WIP: cleaned up the update_frequency_file script and started adding tests.

Tests seem to be choking when I run the entire test suite; to get them
to run I had to move some test files out of place!

Author: rhliang

pyproject.toml

@@ -63,6 +63,7 @@ clinical_hla = "easyhla.clinical_hla:main"
 interpret_from_json = "easyhla.interpret_from_json:main"
 bblab = "easyhla.bblab:main"
 update_alleles = "easyhla.update_alleles:main"
+update_frequency_file = "easyhla.update_frequency_file:main"
 
 [project.optional-dependencies]
 database = [
@@ -116,6 +117,7 @@ omit = [
   "src/easyhla/clinical_hla.py",
   "src/easyhla/interpret_from_json.py",
   "src/easyhla/update_alleles.py",
+  "src/easyhla/update_frequency_file.py",
   "src/scripts/*.py",
 ]
 

src/easyhla/models.py

@@ -133,46 +133,46 @@ def __lt__(self, other: "HLAProteinPair") -> bool:
         )
         return me_tuple < other_tuple
 
-    UNKNOWN: ClassVar[Final[str]] = "unknown"
+    UNMAPPED: ClassVar[Final[str]] = "unmapped"
     DEPRECATED: ClassVar[Final[str]] = "deprecated"
 
     class NonAlleleException(Exception):
         def __init__(
             self,
-            first_unknown: bool = False,
+            first_unmapped: bool = False,
             first_deprecated: bool = False,
-            second_unknown: bool = False,
+            second_unmapped: bool = False,
             second_deprecated: bool = False,
         ):
-            self.first_unknown = first_unknown
+            self.first_unmapped = first_unmapped
             self.first_deprecated = first_deprecated
-            self.second_unknown = second_unknown
+            self.second_unmapped = second_unmapped
             self.second_deprecated = second_deprecated
 
         @classmethod
         def from_frequency_entry(
             cls, raw_first_allele: str, raw_second_allele: str
         ) -> Optional[Self]:
-            first_unknown: bool = False
+            first_unmapped: bool = False
             first_deprecated: bool = False
-            second_unknown: bool = False
+            second_unmapped: bool = False
             second_deprecated: bool = False
 
-            if raw_first_allele == HLAProteinPair.UNKNOWN:
-                first_unknown = True
+            if raw_first_allele == HLAProteinPair.UNMAPPED:
+                first_unmapped = True
             elif raw_first_allele == HLAProteinPair.DEPRECATED:
                 first_deprecated = True
 
-            if raw_second_allele == HLAProteinPair.UNKNOWN:
-                second_unknown = True
+            if raw_second_allele == HLAProteinPair.UNMAPPED:
+                second_unmapped = True
             elif raw_second_allele == HLAProteinPair.DEPRECATED:
                 second_deprecated = True
 
             if any(
-                (first_unknown, first_deprecated, second_unknown, second_deprecated)
+                (first_unmapped, first_deprecated, second_unmapped, second_deprecated)
             ):
                 return cls(
-                    first_unknown, first_deprecated, second_unknown, second_deprecated
+                    first_unmapped, first_deprecated, second_unmapped, second_deprecated
                 )
             return None
 

src/easyhla/update_frequency_file.py

@@ -0,0 +1,116 @@
+#! /usr/bin/env python
+
+import argparse
+import csv
+import logging
+from collections import Counter
+
+from .update_frequency_file_lib import (
+    FREQUENCY_FIELDS,
+    FrequencyRowDict,
+    NewName,
+    OldName,
+    parse_nomenclature,
+    update_old_frequencies,
+)
+from .utils import HLA_LOCUS
+
+logging.basicConfig()
+logger: logging.Logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
+
+
+def main():
+    parser: argparse.ArgumentParser = argparse.ArgumentParser(
+        "Update the format of the old HLA frequencies file"
+    )
+    parser.add_argument(
+        "old_frequency_file",
+        help="Old frequency file path (6-column CSV without header)",
+        type=argparse.FileType("r"),
+    )
+    parser.add_argument(
+        "name_mapping",
+        help=(
+            "File mapping old allele names to new allele names in the format "
+            "kept by IMGT/HLA"
+        ),
+        type=argparse.FileType("r"),
+    )
+    parser.add_argument(
+        "--output",
+        help="Output CSV file",
+        type=argparse.FileType("w"),
+        default="hla_frequencies.csv",
+    )
+    args: argparse.Namespace = parser.parse_args()
+
+    logger.info("Reading in the update mapping....")
+    with args.name_mapping:
+        old_to_new: dict[OldName, NewName]
+        deprecated: list[str]
+        deprecated_maps_to_other: list[tuple[str, str]]
+        mapping_overrides_deprecated: list[tuple[str, str]]
+        (
+            old_to_new,
+            deprecated,
+            deprecated_maps_to_other,
+            mapping_overrides_deprecated,
+        ) = parse_nomenclature(args.name_mapping.read())
+
+    for old_name_str in deprecated:
+        logger.info(f"Allele {old_name_str} is deprecated.")
+
+    for old_name_str, existing_mapping in deprecated_maps_to_other:
+        logger.info(
+            f"Allele {old_name_str} is deprecated but another allele "
+            "with the same first two coordinates maps to "
+            f"{existing_mapping}; retaining that mapping."
+        )
+
+    for old_name_str, new_name_str in mapping_overrides_deprecated:
+        logger.info(
+            f"Allele {old_name_str} maps to {new_name_str} but another "
+            f"allele with the same first two coordinates was "
+            f"deprecated; updating the mapping."
+        )
+
+    logger.info("Updating old alleles....")
+    with args.old_frequency_file:
+        updated_frequencies: list[FrequencyRowDict]
+        unmapped_alleles: Counter[tuple[HLA_LOCUS, str]]
+        deprecated_alleles_seen: Counter[tuple[HLA_LOCUS, str]]
+        updated_frequencies, unmapped_alleles, deprecated_alleles_seen = (
+            update_old_frequencies(args.old_frequency_file, old_to_new)
+        )
+
+    if len(unmapped_alleles) > 1:
+        logger.info(
+            "Alleles present in the old frequencies that do not have a mapping "
+            "in the new nomenclature, and their numbers of occurrences:"
+        )
+        for locus, name in unmapped_alleles:
+            logger.info(
+                f'HLA-{locus} allele "{name}": {unmapped_alleles[(locus, name)]}'
+            )
+
+    if len(deprecated_alleles_seen) > 1:
+        logger.info(
+            "Alleles present in the old frequencies that are deprecated "
+            "in the new nomenclature, and their numbers of occurrences:"
+        )
+        for locus, name in deprecated_alleles_seen:
+            logger.info(
+                f'HLA-{locus} allele "{name}": {deprecated_alleles_seen[(locus, name)]}'
+            )
+
+    with args.output:
+        frequencies_csv: csv.DictWriter = csv.DictWriter(args.output, FREQUENCY_FIELDS)
+        frequencies_csv.writeheader()
+        frequencies_csv.writerows(updated_frequencies)
+
+    logger.info("... done.")
+
+
+if __name__ == "__main__":
+    main()