Cleaned up some unused imports and cleaned up the clinical HLA script's reporting of mismatches when there aren't any.

Author: Richard Liang

src/easyhla/clinical_hla_lib.py

@@ -37,7 +37,7 @@ class HLASequenceCommonFields(TypedDict):
     ambiguous: str
     homozygous: str
     mismatch_count: int
-    mismatches: str
+    mismatches: Optional[str]
     enterdate: datetime
 
 
@@ -62,10 +62,13 @@ def get_common_serialization_fields(
         rep_cs: HLACombinedStandard
         rep_ap, alleles_clean, rep_cs = interpretation.best_common_allele_pair()
 
-        match_details: HLAMatchDetails = interpretation.matches[rep_cs]
-        mismatches_str: str = f"({rep_ap[0]} - {rep_ap[1]}) " + ";".join(
-            str(x) for x in match_details.mismatches
-        )
+        mismatches_str: Optional[str] = None
+        mismatch_count: int = interpretation.lowest_mismatch_count()
+        if mismatch_count > 0:
+            match_details: HLAMatchDetails = interpretation.matches[rep_cs]
+            mismatches_str = f"({rep_ap[0]} - {rep_ap[1]}) " + ";".join(
+                str(x) for x in match_details.mismatches
+            )
 
         return {
             "enum": interpretation.hla_sequence.name,

src/easyhla/interpret_from_json.py

@@ -3,15 +3,10 @@
 import argparse
 import json
 import logging
-from typing import Optional
 
 from .easyhla import EasyHLA
 from .interpret_from_json_lib import HLAInput, HLAResult
-from .models import (
-    HLAInterpretation,
-    HLAProteinPair,
-    HLAStandard,
-)
+from .models import HLAInterpretation
 
 logger: logging.Logger = logging.getLogger(__name__)
 

tests/clinical_hla_lib_test.py

@@ -73,6 +73,17 @@ def dummy_matches(locus: HLA_LOCUS) -> dict[HLACombinedStandard, HLAMatchDetails
     }
 
 
+def dummy_matches_no_mismatches(
+    locus: HLA_LOCUS,
+) -> dict[HLACombinedStandard, HLAMatchDetails]:
+    return {
+        HLACombinedStandard(
+            standard_bin=(2, 2, 1, 2, 1, 4, 4, 2, 8),
+            possible_allele_pairs=((f"{locus}*01:01:01", f"{locus}*02:02:02"),),
+        ): HLAMatchDetails(mismatch_count=0, mismatches=[]),
+    }
+
+
 DUMMY_FREQUENCIES: Final[dict[HLAProteinPair, int]] = {
     HLAProteinPair(
         first_field_1="01",
@@ -119,6 +130,33 @@ def test_hla_sequence_a_build_from_interpretation():
     assert seq_a == expected_result
 
 
+def test_hla_sequence_a_build_from_interpretation_no_mismatches():
+    interp: HLAInterpretation = HLAInterpretation(
+        hla_sequence=dummy_hla_sequence("A"),
+        matches=dummy_matches_no_mismatches("A"),
+        allele_frequencies=DUMMY_FREQUENCIES,
+    )
+    processing_datetime: datetime = datetime(2025, 5, 9, 11, 0, 0)
+
+    seq_a: HLASequenceA = HLASequenceA.build_from_interpretation(
+        interp, processing_datetime
+    )
+
+    expected_result: HLASequenceA = HLASequenceA(
+        enum="dummy_seq",
+        alleles_clean="A*01:01:01 - A*02:02:02",
+        alleles_all="A*01:01:01 - A*02:02:02",
+        ambiguous="False",
+        homozygous="False",
+        mismatch_count=0,
+        mismatches=None,
+        seq="CCACAGGCT",
+        enterdate=processing_datetime,
+    )
+
+    assert seq_a == expected_result
+
+
 def test_hla_sequence_b_build_from_interpretation_non_b5701():
     b5701_standards: list[HLAStandard] = [
         # "Forgiving distance" from sequence: 8
@@ -175,6 +213,58 @@ def test_hla_sequence_b_build_from_interpretation_non_b5701():
     assert seq_b == expected_result
 
