working on centralizing config information in msgspec.Struct objects

vaxrank/cli/parser.py → vaxrank/cli/arg_parser.py

@@ -10,37 +10,18 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-import sys
-import logging
-import logging.config
-import pkg_resources
 
-import msgspec 
+
 from argparse import ArgumentParser
 
 from isovar.cli import make_isovar_arg_parser
 from mhctools.cli import add_mhc_args
 
-import pandas as pd
-import serializable
-
 
-from .version import __version__
-from .core_logic import run_vaxrank
-from .epitope_config import DEFAULT_MIN_EPITOPE_SCORE
-from .gene_pathway_check import GenePathwayCheck
-from .report import (
-    make_ascii_report,
-    make_html_report,
-    make_pdf_report,
-    make_csv_report,
-    make_minimal_neoepitope_report,
-    TemplateDataCreator,
-)
-from .patient_info import PatientInfo
-from .epitope_config import epitope_config_from_args
+from .epitope_config_args import add_epitope_prediction_args
+from .vaccine_config_args import add_vaccine_peptide_args
+from ..version import __version__
 
-logger = logging.getLogger(__name__)
 
 
 def make_vaxrank_arg_parser():
@@ -199,39 +180,6 @@ def add_output_args(arg_parser):
         help="Number of mutations to report")
 
 
-def add_vaccine_peptide_args(arg_parser):
-    vaccine_peptide_group = arg_parser.add_argument_group("Vaccine peptide options")
-    vaccine_peptide_group.add_argument(
-        "--vaccine-peptide-length",
-        default=25,
-        type=int,
-        help="Number of amino acids in the vaccine peptides. (default: %(default)s)")
-
-    vaccine_peptide_group.add_argument(
-        "--padding-around-mutation",
-        default=5,
-        type=int,
-        help=(
-            "Number of off-center windows around the mutation to consider "
-            "as vaccine peptides. (default: %(default)s)"
-        ))
-
-    vaccine_peptide_group.add_argument(
-        "--max-vaccine-peptides-per-mutation",
-        default=1,
-        type=int,
-        help=(
-            "Number of vaccine peptides to generate for each mutation. "
-            "(default: %(default)s)"
-        ))
-
-    vaccine_peptide_group.add_argument(
-        "--num-epitopes-per-vaccine-peptide",
-        type=int,
-        help=(
-            "Maximum number of mutant epitopes to consider when scoring "
-            "each vaccine peptide. (default: %(default)s)"))
-
 
 def add_supplemental_report_args(arg_parser):
     report_args_group = arg_parser.add_argument_group("Supplemental report options")
@@ -262,12 +210,6 @@ def check_args(args):
             "--output-passing-variants-csv, "
             "--output-isovar-csv")
 
-def configure_logging(args):
-    logging.config.fileConfig(
-        pkg_resources.resource_filename(
-            __name__,
-            'logging.conf'),
-        defaults={'logfilename': args.log_path})
 
 def choose_arg_parser(args_list):
     # TODO: replace this with a command sub-parser

vaxrank/cli/entry_point.py

@@ -11,18 +11,30 @@
 # limitations under the License.
 
 
+
+import logging
+import logging.config
+
+import sys
+import pkg_resources
+
+
 import pandas as pd
 import serializable
 
+
 from varcode.cli import variant_collection_from_args
 from isovar import isovar_results_to_dataframe
 from mhctools.cli import (
     mhc_alleles_from_args,
     mhc_binding_predictor_from_args,
 )
 
-from .parser import parse_vaxrank_args
-from ..core_logic import run_vaxrank
+from .arg_parser import parse_vaxrank_args
+from .epitope_config_args import epitope_config_from_args
+from .vaccine_config_args import vaccine_config_from_args
+
+from ..core_logic import run_vaxrank, run_vaxrank_from_parsed_args
 from ..gene_pathway_check import GenePathwayCheck
 from ..report import (
     make_ascii_report,
@@ -34,6 +46,16 @@
 )
 from ..patient_info import PatientInfo
 
