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#!/usr/bin/env python3
import unittest
import os
import subprocess
test_names = ["test1", "test3"]
test_data = {
test_names[0]: "data/test_isolate_01.fa", # Test published resistance
test_names[1]: "data/test_isolate_03.fa", # Test no resistance
}
run_test_dir = "unit_tests"
blast_out_dir = "blast_out"
configs = {}
class ResFinderTest(unittest.TestCase):
def setUp(self):
# Change working dir to test dir
os.chdir(os.path.dirname(os.path.realpath(__file__)))
# Does not allow running two tests in parallel
os.makedirs(run_test_dir, exist_ok=False)
with open("test_config.txt", "r") as fh:
for line in fh:
line = line.rstrip()
if not(line):
continue
if(line.startswith("#")):
continue
key, path = line.split()
configs[key] = path
def test_run_resfinder(self):
test1_dir = run_test_dir + "/" + test_names[0]
test1_blast_dir = test1_dir + "/" + blast_out_dir
os.makedirs(test1_dir)
os.makedirs(test1_blast_dir)
cmd = ("python3 ../ResFinder.py"
+ " -i " + test_data[test_names[0]]
+ " -o " + test1_blast_dir
+ " -p " + configs["resfinder_dbs"]
+ " -l 0.6"
+ " -t 0.9")
print("Run cmd: " + cmd)
process = subprocess.run(cmd, shell=True, stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
outs = process.stdout.decode()
errs = process.stderr.decode()
self.assertNotIn("Error", errs)
if __name__ == "__main__":
unittest.main()
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