Mercurial > repos > bgruening > pharmcat
diff test-data/test_2.json @ 1:891283e0ee89 draft default tip
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
| author | bgruening |
|---|---|
| date | Thu, 05 May 2022 20:27:17 +0000 |
| parents | d67642a21a1d |
| children |
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--- a/test-data/test_2.json Fri Jan 28 21:18:23 2022 +0000 +++ b/test-data/test_2.json Thu May 05 20:27:17 2022 +0000 @@ -3,11 +3,50 @@ "namedAlleleMatcherVersion": "1.0.0", "genomeBuild": "GRCh38.p13", "inputFilename": "input.vcf", - "timestamp": "Jan 27, 2022, 11:53:07 PM" + "timestamp": "May 4, 2022, 8:57:03 PM" }, "results": [ { - "alleleDefinitionVersion": "01/10/22", + "alleleDefinitionVersion": "04/20/22", + "chromosome": "chr4", + "gene": "ABCG2", + "diplotypes": [], + "haplotypes": [], + "phased": true, + "variants": [], + "variantsOfInterest": [], + "matchData": { + "missingPositions": [ + { + "chromosome": "chr4", + "position": 88131171, + "cpicPosition": 88131171, + "rsid": "rs2231142", + "chromosomeHgvsName": "g.88131171G\u003eT", + "cpicAlleles": [ + "G", + "T" + ], + "cpicToVcfAlleleMap": { + "T": "T", + "G": "G" + }, + "ref": "G", + "alts": [ + "T" + ] + } + ], + "mismatchedAlleles": [] + }, + "uncallableHaplotypes": [ + "rs2231142 variant (T)", + "rs2231142 reference (G)" + ], + "ignoredHaplotypes": [] + }, + { + "alleleDefinitionVersion": "04/20/22", "chromosome": "chr1", "gene": "CACNA1S", "diplotypes": [ @@ -58,7 +97,7 @@ "ignoredHaplotypes": [] }, { - "alleleDefinitionVersion": "01/10/22", + "alleleDefinitionVersion": "04/20/22", "chromosome": "chr7", "gene": "CFTR", "diplotypes": [ @@ -294,7 +333,7 @@ "ignoredHaplotypes": [] }, { - "alleleDefinitionVersion": "01/10/22", + "alleleDefinitionVersion": "04/20/22", "chromosome": "chr19", "gene": "CYP2B6", "diplotypes": [ @@ -510,7 +549,7 @@ "ignoredHaplotypes": [] }, { - "alleleDefinitionVersion": "01/10/22", + "alleleDefinitionVersion": "04/20/22", "chromosome": "chr10", "gene": "CYP2C19", "diplotypes": [ @@ -721,7 +760,7 @@ "ignoredHaplotypes": [] }, { - "alleleDefinitionVersion": "01/10/22", + "alleleDefinitionVersion": "04/20/22", "chromosome": "chr10", "gene": "CYP2C9", "diplotypes": [ @@ -1094,6 +1133,101 @@ "missingPositions": [ { "chromosome": "chr10", + "position": 94938719, + "cpicPosition": 94938719, + "rsid": null, + "chromosomeHgvsName": "g.94938719T\u003eG", + "cpicAlleles": [ + "G", + "T" + ], + "cpicToVcfAlleleMap": { + "T": "T", + "G": "G" + }, + "ref": "T", + "alts": [ + "G" + ] + }, + { + "chromosome": "chr10", + "position": 94938788, + "cpicPosition": 94938788, + "rsid": null, + "chromosomeHgvsName": "g.94938788C\u003eT", + "cpicAlleles": [ + "C", + "T" + ], + "cpicToVcfAlleleMap": { + "C": "C", + "T": "T" + }, + "ref": "C", + "alts": [ + "T" + ] + }, + { + "chromosome": "chr10", + "position": 