updated tests to include example data and generate 'run_tests' folder automatically

Author: kbessonov1984

MANIFEST.in

@@ -5,6 +5,7 @@ include setup.py
 include mob_suite/config.json
 include mob_suite/tests/TestData/*
 include mob_suite/tests/*.py
+include mob_suite/example/*
 
 
 

mob_suite/tests/test_mobtyper.py

@@ -12,6 +12,8 @@
 
 def test_mean_and_multireplicon_frame():
     logger.info("Testing MOB-typer")
+    if os.path.exists("run_test") == False:
+        os.mkdir("run_test")
     args = [
         "--infile", os.path.dirname(__file__) + "/TestData/pCAV1453-208.fasta",
         "--out_file", TEST_ROOT + "/run_test/mobtyper_pCAV1453-208_results.txt",

mob_suite/tests/test_mobtyper_vs_biomarker_report.py

@@ -1,4 +1,4 @@
-import subprocess, os, time, random, sys
+import os, time, random, sys
 from statistics import mean
 from Bio import SeqIO
 import pandas as pd
@@ -25,6 +25,9 @@ def clean_missing_dashes(L):
 
 
 def test_mean_and_multireplicon_frame(mode = None):
+    if os.path.exists("run_test") == False:
+        os.mkdir("run_test")
+
     if mode == None:
         return 0
     logger.info("Testing MOB-typer for biomarker and mobtyper reports consistency in terms of biomarker names (not accessions)")