A number of minor fixes.

Author: Richard Liang

src/easyhla/bblab_lib.py

@@ -230,7 +230,7 @@ def summary_row(cls, interpretation: HLAInterpretation) -> "HLAInterpretationRow
             )
 
         allele_pairs: AllelePairs = interpretation.best_matching_allele_pairs()
-        alleles_all_str = allele_pairs.stringify()
+        alleles_all_str = allele_pairs.stringify(sorted=True)
 
         alleles_clean: str
         _, alleles_clean, __ = interpretation.best_common_allele_pair()

src/easyhla/hla_algorithm.rb

@@ -44,16 +44,10 @@ def initialize(raw_result)
 
 class HLAAlgorithm
   def initialize(
-    hla_a_std_path=nil,
-    hla_b_std_path=nil,
-    hla_c_std_path=nil,
+    hla_std_path=nil,
     hla_freq_path=nil
   )
-    @hla_std_paths = {
-      'A' => hla_a_std_path,
-      'B' => hla_b_std_path,
-      'C' => hla_c_std_path
-    }
+    @hla_std_path = hla_std_path
     @hla_freq_path = hla_freq_path
   end
 
@@ -62,10 +56,17 @@ def analyze(seqs, locus='B')
       "seq1" => seqs[0],
       "seq2" => seqs[1],
       "locus" => locus,
-      "hla_std_path" => File.expand_path(@hla_std_paths[locus]),
+      "hla_std_path" => File.expand_path(@hla_std_path),
       "hla_freq_path" => File.expand_path(@hla_freq_path)
     }
 
+    if (!@hla_std_path.nil?)
+      hla_input["hla_std_path"] = File.expand_path(@hla_std_path)
+    end
+    if (!@hla_freq_path.nil?)
+      hla_input["hla_freq_path"] = File.expand_path(@hla_freq_path)
+    end
+
     python_stdout, python_stderr, wait_thread = Open3.capture3(
       "#{HLA_INTERPRET_FROM_JSON} -",
       stdin_data: JSON.generate(hla_input)

src/easyhla/interpret_from_json_lib.py

@@ -117,7 +117,7 @@ def build_from_interpretation(cls, interp: HLAInterpretation) -> "HLAResult":
 
         return HLAResult(
             seqs=seqs,
-            alleles_all=[f"{x[0]} - {x[1]}" for x in aps.allele_pairs],
+            alleles_all=[f"{x[0]} - {x[1]}" for x in aps.sort_pairs()],
             alleles_clean=alleles_clean,
             alleles_for_mismatches=f"{rep_ap[0]} - {rep_ap[1]}",
             mismatches=[str(x) for x in match_details.mismatches],

tests/bblab_lib_test.py

@@ -759,7 +759,7 @@ def test_pair_exons(
                 alleles_clean="B*10:01 - B*20",
                 alleles=(
                     "B*01:01:01 - B*02:02:02;B*10:01:10 - B*20:01;"
-                    "B*10:01:10 - B*22:22:22;B*10:01:15 - B*20:02:03"
+                    "B*10:01:10 - B*111:22:22;B*10:01:15 - B*20:02:03"
                 ),
                 ambiguous=1,
                 homozygous=0,

tests/clinical_hla_lib_test.py

@@ -61,7 +61,7 @@ def dummy_matches(locus: HLA_LOCUS) -> dict[HLACombinedStandard, HLAMatchDetails
             standard_bin=(2, 4, 10, 2),
             possible_allele_pairs=(
                 (f"{locus}*10:01:10", f"{locus}*20:01"),
-                (f"{locus}*10:01:10", f"{locus}*22:22:22"),
+                (f"{locus}*10:01:10", f"{locus}*111:22:22"),
             ),
         ): HLAMatchDetails(
             mismatch_count=1,
@@ -117,7 +117,7 @@ def test_hla_sequence_a_build_from_interpretation():
         alleles_clean="A*10:01 - A*20",
         alleles_all=(
             "A*01:01:01 - A*02:02:02;A*10:01:10 - A*20:01;"
-            "A*10:01:10 - A*22:22:22;A*10:01:15 - A*20:02:03"
+            "A*10:01:10 - A*111:22:22;A*10:01:15 - A*20:02:03"
         ),
         ambiguous="True",
         homozygous="False",
@@ -196,7 +196,7 @@ def test_hla_sequence_b_build_from_interpretation_non_b5701():
         alleles_clean="B*10:01 - B*20",
         alleles_all=(
             "B*01:01:01 - B*02:02:02;B*10:01:10 - B*20:01;"
-            "B*10:01:10 - B*22:22:22;B*10:01:15 - B*20:02:03"
+            "B*10:01:10 - B*111:22:22;B*10:01:15 - B*20:02:03"
         ),
         ambiguous="True",
         homozygous="False",
@@ -384,7 +384,7 @@ def test_hla_sequence_c_build_from_interpretation():
         alleles_clean="C*10:01 - C*20",
         alleles_all=(
             "C*01:01:01 - C*02:02:02;C*10:01:10 - C*20:01;"
-            "C*10:01:10 - C*22:22:22;C*10:01:15 - C*20:02:03"
+            "C*10:01:10 - C*111:22:22;C*10:01:15 - C*20:02:03"
         ),
         ambiguous="True",
         homozygous="False",

tests/interpret_from_json_lib_test.py

@@ -231,7 +231,7 @@ def test_hla_input_hla_sequence_locus_bc():
                 alleles_all=[
                     "A*01:01:01 - A*02:02:02",
                     "A*10:01:10 - A*20:01",
-                    "A*10:01:10 - A*22:22:22",
+                    "A*10:01:10 - A*111:22:22",
                     "A*10:01:15 - A*20:02:03",
                 ],
                 alleles_clean="A*10:01 - A*20",
@@ -279,7 +279,7 @@ def test_hla_input_hla_sequence_locus_bc():
                 alleles_all=[
                     "C*01:01:01 - C*02:02:02",
                     "C*10:01:10 - C*20:01",
-                    "C*10:01:10 - C*22:22:22",
+                    "C*10:01:10 - C*111:22:22",
                     "C*10:01:15 - C*20:02:03",
                 ],
                 alleles_clean="C*10:01 - C*20",