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hotfix-4.5.x: new test added to VariantAnnotationCalculatorTest to ch…
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…eck normalisation of mitochondrial chromosome name chrM -> MT
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@javild
javild committed Jul 30, 2018
1 parent a7c3530 commit 0c61d5f
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7 changes: 7 additions & 0 deletions cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/VariantAnnotationCalculatorTest.java
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Expand Up @@ -1170,6 +1170,13 @@ public void testGetAllConsequenceTypesByVariant() throws IOException, URISyntaxE
assertObjectListEquals("[{\"geneName\":\"MT-CO2\",\"ensemblGeneId\":\"ENSG00000198712\",\"ensemblTranscriptId\":\"ENST00000361739\",\"strand\":\"+\",\"biotype\":\"protein_coding\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001632\",\"name\":\"downstream_variant\"}]},{\"geneName\":\"MT-TK\",\"ensemblGeneId\":\"ENSG00000210156\",\"ensemblTranscriptId\":\"ENST00000387421\",\"strand\":\"+\",\"biotype\":\"Mt_tRNA\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001632\",\"name\":\"downstream_variant\"}]},{\"geneName\":\"MT-ATP8\",\"ensemblGeneId\":\"ENSG00000228253\",\"ensemblTranscriptId\":\"ENST00000361851\",\"strand\":\"+\",\"biotype\":\"protein_coding\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001632\",\"name\":\"downstream_variant\"}]},{\"geneName\":\"MT-ATP6\",\"ensemblGeneId\":\"ENSG00000198899\",\"ensemblTranscriptId\":\"ENST00000361899\",\"strand\":\"+\",\"biotype\":\"protein_coding\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001632\",\"name\":\"downstream_variant\"}]},{\"geneName\":\"MT-CO3\",\"ensemblGeneId\":\"ENSG00000198938\",\"ensemblTranscriptId\":\"ENST00000362079\",\"strand\":\"+\",\"biotype\":\"protein_coding\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001632\",\"name\":\"downstream_variant\"}]},{\"geneName\":\"MT-TG\",\"ensemblGeneId\":\"ENSG00000210164\",\"ensemblTranscriptId\":\"ENST00000387429\",\"strand\":\"+\",\"biotype\":\"Mt_tRNA\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001632\",\"name\":\"downstream_variant\"}]},{\"geneName\":\"MT-ND3\",\"ensemblGeneId\":\"ENSG00000198840\",\"ensemblTranscriptId\":\"ENST00000361227\",\"strand\":\"+\",\"biotype\":\"protein_coding\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001632\",\"name\":\"downstream_variant\"}]},{\"geneName\":\"MT-TR\",\"ensemblGeneId\":\"ENSG00000210174\",\"ensemblTranscriptId\":\"ENST00000387439\",\"strand\":\"+\",\"biotype\":\"Mt_tRNA\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001632\",\"name\":\"downstream_variant\"}]},{\"geneName\":\"MT-ND4L\",\"ensemblGeneId\":\"ENSG00000212907\",\"ensemblTranscriptId\":\"ENST00000361335\",\"strand\":\"+\",\"biotype\":\"protein_coding\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001632\",\"name\":\"downstream_variant\"}]},{\"geneName\":\"MT-ND4\",\"ensemblGeneId\":\"ENSG00000198886\",\"ensemblTranscriptId\":\"ENST00000361381\",\"strand\":\"+\",\"biotype\":\"protein_coding\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0002083\",\"name\":\"2KB_downstream_variant\"}]},{\"geneName\":\"MT-TH\",\"ensemblGeneId\":\"ENSG00000210176\",\"ensemblTranscriptId\":\"ENST00000387441\",\"strand\":\"+\",\"biotype\":\"Mt_tRNA\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0002083\",\"name\":\"2KB_downstream_variant\"}]},{\"geneName\":\"MT-TS2\",\"ensemblGeneId\":\"ENSG00000210184\",\"ensemblTranscriptId\":\"ENST00000387449\",\"strand\":\"+\",\"biotype\":\"Mt_tRNA\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0002083\",\"name\":\"2KB_downstream_variant\"}]},{\"geneName\":\"MT-TL2\",\"ensemblGeneId\":\"ENSG00000210191\",\"ensemblTranscriptId\":\"ENST00000387456\",\"strand\":\"+\",\"biotype\":\"Mt_tRNA\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0002083\",\"name\":\"2KB_downstream_variant\"}]},{\"geneName\":\"MT-ND5\",\"ensemblGeneId\":\"ENSG00000198786\",\"ensemblTranscriptId\":\"ENST00000361567\",\"strand\":\"+\",\"biotype\":\"protein_coding\",\"exonOverlap\":[{\"percentage\":0.05518763796909492,\"number\":\"1/1\"}],\"transcriptAnnotationFlags\":[\"basic\"],\"cdnaPosition\":570,\"cdsPosition\":570,\"codon\":\"atC/atA\",\"proteinVariantAnnotation\":{\"uniprotAccession\":\"P03915\",\"position\":190,\"reference\":\"ILE\",\"alternate\":\"MET\",\"substitutionScores\":[{\"score\":0.31,\"source\":\"sift\",\"description\":\"tolerated\"},{\"score\":0.052,\"source\":\"polyphen\",\"description\":\"benign\"}],\"keywords\":[\"Complete proteome\",\"Disease mutation\",\"Electron transport\",\"Leber hereditary optic neuropathy\",\"Leigh syndrome\",\"MELAS syndrome\",\"Membrane\",\"Mitochondrion\",\"Mitochondrion inner membrane\",\"NAD\",\"Oxidoreductase\",\"Polymorphism\",\"Reference proteome\",\"Respiratory chain\",\"Transmembrane\",\"Transmembrane helix\",\"Transport\",\"Ubiquinone\"],\"features\":[{\"id\":\"IPR003945\",\"start\":8,\"end\":501,\"description\":\"NADH-plastoquinone oxidoreductase, chain 5\"},{\"id\":\"IPR001750\",\"start\":134,\"end\":418,\"description\":\"NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit\"},{\"start\":171,\"end\":191,\"type\":\"transmembrane region\",\"description\":\"Helical\"},{\"id\":\"PRO_0000118101\",\"start\":1,\"end\":603,\"type\":\"chain\",\"description\":\"NADH-ubiquinone oxidoreductase chain 5\"}]},\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001583\",\"name\":\"missense_variant\"}]},{\"geneName\":\"MT-ND6\",\"ensemblGeneId\":\"ENSG00000198695\",\"ensemblTranscriptId\":\"ENST00000361681\",\"strand\":\"-\",\"biotype\":\"protein_coding\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0002083\",\"name\":\"2KB_downstream_variant\"}]},{\"geneName\":\"MT-TE\",\"ensemblGeneId\":\"ENSG00000210194\",\"ensemblTranscriptId\":\"ENST00000387459\",\"strand\":\"-\",\"biotype\":\"Mt_tRNA\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0002083\",\"name\":\"2KB_downstream_variant\"}]},{\"geneName\":\"MT-CYB\",\"ensemblGeneId\":\"ENSG00000198727\",\"ensemblTranscriptId\":\"ENST00000361789\",\"strand\":\"+\",\"biotype\":\"protein_coding\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001636\",\"name\":\"2KB_upstream_variant\"}]},{\"geneName\":\"MT-TT\",\"ensemblGeneId\":\"ENSG00000210195\",\"ensemblTranscriptId\":\"ENST00000387460\",\"strand\":\"+\",\"biotype\":\"Mt_tRNA\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001631\",\"name\":\"upstream_variant\"}]},{\"geneName\":\"MT-TP\",\"ensemblGeneId\":\"ENSG00000210196\",\"ensemblTranscriptId\":\"ENST00000387461\",\"strand\":\"-\",\"biotype\":\"Mt_tRNA\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001632\",\"name\":\"downstream_variant\"}]},{\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001566\",\"name\":\"regulatory_region_variant\"}]},{\"geneName\":null,\"ensemblGeneId\":null,\"ensemblTranscriptId\":null,\"strand\":null,\"biotype\":null,\"exonOverlap\":null,\"transcriptAnnotationFlags\":null,\"cdnaPosition\":null,\"cdsPosition\":null,\"codon\":null,\"proteinVariantAnnotation\":null,\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001782\",\"name\":\"TF_binding_site_variant\"}]}]",
