diff --git a/src/dcd_mapping/schemas.py b/src/dcd_mapping/schemas.py index 45f70e2..366943c 100644 --- a/src/dcd_mapping/schemas.py +++ b/src/dcd_mapping/schemas.py @@ -21,9 +21,9 @@ class TargetSequenceType(str, Enum): class TargetType(str, Enum): """Define target gene types.""" - PROTEIN_CODING = "Protein coding" - REGULATORY = "Regulatory" - OTHER_NC = "Other noncoding" + PROTEIN_CODING = "protein_coding" + REGULATORY = "regulatory" + OTHER_NC = "other_noncoding" class VrsVersion(str, Enum): diff --git a/tests/fixtures/scoreset_metadata.json b/tests/fixtures/scoreset_metadata.json index 04e8b67..f0465db 100644 --- a/tests/fixtures/scoreset_metadata.json +++ b/tests/fixtures/scoreset_metadata.json @@ -3,7 +3,7 @@ { "urn": "urn:mavedb:00000002-a-2", "target_gene_name": "hYAP65 WW domain", - "target_gene_category": "Protein coding", + "target_gene_category": "protein_coding", "target_sequence": "GACGTTCCACTGCCGGCTGGTTGGGAAATGGCTAAAACTAGTTCTGGTCAGCGTTACTTCCTGAACCACATCGACCAGACCACCACGTGGCAGGACCCGCGT", "target_sequence_type": "dna", "target_uniprot_ref": { @@ -14,7 +14,7 @@ { "urn": "urn:mavedb:00000099-a-1", "target_gene_name": "RHO", - "target_gene_category": "Protein coding", + "target_gene_category": "protein_coding", "target_sequence": "ATGAATGGCACAGAAGGCCCTAACTTCTACGTGCCCTTCTCCAATGCGACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTGGCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTGGGCTTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCTCTCAACTACATCCTGCTCAACCTAGCCGTGGCTGACCTCTTCATGGTCCTAGGTGGCTTCACCAGCACCCTCTACACCTCTCTGCATGGATACTTCGTCTTCGGGCCCACAGGATGCAATTTGGAGGGCTTCTTTGCCACCCTGGGCGGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTGGCCATCGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTCGGGGAGAACCATGCCATCATGGGCGTTGCCTTCACCTGGGTCATGGCGCTGGCCTGCGCCGCACCCCCACTCGCCGGCTGGTCCAGGTACATCCCCGAGGGCCTGCAGTGCTCGTGTGGAATCGACTACTACACGCTCAAGCCGGAGGTCAACAACGAGTCTTTTGTCATCTACATGTTCGTGGTCCACTTCACCATCCCCATGATTATCATCTTTTTCTGCTATGGGCAGCTCGTCTTCACCGTCAAGGAGGCCGCTGCCCAGCAGCAGGAGTCAGCCACCACACAGAAGGCAGAGAAGGAGGTCACCCGCATGGTCATCATCATGGTCATCGCTTTCCTGATCTGCTGGGTGCCCTACGCCAGCGTGGCATTCTACATCTTCACCCACCAGGGCTCCAACTTCGGTCCCATCTTCATGACCATCCCAGCGTTCTTTGCCAAGAGCGCCGCCATCTACAACCCTGTCATCTATATCATGATGAACAAGCAGTTCCGGAACTGCATGCTCACCACCATCTGCTGCGGCAAGAACCCACTGGGTGACGATGAGGCCTCTGCTACCGTGTCCAAGACGGAGACGAGCCAGGTGGCCCCGGCCTAA", "target_sequence_type": "dna", "target_uniprot_ref": null @@ -22,7 +22,7 @@ { "urn": "urn:mavedb:00000103-c-1", "target_gene_name": "MAPK1", - "target_gene_category": "Protein coding", + "target_gene_category": "protein_coding", "target_sequence": "MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS", "target_sequence_type": "protein", "target_uniprot_ref": null @@ -30,7 +30,7 @@ { "urn": "urn:mavedb:00000041-a-1", "target_gene_name": "Src catalytic domain", - "target_gene_category": "Protein