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Merged
bencap merged 1 commit into from
Nov 21, 2024
Merged

New API values for protein categories #28

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6 changes: 3 additions & 3 deletions src/dcd_mapping/schemas.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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):
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24 changes: 12 additions & 12 deletions tests/fixtures/scoreset_metadata.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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": {
Expand All @@ -14,23 +14,23 @@
{
"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
},
{
"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
},
{
"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",
Expand All @@ -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",
Expand All @@ -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",
Expand All @@ -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",
Expand All @@ -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",
Expand All @@ -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",
Expand All @@ -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",
Expand All @@ -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",
Expand All @@ -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": {
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2 changes: 1 addition & 1 deletion tests/fixtures/scoreset_metadata_response.json
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Expand Up @@ -166,7 +166,7 @@
"targetGenes": [
{
"name": "BRCA1 translation start through RING domain",
"category": "Protein coding",
"category": "protein_coding",
"externalIdentifiers": [
{
"identifier": {
Expand Down