- version 0.10.1 (#13)

- fixed issue12: checking the --cutoffs parameter at inappropriate position would cause profile mode to fail

cayman/__init__.py

@@ -1,3 +1,3 @@
 """ module docstring """
-__version__ = "0.10.0"
+__version__ = "0.10.1"
 __toolname__ = "cayman"

cayman/__main__.py

@@ -24,8 +24,6 @@
 def main():
 
     args = handle_args(sys.argv[1:])
-    if args.cutoffs is None:
-        args.cutoffs = os.path.join(args.hmmdb, "cutoffs.csv")
     args.aligner = "bwa"
 
     logger.info("Version: %s gqlib: %s", __version__, gqlib_version)

cayman/functions.py

@@ -98,15 +98,17 @@ def run_profile(args):
 
 
 def run_proteome_annotation(args):
-    #raise NotImplementedError("run_proteome_annotation")
-
-	annotator = CazyAnnotator()
-	print("Reading HMMs")
-	annotator.read_hmms(os.path.join(args.hmmdb, "hmms"))
-	print("Reading sequences")
-	annotator.read_sequences(path_to_sequences=args.proteins)
-	print("Annotating sequences (can take a few minutes; be patient)")
-	annotator.annotate_sequences_with_all_hmms(threads=args.threads)
-	print("Filtering and merging annotations over folds")
-	annotator.curate_annotations(precomputed_hmm_cutoffs=args.cutoffs)
-	annotator.annotations_filtered.to_csv(args.output_file, index=False)
+
+    if args.cutoffs is None:
+        args.cutoffs = os.path.join(args.hmmdb, "cutoffs.csv")
+
+    annotator = CazyAnnotator()
+    print("Reading HMMs")
+    annotator.read_hmms(os.path.join(args.hmmdb, "hmms"))
+    print("Reading sequences")
+    annotator.read_sequences(path_to_sequences=args.proteins)
+    print("Annotating sequences (can take a few minutes; be patient)")
+    annotator.annotate_sequences_with_all_hmms(threads=args.threads)
+    print("Filtering and merging annotations over folds")
+    annotator.curate_annotations(precomputed_hmm_cutoffs=args.cutoffs)
+    annotator.annotations_filtered.to_csv(args.output_file, index=False)