Automatically update parent-child lineage info when doing a match usi…

…ng --with-sublineage. Disable with --no-lineage-update.

lib/Lineages_UPDATER.py

@@ -5,6 +5,7 @@
 # We just adapt and change some parts to be used in covsonar, vocal etc.
 import json
 import os
+import sys
 
 import pandas as pd
 import requests
@@ -88,12 +89,12 @@ def download_source(tmp_dir):
     alias_key_url = "https://raw.githubusercontent.com/cov-lineages/pango-designation/master/pango_designation/alias_key.json"
     lineag = os.path.join(tmp_dir, "lineags.csv")
     alias_key = os.path.join(tmp_dir, "alias_key.json")
-    print("Download lineages")
+    print("Download lineages", file=sys.stderr)
     url_content = requests.get(lineages_url).content
     csv_file = open(lineag, "wb")
     csv_file.write(url_content)
     csv_file.close()
-    print("Download alias_key")
+    print("Download alias_key", file=sys.stderr)
     items = requests.get(alias_key_url)
     data = items.json()
     with open(alias_key, "w") as f:
@@ -115,7 +116,7 @@ def process_lineage(alias_key_path, lineages_path, output):
     with open(alias_key_path ,'w') as nf:
         json.dump(data_dict, nf)
     """
-    print("Create all lineages")
+    print("Create all lineages", file=sys.stderr)
     aliasor = Aliasor(alias_key_path)
     df_lineages = pd.read_csv(lineages_path)
     lineages = df_lineages.lineage.unique()
@@ -127,7 +128,7 @@ def process_lineage(alias_key_path, lineages_path, output):
     uncompressed_lineages.sort(key=lts)
 
     sorted_lineages = list(map(aliasor.compress, uncompressed_lineages))
-    print("Calculate parent-child relationship")
+    print("Calculate parent-child relationship", file=sys.stderr)
     # -- Fill the sub child --
     # the current method is working, but it is not good in term of performance
     # the algoritm use 3 loops
@@ -157,7 +158,7 @@ def process_lineage(alias_key_path, lineages_path, output):
             row_dict["lineage"] = _id
             row_dict["sublineage"] = "none"
         _final_list.append(row_dict)
-    print("Write output:", output)
+    print("Write output:", output, file=sys.stderr)
     df = pd.DataFrame.from_dict(_final_list, orient="columns")
     df = df[df.lineage != ""]
     df.sort_values(by=["lineage"]).to_csv(output, sep="\t", index=False)

sonar.py

@@ -179,7 +179,6 @@ def parse_args():
         help="recursively get all sublineages from a given lineage (--lineage) (only child) ",
         action="store_true",
     )
-    # parser_match.add_argument('--recursion',  help="recursively get all sublineages of a given lineage (--lineage). this will work only if '--with-sublineage' is used",action="store_true")
     parser_match.add_argument(
         "--lineage",
         metavar="STR",
@@ -336,6 +335,11 @@ def parse_args():
     parser_match.add_argument(
         "--debug", help="show database query for debugging", action="store_true"
     )
+    parser_match.add_argument(
+        "--no-lineage-update",
+        help="do not automatically update parent-child lineage relationship information",
+        action="store_true",
+    )
 
     # create the parser for the "restore" command
     parser_restore = subparsers.add_parser(
@@ -975,13 +979,16 @@ def process_update_expressions(expr):
     else:
         debug = False
     # update-lineage-info
-    if args.tool == "update-lineage-info":
+    if args.tool == "update-lineage-info" or (
+        args.tool == "match" and args.with_sublineage and not args.no_lineage_update
+    ):
         tmp_dirname = mkdtemp(prefix=".tmp_")
         alias_key, lineage = Lineages_UPDATER.download_source(tmp_dirname)
         Lineages_UPDATER.process_lineage(alias_key, lineage, "lib/lineage.all.tsv")
         if os.path.isdir(tmp_dirname):
             shutil.rmtree(tmp_dirname)
-        sys.exit("Complete!")
+        if args.tool == "update-lineage-info":
+            sys.exit("Complete!")
 
     if not args.db is None and args.tool != "add" and not os.path.isfile(args.db):
         sys.exit("input error: database does not exist.")