resfinder4: resfinder/tests/unit

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--1:000000000000
+:55051a9bc58d
+#!/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()

Mercurial > repos > dcouvin > resfinder4