Mercurial > repos > bgruening > pharmcat
diff test-data/test_4.json @ 0:d67642a21a1d draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit c6a098eb0cbfa87b0feaebf10ef6b24da659fa54"
| author | bgruening |
|---|---|
| date | Fri, 28 Jan 2022 21:18:23 +0000 |
| parents | |
| children | 891283e0ee89 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_4.json Fri Jan 28 21:18:23 2022 +0000 @@ -0,0 +1,6480 @@ +[ + { + "geneSymbol": "CACNA1S", + "chr": "chr1", + "phased": true, + "callSource": "MATCHER", + "uncalledHaplotypes": [], + "messages": [], + "relatedDrugs": [], + "matcherDiplotypes": [ + { + "allele1": { + "gene": "CACNA1S", + "name": "Reference", + "function": "Normal Function", + "reference": true + }, + "allele2": { + "gene": "CACNA1S", + "name": "Reference", + "function": "Normal Function", + "reference": true + }, + "gene": "CACNA1S", + "phenotype": "Uncertain Susceptibility", + "variant": null, + "lookupKey": "Uncertain Susceptibility", + "label": "Reference/Reference" + } + ], + "diplotypes": [ + { + "allele1": { + "gene": "CACNA1S", + "name": "Reference", + "function": "Normal Function", + "reference": true + }, + "allele2": { + "gene": "CACNA1S", + "name": "Reference", + "function": "Normal Function", + "reference": true + }, + "gene": "CACNA1S", + 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"highlightedVariants": [] + }, + { + "geneSymbol": "UGT1A1", + "chr": "chr2", + "phased": true, + "callSource": "MATCHER", + "uncalledHaplotypes": [], + "messages": [ + { + "rule_name": "UGT1A1 repeat warning", + "version": "1", + "matches": { + "gene": "UGT1A1", + "hapsCalled": [], + "hapsMissing": [], + "variantsMissing": [], + "variant": "", + "dips": [], + "drugs": [] + }, + "exception_type": "footnote", + "message": "Some alleles in UGT1A1 are distinguished by a repeat sequence; some genotyping technologies may not accurately call the repeat." + } + ], + "relatedDrugs": [], + "matcherDiplotypes": [ + { + "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" + } + ], + "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": false, + "wildtypeAllele": "C", + "mismatch": false + }, + { + "gene": "UGT1A1", + "chromosome": "chr2", + "position": 233760233, + "dbSnpId": "rs3064744", + "call": "CAT|CAT", + "alleles": [ + "*28", + "*36", + "*37", + "*80+*28", + "*80+*37" + ], + "phased": false, + "wildtypeAllele": "CAT", + "mismatch": false + }, + { + "gene": "UGT1A1", + "chromosome": "chr2", + "position": 233760498, + "dbSnpId": "rs4148323", + "call": "G|G", + "alleles": [ + "*6" + ], + "phased": false, + "wildtypeAllele": "G", + "mismatch": false + }, + { + "gene": "UGT1A1", + "chromosome": "chr2", + "position": 233760973, + "dbSnpId": "rs35350960", + "call": "C|C", + "alleles": [ + "*27" + ], + "phased": false, + "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": [], + "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": false, + "wildtypeAllele": "C", + "mismatch": false + } + ], + "variantsOfInterest": [], + "highlightedVariants": [] + } +] \ No newline at end of file