+logger = logging.getLogger(__name__)
+
+def configure_logging(args):
+    logging.config.fileConfig(
+        pkg_resources.resource_filename(
+            __name__,
+            'logging.conf'),
+        defaults={'logfilename': args.log_path})
+
+
 def main(args_list=None):
     """
     Script to generate vaccine peptide predictions from somatic cancer variants,

vaxrank/cli/epitope_config.py → vaxrank/cli/epitope_config_args.py

@@ -10,21 +10,11 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-import msgspec
-
 import argparse
 
-DEFAULT_MIN_EPITOPE_SCORE = 0.00001
-DEFAULT_BINDING_AFFINITY_CUTOFF = 5000.0
-
-class EpitopeConfig(msgspec.Struct):
+import msgspec 
 
-    """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 = DEFAULT_MIN_EPITOPE_SCORE
-    binding_affinity_cutoff : float = DEFAULT_BINDING_AFFINITY_CUTOFF
+from ..epitope_config import EpitopeConfig
 
 
 def add_epitope_prediction_args(arg_parser : argparse.ArgumentParser):

vaxrank/cli/vaccine_config_args.py

@@ -0,0 +1,70 @@
+# 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 argparse 
+
+import msgspec 
+
+from ..vaccine_config import VaccineConfig
+
+
+
+def add_vaccine_peptide_args(arg_parser : argparse.ArgumentParser) -> None:
+    vaccine_peptide_group = arg_parser.add_argument_group("Vaccine peptide options")
+    vaccine_peptide_group.add_argument(
+        "--vaccine-peptide-length",
+        default=25,
+        type=int,
+        help="Number of amino acids in the vaccine peptides. (default: %(default)s)")
+
+    vaccine_peptide_group.add_argument(
+        "--padding-around-mutation",
+        default=5,
+        type=int,
+        help=(
+            "Number of off-center windows around the mutation to consider "
+            "as vaccine peptides. (default: %(default)s)"
+        ))
+
+    vaccine_peptide_group.add_argument(
+        "--max-vaccine-peptides-per-mutation",
+        default=1,
+        type=int,
+        help=(
+            "Number of vaccine peptides to generate for each mutation. "
+            "(default: %(default)s)"
+        ))
+
+    vaccine_peptide_group.add_argument(
+        "--num-epitopes-per-vaccine-peptide",
+        type=int,
+        help=(
+            "Maximum number of mutant epitopes to consider when scoring "
+            "each vaccine peptide. (default: %(default)s)"))
+
+
+
+
+
+def vaccine_config_from_args(args : argparse.Namespace) -> VaccineConfig:
+    """
+    Extract config path and overrides from argument namespace
+    """
+    epitope_config_kwargs = {}
+    if args.epitope_prediction_config:
+        with open(args.epitope_prediction_config) as f:
+            epitope_config_kwargs.update(msgspec.yaml.decode(f.read()))
+
+    if args.min_epitope_score is not None:
+        epitope_config_kwargs["min_epitope_score"] = args.min_epitope_score
+    epitope_config = msgspec.convert(epitope_config_kwargs, EpitopeConfig)
+    return epitope_config

vaxrank/core_logic.py

@@ -19,6 +19,7 @@
 from mhctools.base_predictor import BasePredictor
 
 from .epitope_config import EpitopeConfig
+from .vaccine_config import VaccineConfig
 from .epitope_logic import slice_epitope_predictions, predict_epitopes
 from .mutant_protein_fragment import MutantProteinFragment
 from .vaccine_peptide import VaccinePeptide
@@ -32,7 +33,8 @@ def run_vaxrank(
         vaccine_peptide_length : int = 25,
         max_vaccine_peptides_per_variant : int = 1,
         num_mutant_epitopes_to_keep : int = 10000,
-        config : EpitopeConfig = None):
+        epitope_config : EpitopeConfig = None,
+        vaccine_config : VaccineConfig = None):
     """
     Parameters
     ----------
@@ -54,16 +56,20 @@ def run_vaxrank(
         Number of top-ranking epitopes for each vaccine peptide to include in
         computation.
 
