Update sv format (#496)

Sage-Bionetworks · Dec 20, 2022 · fc284fc · fc284fc
1 parent 0de905b
commit fc284fc
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Showing 2 changed files with 13 additions and 5 deletions.
diff --git a/genie_registry/structural_variant.py b/genie_registry/structural_variant.py
@@ -150,7 +150,15 @@ def _validate(self, sv_df):
                 "column(s): {}.\n".format(", ".join(non_ints))
             )
 
-        region_allow_vals = ["5_PRIME_UTR", "3_PRIME_UTR", "PROMOTER", "EXON", "INTRON"]
+        region_allow_vals = [
+            "5_prime_UTR",
+            "3_prime_UTR",
+            "Promoter",
+            "Exon",
+            "Intron",
+            "5'UTR",
+            "3'UTR",
+        ]
         warn, error = process_functions.check_col_and_values(
             sv_df,
             "SITE1_REGION",
@@ -196,13 +204,13 @@ def _validate(self, sv_df):
         total_error.write(error)
 
         warn, error = process_functions.check_col_and_values(
-            sv_df, "DNA_SUPPORT", ["yes", "no"], "Structural Variant", required=False
+            sv_df, "DNA_SUPPORT", ["Yes", "No"], "Structural Variant", required=False
         )
         # total_warning.write(warn)
         total_error.write(error)
 
         warn, error = process_functions.check_col_and_values(
-            sv_df, "RNA_SUPPORT", ["yes", "no"], "Structural Variant", required=False
+            sv_df, "RNA_SUPPORT", ["Yes", "No"], "Structural Variant", required=False
         )
         # total_warning.write(warn)
         total_error.write(error)

diff --git a/tests/test_sv.py b/tests/test_sv.py
@@ -117,8 +117,8 @@ def test_validation_no_errors(self):
                 "NCBI_BUILD": ["GRCh38", "GRCh37"],
                 "BREAKPOINT_TYPE": ["PRECISE", "IMPRECISE"],
                 "CONNECTION_TYPE": ["3to5", "5to5"],
-                "DNA_SUPPORT": ["yes", "no"],
-                "RNA_Support": ["yes", "no"],
+                "DNA_SUPPORT": ["Yes", "No"],
+                "RNA_Support": ["Yes", "No"],
             }
         )
         error, warning = self.sv_cls._validate(sv_df)