def test_untrimmed_paired_output():
with temporary_path("tmp-untrimmed.1.fastq") as untrimmed1:
with temporary_path("tmp-untrimmed.2.fastq") as untrimmed2:
def callback(aligner, infiles, outfiles, result):
assert files_equal(cutpath('paired-untrimmed.1.fastq'),
untrimmed1)
assert files_equal(cutpath('paired-untrimmed.2.fastq'),
untrimmed2)
run_paired(
[
'-a',
'TTAGACATAT',
'--untrimmed-output',
untrimmed1,
'--untrimmed-paired-output',
untrimmed2,
],
in1='paired.1.fastq',
in2='paired.2.fastq',
expected1='paired-trimmed.1.fastq',
expected2='paired-trimmed.2.fastq',
callback=callback,
)
def test_interleaved_no_paired_output():
with temporary_path("temp-paired.1.fastq") as p1:
with temporary_path("temp-paired.2.fastq") as p2:
params = '-a XX --interleaved'.split()
with raises(SystemExit), redirect_stderr():
params += [
'-o', p1, '-p1', p2, 'paired.1.fastq', 'paired.2.fastq'
]
execute_cli(params)
def test_explicit_format_with_paired():
# Use --format=fastq with input files whose extension is .txt
with temporary_path("paired.1.txt") as txt1:
with temporary_path("paired.2.txt") as txt2:
shutil.copyfile(datapath("paired.1.fastq"), txt1)
shutil.copyfile(datapath("paired.2.fastq"), txt2)
run_paired(
'--format=fastq -a TTAGACATAT -m 14',
in1=txt1,
in2=txt2,
expected1='paired.m14.1.fastq',
expected2='paired.m14.2.fastq',
)
def run_paired(
params,
in1,
in2,
expected1,
expected2,
aligners=('adapter', ),
callback=None,
assert_files_equal=True,
error_on_rc=True,
):
if type(params) is str:
params = params.split()
for aligner in aligners:
with temporary_path('tmp1-' + expected1.format(aligner=aligner)) as p1:
with temporary_path('tmp2-' +
expected2.format(aligner=aligner)) as p2:
p = params.copy()
p += ['--aligner', aligner, '-o', p1, '-p', p2]
infiles = [
datapath(i.format(aligner=aligner)) for i in (in1, in2)
]
for infile_args in zip(('-pe1', '-pe2'), infiles):
p.extend(infile_args)
command = get_command('trim')
result = command.execute(p)
assert isinstance(result, tuple)
assert len(result) == 2
if error_on_rc:
err = result[1]['exception'] if result[
1] and 'exception' in result[1] else None
# from traceback import format_exception
if result[0] != 0:
if err is None:
raise AssertionError("Return code {} != 0".format(
result[0]))
else:
raise AssertionError("Return code {} != 0".format(
result[0])) from err['details'][1]
if assert_files_equal:
assert files_equal(
cutpath(expected1.format(aligner=aligner)), p1)
assert files_equal(
cutpath(expected2.format(aligner=aligner)), p2)
if callback:
callback(aligner, infiles, (p1, p2), result)
def test_path_pointing_to_filename(self):
with temporary_path("custom.perf.yml"):
with record(path="custom.perf.yml"):
caches["default"].get("foo")
assert os.path.exists("custom.perf.yml")
def test_path_pointing_to_filename_record_twice(self):
with temporary_path("custom.perf.yml"):
with record(path="custom.perf.yml"):
caches["default"].get("foo")
with record(path="custom.perf.yml"):
caches["default"].get("foo")
def test_too_short_paired_output():
with temporary_path("temp-too-short.1.fastq") as p1:
with temporary_path("temp-too-short.2.fastq") as p2:
def callback(aligner, infiles, outfiles, result):
assert files_equal(cutpath('paired-too-short.1.fastq'), p1)
assert files_equal(cutpath('paired-too-short.2.fastq'), p2)
run_paired(
'-a TTAGACATAT -A CAGTGGAGTA -m 14 --too-short-output '
'{0} --too-short-paired-output {1}'.format(p1, p2),
in1='paired.1.fastq',
in2='paired.2.fastq',
expected1='paired_{aligner}.1.fastq',
expected2='paired_{aligner}.2.fastq',
aligners=BACK_ALIGNERS,
callback=callback,
)
def test_mode_once(self):
temp_dir = os.path.join(FILE_DIR, "perf_files/")
with temporary_path(temp_dir):
with record(path="perf_files/api/"):
caches["default"].get("foo")
full_path = os.path.join(FILE_DIR, "perf_files", "api", "test_api.perf.yml")
assert os.path.exists(full_path)
def test_too_short_output_paired_option_missing():
with raises(SystemExit), temporary_path("temp-too-short.1.fastq") as p1:
run_paired(
'-a TTAGACATAT -A CAGTGGAGTA -m 14 --too-short-output '
'{0}'.format(p1),
in1='paired.1.fastq',
in2='paired.2.fastq',
expected1='paired.1.fastq',
expected2='paired.2.fastq',
aligners=BACK_ALIGNERS,
)
def test_second_too_short():
with temporary_path("truncated.2.fastq") as trunc2:
# Create a truncated file in which the last read is missing
with open(datapath('paired.2.fastq')) as f:
lines = f.readlines()
lines = lines[:-4]
with open(trunc2, 'w') as f:
f.writelines(lines)
with raises(SystemExit), redirect_stderr():
execute_cli('-a XX --paired-output out.fastq'.split() +
[datapath('paired.1.fastq'), trunc2])
def test_mode_all(self):
temp_dir = os.path.join(FILE_DIR, "perf_files/")
with temporary_path(temp_dir):
with pytest.raises(AssertionError) as excinfo:
with record(path="perf_files/api/"):
caches["default"].get("foo")
assert "Original performance record did not exist" in str(excinfo.value)
full_path = os.path.join(FILE_DIR, "perf_files", "api", "test_api.perf.yml")
assert os.path.exists(full_path)
def run_interleaved(params, inpath, expected, aligners=('adapter', )):
if type(params) is str:
params = params.split()
for aligner in aligners:
with temporary_path(expected.format(aligner=aligner)) as tmp:
p = params.copy()
p += [
'--aligner',
aligner,
'-l',
datapath(inpath.format(aligner=aligner)),
'-L',
tmp,
]
command = get_command('trim')
result = command.execute(p)
assert isinstance(result, tuple)
assert len(result) == 2
assert files_equal(cutpath(expected.format(aligner=aligner)), tmp)
def test_unmatched_read_names():
with temporary_path("swapped.1.fastq") as swapped:
try:
# Create a file in which reads 2 and are swapped
with open(datapath('paired.1.fastq')) as f:
lines = f.readlines()
lines = lines[0:4] + lines[8:12] + lines[4:8] + lines[12:]
with open(swapped, 'w') as f:
f.writelines(lines)
with redirect_stderr():
command = get_command('trim')
result = command.execute(
'-a XX -o out1.fastq -p out2.fastq'.split() +
['-pe1', swapped, '-pe2',
datapath('paired.2.fastq')])
assert isinstance(result, tuple)
assert len(result) == 2
assert result[0] != 0
finally:
os.remove('out1.fastq')
os.remove('out2.fastq')