94938800, + "cpicPosition": 94938800, + "rsid": "rs1364419386", + "chromosomeHgvsName": "g.94938800G\u003eA", + "cpicAlleles": [ + "A", + "G" + ], + "cpicToVcfAlleleMap": { + "A": "A", + "G": "G" + }, + "ref": "G", + "alts": [ + "A" + ] + }, + { + "chromosome": "chr10", + "position": 94941975, + "cpicPosition": 94941975, + "rsid": null, + "chromosomeHgvsName": "g.94941975G\u003eA", + "cpicAlleles": [ + "A", + "G" + ], + "cpicToVcfAlleleMap": { + "A": "A", + "G": "G" + }, + "ref": "G", + "alts": [ + "A" + ] + }, + { + "chromosome": "chr10", + "position": 94942243, + "cpicPosition": 94942243, + "rsid": "rs1375956433", + "chromosomeHgvsName": "g.94942243T\u003eG", + "cpicAlleles": [ + "G", + "T" + ], + "cpicToVcfAlleleMap": { + "T": "T", + "G": "G" + }, + "ref": "T", + "alts": [ + "G" + ] + }, + { + "chromosome": "chr10", "position": 94942306, "cpicPosition": 94942306, "rsid": "rs1289704600", @@ -1151,6 +1285,82 @@ }, { "chromosome": "chr10", + "position": 94949145, + "cpicPosition": 94949145, + "rsid": "rs772782449", + "chromosomeHgvsName": "g.94949145C\u003eT", + "cpicAlleles": [ + "C", + "T" + ], + "cpicToVcfAlleleMap": { + "C": "C", + "T": "T" + }, + "ref": "C", + "alts": [ + "T" + ] + }, + { + "chromosome": "chr10", + "position": 94949161, + "cpicPosition": 94949163, + "rsid": null, + "chromosomeHgvsName": "g.94949163del", + "cpicAlleles": [ + "T", + "delT" + ], + "cpicToVcfAlleleMap": { + "T": "AT", + "delT": "A" + }, + "ref": "AT", + "alts": [ + "A" + ] + }, + { + "chromosome": "chr10", + "position": 94972183, + "cpicPosition": 94972183, + "rsid": null, + "chromosomeHgvsName": "g.94972183A\u003eT", + "cpicAlleles": [ + "A", + "T" + ], + "cpicToVcfAlleleMap": { + "A": "A", + "T": "T" + }, + "ref": "A", + "alts": [ + "T" + ] + }, + { + "chromosome": "chr10", + "position": 94981258, + "cpicPosition": 94981258, + "rsid": "rs1297714792", + "chromosomeHgvsName": "g.94981258C\u003eT", + "cpicAlleles": [ + "C", + "T" + ], + "cpicToVcfAlleleMap": { + "C": "C", + "T": "T" + }, + "ref": "C", + "alts": [ + "T" + ] + }, + { + "chromosome": "chr10", "position": 94986136, "cpicPosition": 94986136, "rsid": "rs1254213342", @@ -1167,20 +1377,49 @@ "alts": [ "C" ] + }, + { + "chromosome": "chr10", + "position": 94986174, + "cpicPosition": 94986174, + "rsid": "rs1441296358", + "chromosomeHgvsName": "g.94986174G\u003eC", + "cpicAlleles": [ + "C", + "G" + ], + "cpicToVcfAlleleMap": { + "C": "C", + "G": "G" + }, + "ref": "G", + "alts": [ + "C" + ] } ], "mismatchedAlleles": [] }, "uncallableHaplotypes": [ + "*80", + "*81", + "*82", "*72", + "*83", "*73", + "*84", "*74", - "*75" + "*85", + "*75", + "*76", + "*77", + "*78", + "*79" ], "ignoredHaplotypes": [] }, { - "alleleDefinitionVersion": "01/10/22", + "alleleDefinitionVersion": "04/20/22", "chromosome": "chr7", "gene": "CYP3A5", "diplotypes": [ @@ -1189,34 +1428,29 @@ "haplotype1": { "name": "*1", "sequences": [ - "99652613:G;99652770:T;99660516:C;99665212:C;99665237:T;99666950:A;99672916:T;99676198:G;" + "99652770:T;99660516:C;99665212:C;99672916:T;99676198:G;" ] }, "haplotype2": { "name": "*1", "sequences": [ - "99652613:G;99652770:T;99660516:C;99665212:C;99665237:T;99666950:A;99672916:T;99676198:G;" + "99652770:T;99660516:C;99665212:C;99672916:T;99676198:G;" ] }, - "score": 16 + "score": 10 } ], "haplotypes": [ { "name": "*1", "sequences": [ - "99652613:G;99652770:T;99660516:C;99665212:C;99665237:T;99666950:A;99672916:T;99676198:G;" + "99652770:T;99660516:C;99665212:C;99672916:T;99676198:G;" ] } ], "phased": true, "variants": [ { - "position": 99652613, - "rsid": "rs28365083", - "vcfCall": "G|G" - }, - { "position": 99652770, "rsid": "rs41303343", "vcfCall": "T|T" @@ -1232,16 +1466,6 @@ "vcfCall": "C|C" }, { - "position": 99665237, - "rsid": "rs56411402", - "vcfCall": "T|T" - }, - { - "position": 99666950, - "rsid": "rs55965422", - "vcfCall": "A|A" - }, - { "position": 99672916, "rsid": "rs776746", "vcfCall": "T|T" @@ -1261,7 +1485,7 @@ "ignoredHaplotypes": [] }, { - "alleleDefinitionVersion": "01/10/22", + "alleleDefinitionVersion": "04/20/22", "chromosome": "chr19", "gene": "CYP4F2", "diplotypes": [ @@ -1312,7 +1536,7 @@ "ignoredHaplotypes": [] }, { - "alleleDefinitionVersion": "01/10/22", + "alleleDefinitionVersion": "04/20/22", "chromosome": "chr1", "gene": "DPYD", "diplotypes": [ @@ -1768,7 +1992,7 @@ "ignoredHaplotypes": [] }, { - "alleleDefinitionVersion": "01/10/22", + "alleleDefinitionVersion": "04/20/22", "chromosome": "chr19", "gene": "IFNL3", "diplotypes": [ @@ -1814,7 +2038,7 @@ "ignoredHaplotypes": [] }, { - "alleleDefinitionVersion": "01/10/22", + "alleleDefinitionVersion": "04/20/22", "chromosome": "chr13", "gene": "NUDT15", "diplotypes": [ @@ -1940,7 +2164,7 @@ "ignoredHaplotypes": [] }, { - "alleleDefinitionVersion": "01/10/22", + "alleleDefinitionVersion": "04/20/22", "chromosome": "chr19", "gene": "RYR1", "diplotypes": [ @@ -2201,7 +2425,7 @@ "ignoredHaplotypes": [] }, { - "alleleDefinitionVersion": "01/10/22", + "alleleDefinitionVersion": "04/20/22", "chromosome": "chr12", "gene": "SLCO1B1", "diplotypes": [ @@ -2500,7 +2724,7 @@ "ignoredHaplotypes": [] }, { - "alleleDefinitionVersion": "01/10/22", + "alleleDefinitionVersion": "04/20/22", "chromosome": "chr6", "gene": "TPMT", "diplotypes": [ @@ -2756,7 +2980,7 @@ "ignoredHaplotypes": [] }, { - "alleleDefinitionVersion": "01/10/22", + "alleleDefinitionVersion": "04/20/22", "chromosome": "chr2", "gene": "UGT1A1", "diplotypes": [ @@ -2817,7 +3041,7 @@ "ignoredHaplotypes": [] }, { - "alleleDefinitionVersion": "01/10/22", + "alleleDefinitionVersion": "04/20/22", "chromosome": "chr16", "gene": "VKORC1", "diplotypes": [