consequenceTypeResult.getResult(), ConsequenceType.class);

// Tests normalisation of chromosome MT: should transform chrM -> MT
consequenceTypeResult =
variantAnnotationCalculator.getAllConsequenceTypesByVariant(new Variant("chrM", 12906, "C", "A"),
new QueryOptions());
assertObjectListEquals("[{\"geneName\":\"MT-CO2\",\"ensemblGeneId\":\"ENSG00000198712\",\"ensemblTranscriptId\":\"ENST00000361739\",\"strand\":\"+\",\"biotype\":\"protein_coding\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001632\",\"name\":\"downstream_variant\"}]},{\"geneName\":\"MT-TK\",\"ensemblGeneId\":\"ENSG00000210156\",\"ensemblTranscriptId\":\"ENST00000387421\",\"strand\":\"+\",\"biotype\":\"Mt_tRNA\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001632\",\"name\":\"downstream_variant\"}]},{\"geneName\":\"MT-ATP8\",\"ensemblGeneId\":\"ENSG00000228253\",\"ensemblTranscriptId\":\"ENST00000361851\",\"strand\":\"+\",\"biotype\":\"protein_coding\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001632\",\"name\":\"downstream_variant\"}]},{\"geneName\":\"MT-ATP6\",\"ensemblGeneId\":\"ENSG00000198899\",\"ensemblTranscriptId\":\"ENST00000361899\",\"strand\":\"+\",\"biotype\":\"protein_coding\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001632\",\"name\":\"downstream_variant\"}]},{\"geneName\":\"MT-CO3\",\"ensemblGeneId\":\"ENSG00000198938\",\"ensemblTranscriptId\":\"ENST00000362079\",\"strand\":\"+\",\"biotype\":\"protein_coding\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001632\",\"name\":\"downstream_variant\"}]},{\"geneName\":\"MT-TG\",\"ensemblGeneId\":\"ENSG00000210164\",\"ensemblTranscriptId\":\"ENST00000387429\",\"strand\":\"+\",\"biotype\":\"Mt_tRNA\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001632\",\"name\":\"downstream_variant\"}]},{\"geneName\":\"MT-ND3\",\"ensemblGeneId\":\"ENSG00000198840\",\"ensemblTranscriptId\":\"ENST00000361227\",\"strand\":\"+\",\"biotype\":\"protein_coding\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001632\",\"name\":\"downstream_variant\"}]},{\"geneName\":\"MT-TR\",\"ensemblGeneId\":\"ENSG00000210174\",\"ensemblTranscriptId\":\"ENST00000387439\",\"strand\":\"+\",\"biotype\":\"Mt_tRNA\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001632\",\"name\":\"downstream_variant\"}]},{\"geneName\":\"MT-ND4L\",\"ensemblGeneId\":\"ENSG00000212907\",\"ensemblTranscriptId\":\"ENST00000361335\",\"strand\":\"+\",\"biotype\":\"protein_coding\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001632\",\"name\":\"downstream_variant\"}]},{\"geneName\":\"MT-ND4\",\"ensemblGeneId\":\"ENSG00000198886\",\"ensemblTranscriptId\":\"ENST00000361381\",\"strand\":\"+\",\"biotype\":\"protein_coding\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0002083\",\"name\":\"2KB_downstream_variant\"}]},{\"geneName\":\"MT-TH\",\"ensemblGeneId\":\"ENSG00000210176\",\"ensemblTranscriptId\":\"ENST00000387441\",\"strand\":\"+\",\"biotype\":\"Mt_tRNA\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0002083\",\"name\":\"2KB_downstream_variant\"}]},{\"geneName\":\"MT-TS2\",\"ensemblGeneId\":\"ENSG00000210184\",\"ensemblTranscriptId\":\"ENST00000387449\",\"strand\":\"+\",\"biotype\":\"Mt_tRNA\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0002083\",\"name\":\"2KB_downstream_variant\"}]},{\"geneName\":\"MT-TL2\",\"ensemblGeneId\":\"ENSG00000210191\",\"ensemblTranscriptId\":\"ENST00000387456\",\"strand\":\"+\",\"biotype\":\"Mt_tRNA\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0002083\",\"name\":\"2KB_downstream