add IMGT pull for TCE; update package specifications

dpb1/genotype.py

@@ -31,7 +31,9 @@ class Genotype(object):
     :param name: A list of two Haplotype objects or a genotype name (str)
     """
 
-    def __init__(self, haplotypes):
+    def __init__(self, haplotypes, index : int = None, prob : float = None):
+        self.index = index
+        self.prob = prob
         self.SLUGs = None
         if isinstance(haplotypes, str):
             self.name = haplotypes

dpb1/tce.py

@@ -19,6 +19,7 @@
 #
 import requests
 import json
+import pandas as pd
 
 class TCE_map(object):
 
@@ -29,8 +30,25 @@ def __init__(self,
         self.ard = ard
 
     def _get_tce_assignments(self):
+        """
+        Obtains TCE assignments from a hard-coded from IMGT.
+        :return: Dictionary of alleles to TCE groups (3, 2, 1, 0).
+        :rtype: Dict[str, str]
+        """
         with open(self.path, 'r') as f:
-            return json.loads(f.readline())
+            tce_map = json.loads(f.readline())
+
+        allele_header = 'Allele'
+        tce_header = 'V2_Assignment'
+        url = 'https://raw.githubusercontent.com/ANHIG/IMGTHLA/Latest/tce/dpb_tce.csv'
+        tce_df = pd.read_csv(url, comment='#')
+        tce_df.replace({'\$' : '', 'a' : ''}, regex=True, inplace=True)
+        tce_df = tce_df[[allele_header, tce_header]]
+        tce_df = tce_df[~tce_df[tce_header].isnull()]
+        tce_df.set_index(allele_header, inplace=True)
+        tce_map_updated = tce_df.to_dict()[tce_header]
+        tce_map.update(tce_map_updated)
+        return tce_map
 
     def assign_tce(self, dpb1_allele):
         if dpb1_allele not in self.tce_assignments:

requirements.txt

@@ -5,10 +5,11 @@ flask-restplus==0.13.0
 behave==1.2.6
 PyHamcrest==1.9.0
 allure-behave==2.8.5
+itsdangerous==2.0.1
 matplotlib==3.1.3
 mpmath==1.1.0
 numpy==1.18.1
-pandas==1.0.1
+pandas>=1.1.4
 requests==2.22.0
 seaborn==0.10.0
 toolz==0.11.1

tests/features/algorithm/call_rest_service.feature

@@ -778,8 +778,15 @@ Feature: Call REST Service
                         "dpb1_genotypes": [
                         {
                             "genotype": "DPB1*04:01+DPB1*04:01",
-                            "tce_groups": "3+3",
-                            "probability": 1
+                            "tce_groups": "3+3"
+                        },
+                        {
+                            "genotype": "DPB1*04:01+DPB1*677:01",
+                            "tce_groups": "3+3"
+                        },
+                        {
+                            "genotype": "DPB1*677:01+DPB1*677:01",
+                            "tce_groups": "3+3"
                         }
                         ]
                     }
@@ -813,13 +820,19 @@ Feature: Call REST Service
                         "dpb1_genotypes": [
                         {
                             "genotype": "DPB1*03:01+DPB1*04:01",
-                            "tce_groups": "2+3",
-                            "probability": 0.5035143163576772
+                            "tce_groups": "2+3"
+                        },
+                        {
+                            "genotype": "DPB1*03:01+DPB1*677:01",
+                            "tce_groups": "2+3"
                         },
                         {
                             "genotype": "DPB1*04:01+DPB1*14:01",
-                            "tce_groups": "2+3",
-                            "probability": 0.4964856836423228
+                            "tce_groups": "2+3"
+                        },
+                        {
+                            "genotype": "DPB1*14:01+DPB1*677:01",
+                            "tce_groups": "2+3"
                         }
                         ]
                     }

tests/steps/dpb1_perm_freq_generation.py

@@ -1,6 +1,6 @@
 from behave import *
 from hamcrest import assert_that, is_
-from validation.dpb1_validator.predicted import Predicted, PredictedPair
+# from validation.dpb1_validator.predicted import Predicted, PredictedPair
 import pandas as pd
 from sigfig import round
 import json

tests/steps/match_tce_groups.py

@@ -3,7 +3,7 @@
 from dpb1.match import Matches, MatchGrade
 from dpb1.dpb1 import DPB1_SLUG
 from dpb1.tce import TCE_SLUG
-from validation.dpb1_validator.observed import ObservedPair
+# from validation.dpb1_validator.observed import ObservedPair
 
 @given('these TCE group pairs and expected match categories')
 def step_impl(context):