working on YAML config

vaxrank/__init__.py

@@ -16,8 +16,8 @@
 from .epitope_logic import predict_epitopes
 from .vaccine_peptide import VaccinePeptide
 from .version import __version__
-from .epitope_config import EpitopeConfig
-from .vaccine_config import VaccineConfig
+from .cli.epitope_config_args import EpitopeConfig
+from .cli.vaccine_config_args import VaccineConfig
 
 __all__ = [
     "__version__",

vaxrank/cli/__init__.py

@@ -0,0 +1,11 @@
+# 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.

vaxrank/cli/entry_point.py

@@ -24,7 +24,7 @@
 
 
 from varcode.cli import variant_collection_from_args
-from isovar import isovar_results_to_dataframe
+from isovar import isovar_results_to_dataframe, run_isovar_from_parsed_args
 from mhctools.cli import (
     mhc_alleles_from_args,
     mhc_binding_predictor_from_args,

vaxrank/cli/vaccine_config_args.py

@@ -19,10 +19,12 @@
 
 
 def add_vaccine_peptide_args(arg_parser : argparse.ArgumentParser) -> None:
+    default_vaccine_config = VaccineConfig()
+
     vaccine_peptide_group = arg_parser.add_argument_group("Vaccine peptide options")
     vaccine_peptide_group.add_argument(
         "--vaccine-peptide-length",
-        default=25,
+        default=default_vaccine_config.vaccine_peptide_length,
         type=int,
         help="Number of amino acids in the vaccine peptides. (default: %(default)s)")
 

vaxrank/core_logic.py

@@ -137,9 +137,7 @@ def create_vaccine_peptides_dict(
 def vaccine_peptides_for_variant(
         isovar_result : IsovarResult,
         mhc_predictor : BasePredictor,
-        vaccine_peptide_length : int,
-        max_vaccine_peptides_per_variant : int,
-        num_mutant_epitopes_to_keep : int = None,
+
         epitope_config : EpitopeConfig = None,
         vaccine_config : VaccineConfig = None):
     """
@@ -179,12 +177,18 @@ def vaccine_peptides_for_variant(
         variant,
         long_protein_fragment)
 
-    epitope_predictions = predict_epitopes(
+    epitope_predictions_dict = predict_epitopes(
         mhc_predictor=mhc_predictor,
         protein_fragment=long_protein_fragment,
         epitope_config=epitope_config,
-        genome=variant.ensembl).values()
+        genome=variant.ensembl)
+    epitope_predictions : list[] = epitope_predictions_dict.values()
+    return vaccine_peptides_from_epitopes(
+        epitope_predictions, 
+        vaccine_config=vaccine_config)
 
+
+def vaccine_peptides_from_epitopes():
     # TODO: make a function called vaccine_peptides_from_epitopes that
     # takes vaccine_config as an option
     candidate_vaccine_peptides = []
@@ -210,7 +214,7 @@ def vaccine_peptides_for_variant(
         candidate_vaccine_peptide = VaccinePeptide(
             mutant_protein_fragment=candidate_fragment,
             epitope_predictions=subsequence_epitope_predictions,
-            num_mutant_epitopes_to_keep=num_mutant_epitopes_to_keep)
+            num_mutant_epitopes_to_keep=vaccine_config.num_mutant_epitopes_to_keep)
 
         logger.debug(
             "%s, combined score: %0.4f",

vaxrank/epitope_logic.py

@@ -20,7 +20,7 @@
 from mhctools.base_predictor import BasePredictor
 
 
-from .epitope_config import EpitopeConfig 
+from .cli.epitope_config_args import EpitopeConfig 
 from .epitope_prediction import EpitopePrediction
 from .mutant_protein_fragment import MutantProteinFragment
 from .reference_proteome import ReferenceProteome
@@ -42,11 +42,14 @@ def slice_epitope_predictions(
         if p.offset >= start_offset and p.offset + p.length <= end_offset
     ]
 
+Peptide = str
+Allele = str
+
 def predict_epitopes(
         mhc_predictor : BasePredictor,
         protein_fragment : MutantProteinFragment,
-        config : EpitopeConfig = None,
-        genome :  Genome = None):
+        epitope_config : EpitopeConfig = None,
+        genome :  Genome = None) -> dict[tuple[Peptide, Allele], EpitopePrediction]
     """
     Parameters
     ----------
@@ -56,7 +59,7 @@ def predict_epitopes(
     protein_fragment 
         Protein sub-sequence to run MHC binding predictor over 
 
-    config
+    epitope_config
         Configuration object with parameters for scoring epitopes, if 
         missing then default values are used
 
@@ -69,8 +72,8 @@ def predict_epitopes(
 
     Uses the input genome to evaluate whether the epitope occurs in reference.
     """
-    if config is None:
-        config = EpitopeConfig()
+    if epitope_config is None:
+        epitope_config = EpitopeConfig()
 
     results = OrderedDict()
     reference_proteome = ReferenceProteome(genome)
@@ -185,11 +188,11 @@ def predict_epitopes(
             offset=peptide_start_offset,
             occurs_in_reference=occurs_in_reference)
         epitope_score = epitope_prediction.logistic_epitope_score(
-            midpoint=config.logistic_epitope_score_midpoint,
-            width=config.logistic_epitope_score_width,
-            ic50_cutoff=config.binding_affinity_cutoff)
+            midpoint=epitope_config.logistic_epitope_score_midpoint,
+            width=epitope_config.logistic_epitope_score_width,
+            ic50_cutoff=epitope_config.binding_affinity_cutoff)
 
-        if epitope_score >= config.min_epitope_score:
+        if epitope_score >= epitope_config.min_epitope_score:
             key = (epitope_prediction.peptide_sequence, epitope_prediction.allele)
             results[key] = epitope_prediction
         else:

vaxrank/vaccine_config.py

@@ -20,4 +20,4 @@ class VaccineConfig(msgspec.Struct):
 
     max_vaccine_peptides_per_variant : int = 1
 
-    num_mutant_epitopes_to_keep : int = 1000 
+    num_mutant_epitopes_to_keep : int = 1000