coding", + "target_gene_category": "protein_coding", "target_sequence": "CTGCGGCTGGAGGTCAAGCTGGGCCAGGGCTGCTTTGGCGAGGTGTGGATGGGGACCTGGAACGGTACCACCAGGGTGGCCATCAAAACCCTGAAGCCTGGCACGATGTCTCCAGAGGCCTTCCTGCAGGAGGCCCAGGTCATGAAGAAGCTGAGGCATGAGAAGCTGGTGCAGTTGTATGCTGTGGTTTCAGAGGAGCCCATTTACATCGTCACGGAGTACATGAGCAAGGGGAGTTTGCTGGACTTTCTCAAGGGGGAGACAGGCAAGTACCTGCGGCTGCCTCAGCTGGTGGACATGGCTGCTCAGATCGCCTCAGGCATGGCGTACGTGGAGCGGATGAACTACGTCCACCGGGACCTTCGTGCAGCCAACATCCTGGTGGGAGAGAACCTGGTGTGCAAAGTGGCCGACTTTGGGCTGGCTCGGCTCATTGAAGACAATGAGTACACGGCGCGGCAAGGTGCCAAATTCCCCATCAAGTGGACGGCTCCAGAAGCTGCCCTCTATGGCCGCTTCACCATCAAGTCGGACGTGTGGTCCTTCGGGATCCTGCTGACTGAGCTCACCACAAAGGGACGGGTGCCCTACCCTGGGATGGTGAACCGCGAGGTGCTGGACCAGGTGGAGCGGGGCTACCGGATGCCCTGCCCGCCGGAGTGTCCCGAGTCCCTGCACGACCTCATGTGCCAGTGCTGGCGGAAGGAGCCTGAGGAGCGGCCCACCTTCGAGTACCTGCAGGCCTTCCTG", "target_sequence_type": "dna", "target_reference_genome": "hg38", @@ -42,7 +42,7 @@ { "urn": "urn:mavedb:00000018-a-1", "target_gene_name": "HBB promoter", - "target_gene_category": "Regulatory", + "target_gene_category": "regulatory", "target_sequence": "GGTGTCTGTTTGAGGTTGCTAGTGAACACAGTTGTGTCAGAAGCAAATGTAAGCAATAGATGGCTCTGCCCTGACTTTTATGCCCAGCCCTGGCTCCTGCCCTCCCTGCTCCTGGGAGTAGATTGGCCAACCCTAGGGTGTGGCTCCACAGGGTGAGGTCTAAGTGATGACAGCCGTACCTGTCCTT", "target_sequence_type": "dna", "target_reference_genome": "hg38", @@ -51,7 +51,7 @@ { "urn": "urn:mavedb:00000001-a-4", "target_gene_name": "UBE2I", - "target_gene_category": "Protein coding", + "target_gene_category": "protein_coding", "target_sequence": "ATGTCGGGGATCGCCCTCAGCAGACTCGCCCAGGAGAGGAAAGCATGGAGGAAAGACCACCCATTTGGTTTCGTGGCTGTCCCAACAAAAAATCCCGATGGCACGATGAACCTCATGAACTGGGAGTGCGCCATTCCAGGAAAGAAAGGGACTCCGTGGGAAGGAGGCTTGTTTAAACTACGGATGCTTTTCAAAGATGATTATCCATCTTCGCCACCAAAATGTAAATTCGAACCACCATTATTTCACCCGAATGTGTACCCTTCGGGGACAGTGTGCCTGTCCATCTTAGAGGAGGACAAGGACTGGAGGCCAGCCATCACAATCAAACAGATCCTATTAGGAATACAGGAACTTCTAAATGAACCAAATATCCAAGACCCAGCTCAAGCAGAGGCCTACACGATTTACTGCCAAAACAGAGTGGAGTACGAGAAAAGGGTCCGAGCACAAGCCAAGAAGTTTGCGCCCTCATAA", "target_sequence_type": "dna", "target_reference_genome": "hg38", @@ -63,7 +63,7 @@ { "urn": "urn:mavedb:00000113-a-2", "target_gene_name": "APP", - "target_gene_category": "Protein coding", + "target_gene_category": "protein_coding", "target_sequence": "DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA", "target_sequence_type": "protein", "target_reference_genome": "hg38", @@ -75,7 +75,7 @@ { "urn": "urn:mavedb:00000098-a-1", "target_gene_name": "SCN5A", - "target_gene_category": "Protein coding", + "target_gene_category": "protein_coding", "target_sequence": "LFRVIRLARIGR", "target_sequence_type": "protein", "target_reference_genome": "hg38", @@ -87,7 +87,7 @@ { "urn": "urn:mavedb:00000061-h-1", "target_gene_name": "RAF", - "target_gene_category": "Protein