Cleanup

- Make `is_valid_allele` public
- misc cleanup

Author: pbashyal-nmdp

pyard/ard_refactored.py

@@ -204,7 +204,7 @@ def _redux_allele(
                 )
                 if "/" in twice_redux_allele:
                     return twice_redux_allele
-                if self._is_valid_allele(twice_redux_allele):
+                if self.is_valid_allele(twice_redux_allele):
                     return twice_redux_allele
 
         return self.allele_reducer.reduce_allele(allele, redux_type, re_ping)
@@ -361,7 +361,7 @@ def _is_who_allele(self, allele: str) -> bool:
     def _is_allele_in_db(self, allele: str) -> bool:
         return allele in self.allele_group.alleles
 
-    def _is_valid_allele(self, allele: str) -> bool:
+    def is_valid_allele(self, allele: str) -> bool:
         if allele.endswith(("P", "G")):
             allele = allele[:-1]
         if "*" in allele:
@@ -402,7 +402,7 @@ def _is_valid(self, allele: str) -> bool:
             and not self.is_v2(allele)
             and not self.is_shortnull(allele)
         ):
-            return self._is_valid_allele(allele)
+            return self.is_valid_allele(allele)
 
         return True
 

pyard/reducers/default_reducer.py

@@ -2,6 +2,7 @@
 from typing_extensions import override
 
 from .base_reducer import Reducer
+from ..exceptions import InvalidAlleleError
 
 
 class DefaultReducer(Reducer):
@@ -18,9 +19,7 @@ def reduce(self, allele: str) -> str:
             if allele in self.ard.ars_mappings.g_group.values():
                 return allele
 
-        if self.ard._is_allele_in_db(allele):
+        if self.ard.is_valid_allele(allele):
             return allele
         else:
-            from ..exceptions import InvalidAlleleError
-
             raise InvalidAlleleError(f"{allele} is an invalid allele.")

pyard/reducers/exon_reducer.py

@@ -2,6 +2,7 @@
 from typing import override
 
 from .base_reducer import Reducer
+from ..constants import expression_chars
 
 
 class ExonReducer(Reducer):
@@ -13,7 +14,6 @@ def reduce(self, allele: str) -> str:
             exon_group_allele = self.ard.ars_mappings.exon_group[allele]
             # Check if the 3 field exon allele has a 4 field alleles
             # that all have the same expression characters
-            from ..constants import expression_chars
 
             last_char = allele[-1]
             if last_char in expression_chars:

pyard/reducers/p_reducer.py

@@ -1,10 +1,10 @@
 # -*- coding: utf-8 -*-
 from typing import override
 
-from .base_reducer import Reducer
+from .default_reducer import DefaultReducer
 
 
-class PGroupReducer(Reducer):
+class PGroupReducer(DefaultReducer):
     """Strategy for P group reduction"""
 
     @override

pyard/reducers/s_reducer.py

@@ -4,16 +4,15 @@
 from typing import override
 
 from .base_reducer import Reducer
+from .. import db
+from ..misc import is_2_field_allele
 
 
 class SReducer(Reducer):
     """Strategy for serology reduction"""
 
     @override
     def reduce(self, allele: str) -> str:
-        from .. import db
-        from ..misc import is_2_field_allele
-
         # find serology equivalent in serology_mapping
         if is_2_field_allele(allele):
             allele = self.ard._redux_allele(allele, "lgx")

pyard/reducers/u2_reducer.py

@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 
 from .base_reducer import Reducer
+from ..misc import get_n_field_allele
 
 
 class U2Reducer(Reducer):
@@ -12,7 +13,6 @@ def reduce(self, allele: str) -> str:
         if len(allele_fields) == 2:
             return allele
         # If the 2 field reduction is unambiguous, reduce to 2 field level
-        from ..misc import get_n_field_allele
 
         allele_2_fields = get_n_field_allele(allele, 2, preserve_expression=True)
         if self.ard._is_allele_in_db(allele_2_fields):

setup.py

@@ -63,10 +63,12 @@
         "Topic :: Scientific/Engineering :: Bio-Informatics",
         "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
         "Natural Language :: English",
+        "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
         "Programming Language :: Python :: 3.12",
+        "Programming Language :: Python :: 3.13",
     ],
     test_suite="tests",
     tests_require=test_requirements,