diff --git a/genie_registry/structural_variant.py b/genie_registry/structural_variant.py index a1ff6318..d8a9688f 100644 --- 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 index efd5ca36..26010cff 100644 --- 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)