add split alleles to broad serology (#78)

* add split alleles to broad serology

* update expected results based on new behavior of serology.feature

* smartsorting broad serology glstrings and updated expected serology.feature results

* formatting of serology.feature

* formatting of serology.feature

* more formatting of serology.feature

* even more formatting of serology.feature

* Bump version: 0.6.1 → 0.6.2

Author: mmaiers-nmdp

pyard/__init__.py

@@ -24,4 +24,4 @@
 from .pyard import ARD
 
 __author__ = """NMDP Bioinformatics"""
-__version__ = '0.6.1'
+__version__ = '0.6.2'

pyard/broad_splits.py

@@ -28,7 +28,7 @@
 #
 # Mapping Generated from `dna_relshp.csv` file
 #
-broad_splits_mapping = {
+broad_splits_dna_mapping = {
     'A*09': ['A*23', 'A*24'],
     'A*10': ['A*25', 'A*26', 'A*34', 'A*66'],
     'A*19': ['A*29', 'A*30', 'A*31', 'A*32', 'A*33', 'A*74'],
@@ -45,3 +45,23 @@
     'DRB1*02': ['DRB1*15', 'DRB1*16'],
     'DRB1*06': ['DRB1*13', 'DRB1*14']
 }
+broad_splits_ser_mapping = {
+    'A9':  ['A23', 'A24'],
+    'A10': ['A25', 'A26', 'A34', 'A66'],
+    'A19': ['A29', 'A30', 'A31', 'A32', 'A33', 'A74'],
+    'A28': ['A68', 'A69'],
+    'B5':  ['B51', 'B52'],
+    'B12': ['B44', 'B45'],
+    'B15': ['B62', 'B63', 'B75', 'B76', 'B77'], 
+    'B16': ['B38', 'B39'],
+    'B17': ['B57', 'B58'],
+    'B21': ['B49', 'B50'],
+    'B22': ['B54', 'B55', 'B56'],
+    'B40': ['B60', 'B61'],
+    'B70': ['B71', 'B72'],
+    'DQ1': ['DQ5',  'DQ6'],
+    'DR2': ['DR15', 'DR16'],
+    'DR3': ['DR17', 'DR18'],
+    'DR5': ['DR11', 'DR12'],
+    'DR6': ['DR13', 'DR14']
+}

pyard/data_repository.py

@@ -26,7 +26,8 @@
 import pandas as pd
 
 from pyard import db
-from pyard.broad_splits import broad_splits_mapping
+from pyard.broad_splits import broad_splits_dna_mapping
+from pyard.broad_splits import broad_splits_ser_mapping
 
 # GitHub URL where IMGT HLA files are downloaded.
 from pyard.smart_sort import smart_sort_comparator
@@ -185,7 +186,7 @@ def generate_alleles_and_xx_codes(db_connection: sqlite3.Connection, imgt_versio
         .to_dict()
 
     # Update xx codes with broads and splits
-    for broad, splits in broad_splits_mapping.items():
+    for broad, splits in broad_splits_dna_mapping.items():
         for split in splits:
             if broad in xx_codes:
                 xx_codes[broad].extend(xx_codes[split])
@@ -318,6 +319,20 @@ def generate_serology_mapping(db_connection: sqlite3.Connection, imgt_version):
             apply(lambda x: '/'.join(sorted(x['Allele']))). \
             to_dict()
 
+        # map alleles for split serology to their corresponding broad
+        # Update xx codes with broads and splits
+        for broad, splits in broad_splits_ser_mapping.items():
+            for split in splits:
+                try:
+                    sero_mapping[broad] = '/'.join([sero_mapping[broad], sero_mapping[split]])
+
+                except KeyError:
+                    sero_mapping[broad] = sero_mapping[split]
+
+        # re-sort allele lists into smartsort order
+        for sero in sero_mapping.keys():
+           sero_mapping[sero] =  '/'.join(sorted(sero_mapping[sero].split('/'), key=functools.cmp_to_key(smart_sort_comparator)))
+
         # Save the serology mapping to db
         db.save_dict(db_connection, table_name='serology_mapping',
                      dictionary=sero_mapping, columns=('serology', 'allele_list'))

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.6.1
+current_version = 0.6.2
 commit = True
 tag = True
 

setup.py

@@ -42,7 +42,7 @@
 
 setup(
     name='py-ard',
-    version='0.6.1',
+    version='0.6.2',
     description="ARD reduction for HLA with Python",
     long_description=readme + '\n\n' + history,
     author="CIBMTR",

tests/features/serology.feature

@@ -12,9 +12,9 @@ Feature: Serology
 
     Examples: Valid A serology typings
       | Serology | Level | Redux Allele                                                |
-      | A10      | G     | A*26:01:01G/A*26:10/A*26:15/A*26:92/A*66:01:01G/A*66:03:01G |
-      | A10      | lg    | A*26:01g/A*26:10g/A*26:15g/A*26:92g/A*66:01g/A*66:03g       |
-      | A10      | lgx   | A*26:01/A*26:10/A*26:15/A*26:92/A*66:01/A*66:03             |
-      | A19      | G     | A*02:65/A*33:09                                             |
-      | DR1403   | G     | DRB1*14:03:01/DRB1*14:03:02                                 |
-      | DR2      | G     | DRB1*15:08/DRB1*16:03                                       |
+      | A10      | G     | A*25:01:01G/A*25:01:02/A*25:01:03/A*25:01:04/A*25:01:05/A*25:01:06/A*25:01:07/A*25:01:08/A*25:01:09/A*25:01:10/A*25:01:11/A*25:02/A*25:03/A*25:04/A*25:05/A*25:06/A*25:08/A*25:09/A*25:10/A*25:11/A*25:13/A*25:14/A*25:15/A*25:16/A*25:17/A*25:18/A*25:19:01/A*25:19:02/A*25:20/A*25:21/A*25:22/A*25:23/A*25:24/A*25:25/A*25:26/A*25:27:01/A*25:27:02/A*25:28/A*25:29/A*25:30/A*25:31/A*25:32/A*25:33/A*25:34/A*25:35/A*25:36/A*25:37/A*25:38/A*25:39/A*25:40/A*25:41/A*25:43/A*25:44/A*25:45/A*26:01:01G/A*26:01:02/A*26:01:03/A*26:01:04/A*26:01:05/A*26:01:06/A*26:01:08/A*26:01:09/A*26:01:10/A*26:01:11/A*26:01:12/A*26:01:13/A*26:01:14/A*26:01:15/A*26:01:16/A*26:01:17/A*26:01:18/A*26:01:19/A*26:01:20/A*26:01:21/A*26:01:22/A*26:01:23/A*26:01:24/A*26:01:26/A*26:01:27/A*26:01:28/A*26:01:29/A*26:01:30/A*26:01:31/A*26:01:33/A*26:01:34/A*26:01:36/A*26:01:37/A*26:01:38/A*26:01:39/A*26:01:41/A*26:01:42/A*26:02:01/A*26:02:02/A*26:03:01/A*26:04/A*26:05/A*26:06/A*26:07:01/A*26:07:02/A*26:08/A*26:09/A*26:10/A*26:12/A*26:13/A*26:14/A*26:15/A*26:16/A*26:17/A*26:18/A*26:19/A*26:20/A*26:21/A*26:22/A*26:23/A*26:27/A*26:28/A*26:29/A*26:30/A*26:31/A*26:32/A*26:33/A*26:34/A*26:35/A*26:36/A*26:37/A*26:38/A*26:39/A*26:40/A*26:41/A*26:42/A*26:43:01/A*26:43:02/A*26:45/A*26:46/A*26:47/A*26:48/A*26:49/A*26:50/A*26:51/A*26:52/A*26:53/A*26:54/A*26:55/A*26:57/A*26:58/A*26:59/A*26:61/A*26:62/A*26:63/A*26:64