Fix: command line arguments to pass to cmalign and stats

persalteas · Aug 17, 2021 · 1eae2e9 · 1eae2e9
1 parent 8038ee3
commit 1eae2e9
Showing 1 changed file with 6 additions and 6 deletions.
diff --git a/RNAnet.py b/RNAnet.py
@@ -1225,12 +1225,12 @@ def process_options(self):
                                 path_to_seq_data + "realigned",
                                 path_to_seq_data + "rfam_sequences"])
                 self.REUSE_ALL = True
-            elif opt == "cmalign-opts":
-                self.ALIGNOPTS = arg
-            elif opt == "cmalign-rrna-opts":
-                self.RRNAALIGNOPTS = " ".split(arg)
-            elif opt == "stats-opts":
-                self.STATSOPTS = " ".split(arg)
+            elif opt == "--cmalign-opts":
+                self.ALIGNOPTS = arg.split(" ")
+            elif opt == "--cmalign-rrna-opts":
+                self.RRNAALIGNOPTS = arg.split(" ")
+            elif opt == "--stats-opts":
+                self.STATSOPTS = arg.split(" ")
             elif opt == "--all":
                 self.REUSE_ALL = True
                 self.USE_KNOWN_ISSUES = False