def test_no_position_file(self):
with tempfile.TemporaryDirectory(prefix='test_grep_vcf') as tmpdir:
pos_file_name = self.find_data('data.txt')
pos_file_name = os.path.join(tmpdir, os.path.basename(pos_file_name))
data_file_name = self.find_data('data.vcf')
data_file_name = shutil.copyfile(data_file_name,
os.path.join(tmpdir, os.path.basename(data_file_name)))
command = f"grep_vcf {pos_file_name}"
with self.assertRaises(FileNotFoundError) as ctx:
main(args=command.split()[1:])
self.assertEqual(str(ctx.exception),
f"The file {pos_file_name} does not exists.")
def test_empty_positions(self):
with tempfile.TemporaryDirectory(prefix='test_grep_vcf') as tmpdir:
pos_file_name = self.find_data('empty.txt')
pos_file_name = shutil.copyfile(pos_file_name,
os.path.join(tmpdir, os.path.basename(pos_file_name)))
data_file_name = self.find_data('data.vcf')
data_file_name = shutil.copyfile(data_file_name,
os.path.join(tmpdir, os.path.basename(data_file_name)))
command = f"grep_vcf --vcf {data_file_name} {pos_file_name}"
with self.catch_io(out=True):
main(args=command.split()[1:])
stdout = sys.stdout.getvalue().strip()
self.assertEqual(stdout, '')
def test_specify_out(self):
with tempfile.TemporaryDirectory(prefix='test_grep_vcf') as tmpdir:
pos_file_name = self.find_data('data.txt')
pos_file_name = shutil.copyfile(pos_file_name,
os.path.join(tmpdir, os.path.basename(pos_file_name)))
data_file_name = self.find_data('data.vcf')
data_file_name = shutil.copyfile(data_file_name,
os.path.join(tmpdir, os.path.basename(data_file_name)))
out_file_name = os.path.join(tmpdir, 'diff.vcf')
command = f"grep_vcf --out {out_file_name} {pos_file_name}"
main(args=command.split()[1:])
with open(out_file_name) as out:
res = out.read()
self.assertEqual(res,
"7\tvcf ligne 1\n9\tvcf ligne 3\n11\tvcf ligne 4\n")