/A*26:65/A*26:66/A*26:67/A*26:68/A*26:69/A*26:70/A*26:72/A*26:73/A*26:74/A*26:75/A*26:76/A*26:77/A*26:78/A*26:79/A*26:80/A*26:81/A*26:83/A*26:84/A*26:85/A*26:86/A*26:87/A*26:88/A*26:89/A*26:90/A*26:91/A*26:92/A*26:93/A*26:94/A*26:95/A*26:96/A*26:97/A*26:100/A*26:101/A*26:102/A*26:103/A*26:104/A*26:105/A*26:106/A*26:108/A*26:109/A*26:110/A*26:111/A*26:112/A*26:113/A*26:114/A*26:115/A*26:116/A*26:118/A*26:119/A*26:120/A*26:121/A*26:122/A*26:123/A*26:124/A*26:125/A*26:126/A*26:128/A*26:129/A*26:130/A*26:131/A*26:132/A*26:133/A*26:134/A*26:135/A*26:136/A*26:137/A*26:138/A*26:139/A*26:140/A*26:141/A*26:142/A*26:143/A*26:144/A*34:01:01/A*34:01:02/A*34:02:01/A*34:02:02/A*34:02:03/A*34:02:04/A*34:03/A*34:04/A*34:05/A*34:06/A*34:07/A*34:08/A*34:09/A*34:11/A*34:12/A*34:13/A*34:14/A*34:15/A*34:16/A*34:17/A*66:01:01G/A*66:01:02/A*66:01:03/A*66:02/A*66:03:01G/A*66:04/A*66:05/A*66:06/A*66:07/A*66:09/A*66:10/A*66:11/A*66:12/A*66:13/A*66:14/A*66:15/A*66:16/A*66:18/A*66:19/A*66:20/A*66:21/A*66:22/A*66:23/A*66:24/A*66:25/A*66:26Q | 
+      | A10      | lg    | A*25:01g/A*25:02g/A*25:03g/A*25:04g/A*25:05g/A*25:06g/A*25:08g/A*25:09g/A*25:10g/A*25:11g/A*25:13g/A*25:14g/A*25:15g/A*25:16g/A*25:17g/A*25:18g/A*25:19g/A*25:20g/A*25:21g/A*25:22g/A*25:23g/A*25:24g/A*25:25g/A*25:26g/A*25:27g/A*25:28g/A*25:29g/A*25:30g/A*25:31g/A*25:32g/A*25:33g/A*25:34g/A*25:35g/A*25:36g/A*25:37g/A*25:38g/A*25:39g/A*25:40g/A*25:41g/A*25:43g/A*25:44g/A*25:45g/A*26:01g/A*26:02g/A*26:03g/A*26:04g/A*26:05g/A*26:06g/A*26:07g/A*26:08g/A*26:09g/A*26:10g/A*26:12g/A*26:13g/A*26:14g/A*26:15g/A*26:16g/A*26:17g/A*26:18g/A*26:19g/A*26:20g/A*26:21g/A*26:22g/A*26:23g/A*26:27g/A*26:28g/A*26:29g/A*26:30g/A*26:31g/A*26:32g/A*26:33g/A*26:34g/A*26:35g/A*26:36g/A*26:37g/A*26:38g/A*26:39g/A*26:40g/A*26:41g/A*26:42g/A*26:43g/A*26:45g/A*26:46g/A*26:47g/A*26:48g/A*26:49g/A*26:50g/A*26:51g/A*26:52g/A*26:53g/A*26:54g/A*26:55g/A*26:57g/A*26:58g/A*26:59g/A*26:61g/A*26:62g/A*26:63g/A*26:64g/A*26:65g/A*26:66g/A*26:67g/A*26:68g/A*26:69g/A*26:70g/A*26:72g/A*26:73g/A*26:74g/A*26:75g/A*26:76g/A*26:77g/A*26:78g/A*26:79g/A*26:80g/A*26:81g/A*26:83g/A*26:84g/A*26:85g/A*26:86g/A*26:87g/A*26:88g/A*26:89g/A*26:90g/A*26:91g/A*26:92g/A*26:93g/A*26:94g/A*26:95g/A*26:96g/A*26:97g/A*26:100g/A*26:101g/A*26:102g/A*26:103g/A*26:104g/A*26:105g/A*26:106g/A*26:108g/A*26:109g/A*26:110g/A*26:111g/A*26:112g/A*26:113g/A*26:114g/A*26:115g/A*26:116g/A*26:118g/A*26:119g/A*26:120g/A*26:121g/A*26:122g/A*26:123g/A*26:124g/A*26:125g/A*26:126g/A*26:128