add CLI to config

vaxrank/__init__.py

@@ -19,8 +19,8 @@
 
 __all__ = [
     "__version__",
-    EpitopePrediction,
-    VaccinePeptide,
-    run_vaxrank,
-    predict_epitopes,
+    "EpitopePrediction",
+    "VaccinePeptide",
+    "run_vaxrank",
+    "predict_epitopes",
 ]

vaxrank/cli.py

@@ -15,6 +15,7 @@
 import logging.config
 import pkg_resources
 
+import msgspec 
 from argparse import ArgumentParser
 from isovar import isovar_results_to_dataframe
 from isovar.cli import (make_isovar_arg_parser, run_isovar_from_parsed_args,)
@@ -28,8 +29,9 @@
 import serializable
 from varcode.cli import variant_collection_from_args
 
-from . import __version__
+from .version import __version__
 from .core_logic import run_vaxrank
+from .config import MIN_EPITOPE_SCORE_DEFAULT
 from .gene_pathway_check import GenePathwayCheck
 from .report import (
     make_ascii_report,
@@ -60,6 +62,7 @@ def make_vaxrank_arg_parser():
     )
     add_mhc_args(arg_parser)
     add_vaccine_peptide_args(arg_parser)
+    add_epitope_prediction_args(arg_parser)
     add_output_args(arg_parser)
     add_optional_output_args(arg_parser)
     add_supplemental_report_args(arg_parser)
@@ -193,6 +196,21 @@ def add_output_args(arg_parser):
         type=int,
         help="Number of mutations to report")
 
+def add_epitope_prediction_args(arg_parser):
+    epitope_prediction_args = arg_parser.add_argument_group("T-cell epitope prediction options")
+    epitope_prediction_args.add_argument(
+        "--min-epitope-score",
+        default=MIN_EPITOPE_SCORE_DEFAULT,
+        type=float,
+        help=(
+            "Ignore predicted MHC ligands whose normalized binding score "
+            "falls below this threshold. (default: %(default)s)"))
+
+    epitope_prediction_args.add_argument(
+        "--epitope-prediction-config",
+        default=None,
+        help="Path to YAML file with options related to epitope prediction, scoring, and filtering.")
+
 
 def add_vaccine_peptide_args(arg_parser):
     vaccine_peptide_group = arg_parser.add_argument_group("Vaccine peptide options")
@@ -220,14 +238,6 @@ def add_vaccine_peptide_args(arg_parser):
             "(default: %(default)s)"
         ))
 
-    vaccine_peptide_group.add_argument(
-        "--min-epitope-score",
-        default=1e-10,
-        type=float,
-        help=(
-            "Ignore predicted MHC ligands whose normalized binding score "
-            "falls below this threshold. (default: %(default)s)"))
-
     vaccine_peptide_group.add_argument(
         "--num-epitopes-per-vaccine-peptide",
         type=int,
@@ -280,7 +290,18 @@ def run_vaxrank_from_parsed_args(args):
         df = isovar_results_to_dataframe(isovar_results)
         df.to_csv(args.output_isovar_csv, index=False)
 
-    config = Config(min_epitope_score=args.min_epitope_score)
+
+
+    if args.epitope_prediction_config:
+        with open(args.epitope_prediction_config) as f:
+            config = msgspec.yaml.decode(f.read(), Config)
+    else:
+        config = Config()
+
+    if args.min_epitope_score != config.min_epitope_score:
+        config.min_epitope_score = args.min_epitope_score
+
+
     return run_vaxrank(
         isovar_results=isovar_results,
         mhc_predictor=mhc_predictor,

vaxrank/config.py

@@ -1,11 +1,27 @@
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#       http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 import msgspec
 
+MIN_EPITOPE_SCORE_DEFAULT = 1e-10
+BINDING_AFFINITY_CUTOFF = 5000.0
+
 class Config(msgspec.Struct):
 
     """Parameters for score, filtering, and ranking both epitopes and vaccine peptides"""
     logistic_epitope_score_midpoint : float = 350.0
     logistic_epitope_score_width : float = 150.0
 
-    min_epitope_score : float = 0.0
-    binding_affinity_cutoff : float = 5000.0
+    min_epitope_score : float = MIN_EPITOPE_SCORE_DEFAULT
+    binding_affinity_cutoff : float = BINDING_AFFINITY_CUTOFF