Reverting some code here and there

Clinical-Genomics · Jun 14, 2024 · 371fd5c · 371fd5c
1 parent fc00685
commit 371fd5c
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Showing 3 changed files with 6 additions and 6 deletions.
diff --git a/scout/build/genes/hgnc_gene.py b/scout/build/genes/hgnc_gene.py
@@ -18,7 +18,7 @@ def build_phenotype(phenotype_info):
 
 
 def build_hgnc_gene(
-    gene_info: dict, cytoband_coords: Dict[str, dict], build: str = "37"
+    gene_info: dict, cytoband_coords: Dict[str, dict] = {}, build: str = "37"
 ) -> Optional[dict]:
     """Build a hgnc_gene object
 

diff --git a/tests/build/test_build_hgnc_gene.py b/tests/build/test_build_hgnc_gene.py
@@ -9,7 +9,7 @@ def test_build_hgnc_genes(genes):
     # WHEN building hgnc gene objecs
     for hgnc_id in genes:
         gene_info = genes[hgnc_id]
-        gene_obj = build_hgnc_gene(gene_info=gene_info, cytoband_coords={})
+        gene_obj = build_hgnc_gene(gene_info)
         # THEN check that the gene models have a hgnc id
         assert gene_obj["hgnc_id"]
 
@@ -23,7 +23,7 @@ def test_build_hgnc_gene():
         "start": 1,
         "end": 1000,
     }
-    gene_obj = build_hgnc_gene(gene_info=gene_info, cytoband_coords={})
+    gene_obj = build_hgnc_gene(gene_info)
 
     assert gene_obj["hgnc_id"] == gene_info["hgnc_id"]
     assert gene_obj["hgnc_symbol"] == gene_info["hgnc_symbol"]
@@ -38,4 +38,4 @@ def test_build_hgnc_gene_missing_hgnc_symbol(test_gene, key):
     # WHEN deleting a required key
     test_gene.pop(key)
     # THEN calling build_hgnc_gene() will return None
-    assert build_hgnc_gene(gene_info=test_gene, cytoband_coords={}) is None
+    assert build_hgnc_gene(gene_info) is None
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -239,7 +239,7 @@ def gene_bulk(genes):
     """Return a list with HgncGene objects"""
     bulk = []
     for gene_key in genes:
-        bulk.append(build_hgnc_gene(genes[gene_key], cytoband_coords={}))
+        bulk.append(build_hgnc_gene(genes[gene_key]))
 
     return bulk
 
@@ -249,7 +249,7 @@ def gene_bulk_38(genes):
     """Return a list with HgncGene objects"""
     bulk = []
     for gene_key in genes:
-        gene_obj = build_hgnc_gene(genes[gene_key], cytoband_coords={})
+        gene_obj = build_hgnc_gene(genes[gene_key])
         gene_obj["build"] = "38"
         bulk.append(gene_obj)