add upper() to input query

luponzo86 · Mar 2, 2020 · 3c68320 · 3c68320
1 parent 60281d1
commit 3c68320
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Showing 2 changed files with 6 additions and 5 deletions.
diff --git a/rhapsody/features/Uniprot.py b/rhapsody/features/Uniprot.py
@@ -884,7 +884,7 @@ def seqScanning(Uniprot_coord, sequence=None):
     sequence will be downloaded from Uniprot.
     '''
     assert isinstance(Uniprot_coord, str), "Must be a string."
-    coord = Uniprot_coord.strip().split()
+    coord = Uniprot_coord.upper().strip().split()
     assert len(coord) < 3, "Invalid format. Examples: 'Q9BW27' or 'Q9BW27 10'."
     aa_list = 'ACDEFGHIKLMNPQRSTVWY'
     if sequence is None:
@@ -928,5 +928,5 @@ def printSAVlist(input_SAVs, filename):
             m = f'error in SAV {i}: '
             assert isinstance(line, str), f'{m} not a string'
             assert len(line) < 25, f'{m} too many characters'
-            print(line, file=f)
+            print(line.upper(), file=f)
     return filename
diff --git a/rhapsody/predict/core.py b/rhapsody/predict/core.py
@@ -193,18 +193,19 @@ def setSAVs(self, query):
             if isfile(query):
                 # 'query' is a filename, with line format 'P17516 135 G E'
                 SAVs = np.loadtxt(query, dtype=SAV_dtype)
-                SAV_list = ['{} {} {} {}'.format(*s) for s in SAVs]
+                SAV_list = ['{} {} {} {}'.format(*s).upper() for s in SAVs]
             elif len(query.split()) < 3:
                 # single Uniprot acc (+ pos), e.g. 'P17516' or 'P17516 135'
                 SAV_list = Uniprot.seqScanning(query)
                 self.saturation_mutagenesis = True
             else:
                 # single SAV
-                SAV = np.array(query.split(), dtype=SAV_dtype)
+                SAV = np.array(query.upper().split(), dtype=SAV_dtype)
                 SAV_list = ['{} {} {} {}'.format(*SAV)]
         else:
             # 'query' is a list or tuple of SAV coordinates
-            SAVs = np.array([tuple(s.split()) for s in query], dtype=SAV_dtype)
+            SAVs = np.array([tuple(s.upper().split()) for s in query],
+                            dtype=SAV_dtype)
             SAV_list = ['{} {} {} {}'.format(*s) for s in SAVs]
         # store SAV coordinates
         numSAVs = len(SAV_list)