Added untested partial matching

src/automlst/cli/program.py

@@ -4,7 +4,7 @@ import datetime
 from os import path
 import os
 
-from automlst.cli import info, type
+from automlst.cli import info, st
 from automlst.cli.meta import get_module_base_name
 from automlst.engine.data.genomics import NamedString
 from automlst.engine.local.abif import read_abif
@@ -16,7 +16,7 @@ root_parser = argparse.ArgumentParser()
 subparsers = root_parser.add_subparsers(required=True)
 
 info.setup_parser(subparsers.add_parser(get_module_base_name(info.__name__)))
-type.setup_parser(subparsers.add_parser(get_module_base_name(type.__name__)))
+st.setup_parser(subparsers.add_parser(get_module_base_name(st.__name__)))
 
 
 def run():

src/automlst/cli/st.py

@@ -38,17 +38,27 @@ def setup_parser(parser: ArgumentParser):
     parser.add_argument(
         "--exact", "-ex",
         action="store_true",
+        dest="exact",
         required=False,
         default=False,
         help="Should run exact matching rather than returning all similar ones"
     )
+
+    parser.add_argument(
+        "--stop-on-fail", "-sof",
+        action="store_true",
+        dest="stop_on_fail",
+        required=False,
+        default=False,
+        help="Should the algorithm stop in the case there are no matches (or partial matches when expecting exact matches)."
+    )
     parser.set_defaults(func=run_asynchronously)
 
 async def run(args):
     async with BIGSdbIndex() as bigsdb_index:
         gen_strings = read_multiple_fastas(args.fastas)
         async with await bigsdb_index.build_profiler_from_seqdefdb(args.seqdefdb, args.schema) as mlst_profiler:
-            mlst_profiles = mlst_profiler.profile_multiple_strings(gen_strings)
+            mlst_profiles = mlst_profiler.profile_multiple_strings(gen_strings, exact=args.exact)
             failed = await write_mlst_profiles_as_csv(mlst_profiles, args.out)
             if len(failed) > 0:
                 print(f"A total of {len(failed)} IDs failed:\n{"\n".join(failed)}")