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#!/usr/bin/env python3
import hashlib
import logging
import os
from os import path
import re
import shutil
import subprocess as sp
import sys
import unittest
if len(sys.argv) < 2:
print("USAGE: axe_cli_tests.py $CMAKE_BINARY_DIR")
exit(-1)
CMAKE_BINARY_DIR = sys.argv.pop(1)
def md5sum(filename):
h = hashlib.md5()
with open(filename, 'rb') as fh:
while True:
hunk = fh.read(1024 ** 2)
if not hunk:
break
h.update(hunk)
return h.hexdigest()
class AxeTest(unittest.TestCase):
maxDiff= None
def __init__(self, methodName='runTest'):
super(AxeTest, self).__init__(methodName)
self.data = path.join(CMAKE_BINARY_DIR, "data")
self.out = path.join(CMAKE_BINARY_DIR, "out", "cli_tests")
self.axe = path.join(CMAKE_BINARY_DIR, "bin", "axe-demux")
self.log = logging.getLogger("AxeTest")
if not path.exists(self.data) or not path.exists(self.axe):
print("Please run axe_cli_tests.py after compiling axe")
exit(-1)
def setUp(self):
if not path.exists(self.out):
os.makedirs(self.out)
def run_and_check_stdout(self, command):
self.log.debug(" ".join(command))
try:
output = sp.check_output(command, stderr=sp.STDOUT)
except sp.CalledProcessError as err:
self.log.info(err.output)
return False
return True
def get_md5_dict(self):
dct = {}
for root, dirs, files in os.walk(self.out):
for fle in files:
md5 = md5sum(path.join(root, fle))
dct[path.basename(fle)] = md5
return dct
def tearDown(self):
if path.exists(self.out):
shutil.rmtree(self.out)
class TestBadUsage(AxeTest):
def __init__(self, methodName='runTest'):
super(TestBadUsage, self).__init__(methodName)
def test_bad_command(self):
command = [self.axe, "-f"]
self.assertFalse(self.run_and_check_stdout(command))
self.assertDictEqual({}, self.get_md5_dict())
class TestPareSE(AxeTest):
def __init__(self, methodName='runTest'):
super(TestPareSE, self).__init__(methodName)
self.infq = path.join(self.data, "pare.fq.gz")
self.barcodes = path.join(self.data, "pare.barcodes")
self.outfq = path.join(self.out, "pare_se")
self.nobcdfq = path.join(self.out, "pare_se_unknown_R1.fastq")
def test_pare_se(self):
command = [self.axe,
"-f", self.infq,
"-F", self.outfq,
'-b', self.barcodes,
]
self.assertTrue(self.run_and_check_stdout(command))
files = {
'pare_se_1_R1.fastq': 'd41d8cd98f00b204e9800998ecf8427e',
'pare_se_2_R1.fastq': 'd41d8cd98f00b204e9800998ecf8427e',
'pare_se_3_R1.fastq': 'd41d8cd98f00b204e9800998ecf8427e',
'pare_se_4_R1.fastq': '8e5eef3323e597b209f79dc9fcd74c9a',
'pare_se_5_R1.fastq': 'd41d8cd98f00b204e9800998ecf8427e',
'pare_se_6_R1.fastq': '7228a165f353920328360dedc3a41205',
'pare_se_7_R1.fastq': 'd41d8cd98f00b204e9800998ecf8427e',
'pare_se_8_R1.fastq': 'b349d3276ba7c7515d0093b1a49b3959',
'pare_se_9_R1.fastq': '74b4763271aefcc135425b06730874ba',
'pare_se_unknown_R1.fastq': 'd450569dd8fd4bdddffbfaeec4980273',
}
self.assertDictEqual(files, self.get_md5_dict())
def test_pare_se_zip(self):
command = [self.axe,
"-f", self.infq,
"-F", self.outfq,
'-b', self.barcodes,
'-z', '9',
]
files = {
'pare_se_1_R1.fastq.gz': '4a4dd3598707603b3f76a2378a4504aa',
