Fix for HFE alleles

Author: pbashyal-nmdp

pyard/ard.py

@@ -540,7 +540,7 @@ def is_v2(self, allele: str) -> bool:
             self._config["reduce_v2"]
             and "*" in allele
             and ":" not in allele
-            and allele.split("*")[0] not in ["MICA", "MICB"]
+            and allele.split("*")[0] not in ["MICA", "MICB", "HFE"]
             and allele != self._map_v2_to_v3(allele)
         )
 

pyard/constants.py

@@ -28,7 +28,7 @@
 VALID_REDUCTION_TYPES = ("G", "P", "lg", "lgx", "W", "exon", "U2", "S")
 expression_chars = ("N", "Q", "L", "S")
 # List of P and G characters
-PandG_chars = ["P", "G"]
+P_and_G_chars = ("P", "G")
 
 # Loci with G group data
 # Retrieved from lgx_group

pyard/misc.py

@@ -24,7 +24,7 @@
 import tempfile
 from typing import List
 
-from pyard.constants import VALID_REDUCTION_TYPES, expression_chars, PandG_chars
+from pyard.constants import VALID_REDUCTION_TYPES, expression_chars, P_and_G_chars
 
 
 def get_n_field_allele(allele: str, n: int, preserve_expression=False) -> str:
@@ -47,15 +47,15 @@ def get_n_field_allele(allele: str, n: int, preserve_expression=False) -> str:
 
 def get_3field_allele(a: str) -> str:
     last_char = a[-1]
-    if last_char in PandG_chars:
+    if last_char in P_and_G_chars:
         a = a[:-1]
 
     return get_n_field_allele(a, 3)
 
 
 def get_2field_allele(a: str) -> str:
     last_char = a[-1]
-    if last_char in PandG_chars:
+    if last_char in P_and_G_chars:
         a = a[:-1]
     return get_n_field_allele(a, 2)
 
@@ -76,7 +76,7 @@ def is_2_field_allele(allele: str) -> bool:
 def get_G_name(a: str) -> str:
     a = a.split("/")[0]
     last_char = a[-1]
-    if last_char in PandG_chars + expression_chars:
+    if last_char in P_and_G_chars + expression_chars:
         a = a[:-1]
     if len(a.split(":")) == 2:
         return ":".join([a, "01"]) + "G"
@@ -88,7 +88,7 @@ def get_G_name(a: str) -> str:
 def get_P_name(a: str) -> str:
     a = a.split("/")[0]
     last_char = a[-1]
-    if last_char in PandG_chars + expression_chars:
+    if last_char in P_and_G_chars + expression_chars:
         a = a[:-1]
     return ":".join(a.split(":")[0:2]) + "P"
 

tests/features/allele.feature

@@ -83,6 +83,7 @@ Feature: Alleles
 
     Examples:
       | Allele   | Level | Redux Allele |
+      | HFE*002  | lgx   | HFE*002      |
       | MICA*040 | lgx   | MICA*040     |
       | MICB*006 | lgx   | MICB*006     |
       | MICB*029 | lgx   | MICB*029     |