g/A*26:129g/A*26:130g/A*26:131g/A*26:132g/A*26:133g/A*26:134g/A*26:135g/A*26:136g/A*26:137g/A*26:138g/A*26:139g/A*26:140g/A*26:141g/A*26:142g/A*26:143g/A*26:144g/A*34:01g/A*34:02g/A*34:03g/A*34:04g/A*34:05g/A*34:06g/A*34:07g/A*34:08g/A*34:09g/A*34:11g/A*34:12g/A*34:13g/A*34:14g/A*34:15g/A*34:16g/A*34:17g/A*66:01g/A*66:02g/A*66:03g/A*66:04g/A*66:05g/A*66:06g/A*66:07g/A*66:09g/A*66:10g/A*66:11g/A*66:12g/A*66:13g/A*66:14g/A*66:15g/A*66:16g/A*66:18g/A*66:19g/A*66:20g/A*66:21g/A*66:22g/A*66:23g/A*66:24g/A*66:25g/A*66:26Qg |
+      | A10      | lgx   | A*25:01/A*25:02/A*25:03/A*25:04/A*25:05/A*25:06/A*25:08/A*25:09/A*25:10/A*25:11/A*25:13/A*25:14/A*25:15/A*25:16/A*25:17/A*25:18/A*25:19/A*25:20/A*25:21/A*25:22/A*25:23/A*25:24/A*25:25/A*25:26/A*25:27/A*25:28/A*25:29/A*25:30/A*25:31/A*25:32/A*25:33/A*25:34/A*25:35/A*25:36/A*25:37/A*25:38/A*25:39/A*25:40/A*25:41/A*25:43/A*25:44/A*25:45/A*26:01/A*26:02/A*26:03/A*26:04/A*26:05/A*26:06/A*26:07/A*26:08/A*26:09/A*26:10/A*26:12/A*26:13/A*26:14/A*26:15/A*26:16/A*26:17/A*26:18/A*26:19/A*26:20/A*26:21/A*26:22/A*26:23/A*26:27/A*26:28/A*26:29/A*26:30/A*26:31/A*26:32/A*26:33/A*26:34/A*26:35/A*26:36/A*26:37/A*26:38/A*26:39/A*26:40/A*26:41/A*26:42/A*26:43/A*26:45/A*26:46/A*26:47/A*26:48/A*26:49/A*26:50/A*26:51/A*26:52/A*26:53/A*26:54/A*26:55/A*26:57/A*26:58/A*26:59/A*26:61/A*26:62/A*26:63/A*26:64/A*26:65/A*26:66/A*26:67/A*26:68/A*26:69/A*26:70/A*26:72/A*26:73/A*26:74/A*26:75/A*26:76/A*26:77/A*26:78/A*26:79/A*26:80/A*26:81/A*26:83/A*26:84/A*26:85/A*26:86/A*26:87/A*26:88/A*26:89/A*26:90/A*26:91/A*26:92/A*26:93/A*26:94/A*26:95/A*26:96/A*26:97/A*26:100/A*26:101/A*26:102/A*26:103/A*26:104/A*26:105/A*26:106/A*26:108/A*26:109/A*26:110/A*26:111/A*26:112/A*26:113/A*26:114/A*26:115/A*26:116/A*26:118/A*26:119/A*26:120/A*26:121/A*26:122/A*26:123/A*26:124/A*26:125/A*26:126/A*26:128/A*26:129/A*26:130/A*26:131/A*26:132/A*26:133/A*26:134/A*26:135/A*26:136/A*26:137/A*26:138/A*26:139/A*26:140/A*26:141/A*26:142/A*26:143/A*26:144/A*34:01/A*34:02/A*34:03/A*34:04/A*34:05/A*34:06/A*34:07/A*34:08/A*34:09/A*34:11/A*34:12/A*34:13/A*34:14/A*34:15/A*34:16/A*34:17/A*66:01/A*66:02/A*66:03/A*66:04/A*66:05/A*66:06/A*66:07/A*66:09/A*66:10/A*66:11/A*66:12/A*66:13/A*66:14/A*66:15/A*66:16/A*66:18/A*66:19/A*66:20/A*66:21/A*66:22/A*66:23/A*66:24/A*66:25/A*66:26Q |
+      | A19      | G     | 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+      | DR1403   | G     | DRB1*14:03:01/DRB1*14:03:02 |
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