-    config 
+    epitope_config 
         Configuration options for epitope scoring, using defaults if not provided
+    
+    vaccine_config
+        Configuration options for vaccine peptide selection, using defaults if not provided
     """
     variant_to_vaccine_peptides_dict = create_vaccine_peptides_dict(
         isovar_results=isovar_results,
         mhc_predictor=mhc_predictor,
         vaccine_peptide_length=vaccine_peptide_length,
         max_vaccine_peptides_per_variant=max_vaccine_peptides_per_variant,
         num_mutant_epitopes_to_keep=num_mutant_epitopes_to_keep,
-        config=config)
+        epitope_config=epitope_config,
+        vaccine_config=vaccine_config)
     ranked_list = ranked_vaccine_peptides(variant_to_vaccine_peptides_dict)
 
     return VaxrankResults(
@@ -78,7 +84,8 @@ def create_vaccine_peptides_dict(
         vaccine_peptide_length : int = 25,
         max_vaccine_peptides_per_variant : int = 1,
         num_mutant_epitopes_to_keep : int = 10 ** 5,
-        config : EpitopeConfig = None):
+        epitope_config : EpitopeConfig = None,
+        vaccine_config : VaccineConfig = None):
     """
     Parameters
     ----------
@@ -99,9 +106,11 @@ def create_vaccine_peptides_dict(
         Number of top-ranking epitopes for each vaccine peptide to include in
         computation.
 
-    config 
+    epitope_config 
         Configuration options for epitope scoring, using defaults if not provided
-   
+    
+    vaccine_config
+        Configuration options for vaccine peptide selection, using defaults if not provided
 
     Returns
     -------
@@ -117,7 +126,8 @@ def create_vaccine_peptides_dict(
             vaccine_peptide_length=vaccine_peptide_length,
             max_vaccine_peptides_per_variant=max_vaccine_peptides_per_variant,
             num_mutant_epitopes_to_keep=num_mutant_epitopes_to_keep,
-            config=config)
+            epitope_config=epitope_config,
+            vaccine_config=vaccine_config)
 
         if any(x.contains_mutant_epitopes() for x in vaccine_peptides):
             vaccine_peptides_dict[variant] = vaccine_peptides
@@ -130,7 +140,8 @@ def vaccine_peptides_for_variant(
         vaccine_peptide_length : int,
         max_vaccine_peptides_per_variant : int,
         num_mutant_epitopes_to_keep : int = None,
-        config : EpitopeConfig = None):
+        epitope_config : EpitopeConfig = None,
+        vaccine_config : VaccineConfig = None):
     """
     Parameters
     ----------
@@ -146,14 +157,10 @@ def vaccine_peptides_for_variant(
     max_vaccine_peptides_per_variant 
         Number of vaccine peptides to generate for each mutation.
 
-    num_mutant_epitopes_to_keep : int, optional
+    num_mutant_epitopes_to_keep 
         Number of top-ranking epitopes for each vaccine peptide to include in
         computation.
-
-    min_epitope_score : float, optional
-        Ignore peptides with binding predictions whose normalized score is less
-        than this.
-
+    
     Returns
     -------
     Sorted list of VaccinePeptide objects. If there are no suitable vaccine
@@ -175,9 +182,11 @@ def vaccine_peptides_for_variant(
     epitope_predictions = predict_epitopes(
         mhc_predictor=mhc_predictor,
         protein_fragment=long_protein_fragment,
-        config=config,
+        epitope_config=epitope_config,
         genome=variant.ensembl).values()
-
+
+    # TODO: make a function called vaccine_peptides_from_epitopes that
+    # takes vaccine_config as an option
     candidate_vaccine_peptides = []
 
     for offset, candidate_fragment in long_protein_fragment.sorted_subsequences(

vaxrank/epitope_config.py

@@ -0,0 +1,25 @@
+# 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 
+
+DEFAULT_MIN_EPITOPE_SCORE = 0.00001
+DEFAULT_BINDING_AFFINITY_CUTOFF = 5000.0
+
+class EpitopeConfig(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 = DEFAULT_MIN_EPITOPE_SCORE
+    binding_affinity_cutoff : float = DEFAULT_BINDING_AFFINITY_CUTOFF