Merge pull request #515 from Sage-Bionetworks/GEN-564-update-site1-2-…

…region [GEN-564] Add support for more values for site1 site2 col in SV file
Sage-Bionetworks · Apr 18, 2023 · f2f9ca3 · f2f9ca3
2 parents c96000b + 3afb070
commit f2f9ca3
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diff --git a/genie_registry/structural_variant.py b/genie_registry/structural_variant.py
@@ -159,6 +159,14 @@ def _validate(self, sv_df):
             "Intron",
             "5'UTR",
             "3'UTR",
+            "5-UTR",
+            "3-UTR",
+            "5_Prime_UTR Intron",
+            "3_Prime_UTR Intron",
+            "Downstream",
+            "Upstream",
+            "Intergenic",
+            "IGR",
         ]
         warn, error = process_functions.check_col_and_values(
             df=sv_df,

diff --git a/tests/test_sv.py b/tests/test_sv.py
@@ -126,6 +126,8 @@ def test_validation_no_errors(self):
                 "RNA_Support": ["Yes", "No", "Unknown"],
                 "SITE1_CHROMOSOME": [1, 22, 22],
                 "SITE2_CHROMOSOME": ["X", "2", "2"],
+                "SITE1_REGION": ["IGR", "Upstream", "5_Prime_UTR Intron"],
+                "SITE2_REGION": ["3-UTR", "3_Prime_UTR Intron", "Exon"],
             }
         )
         error, warning = self.sv_cls._validate(sv_df)