_variant\"}]},{\"geneName\":\"MT-ND5\",\"ensemblGeneId\":\"ENSG00000198786\",\"ensemblTranscriptId\":\"ENST00000361567\",\"strand\":\"+\",\"biotype\":\"protein_coding\",\"exonOverlap\":[{\"percentage\":0.05518763796909492,\"number\":\"1/1\"}],\"transcriptAnnotationFlags\":[\"basic\"],\"cdnaPosition\":570,\"cdsPosition\":570,\"codon\":\"atC/atA\",\"proteinVariantAnnotation\":{\"uniprotAccession\":\"P03915\",\"position\":190,\"reference\":\"ILE\",\"alternate\":\"MET\",\"substitutionScores\":[{\"score\":0.31,\"source\":\"sift\",\"description\":\"tolerated\"},{\"score\":0.052,\"source\":\"polyphen\",\"description\":\"benign\"}],\"keywords\":[\"Complete proteome\",\"Disease mutation\",\"Electron transport\",\"Leber hereditary optic neuropathy\",\"Leigh syndrome\",\"MELAS syndrome\",\"Membrane\",\"Mitochondrion\",\"Mitochondrion inner membrane\",\"NAD\",\"Oxidoreductase\",\"Polymorphism\",\"Reference proteome\",\"Respiratory chain\",\"Transmembrane\",\"Transmembrane helix\",\"Transport\",\"Ubiquinone\"],\"features\":[{\"id\":\"IPR003945\",\"start\":8,\"end\":501,\"description\":\"NADH-plastoquinone oxidoreductase, chain 5\"},{\"id\":\"IPR001750\",\"start\":134,\"end\":418,\"description\":\"NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit\"},{\"start\":171,\"end\":191,\"type\":\"transmembrane region\",\"description\":\"Helical\"},{\"id\":\"PRO_0000118101\",\"start\":1,\"end\":603,\"type\":\"chain\",\"description\":\"NADH-ubiquinone oxidoreductase chain 5\"}]},\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001583\",\"name\":\"missense_variant\"}]},{\"geneName\":\"MT-ND6\",\"ensemblGeneId\":\"ENSG00000198695\",\"ensemblTranscriptId\":\"ENST00000361681\",\"strand\":\"-\",\"biotype\":\"protein_coding\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0002083\",\"name\":\"2KB_downstream_variant\"}]},{\"geneName\":\"MT-TE\",\"ensemblGeneId\":\"ENSG00000210194\",\"ensemblTranscriptId\":\"ENST00000387459\",\"strand\":\"-\",\"biotype\":\"Mt_tRNA\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0002083\",\"name\":\"2KB_downstream_variant\"}]},{\"geneName\":\"MT-CYB\",\"ensemblGeneId\":\"ENSG00000198727\",\"ensemblTranscriptId\":\"ENST00000361789\",\"strand\":\"+\",\"biotype\":\"protein_coding\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001636\",\"name\":\"2KB_upstream_variant\"}]},{\"geneName\":\"MT-TT\",\"ensemblGeneId\":\"ENSG00000210195\",\"ensemblTranscriptId\":\"ENST00000387460\",\"strand\":\"+\",\"biotype\":\"Mt_tRNA\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001631\",\"name\":\"upstream_variant\"}]},{\"geneName\":\"MT-TP\",\"ensemblGeneId\":\"ENSG00000210196\",\"ensemblTranscriptId\":\"ENST00000387461\",\"strand\":\"-\",\"biotype\":\"Mt_tRNA\",\"transcriptAnnotationFlags\":[\"basic\"],\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001632\",\"name\":\"downstream_variant\"}]},{\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001566\",\"name\":\"regulatory_region_variant\"}]},{\"geneName\":null,\"ensemblGeneId\":null,\"ensemblTranscriptId\":null,\"strand\":null,\"biotype\":null,\"exonOverlap\":null,\"transcriptAnnotationFlags\":null,\"cdnaPosition\":null,\"cdsPosition\":null,\"codon\":null,\"proteinVariantAnnotation\":null,\"sequenceOntologyTerms\":[{\"accession\":\"SO:0001782\",\"name\":\"TF_binding_site_variant\"}]}]",
consequenceTypeResult.getResult(), ConsequenceType.class);

consequenceTypeResult =
variantAnnotationCalculator.getAllConsequenceTypesByVariant(new Variant("1:818401-819973:<CN10>"),
new QueryOptions());
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