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1 #!/usr/bin/env python3
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2 import unittest
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3 import os
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4 import subprocess
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5
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6
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7 test_names = ["test1", "test3"]
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8 test_data = {
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9 test_names[0]: "data/test_isolate_01.fa", # Test published resistance
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10 test_names[1]: "data/test_isolate_03.fa", # Test no resistance
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11 }
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12 run_test_dir = "unit_tests"
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13 blast_out_dir = "blast_out"
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14
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15 configs = {}
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16
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17
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18 class ResFinderTest(unittest.TestCase):
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19
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20 def setUp(self):
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21 # Change working dir to test dir
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22 os.chdir(os.path.dirname(os.path.realpath(__file__)))
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23 # Does not allow running two tests in parallel
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24 os.makedirs(run_test_dir, exist_ok=False)
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25 with open("test_config.txt", "r") as fh:
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26 for line in fh:
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27 line = line.rstrip()
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28
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29 if not(line):
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30 continue
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31
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32 if(line.startswith("#")):
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33 continue
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34
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35 key, path = line.split()
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36 configs[key] = path
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37
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38 def test_run_resfinder(self):
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39
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40 test1_dir = run_test_dir + "/" + test_names[0]
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41 test1_blast_dir = test1_dir + "/" + blast_out_dir
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42 os.makedirs(test1_dir)
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43 os.makedirs(test1_blast_dir)
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44
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45 cmd = ("python3 ../ResFinder.py"
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46 + " -i " + test_data[test_names[0]]
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47 + " -o " + test1_blast_dir
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48 + " -p " + configs["resfinder_dbs"]
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49 + " -l 0.6"
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50 + " -t 0.9")
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51
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52 print("Run cmd: " + cmd)
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53
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54 process = subprocess.run(cmd, shell=True, stdout=subprocess.PIPE,
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55 stderr=subprocess.PIPE)
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56
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57 outs = process.stdout.decode()
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58 errs = process.stderr.decode()
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59
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60 self.assertNotIn("Error", errs)
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61
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62
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63 if __name__ == "__main__":
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64 unittest.main()
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