Merge pull request #28 from cov-lineages/dev

Fix bugs with define

Author: rmcolq

scorpio/__init__.py

@@ -1,2 +1,2 @@
 _program = "scorpio"
-__version__ = "0.3.11"
+__version__ = "0.3.12"

scorpio/scripts/extract_definitions.py

@@ -163,7 +163,7 @@ def define_mutations(list_variants, feature_dict, reference_seq):
                 merged_list.append(new_var)
         elif var.startswith("ins") or var.startswith("del"):
             i, pos, add = var.split("_")
-            new_var = "%s:%i+%s" % (i, pos, add)
+            new_var = "%s:%s+%s" % (i, pos, add)
             if freq:
                 merged_list.append("%s:%s" % (new_var, freq))
             else:

scorpio/scripts/type_constellations.py

@@ -55,7 +55,7 @@ def load_feature_coordinates(reference_json):
                         features_dict[name] = (start, end, json_dict[feature][item]["gene"])
                     else:
                         features_dict[name] = (start, end)
-                    logging.info("Found reference feature %s with coordinates" % name, features_dict[name])
+                    logging.info("Found reference feature %s with coordinates %s" % (name, features_dict[name]))
     if len(features_dict) == 0:
         sys.stderr.write("No features (keys \"genes\", \"proteins\" or \"features\" ) provided in JSON %s " %
                          reference_json)