
"modificationDate": "2020-12-09T23:49:04.141Z",
"gene": "NUDT15",
"chromosome": "chr13",
"genomeBuild": "b38",
Expand All @@ -13,18 +13,6 @@
"rs554405994 was merged into rs869320766 which was merged into rs746071566"
],
"variants": [
{
"chromosome": "chr13",
"position": 48037801,
"rsid": "rs746071566",
"chromosomeHgvsName": "g.48037801_48037802insGAGTCG",
"geneHgvsName": "g.5235_5326insGAGTCG",
"proteinNote": "V18_V19insGV",
"resourceNote": "55_56insGAGTCG",
"type": "INS",
"referenceRepeat": null,
"sequenceLocationId": 263279
},
{
"chromosome": "chr13",
"position": 48037748,
Expand Down Expand Up @@ -73,6 +61,18 @@
"referenceRepeat": null,
"sequenceLocationId": 263278
},
{
"chromosome": "chr13",
"position": 48037801,
"rsid": "rs746071566",
"chromosomeHgvsName": "g.48037801_48037802insGAGTCG",
"geneHgvsName": "g.5235_5326insGAGTCG",
"proteinNote": "V18_V19insGV",
"resourceNote": "55_56insGAGTCG",
"type": "INS",
"referenceRepeat": null,
"sequenceLocationId": 263279
},
{
"chromosome": "chr13",
"position": 48037826,
Expand Down Expand Up @@ -243,10 +243,6 @@
}
],
"variantAlleles": [
[
"del",
"insGAGTCG"
],
[
"C",
"T"
Expand All @@ -263,6 +259,10 @@
"A",
"G"
],
[
"del",
"insGAGTCG"
],
[
"del",
"insCGGG"
Expand Down Expand Up @@ -325,12 +325,12 @@
"name": "*1",
"id": "263294",
"alleles": [
"del",
"T",
"G",
"GGAGTC",
"G",
"del",
"del",
"C",
"G",
"A",
Expand All @@ -350,7 +350,6 @@
"name": "*10",
"id": "263312",
"alleles": [
null,
"C",
null,
null,
Expand All @@ -368,6 +367,7 @@
null,
null,
null,
null,
null
]
},
Expand Down Expand Up @@ -575,7 +575,6 @@
"name": "*19",
"id": "263330",
"alleles": [
null,
null,
"C",
null,
Expand All @@ -593,18 +592,19 @@
null,
null,
null,
null,
null
]
},
{
"name": "*2",
"id": "263296",
"alleles": [
"insGAGTCG",
null,
null,
null,
null,
"insGAGTCG",
null,
null,
null,
Expand Down Expand Up @@ -703,7 +703,6 @@
null,
null,
null,
null,
"A",
null,
null,
Expand All @@ -718,18 +717,19 @@
null,
null,
null,
null,
null
]
},
{
"name": "*6",
"id": "263304",
"alleles": [
"insGAGTCG",
null,
null,
null,
null,
"insGAGTCG",
null,
null,
null,
Expand Down Expand Up @@ -800,7 +800,6 @@
"name": "*9",
"id": "263310",
"alleles": [
null,
null,
null,
"delGGAGTC",
Expand All @@ -818,6 +817,7 @@
null,
null,
null,
null,
null
]
}
Expand Down
72 changes: 36 additions & 36 deletions src/main/resources/org/pharmgkb/pharmcat/definition/alleles/SLCO1B1_translation.json
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"formatVersion": 1,
"modificationDate": "2020-12-08T21:17:58.950Z",
"modificationDate": "2020-12-09T23:49:04.161Z",
"gene": "SLCO1B1",
"chromosome": "chr12",
"genomeBuild": "b38",
Expand Down Expand Up @@ -482,6 +482,41 @@
]
],
"namedAlleles": [
{
"name": "*1A",
"id": "263505",
"alleles": [
"G",
"C",
"G",
"T",
"T",
"A",
"G",
"A",
"C",
"A",
"T",
"T",
"T",
"C",
"A",
"A",
"G",
"T",
"T",
"C",
"A",
"G",
"A",
"G",
"A",
"A",
"A",
"C",
"C"
]
},
{
"name": "*10",
"id": "263525",
Expand Down Expand Up @@ -832,41 +867,6 @@
null
]
},
{
"name": "*1A",
"id": "263505",
"alleles": [
"G",
"C",
"G",
"T",
"T",
"A",
"G",
"A",
"C",
"A",
"T",
"T",
"T",
"C",
"A",
"A",
"G",
"T",
"T",
"C",
"A",
"G",
"A",
"G",
"A",
"A",
"A",
"C",
"C"
]
},
{
"name": "*1B",
"id": "263507",
Expand Down
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