Louis BECQUEY / RNANet

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Louis BECQUEY
1eae2e9c 1 parent 8038ee37

Fix: command line arguments to pass to cmalign and stats

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Showing 1 changed file with 6 additions and 6 deletions
...@@ -1225,12 +1225,12 @@ class Pipeline: ...@@ -1225,12 +1225,12 @@ class Pipeline:
1225 path_to_seq_data + "realigned", 1225 path_to_seq_data + "realigned",
1226 path_to_seq_data + "rfam_sequences"]) 1226 path_to_seq_data + "rfam_sequences"])
1227 self.REUSE_ALL = True 1227 self.REUSE_ALL = True
1228 - elif opt == "cmalign-opts": 1228 + elif opt == "--cmalign-opts":
1229 - self.ALIGNOPTS = arg 1229 + self.ALIGNOPTS = arg.split(" ")
1230 - elif opt == "cmalign-rrna-opts": 1230 + elif opt == "--cmalign-rrna-opts":
1231 - self.RRNAALIGNOPTS = " ".split(arg) 1231 + self.RRNAALIGNOPTS = arg.split(" ")
1232 - elif opt == "stats-opts": 1232 + elif opt == "--stats-opts":
1233 - self.STATSOPTS = " ".split(arg) 1233 + self.STATSOPTS = arg.split(" ")
1234 elif opt == "--all": 1234 elif opt == "--all":
1235 self.REUSE_ALL = True 1235 self.REUSE_ALL = True
1236 self.USE_KNOWN_ISSUES = False 1236 self.USE_KNOWN_ISSUES = False
......