Merge pull request #249 from cov-lineages/patch

Add robustness to scorpio overwrite for missing lineages and unusual constellation names

pangolin/__init__.py

@@ -1,6 +1,5 @@
 _program = "pangolin"
-__version__ = "3.1.2"
-
+__version__ = "3.1.3"
 
 __all__ = ["pangolearn",
     "utils"]

pangolin/command.py

@@ -87,7 +87,7 @@ def main(sysargs = sys.argv[1:]):
     parser.add_argument("-t","--threads",action="store",default=1,type=int, help="Number of threads")
     parser.add_argument("-v","--version", action='version', version=f"pangolin {__version__}")
     parser.add_argument("-pv","--pangoLEARN-version", action='version', version=f"pangoLEARN {pangoLEARN.__version__}",help="show pangoLEARN's version number and exit")
-    parser.add_argument("-dv","--pango-designation-version", action='version', version=f"pango-designation {PANGO_VERSION}",help="show pango-designation version number and exit")
+    parser.add_argument("-dv","--pango-designation-version", action='version', version=f"pango-designation {PANGO_VERSION} used for pangoLEARN and UShER training",help="show pango-designation version number used for training and exit")
     parser.add_argument("--aliases", action='store_true', default=False, help="print pango-designation alias_key.json and exit")
     parser.add_argument("--update", action='store_true', default=False, help="Automatically updates to latest release of pangolin, pangoLEARN and constellations, then exits")
     parser.add_argument("--update-data", action='store_true',dest="update_data", default=False, help="Automatically updates to latest release of pangoLEARN and constellations, then exits")

pangolin/scripts/pangolearn.smk

@@ -18,8 +18,8 @@ if config.get("header_file"):
 ##### Utility functions #####
 
 def expand_alias(pango_lineage, alias_dict):
-    if not pango_lineage or pango_lineage == "":
-        return pango_lineage
+    if not pango_lineage or pango_lineage in ["None", None, ""] or "/" in pango_lineage:
+        return None
 
     lineage_parts = pango_lineage.split(".")
     if lineage_parts[0].startswith('X'):
@@ -31,7 +31,7 @@ def expand_alias(pango_lineage, alias_dict):
             pango_lineage = alias_dict[lineage_parts[0]]
         lineage_parts = pango_lineage.split(".")
     if lineage_parts[0] not in ["A","B"]:
-        sys.exit("Pango lineage %s has no alias provided. Please update aliases JSON" %lineage_parts[0])
+        return None
     return pango_lineage
 
 
@@ -225,7 +225,7 @@ rule generate_report:
                             scorpio_lineage = new_row["scorpio_call"].split("+")[0].split("-like")[0]
                         expanded_scorpio_lineage = expand_alias(scorpio_lineage, alias_dict)
                         expanded_pango_lineage = expand_alias(row['lineage'], alias_dict)
-                        if not expanded_pango_lineage.startswith(expanded_scorpio_lineage):
+                        if expanded_scorpio_lineage and expanded_pango_lineage and not expanded_pango_lineage.startswith(expanded_scorpio_lineage):
                             new_row["note"] += f'; scorpio replaced lineage assignment {row["lineage"]}'
                             new_row['lineage'] = scorpio_lineage
 
@@ -351,7 +351,7 @@ rule usher_to_report:
                             scorpio_lineage = scorpio_call.split("+")[0].split("-like")[0]
                         expanded_scorpio_lineage = expand_alias(scorpio_lineage, alias_dict)
                         expanded_pango_lineage = expand_alias(lineage, alias_dict)
-                        if not expanded_pango_lineage.startswith(expanded_scorpio_lineage):
+                        if expanded_scorpio_lineage and expanded_pango_lineage and not expanded_pango_lineage.startswith(expanded_scorpio_lineage):
                             note += f'; scorpio replaced lineage assignment {lineage}'
                             lineage = scorpio_lineage