'pare_se_2_R1.fastq.gz': '4a4dd3598707603b3f76a2378a4504aa',
'pare_se_3_R1.fastq.gz': '4a4dd3598707603b3f76a2378a4504aa',
'pare_se_4_R1.fastq.gz': '96d21b860a0fc70641ea43d350433d11',
'pare_se_5_R1.fastq.gz': '4a4dd3598707603b3f76a2378a4504aa',
'pare_se_6_R1.fastq.gz': 'd6044c04f79c358e4a1d443f8828df18',
'pare_se_7_R1.fastq.gz': '4a4dd3598707603b3f76a2378a4504aa',
'pare_se_8_R1.fastq.gz': 'da77b8e95827d362a1702ce4fe75c7a9',
'pare_se_9_R1.fastq.gz': '9c160b0daa0c73e5ef0994206774a5a0',
'pare_se_unknown_R1.fastq.gz': 'afd5737935814d756e89c365d2d61c7b',
}
self.assertTrue(self.run_and_check_stdout(command))
self.assertDictEqual(files, self.get_md5_dict())
class TestFakeSE(AxeTest):
files = {
'fake_se_1_R1.fastq': '836eaf06938d4a41122f284ed487a9c7',
'fake_se_2_R1.fastq': '836eaf06938d4a41122f284ed487a9c7',
'fake_se_unknown_R1.fastq': '836eaf06938d4a41122f284ed487a9c7',
}
zfiles = {
'fake_se_1_R1.fastq.gz': '3e07353d24a3ecd315067250a6be6047',
'fake_se_2_R1.fastq.gz': '3e07353d24a3ecd315067250a6be6047',
'fake_se_unknown_R1.fastq.gz': '3e07353d24a3ecd315067250a6be6047',
}
def __init__(self, methodName='runTest'):
super(TestFakeSE, self).__init__(methodName)
self.barcodes = path.join(self.data, "fake.barcodes")
self.outfq = path.join(self.out, "fake_se")
self.nobcdfq = path.join(self.out, "fake_se_unknown_R1.fastq")
def _do_test(self, mm_level):
infq = path.join(self.data, "fake_{}mm_R1.fq.gz".format(mm_level))
command = [self.axe,
"-f", infq,
"-F", self.outfq,
'-b', self.barcodes,
]
self.assertTrue(self.run_and_check_stdout(command))
def _do_test_zip(self, mm_level):
infq = path.join(self.data, "fake_{}mm_R1.fq.gz".format(mm_level))
command = [self.axe,
"-f", infq,
"-F", self.outfq,
'-b', self.barcodes,
'-z', '9',
]
self.assertTrue(self.run_and_check_stdout(command))
def test_fake_se_0mm(self):
self._do_test(0)
self.assertDictEqual(self.files, self.get_md5_dict())
def test_fake_se_0mm_zip(self):
self._do_test_zip(0)
self.assertDictEqual(self.zfiles, self.get_md5_dict())
def test_fake_se_1mm(self):
self._do_test(1)
self.assertDictEqual(self.files, self.get_md5_dict())
def test_fake_se_1mm_zip(self):
self._do_test_zip(1)
self.assertDictEqual(self.zfiles, self.get_md5_dict())
def test_fake_se_2mm(self):
self._do_test(2)
files = {
'fake_se_1_R1.fastq': 'd41d8cd98f00b204e9800998ecf8427e',
'fake_se_2_R1.fastq': 'd41d8cd98f00b204e9800998ecf8427e',
'fake_se_unknown_R1.fastq': 'a6de105b6c5abbc2d0d16440333adc64',
}
self.assertDictEqual(files, self.get_md5_dict())
def test_fake_se_2mm_zip(self):
self._do_test_zip(2)
zfiles = {
'fake_se_1_R1.fastq.gz': '4a4dd3598707603b3f76a2378a4504aa',
'fake_se_2_R1.fastq.gz': '4a4dd3598707603b3f76a2378a4504aa',
'fake_se_unknown_R1.fastq.gz': 'ee6979b139dbd898f058fd7649f87da2',
}
self.assertDictEqual(zfiles, self.get_md5_dict())
if __name__ == '__main__':
log = logging.getLogger("AxeTest")
fmt = logging.Formatter('%(message)s')
cons = logging.StreamHandler()
cons.setLevel(logging.DEBUG)
cons.setFormatter(fmt)
log.addHandler(cons)
log.setLevel(logging.DEBUG)
unittest.main()
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