removed old test files

setup.py

@@ -31,7 +31,7 @@
     python_requires=">=3.8, <4",
     packages=find_packages(exclude=["contrib", "docs", "tests"]),
     zip_safe=False,
-    install_requires=["pandas","xlsxwriter","psutil","tqdm","requests"],
+    install_requires=["pandas","xlsxwriter","psutil","tqdm","requests","pytest"],
     test_suite="nose.collector",
     tests_require=["nose", "pytest","psutil"],
     entry_points={

tbtamr/Collate.py

@@ -81,8 +81,8 @@ def __init__(self,args):
         self.low_level = self._get_low_level()
         self.not_reportable = self._get_not_reportable()
         self.exclude_not_reportable = args.exclude_not_reportable
-        self.prop_mtb = args.prop_mtb
-        self.min_cov = args.min_cov
+        self.prop_mtb = float(args.prop_mtb)
+        self.min_cov = float(args.min_cov)
 
     def _get_db(self,path):
 
@@ -274,7 +274,7 @@ def _save_data(self, _data, prefix):
 
     def _check_quality(self, cov, perc):
 
-        if cov >= self.min_cov and perc >= self.prop_mtb:
+        if float(cov) >= self.min_cov and float(perc) >= self.prop_mtb:
 
             return 'Pass QC'
         elif perc < self.prop_mtb:

tbtamr/TbTamr.py

@@ -7,34 +7,12 @@ class Tbtamr(object):
     A base class for setting up tbtamr return a valid input object for subsequent steps
     """
     def __init__(self):
-
-
+
 
         self.one,self.five,self.fifteen = psutil.getloadavg()
         self.total_cores = os.cpu_count()
         self._cwd = pathlib.Path.cwd()
-        # self.jobs = args.jobs # number of tbprofilers to run at a time
-        # self.read1 = args.read1
-        # self.read2 = args.read2
-        # self.prefix = args.prefix
-        # self.datafile = args.data
-        # self.database = args.database
-
-    # def _get_logger(self):
-    #     logger =logging.getLogger(__name__) 
-    #     logger.setLevel(logging.DEBUG)
-    #     ch = logging.StreamHandler()
-    #     ch.setLevel(logging.DEBUG)
-    #     ch.setFormatter(CustomFormatter())
-    #     fh = logging.FileHandler('tbtamr.log')
-    #     fh.setLevel(logging.DEBUG)
-    #     formatter = logging.Formatter('[%(levelname)s:%(asctime)s] %(message)s', datefmt='%Y%m-%d %I:%M:%S %p') 
-    #     fh.setFormatter(formatter)
-    #     logger.addHandler(ch) 
-    #     logger.addHandler(fh)
-
-    #     return logger
-
+
     def _run_cmd(self, cmd):
 
         """

tests/results/data/iso.list

@@ -0,0 +1,25 @@
+A
+B
+C
+D
+E
+F
+G
+H
+I
+iso.list
+K
+L
+M
+N
+O
+P
+Q
+R
+S
+T
+U
+V
+W
+X
+Y