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#!/usr/bin/env python3
import unittest
from subprocess import PIPE, run
import os
import shutil
import sys
import argparse
# This is not best practice but for testing, this is the best I could
# come up with
sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
# TODO: Species specific aqquired genes only pheno results, not spec specific?
test_names = ["test1", "test2", "test3", "test4"]
test_data = {
# Test published acquired resistance
test_names[0]: "data/test_isolate_01.fa",
test_names[1]: "data/test_isolate_01_1.fq data/test_isolate_01_2.fq",
# Test published point mut resistance
test_names[2]: "data/test_isolate_05.fa",
test_names[3]: "data/test_isolate_05_1.fq data/test_isolate_05_2.fq",
}
run_test_dir = "running_test"
working_dir = os.path.dirname(os.path.realpath(__file__))
class ResFinderRunTest(unittest.TestCase):
@classmethod
def setUpClass(cls):
# Delete "running_test" folder from previous tests if still exists
if os.path.isdir(run_test_dir):
try:
shutil.rmtree(run_test_dir)
# The following error has occured using VirtualBox under Windows 10
# with ResFinder installed in a shared folder:
# OSError [Errno: 26] Text file busy: 'tmp'
except OSError:
procs = run(["rm", "-r", run_test_dir])
# Set absolute path for database folders and external programs
cls.db_path_res = os.path.abspath(args.db_path_res)
cls.blastPath = os.path.abspath(args.blast_path)
cls.kmaPath = os.path.abspath(args.kma_path)
cls.db_path_point = os.path.abspath(args.db_path_point)
cls.dir_res = os.path.join(os.path.dirname(__file__), '../', )
cls.dir_res = os.path.abspath(cls.dir_res)
# Change working dir to test dir
os.chdir(working_dir)
# Does not allow running two tests in parallel
os.makedirs(run_test_dir, exist_ok=False)
@classmethod
def tearDownClass(cls):
try:
shutil.rmtree(run_test_dir)
# The following error has occured using VirtualBox under Windows 10
# with ResFinder installed in a shared folder:
# OSError [Errno: 26] Text file busy: 'tmp'
except OSError:
procs = run(["rm", "-r", run_test_dir])
def test_on_data_with_just_acquired_resgene_using_blast(self):
# Maria has an E. coli isolate, with unknown resistance.
# At first, she just wants to know which acquired resistance genes are
# found in the genome.
# She therefore runs resfinder cmd line.
# First Maria checks out the documentation.
procs = run("run_resfinder.py -h", shell=True, stdout=PIPE,
check=True)
output = procs.stdout.decode()
self.assertIn("--help", output)
# Maria goes on to run ResFinder for acquired genes with her E. coli
# isolate.
# First she creates a few directories to store her output.
test1_dir = run_test_dir + "/" + test_names[0]
os.makedirs(test1_dir)
# Then she runs run_resfinder with her first isolate.
cmd_acquired = ("run_resfinder.py"
+ " -ifa " + test_data[test_names[0]]
+ " -o " + test1_dir
+ " -s 'Escherichia coli'"
+ " --min_cov 0.6"
+ " -t 0.8"
+ " --acquired"
+ " --db_path_res " + self.db_path_res
+ " --blastPath " + self.blastPath)
procs = run(cmd_acquired, shell=True, stdout=PIPE, stderr=PIPE,
check=True)
fsa_hit = test1_dir + "/ResFinder_Hit_in_genome_seq.fsa"
fsa_res = test1_dir + "/ResFinder_Resistance_gene_seq.fsa"
res_table = test1_dir + "/ResFinder_results_table.txt"
res_tab = test1_dir + "/ResFinder_results_tab.txt"
results = test1_dir + "/ResFinder_results.txt"
with open(fsa_hit, "r") as fh:
check_result = fh.readline()
self.assertIn("blaB-2_1_AF189300", check_result)
with open(fsa_res, "r") as fh:
check_result = fh.readline()
self.assertIn("blaB-2_AF189300", check_result)
with open(res_table, "r") as fh:
for line in fh:
if(line.startswith("blaB-2")):
check_result = line
break
self.assertIn("blaB-2_1_AF189300", check_result)
with open(res_tab, "r") as fh:
fh.readline()
check_result = fh.readline()
self.assertIn("blaB-2_1_AF189300", check_result)
with open(results, "r") as fh:
fh.readline()
fh.readline()
fh.readline()
fh.readline()
fh.readline()
check_result = fh.readline()
self.assertIn("blaB-2_1_AF189300", check_result)
def test_on_data_with_just_acquired_resgene_using_kma(self):
