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#!/usr/bin/env python3
import sys
import os
import filecmp
import unittest
from pyfastaq import utils
modules_dir = os.path.dirname(os.path.abspath(utils.__file__))
data_dir = os.path.join(modules_dir, 'tests', 'data')
class TestUtils(unittest.TestCase):
def test_write_and_read(self):
'''open_file_write() and open_file_read() should do the right thing depending gzipped or not'''
for filename in ['utils.tmp', 'utils.tmp.gz', 'utils.tmp.bgz']:
f = utils.open_file_write(filename)
for i in range(3):
print(i, file=f)
utils.close(f)
counter = 0
f = utils.open_file_read(filename)
for line in f:
self.assertEqual(counter, int(line.strip()))
counter += 1
utils.close(f)
os.unlink(filename)
f = utils.open_file_read('-')
self.assertEqual(sys.stdin, f)
f = utils.open_file_write('-')
self.assertEqual(sys.stdout, f)
def test_raise_exception(self):
'''open_file_write() and open_file_read() should raise an exception when can't do the opening'''
with self.assertRaises(utils.Error):
utils.open_file_read('this_file_is_not_here_so_throw_error')
with self.assertRaises(utils.Error):
utils.open_file_read('this_file_is_not_here_so_throw_error.gz')
with self.assertRaises(utils.Error):
utils.open_file_read(os.path.join(data_dir, 'utils_test_not_really_zipped.gz'))
with self.assertRaises(utils.Error):
utils.open_file_write(os.path.join('not_a_directory', 'this_file_is_not_here_so_throw_error'))
with self.assertRaises(utils.Error):
utils.open_file_write(os.path.join('not_a_directory', 'this_file_is_not_here_so_throw_error.gz'))
def test_file_transpose(self):
'''Test that file_transpose() does what it should'''
infile = os.path.join(data_dir, 'utils_test_file_transpose.txt')
tmp_out = 'utils_test_file_transpose.tmp'
correct_file = os.path.join(data_dir, 'utils_test_file_transposed.txt')
utils.file_transpose(infile, tmp_out)
self.assertTrue(filecmp.cmp(tmp_out, correct_file))
os.unlink(tmp_out)
def test_system_call(self):
'''Test that system call appears to work and die as it should'''
test_file = os.path.join(data_dir, 'utils_test_system_call.txt')
tmp_out = 'utils_test_syscall.tmp'
utils.syscall('cat ' + test_file + ' > ' + tmp_out)
self.assertTrue(filecmp.cmp(tmp_out, test_file))
os.unlink(tmp_out)
with self.assertRaises(utils.Error):
utils.syscall('thisisveryunlikelytoebarealcommandandshouldthrowerror')
utils.syscall('echo "this is not the right string" > ' + tmp_out)
self.assertFalse(filecmp.cmp(tmp_out, test_file))
os.unlink(tmp_out)
s = utils.syscall_get_stdout('echo bingo')
self.assertListEqual(["bingo"], s)
with self.assertRaises(utils.Error):
utils.syscall_get_stdout('thisisveryunlikelytoebarealcommandandshouldthrowerror')
if __name__ == '__main__':
unittest.main()
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