change field name and update tests for ensembl 113

EBIvariation · Oct 17, 2024 · 96050a0 · 96050a0
1 parent e0fd239
commit 96050a0
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Showing 6 changed files with 1,090 additions and 1,089 deletions.
diff --git a/cmat/output_generation/clinvar_to_evidence_strings.py b/cmat/output_generation/clinvar_to_evidence_strings.py
@@ -238,7 +238,7 @@ def generate_evidence_string(clinvar_record, allele_origins, disease_name, disea
         'variantFunctionalConsequenceId': consequence_attributes.so_term.accession,
         'variantId': clinvar_record.measure.vcf_full_coords,  # CHROM_POS_REF_ALT notation.
         'variantRsId': clinvar_record.measure.rs_id,
-        'variantIdFromSource': clinvar_record.vcv_id,
+        'variantFromSourceId': clinvar_record.vcv_id,
 
         # PHENOTYPE ATTRIBUTES.
         # The alphabetical list of *all* valid disease names from all traits from that ClinVar record, reported as a

diff --git a/tests/output_generation/resources/expected_genetics_evidence_string.json b/tests/output_generation/resources/expected_genetics_evidence_string.json
@@ -25,6 +25,6 @@
   "variantFunctionalConsequenceId": "SO_0001583",
   "variantHgvsId": "NC_000014.9:g.67729209A>G",
   "variantId": "14_67729209_A_G",
-  "variantIdFromSource": "VCV000002046",
+  "variantFromSourceId": "VCV000002046",
   "variantRsId": "rs28940313"
 }
diff --git a/tests/output_generation/resources/expected_multiple_names_evidence_string.json b/tests/output_generation/resources/expected_multiple_names_evidence_string.json
@@ -22,6 +22,6 @@
   "variantFunctionalConsequenceId": "SO_0001583",
   "variantHgvsId": "NC_000007.14:g.94423102G>A",
   "variantId": "7_94423102_G_A",
-  "variantIdFromSource": "VCV000374196",
+  "variantFromSourceId": "VCV000374196",
   "variantRsId": "rs1057518967"
 }
diff --git a/tests/output_generation/resources/expected_somatic_evidence_string.json b/tests/output_generation/resources/expected_somatic_evidence_string.json
@@ -25,6 +25,6 @@
   "variantFunctionalConsequenceId": "SO_0001583",
   "variantHgvsId": "NC_000014.9:g.67729209A>G",
   "variantId": "14_67729209_A_G",
-  "variantIdFromSource": "VCV000002046",
+  "variantFromSourceId": "VCV000002046",
   "variantRsId": "rs28940313"
 }
diff --git a/tests/pipelines/resources/expected/consequences_snp.tsv b/tests/pipelines/resources/expected/consequences_snp.tsv
@@ -396,6 +396,7 @@
 17:63957460:A:G	ENSG00000007314	SCN4A	missense_variant
 17:63971780:C:T	ENSG00000007314	SCN4A	missense_variant
 17:64485735:TG:T	ENSG00000256525	POLG2	frameshift_variant
+17:64485735:TG:T	ENSG00000271605	MILR1	intron_variant
 17:6453135:C:T	ENSG00000091622	PITPNM3	3_prime_UTR_variant
 17:65177778:A:G	ENSG00000108370	RGS9	missense_variant
 17:65538242:G:C	ENSG00000168646	AXIN2	missense_variant