Mercurial > repos > bgruening > pharmcat
diff test-data/test_1.pheno.json @ 0:d67642a21a1d draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
author | bgruening |
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date | Fri, 28 Jan 2022 21:18:23 +0000 |
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children | 891283e0ee89 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_1.pheno.json Fri Jan 28 21:18:23 2022 +0000 @@ -0,0 +1,6974 @@ +[ + { + "geneSymbol": "CACNA1S", + "chr": "chr1", + "phased": true, + "callSource": "MATCHER", + "uncalledHaplotypes": [], + "messages": [], + "relatedDrugs": [ + { + "name": "desflurane", + "guidelineId": "RxNorm:27340" + }, + { + "name": "enflurane", + "guidelineId": "RxNorm:3920" + }, + { + "name": "halothane", + "guidelineId": "RxNorm:5095" + }, + { + "name": "isoflurane", + "guidelineId": "RxNorm:6026" + }, + { + "name": "methoxyflurane", + "guidelineId": "RxNorm:6857" + }, + { + "name": "sevoflurane", + "guidelineId": "RxNorm:36453" + }, + { + "name": "succinylcholine", + "guidelineId": "RxNorm:10154" + } + ], + "matcherDiplotypes": [ + { + "allele1": { + "gene": "CACNA1S", + "name": "Reference", + "function": "Normal Function", + "reference": true + }, + "allele2": { + "gene": "CACNA1S", + "name": "Reference", + "function": "Normal Function", + 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"phased": true, + "wildtypeAllele": "A", + "mismatch": false + }, + { + "gene": "CYP2C9", + "chromosome": "chr10", + "position": 94988955, + "dbSnpId": "rs767284820", + "call": "T|T", + "alleles": [ + "*60" + ], + "phased": true, + "wildtypeAllele": "T", + "mismatch": false + }, + { + "gene": "CYP2C9", + "chromosome": "chr10", + "position": 94988984, + "dbSnpId": "rs781583846", + "call": "G|G", + "alleles": [ + "*30" + ], + "phased": true, + "wildtypeAllele": "G", + "mismatch": false + }, + { + "gene": "CYP2C9", + "chromosome": "chr10", + "position": 94989020, + "dbSnpId": "rs9332239", + "call": "C|C", + "alleles": [ + "*12", + "*71" + ], + "phased": true, + "wildtypeAllele": "C", + "mismatch": false + }, + { + "gene": "CYP2C9", + "chromosome": "chr10", + "position": 94989023, + "dbSnpId": "rs868182778", + "call": "G|G", + "alleles": [ + "*32" + ], + "phased": true, + "wildtypeAllele": "G", + "mismatch": false + }, + { + "gene": "CYP2C9", + "chromosome": "chr10", + "position": 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"mismatch": false + } + ], + "highlightedVariants": [] + }, + { + "geneSymbol": "CYP2D6", + "chr": null, + "phased": false, + "callSource": "OUTSIDE", + "uncalledHaplotypes": [], + "messages": [ + { + "rule_name": "CYP2D6 warning", + "version": "1", + "matches": { + "gene": "CYP2D6", + "hapsCalled": [], + "hapsMissing": [], + "variantsMissing": [], + "variant": "", + "dips": [], + "drugs": [] + }, + "exception_type": "note", + "message": "CYP2D6 genotypes are called by a separate algorithm from other genes in the PharmCAT report. Please refer to \u003ca href\u003d\"https://github.com/PharmGKB/PharmCAT/wiki/Determining-Alleles\"\u003ethe PharmCAT wiki\u003c/a\u003e for more information." + } + ], + "relatedDrugs": [ + { + "name": "amitriptyline", + "guidelineId": "RxNorm:704" + }, + { + "name": "atomoxetine", + "guidelineId": "RxNorm:38400" + }, + { + "name": "clomipramine", + "guidelineId": "RxNorm:2597" + }, + { + "name": "codeine", + "guidelineId": "RxNorm:2670" + }, + { + "name": "desipramine", + "guidelineId": "RxNorm:3247" + }, + { + "name": "doxepin", + "guidelineId": "RxNorm:3638" + }, + { + "name": "fluvoxamine", + "guidelineId": "RxNorm:42355" + }, + { + "name": "hydrocodone", + "guidelineId": "RxNorm:5489" + }, + { + "name": "imipramine", + "guidelineId": "RxNorm:5691" + }, + { + "name": "nortriptyline", + "guidelineId": "RxNorm:7531" + }, + { + "name": "ondansetron", + "guidelineId": "RxNorm:26225" + }, + { + "name": "paroxetine", + "guidelineId": "RxNorm:32937" + }, + { + "name": "tamoxifen", + "guidelineId": "RxNorm:10324" + }, + { + "name": "tramadol", + "guidelineId": "RxNorm:10689" + }, + { + "name": "trimipramine", + "guidelineId": "RxNorm:10834" + }, + { + "name": "tropisetron", + "guidelineId": "RxNorm:27392" + } + ], + "matcherDiplotypes": [ + { + "allele1": { + "gene": "CYP2D6", + "name": "*1", + "function": "Normal function", + "reference": true + }, + "allele2": { + "gene": "CYP2D6", + "name": "*3", + "function": "No function", + "reference": false + }, + "gene": "CYP2D6", + "phenotype": "Intermediate Metabolizer", + "variant": null, + "lookupKey": "1", + "label": "*1/*3" + } + ], + "diplotypes": [ + { + "allele1": { + "gene": "CYP2D6", + "name": "*1", + "function": "Normal function", + "reference": true + }, + "allele2": { + "gene": "CYP2D6", + "name": "*3", + "function": "No function", + "reference": false + }, + "gene": "CYP2D6", + "phenotype": "Intermediate Metabolizer", + "variant": null, + "lookupKey": "1", + "label": "*1/*3" + } + ], + "variants": [], + "variantsOfInterest": [], + "highlightedVariants": [] + }, + { + "geneSymbol": "CYP3A5", + "chr": "chr7", + "phased": true, + "callSource": "MATCHER", + "uncalledHaplotypes": [], + "messages": [ + { + "rule_name": "CYP3A5 reverse complement footnote", + "version": "1", + "matches": { + "gene": "CYP3A5", + "hapsCalled": [], + "hapsMissing": [], + "variantsMissing": [], + "variant": "", + "dips": [], + "drugs": [] + }, + "exception_type": "footnote", + "message": "The CYP3A5 gene is on the negative chromosomal strand, all genotype calls for CYP3A5 in this report refer to the positive chromosomal strand. 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"phased": true, + "wildtypeAllele": "G", + "mismatch": false + }, + { + "gene": "TPMT", + "chromosome": "chr6", + "position": 18149022, + "dbSnpId": "rs750424422", + "call": "C|C", + "alleles": [ + "*30" + ], + "phased": true, + "wildtypeAllele": "C", + "mismatch": false + }, + { + "gene": "TPMT", + "chromosome": "chr6", + "position": 18149032, + "dbSnpId": "rs759836180", + "call": "C|C", + "alleles": [ + "*42" + ], + "phased": true, + "wildtypeAllele": "C", + "mismatch": false + }, + { + "gene": "TPMT", + "chromosome": "chr6", + "position": 18149045, + "dbSnpId": "rs72552742", + "call": "T|T", + "alleles": [ + "*13" + ], + "phased": true, + "wildtypeAllele": "T", + "mismatch": false + }, + { + "gene": "TPMT", + "chromosome": "chr6", + "position": 18149126, + "dbSnpId": "rs267607275", + "call": "A|A", + "alleles": [ + "*29" + ], + "phased": true, + "wildtypeAllele": "A", + "mismatch": false + }, + { + "gene": "TPMT", + "chromosome": "chr6", + "position": 18149127, + "dbSnpId": 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"*1", + "function": "Normal function", + "reference": true + }, + "gene": "UGT1A1", + "phenotype": "Normal Metabolizer", + "variant": null, + "lookupKey": "Normal Metabolizer", + "label": "*1/*1" + } + ], + "diplotypes": [ + { + "allele1": { + "gene": "UGT1A1", + "name": "*1", + "function": "Normal function", + "reference": true + }, + "allele2": { + "gene": "UGT1A1", + "name": "*1", + "function": "Normal function", + "reference": true + }, + "gene": "UGT1A1", + "phenotype": "Normal Metabolizer", + "variant": null, + "lookupKey": "Normal Metabolizer", + "label": "*1/*1" + } + ], + "variants": [ + { + "gene": "UGT1A1", + "chromosome": "chr2", + "position": 233759924, + "dbSnpId": "rs887829", + "call": "C|C", + "alleles": [ + "*80", + "*80+*28", + "*80+*37" + ], + "phased": true, + "wildtypeAllele": "C", + "mismatch": false + }, + { + "gene": "UGT1A1", + "chromosome": "chr2", + "position": 233760233, + "dbSnpId": "rs3064744", + "call": "CAT|CAT", + "alleles": [ + "*28", + "*36", + "*37", + "*80+*28", + "*80+*37" + ], + "phased": true, + "wildtypeAllele": "CAT", + "mismatch": false + }, + { + "gene": "UGT1A1", + "chromosome": "chr2", + "position": 233760498, + "dbSnpId": "rs4148323", + "call": "G|G", + "alleles": [ + "*6" + ], + "phased": true, + "wildtypeAllele": "G", + "mismatch": false + }, + { + "gene": "UGT1A1", + "chromosome": "chr2", + "position": 233760973, + "dbSnpId": "rs35350960", + "call": "C|C", + "alleles": [ + "*27" + ], + "phased": true, + "wildtypeAllele": "C", + "mismatch": false + } + ], + "variantsOfInterest": [], + "highlightedVariants": [] + }, + { + "geneSymbol": "VKORC1", + "chr": "chr16", + "phased": true, + "callSource": "MATCHER", + "uncalledHaplotypes": [], + "messages": [ + { + "rule_name": "VKORC1", + "version": "1", + "matches": { + "gene": "VKORC1", + "hapsCalled": [], + "hapsMissing": [], + "variantsMissing": [], + "variant": "", + "dips": [], + "drugs": [] + }, + "exception_type": "footnote", + "message": "CPIC recommendations for warfarin use only rs9923231; however, other variants in VKORC1 may have functional consequences and may be more common in some populations." + }, + { + "rule_name": "VKORC1 reverse complement footnote", + "version": "1", + "matches": { + "gene": "VKORC1", + "hapsCalled": [], + "hapsMissing": [], + "variantsMissing": [], + "variant": "", + "dips": [], + "drugs": [] + }, + "exception_type": "footnote", + "message": "The VKORC1 gene is on the negative chromosomal strand, all genotype calls for VKORC1 in this report refer to the positive chromosomal strand. Therefore, genotype calls are complemented from gene bases." + } + ], + "relatedDrugs": [ + { + "name": "warfarin", + "guidelineId": "RxNorm:11289" + } + ], + "matcherDiplotypes": [ + { + "allele1": { + "gene": "VKORC1", + "name": "rs9923231 reference (C)", + "function": null, + "reference": true + }, + "allele2": { + "gene": "VKORC1", + "name": "rs9923231 reference (C)", + "function": null, + "reference": true + }, + "gene": "VKORC1", + "phenotype": null, + "variant": null, + "lookupKey": null, + "label": "rs9923231 reference (C)/rs9923231 reference (C)" + } + ], + "diplotypes": [ + { + "allele1": { + "gene": "VKORC1", + "name": "rs9923231 reference (C)", + "function": null, + "reference": true + }, + "allele2": { + "gene": "VKORC1", + "name": "rs9923231 reference (C)", + "function": null, + "reference": true + }, + "gene": "VKORC1", + "phenotype": null, + "variant": null, + "lookupKey": null, + "label": "rs9923231 reference (C)/rs9923231 reference (C)" + } + ], + "variants": [ + { + "gene": "VKORC1", + "chromosome": "chr16", + "position": 31096368, + "dbSnpId": "rs9923231", + "call": "C|C", + "alleles": [ + "rs9923231 variant (T)" + ], + "phased": true, + "wildtypeAllele": "C", + "mismatch": false + } + ], + "variantsOfInterest": [], + "highlightedVariants": [] + } +] \ No newline at end of file