Updated to reflect changes in Engine 0.10.*

pyproject.toml

@@ -8,7 +8,7 @@ dynamic = ["version"]
 readme = "README.md"
 license = {file = "LICENSE"}
 dependencies = [
-    "autoBIGS-engine"
+    "autoBIGS-engine==0.10.*"
 ]
 requires-python = ">=3.12"
 description = "A CLI tool to rapidly fetch fetch MLST profiles given sequences for various diseases."

requirements.txt

@@ -4,4 +4,4 @@ pytest-cov
 build
 twine
 setuptools_scm
-autoBIGS.engine
+autoBIGS.engine==0.10.*

src/autobigs/cli/info.py

@@ -1,6 +1,6 @@
 from argparse import ArgumentParser, Namespace
 import asyncio
-from autobigs.engine.data.remote.databases.bigsdb import BIGSdbIndex
+from autobigs.engine.analysis.bigsdb import BIGSdbIndex
 
 def setup_parser(parser: ArgumentParser):
     parser.description = "Fetches the latest BIGSdb MLST database definitions."

src/autobigs/cli/st.py

@@ -2,9 +2,9 @@
 from argparse import ArgumentParser, Namespace
 import asyncio
 import datetime
-from autobigs.engine.data.local.csv import write_mlst_profiles_as_csv
-from autobigs.engine.data.local.fasta import read_multiple_fastas
-from autobigs.engine.data.remote.databases.bigsdb import BIGSdbIndex
+from autobigs.engine.writing import write_mlst_profiles_as_csv
+from autobigs.engine.reading import read_multiple_fastas
+from autobigs.engine.analysis.bigsdb import BIGSdbIndex
 
 
 def setup_parser(parser: ArgumentParser):
@@ -35,15 +35,6 @@ def setup_parser(parser: ArgumentParser):
         help="The output CSV name (.csv will be appended)."
     )
 
-    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",
@@ -58,7 +49,7 @@ def setup_parser(parser: ArgumentParser):
 async def run(args: Namespace):
     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:
+        async with await bigsdb_index.build_profiler_from_seqdefdb(False, args.seqdefdb, args.schema) as mlst_profiler:
             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: