Merge pull request #82 from pbashyal-nmdp/map_drbx

Map DRB3, DRB4 and DRB5 typings to DRBX.

Author: mmaiers-nmdp

pyard/drbx.py

@@ -0,0 +1,43 @@
+from typing import Tuple, List
+
+
+def map_drbx(drb_alleles: List, locus_in_allele_name: bool) -> Tuple:
+    """
+    Generates a pair of DRBX Typings based on DRB3, DRB4 and DRB5 typings.
+    Expects Type1 and Type2 DRB3, DRB4 and DRB5 typings in that order
+    in `drb_alleles` list.
+
+    Reference:
+    World Marrow Donor Association guidelines for use of HLA nomenclature
+    and its validation in the data exchange among hematopoietic
+    stem cell donor registries and cord blood banks
+    https://www.nature.com/articles/1705672
+
+    :param drb_alleles: Type1/Type2 DRB3, DRB4 and DRB5 typings.
+    :param locus_in_allele_name: Does typing include DRBn prefix?
+    :return: Tuple of DRBX type1/type2
+    """
+
+    nnnn = 'NNNN'
+    if locus_in_allele_name:
+        nnnn = 'DRBX*NNNN'
+
+    # Get the ones DRBs without NNNNs
+    drbx_non_nns = list(filter(lambda x: x != '' and not x.endswith('NNNN'), drb_alleles))
+    if len(drbx_non_nns) == 0:
+        return nnnn, nnnn
+
+    # There can only be at most 2 DRBn loci present
+    if len(drbx_non_nns) == 2:
+        # If they are homozygous, return a single DRBn only
+        if drbx_non_nns[0] == drbx_non_nns[1]:
+            return drbx_non_nns[0], ''
+        # Else return drbx_1 and drbx_2
+        return tuple(drbx_non_nns)
+
+    # If there's only a single DRBn, return NNNN as the second typing
+    if len(drbx_non_nns) == 1:
+        return drbx_non_nns[0], nnnn
+
+    # Everything else is NNNNs
+    return nnnn, nnnn

tests/features/drbx.feature

@@ -0,0 +1,32 @@
+Feature: DRBX Mapping
+
+  Create a single DRBX genotype from DRB3, DRB4, DRB5 alleles
+
+  Scenario Outline:
+
+    Given a subject has <DRB3_Type1> and <DRB3_Type2> DRB3 alleles
+    And a subject has <DRB4 Type1> and <DRB4 Type2> DRB4 alleles
+    And a subject has <DRB5 Type1> and <DRB5 Type2> DRB5 alleles
+    When I create a DRBX genotype
+    Then it should be <DRBX_Type1> and <DRBX_Type2>
+
+    Examples: All NNNS
+      | DRB3_Type1 | DRB3_Type2 | DRB4 Type1 | DRB4 Type2 | DRB5 Type1 | DRB5 Type2 | DRBX_Type1 | DRBX_Type2 |
+      | DRB3*NNNN  | x          | DRB4*NNNN  | x          | DRB5*NNNN  | x          | DRBX*NNNN  | DRBX*NNNN  |
+      | DRB3*NNNN  | x          | x          | x          | x          | x          | DRBX*NNNN  | DRBX*NNNN  |
+      | DRB3*NNNN  | x          | DRB4*NNNN  | x          | x          | x          | DRBX*NNNN  | DRBX*NNNN  |
+
+    Examples: Some NNNS
+      | DRB3_Type1 | DRB3_Type2 | DRB4 Type1 | DRB4 Type2 | DRB5 Type1 | DRB5 Type2 | DRBX_Type1 | DRBX_Type2 |
+      | DRB3*02:02 | x          | x          | x          | x          | x          | DRB3*02:02 | DRBX*NNNN  |
+      | DRB3*02:02 | x          | DRB4*01:01 | x          | DRB5*NNNN  | x          | DRB3*02:02 | DRB4*01:01 |
+
+    Examples: No NNNS
+      | DRB3_Type1 | DRB3_Type2 | DRB4 Type1 | DRB4 Type2 | DRB5 Type1 | DRB5 Type2 | DRBX_Type1 | DRBX_Type2 |
+      | DRB3*02:02 | x          | DRB4*01:01 | x          | x          | x          | DRB3*02:02 | DRB4*01:01 |
+      | DRB3*02:02 | DRB3*01:01 | x          | x          | x          | x          | DRB3*02:02 | DRB3*01:01 |
+      | DRB3*01:01 | x          | DRB4*01:01 | x          | x          | x          | DRB3*01:01 | DRB4*01:01 |
+
+    Examples: Homozygous
+      | DRB3_Type1 | DRB3_Type2 | DRB4 Type1 | DRB4 Type2 | DRB5 Type1 | DRB5 Type2 | DRBX_Type1 | DRBX_Type2 |
+      | DRB3*02:02 | DRB3*02:02 | x          | x          | x          | x          | DRB3*02:02 | x          |

tests/steps/generate_drbx.py

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+from behave import *
+from hamcrest import assert_that, is_
+
+from pyard.drbx import map_drbx
+
+
+@given("a subject has {arg0} and {arg1} DRB3 alleles")
+def step_impl(context, arg0, arg1):
+    context.drb3_1 = '' if arg0 == 'x' else arg0
+    context.drb3_2 = '' if arg1 == 'x' else arg1
+
+
+@step("a subject has {arg0} and {arg1} DRB4 alleles")
+def step_impl(context, arg0, arg1):
+    context.drb4_1 = '' if arg0 == 'x' else arg0
+    context.drb4_2 = '' if arg1 == 'x' else arg1
+
+
+@step("a subject has {arg0} and {arg1} DRB5 alleles")
+def step_impl(context, arg0, arg1):
+    context.drb5_1 = '' if arg0 == 'x' else arg0
+    context.drb5_2 = '' if arg1 == 'x' else arg1
+
+
+@when("I create a DRBX genotype")
+def step_impl(context):
+    drbs = [
+        context.drb3_1, context.drb3_2,
+        context.drb4_1, context.drb4_2,
+        context.drb5_1, context.drb5_2
+    ]
+    context.drbx = map_drbx(drbs, True)
+
+
+@then("it should be {drbx1} and {drbx2}")
+def step_impl(context, drbx1, drbx2):
+    expected_drbx_1 = '' if drbx1 == 'x' else drbx1
+    expected_drbx_2 = '' if drbx2 == 'x' else drbx2
+    expected_drbx = (expected_drbx_1, expected_drbx_2)
+    assert_that(context.drbx, is_(expected_drbx))