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tongzhouxu · Mar 21, 2024 · 52f8901 · 52f8901
1 parent 0e4b990
commit 52f8901
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/mashpit/mashpit.py b/mashpit/mashpit.py
@@ -46,8 +46,8 @@ def commandToArgs(commandline):
     subparser_update.set_defaults(func=update.update)
 
     # "query" subcommand
-    subparser_query.add_argument(dest="sample", type=str, help="file path of the query sample")
-    subparser_query.add_argument(dest="database", type=str, help="path for the database folder")
+    subparser_query.add_argument(dest="sample", type=str, help="file path to the query sample")
+    subparser_query.add_argument(dest="database", type=str, help="path to the database folder")
     subparser_query.add_argument("--number", type=int, help="number of isolates in the query output, default is 200",default=200)
     subparser_query.add_argument("--threshold", type=float, help="minimum jaccard similarity for mashtree, default is 0.85",default=0.85)
     subparser_query.add_argument("--annotation", type=str, help="mashtree tip annoatation, default is none")

diff --git a/mashpit/query.py b/mashpit/query.py
@@ -153,8 +153,9 @@ def query(args):
     if not os.path.exists(db_folder):
         logging.error('Database path not found.')
         exit(1)
-    sql_path = os.path.join(db_folder,f'{args.database}.db')
-    sig_path = os.path.join(db_folder, f'{args.database}.sig')
+    folder_name = os.path.basename(db_folder)
+    sql_path = os.path.join(db_folder,f'{folder_name}.db')
+    sig_path = os.path.join(db_folder, f'{folder_name}.sig')
     if not (os.path.exists(sql_path) and os.path.exists(sig_path)):
         logging.error('Database incomplete.')
         exit(1)