coding", + "target_gene_category": "protein_coding", "target_sequence": "TCTAAGACAAGCAACACTATCCGTGTTTTCTTGCCGAACAAGCAAAGAACAGTGGTCAATGTGCGAAATGGAATGAGCTTGCATGACTGCCTTATGAAAGCACTCAAGGTGAGGGGC", "target_sequence_type": "dna", "target_reference_genome": "hg38", @@ -99,7 +99,7 @@ { "urn": "urn:mavedb:00000068-a-1", "target_gene_name": "TP53 (P72R)", - "target_gene_category": "Protein coding", + "target_gene_category": "protein_coding", "target_sequence": "ATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCAGACCTATGGAAACTACTTCCTGAAAACAACGTTCTGTCCCCCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAGAATGCCAGAGGCTGCTCCCCGCGTGGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACTCCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCGACATAGTGTGGTGGTGCCCTATGAGCCGCCTGAGGTTGGCTCTGACTGTACCACCATCCACTACAACTACATGTGTAACAGTTCCTGCATGGGCGGCATGAACCGGAGGCCCATCCTCACCATCATCACACTGGAAGACTCCAGTGGTAATCTACTGGGACGGAACAGCTTTGAGGTGCGTGTTTGTGCCTGTCCTGGGAGAGACCGGCGCACAGAGGAAGAGAATCTCCGCAAGAAAGGGGAGCCTCACCACGAGCTGCCCCCAGGGAGCACTAAGCGAGCACTGCCCAACAACACCAGCTCCTCTCCCCAGCCAAAGAAGAAACCACTGGATGGAGAATATTTCACCCTTCAGATCCGTGGGCGTGAGCGCTTCGAGATGTTCCGAGAGCTGAATGAGGCCTTGGAACTCAAGGATGCCCAGGCTGGGAAGGAGCCAGGGGGGAGCAGGGCTCACTCCAGCCACCTGAAGTCCAAAAAGGGTCAGTCTACCTCCCGCCATAAAAAACTCATGTTCAAGACAGAAGGGCCTGACTCAGACTAG", "target_sequence_type": "dna", "target_reference_genome": "hg38", @@ -108,7 +108,7 @@ { "urn": "urn:mavedb:00000093-a-1", "target_gene_name": "BRCA1 translation start through RING domain", - "target_gene_category": "Protein coding", + "target_gene_category": "protein_coding", "target_sequence": "ATGGATTTATCTGCTCTTCGCGTTGAAGAAGTACAAAATGTCATTAATGCTATGCAGAAAATCTTAGAGTGTCCCATCTGTCTGGAGTTGATCAAGGAACCTGTCTCCACAAAGTGTGACCACATATTTTGCAAATTTTGCATGCTGAAACTTCTCAACCAGAAGAAAGGGCCTTCACAGTGTCCTTTATGTAAGAATGATATAACCAAAAGGAGCCTACAAGAAAGTACGAGATTTAGTCAACTTGTTGAAGAGCTATTGAAAATCATTTGTGCTTTTCAGCTTGACACAGGTTTGGAG", "target_sequence_type": "dna", "target_reference_genome": "hg19", @@ -120,7 +120,7 @@ { "urn": "urn:mavedb:00000001-b-2", "target_gene_name": "SUMO1", - "target_gene_category": "Protein coding", + "target_gene_category": "protein_coding", "target_sequence": "ATGTCTGACCAGGAGGCAAAACCTTCAACTGAGGACTTGGGGGATAAGAAGGAAGGTGAATATATTAAACTCAAAGTCATTGGACAGGATAGCAGTGAGATTCACTTCAAAGTGAAAATGACAACACATCTCAAGAAACTCAAAGAATCATACTGTCAAAGACAGGGTGTTCCAATGAATTCACTCAGGTTTCTCTTTGAGGGTCAGAGAATTGCTGATAATCATACTCCAAAAGAACTGGGAATGGAGGAAGAAGATGTGATTGAAGTTTATCAGGAACAAACGGGGGGTCATTCAACAGTTTAG", "target_sequence_type": "dna", "target_uniprot_ref": { diff --git a/tests/fixtures/scoreset_metadata_response.json b/tests/fixtures/scoreset_metadata_response.json index 58ad764..74187d4 100644 --- a/tests/fixtures/scoreset_metadata_response.json +++ b/tests/fixtures/scoreset_metadata_response.json @@ -166,7 +166,7 @@ "targetGenes": [ { "name": "BRCA1 translation start through RING domain", - "category": "Protein coding", + "category": "protein_coding", "externalIdentifiers": [ { "identifier": {