# Maria has another E. coli isolate, with unknown resistance.
# This time she does not have an assembly, but only raw data.
# She therefore runs resfinder cmd line using KMA.
# First she creates a few directories to store her output.
test2_dir = run_test_dir + "/" + test_names[1]
os.makedirs(test2_dir, exist_ok=False)
# Then she runs run_resfinder with her first isolate.
cmd_acquired = ("run_resfinder.py"
+ " -ifq " + test_data[test_names[1]]
+ " -o " + test2_dir
+ " -s 'Escherichia coli'"
+ " --min_cov 0.6"
+ " -t 0.8"
+ " --acquired"
+ " --db_path_res " + self.db_path_res
+ " --kmaPath " + self.kmaPath)
procs = run(cmd_acquired, shell=True, stdout=PIPE, stderr=PIPE,
check=True)
fsa_hit = test2_dir + "/ResFinder_Hit_in_genome_seq.fsa"
fsa_res = test2_dir + "/ResFinder_Resistance_gene_seq.fsa"
res_table = test2_dir + "/ResFinder_results_table.txt"
res_tab = test2_dir + "/ResFinder_results_tab.txt"
results = test2_dir + "/ResFinder_results.txt"
with open(fsa_hit, "r") as fh:
check_result = fh.readline()
self.assertIn("blaB-2", check_result)
with open(fsa_res, "r") as fh:
check_result = fh.readline()
self.assertIn("blaB-2_AF189300", check_result)
with open(res_table, "r") as fh:
for line in fh:
if(line.startswith("blaB-2")):
check_result = line
break
self.assertIn("blaB-2", check_result)
with open(res_tab, "r") as fh:
fh.readline()
check_result = fh.readline()
self.assertIn("blaB-2", check_result)
with open(results, "r") as fh:
fh.readline()
fh.readline()
fh.readline()
fh.readline()
fh.readline()
check_result = fh.readline()
self.assertIn("blaB-2", check_result)
def test_on_data_with_just_point_mut_using_blast(self):
# Maria also wants to check her assembled E. coli isolate for
# resistance caused by point mutations.
# First she creates a few directories to store her output.
test3_dir = run_test_dir + "/" + test_names[2]
os.makedirs(test3_dir)
# Then she runs run_resfinder with her first isolate.
cmd_point = ("run_resfinder.py"
+ " -ifa " + test_data[test_names[2]]
+ " -o " + test3_dir
+ " -s 'Escherichia coli'"
+ " --min_cov 0.6"
+ " --threshold 0.8"
+ " --point"
+ " --db_path_point " + self.db_path_point
+ " --db_path_res " + self.db_path_res
+ " --blastPath " + self.blastPath)
procs = run(cmd_point, shell=True, stdout=PIPE, stderr=PIPE,
check=True)
# Expected output files
pf_pred = test3_dir + "/PointFinder_prediction.txt"
pf_res = test3_dir + "/PointFinder_results.txt"
pf_table = test3_dir + "/PointFinder_table.txt"
with open(pf_res, "r") as fh:
fh.readline()
check_result = fh.readline()
self.assertIn("gyrA", check_result)
self.assertIn("p.S83A", check_result)
point_mut_found = False
with open(pf_table, "r") as fh:
for line in fh:
if(line.startswith("gyrA p.S83A")):
check_result = line
point_mut_found = True
break
self.assertEqual(point_mut_found, True)
def test_on_data_with_just_point_mut_using_kma(self):
# Maria has another E. coli isolate, with unknown resistance.
# This time she does not have an assembly, but only raw data.
# She therefore runs resfinder cmd line using KMA.
# First she creates a few directories to store her output.
test4_dir = run_test_dir + "/" + test_names[3]
os.makedirs(test4_dir, exist_ok=False)
# Then she runs run_resfinder with her first isolate.
cmd_acquired = ("run_resfinder.py"
+ " -ifq " + test_data[test_names[3]]
+ " -o " + test4_dir
+ " -s 'Escherichia coli'"
+ " --min_cov 0.6"
+ " --threshold 0.8"
+ " --point"
+ " --db_path_point " + self.db_path_point
+ " --db_path_res " + self.db_path_res
+ " --kmaPath " + self.kmaPath)
procs = run(cmd_acquired, shell=True, stdout=PIPE, stderr=PIPE,
check=True)
# Expected output files
pf_pred = test4_dir + "/PointFinder_prediction.txt"
pf_res = test4_dir + "/PointFinder_results.txt"
pf_table = test4_dir + "/PointFinder_table.txt"
with open(pf_res, "r") as fh:
fh.readline()
check_result = fh.readline()
self.assertIn("gyrA", check_result)
self.assertIn("p.S83A", check_result)
point_mut_found = False
with open(pf_table, "r") as fh:
for line in fh:
if(line.startswith("gyrA p.S83A")):
check_result = line
point_mut_found = True
break
self.assertEqual(point_mut_found, True)
def parse_args():
parser = argparse.ArgumentParser(add_help=False, allow_abbrev=False)
group = parser.add_argument_group("Options")
group.add_argument('-res_help', "--resfinder_help",
action="help")
group.add_argument("-db_res", "--db_path_res",
help="Path to the databases for ResFinder",
default="./db_resfinder")
group.add_argument("-b", "--blastPath",
dest="blast_path",
help="Path to blastn",
default="./cge/blastn")
group.add_argument("-k", "--kmaPath",
dest="kma_path",
help="Path to KMA",
default="./cge/kma/kma")
group.add_argument("-db_point", "--db_path_point",
help="Path to the databases for PointFinder",
default="./db_pointfinder")
ns, args = parser.parse_known_args(namespace=unittest)
return ns, sys.argv[:1] + args
if __name__ == "__main__":
args, argv = parse_args() # run this first
sys.argv[:] = argv # create cleans argv for main()
unittest.main()
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