 
+def test_hla_sequence_b_build_from_interpretation_no_mismatches():
+    b5701_standards: list[HLAStandard] = [
+        # "Forgiving distance" from sequence: 8
+        HLAStandard(
+            allele="B*57:01:01",
+            two=(8, 8, 8, 8),
+            three=(8, 8, 8, 8, 8),
+        ),
+        # "Forgiving distance" from sequence: 7
+        HLAStandard(
+            allele="B*57:01:02:01N",
+            two=(4, 8, 4, 8),
+            three=(8, 4, 8, 4, 8),
+        ),
+        # "Forgiving distance" from sequence: 6, because 12 "contains" 8
+        HLAStandard(
+            allele="B*57:01:03",
+            two=(4, 4, 8, 8),
+            three=(8, 4, 4, 8, 12),
+        ),
+    ]
+    interp: HLAInterpretation = HLAInterpretation(
+        hla_sequence=dummy_hla_sequence("B"),
+        matches=dummy_matches_no_mismatches("B"),
+        allele_frequencies=DUMMY_FREQUENCIES,
+        b5701_standards=b5701_standards,
+    )
+    processing_datetime: datetime = datetime(2025, 5, 9, 11, 0, 0)
+
+    seq_b: HLASequenceB = HLASequenceB.build_from_interpretation(
+        interp, processing_datetime
+    )
+
+    expected_result: HLASequenceB = HLASequenceB(
+        enum="dummy_seq",
+        alleles_clean="B*01:01:01 - B*02:02:02",
+        alleles_all="B*01:01:01 - B*02:02:02",
+        ambiguous="False",
+        homozygous="False",
+        mismatch_count=0,
+        mismatches=None,
+        b5701="False",
+        b5701_dist=6,
+        seqa="CCAC",
+        seqb="AGGCT",
+        reso_status=None,
+        enterdate=processing_datetime,
+    )
+
+    assert seq_b == expected_result
+
+
 MATCHES_FOR_B5701_CASES: dict[HLACombinedStandard, HLAMatchDetails] = {
     HLACombinedStandard(
         standard_bin=(1, 4, 9, 4),
@@ -241,6 +331,7 @@ def test_hla_sequence_b_build_from_interpretation_non_b5701():
     ),
 ]
 
+
 def test_hla_sequence_b_build_from_interpretation_is_b5701():
     interp: HLAInterpretation = HLAInterpretation(
         hla_sequence=dummy_hla_sequence("B"),
@@ -307,6 +398,34 @@ def test_hla_sequence_c_build_from_interpretation():
     assert seq_c == expected_result
 
 
+def test_hla_sequence_c_build_from_interpretation_no_mismatches():
+    interp: HLAInterpretation = HLAInterpretation(
+        hla_sequence=dummy_hla_sequence("C"),
+        matches=dummy_matches_no_mismatches("C"),
+        allele_frequencies=DUMMY_FREQUENCIES,
+    )
+    processing_datetime: datetime = datetime(2025, 5, 9, 11, 0, 0)
+
+    seq_c: HLASequenceC = HLASequenceC.build_from_interpretation(
+        interp, processing_datetime
+    )
+
+    expected_result: HLASequenceC = HLASequenceC(
+        enum="dummy_seq",
+        alleles_clean="C*01:01:01 - C*02:02:02",
+        alleles_all="C*01:01:01 - C*02:02:02",
+        ambiguous="False",
+        homozygous="False",
+        mismatch_count=0,
+        mismatches=None,
+        seqa="CCAC",
+        seqb="AGGCT",
+        enterdate=processing_datetime,
+    )
+
+    assert seq_c == expected_result
+
+
 @pytest.mark.parametrize(
     "raw_contents, locus, sample_name, expected_sanitized_contents",
     [