bug fix in PolyPhen2 output: path. class = 'none' is sometimes used i…

…nstead of '?'
luponzo86 · Dec 10, 2019 · ca48d4a · ca48d4a
1 parent 5b69dee
commit ca48d4a
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/rhapsody/predict/core.py b/rhapsody/predict/core.py
@@ -594,7 +594,8 @@ def _calcPolyPhen2Predictions(self):
             return
         PP2_score = [x if x != '?' else 'nan' for x in
                      self.PolyPhen2output['pph2_prob']]
-        PP2_class = self.PolyPhen2output['pph2_class']
+        PP2_class = [x if x not in ['none', '?'] else '?' for x in
+                     self.PolyPhen2output['pph2_class']
         self.data['PolyPhen-2 score'] = PP2_score
         self.data['PolyPhen-2 path. class'] = PP2_class