Osteoarithritis snp score

Osteoarthritis.py

@@ -0,0 +1,112 @@
+## TODO: Scores should be LOD risk ratios I think...
+import pathlib
+import json
+import os
+import pandas as pd
+class Osteo:
+
+  def __init__(self):
+    pass
+
+  def read_json_osteo(self):
+
+  #  filename = pathlib.Path(path).name
+    #print(filename)
+    with open("/Users/tanvisingh/Documents/Geromics/covcheck/tests/data/Osteoarithritis.json") as f:
+        data = json.load(f)
+
+    return data
+
+
+  def read_json_individual(self):
+
+  #  filename = pathlib.Path(path).name
+    #print(filename)
+    with open("/Users/tanvisingh/Documents/Geromics/covcheck/tests/data/dan_osteo.json") as f:
+        data = json.load(f)
+
+    return data
+
+  def calculate_score(self,count,OR):
+    score = float(count*OR)
+    return score
+
+  def display_score(self,snp,ORatio,Effect_Allele,Geneotype,scores):
+    df = pd.DataFrame()
+    df['snp']= snp
+    df['Effect_Allele']=Effect_Allele
+    df['Geneotype']=Geneotype
+    df['ORatio']= ORatio
+    df['scores']= scores
+    print("Snp details")
+    print("-----------------------")
+    print(df)
+
+  def score_report(self,snp,scores):
+    l=len(snp)
+    result=sum(scores)/l
+    print()
+    if result < 1:
+        print("Your score is ", result)
+        print("You are at less risk of developing Osteoarthritis")
+    else:
+        print("Your score is " , result)
+        print("You are at high risk of developing Osteoarthritis")
+
+
+
+
+  def parse_data_json(self,data,data1):
+    scores = []
+    snp = []
+    ORatio = []
+    Effect_Allele = []
+    Geneotype = []
+   # data = read_json_osteo()
+   # data1 = read_json_individual()
+
+    k = 0
+    for i in data['groups']:
+
+         if i['group_id'] == "44" and data1['age'] == 44:
+               #print("Hello", list(data1['snps'].keys())[0])
+               #print("Bye", list(i['snps'].keys())[0])
+               l=len(list(i['snps'].keys()))
+               l1=len(list(data1['snps'].keys()))
+               #print(l1)
+               for k in range(l):
+                   for m in range(l1):
+                       a = str(list(data1['snps'].keys())[m])
+                       b = str(list(i['snps'].keys())[k])
+                       #print ("a=" +a , "b="+b)
+                       if a in b:
+                          c1 = list(data1['snps'].values())[m]
+                          c2 = list(i['snps'].values())[k]['effect_allele']
+                          #print("match a=" + a, "b=" + b)
+                          #print("----------------------------")
+                          snp.append(a)
+                          Effect_Allele.append(c2)
+                          Geneotype.append(c1)
+                          if c2 in c1:
+                              count=c1.count(c2)
+                              OR=list(i['snps'].values())[k]['OR']
+                              score = float(count * OR)
+                              s = score
+                               # print(s)
+                              ORatio.append(OR)
+                              scores.append(s)
+                          else:
+                              s=0
+                              OR = list(i['snps'].values())[k]['OR']
+                              ORatio.append(OR)
+                              scores.append(s)
+
+    return snp,Effect_Allele,Geneotype,ORatio,scores
+
+
+snp_osteo = Osteo()
+data2=snp_osteo.read_json_osteo()
+data3=snp_osteo.read_json_individual()
+snp,Effect_Allele,Geneotype,ORatio,scores = snp_osteo.parse_data_json(data2,data3)
+snp_osteo.display_score(snp,ORatio,Effect_Allele,Geneotype,scores)
+snp_osteo.score_report(snp,scores)

tests/data/Osteoarithritis.json

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+{
+    "trait": "Osteoarthritis",   
+    "groups": [
+        {
+            "group_id": "age",
+            "note": "This is literally the first idea that came to mind..."
+        },
+        {
+            "group_id": "44",
+            "snps": {
+                "rs6976":{"effect_allele": "T", "other_allele": "C", "OR": 1.09},
+                "rs11177": {"effect_allele": "A", "other_allele": "G", "OR": 1.09},
+               "rs4836732":{"effect_allele": "C", "other_allele": "T", "OR": 1.04},
+               "rs9350591":{"effect_allele": "T", "other_allele": "C", "OR": 1.09},
+               "rs10492367":{"effect_allele": "T", "other_allele": "G", "OR": 1.06},
+                "rs835487":{"effect_allele": "G", "other_allele": "A", "OR": 1.05},
+                "rs12107036":{"effect_allele": "G", "other_allele": "A", "OR": 1.05},
+                "rs8044769":{"effect_allele": "C", "other_allele": "T", "OR": 1.07},
+                "rs10948172":{"effect_allele": "G", "other_allele": "A", "OR": 1.08}
+            }
+
+        }
+    ]
+}

tests/test_snp.py

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+import sys
+import unittest
+sys.path.insert(0, '/Users/tanvisingh/Documents/Geromics/covcheck')
+from Osteoarthritis import Osteo
+
+class TestSNP_age(unittest.TestCase):
+    def test_snp(self):
+        Ot = Osteo()
+        data = Ot.read_json_individual()
+        assert data['age'] == 44
+        assert list(data['snps'].keys())[0]== 'rs6976'
+        assert list(data['snps'].keys())[0] == 'rs835488'
+        assert data['id'] =='dan.geromics'
+        data1= Ot.read_json_osteo()
+        assert data1['trait']=='Osteoarthritis'
+        #assert list(data1['groups'])[1]== '44'
+if __name__ == '__main__':
+    unittest.main()
+    test_snp()