Update consistency checks to be fully in python.

Please fill in the appropriate checklist below (delete those which are not relevant). These are the most common things requested on pull requests.

PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated
• Replace dag.png with the most recent CI pipleine integrated_pe artifact
• CHANGELOG.md is updated
• README.md is updated
• LICENSE.md is updated with new contributors
• Docker images moved to production release and changed in pipeline
• Docker images used in the CI unit tests match those used in pipeline

• Close issue
  Closes #60 (closed)

/cc @ghenry @venkat.malladi

workflow/tests/test_consistency.py

@@ -4,6 +4,7 @@ import pytest
 import pandas as pd
 from io import StringIO
 import os
+import json
 
 test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
     '/../../'
@@ -13,23 +14,21 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 def test_consistencySE():
     assert os.path.exists(os.path.join(
         test_output_path, 'SE_multiqc_data.json'))
-    assert readAssigned("assignedSE.txt", "assignedExpectSE.txt")
+
+    with open(os.path.join(
+        test_output_path, 'SE_multiqc_data.json')) as f:
+        assigned_reads_json = json.load(f)
+    assigned_reads = assigned_reads_json['report_general_stats_data'][4]['16-1ZX4']['Assigned']
+    assert  assigned_reads == 7742416
 
 
 @pytest.mark.consistencyPE
 def test_consistencyPE():
     assert os.path.exists(os.path.join(
         test_output_path, 'PE_multiqc_data.json'))
-    assert readAssigned("assignedPE.txt", "assignedExpectPE.txt")
-
-
-def readAssigned(fileAssigned, fileExpectAssigned):
-    data = False
-    assigned = open(fileAssigned, "r")
-    expect = open(fileExpectAssigned, "r")
-    lineAssigned = assigned.readline()
-    lineExpect = expect.readline()
-    if int(lineAssigned.strip()) < (int(lineExpect.strip())+(int(lineExpect.strip())*0.00001)) and int(lineAssigned.strip()) > (int(lineExpect.strip())-(int(lineExpect.strip())*0.00001)):
-        data = True
 
-    return data
+    with open(os.path.join(
+        test_output_path, 'PE_multiqc_data.json')) as f:
+        assigned_reads_json = json.load(f)
+    assigned_reads = assigned_reads_json['report_general_stats_data'][4]['Q-Y5JA']['Assigned']
+    assert  assigned_reads == 2599149