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_no_trimming_legacy():
# make sure that this doesn't divide by zero
execute_cli([
'-a', 'XXXXX', '-o', '/dev/null', '-p', '/dev/null', '-pe1',
datapath('paired.1.fastq'), '-pe2',
datapath('paired.2.fastq')
])
def test_two_fastqs():
with raises(SystemExit), redirect_stderr():
execute_cli([
'-pe1',
datapath('paired.1.fastq'), '-pe2',
datapath('paired.2.fastq')
])
def test_E3M():
'''Read the E3M dataset'''
# not really colorspace, but a fasta/qual file pair
execute_cli([
'-o', '/dev/null', '-se',
datapath("E3M.fasta"), '-sq',
datapath("E3M.qual")
])
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_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_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_quiet_is_quiet():
captured_standard_output = StringIO()
captured_standard_error = StringIO()
try:
old_stdout = sys.stdout
old_stderr = sys.stderr
sys.stdout = captured_standard_output
sys.stderr = captured_standard_error
execute_cli(['-o', '/dev/null', '--quiet', '-a', 'XXXX', '-se', datapath('illumina.fastq.gz')])
finally:
sys.stdout = old_stdout
sys.stderr = old_stderr
print(captured_standard_output.getvalue())
assert captured_standard_output.getvalue() == ''
assert captured_standard_error.getvalue() == ''
def test_quiet_is_quiet():
captured_standard_output = StringIO()
captured_standard_error = StringIO()
try:
old_stdout = sys.stdout
old_stderr = sys.stderr
sys.stdout = captured_standard_output
sys.stderr = captured_standard_error
execute_cli([
'-o', '/dev/null', '--quiet', '-a', 'XXXX', '-se',
datapath('illumina.fastq.gz')
])
finally:
sys.stdout = old_stdout
sys.stderr = old_stderr
print(captured_standard_output.getvalue())
assert captured_standard_output.getvalue() == ''
assert captured_standard_error.getvalue() == ''
def test_missing_file():
with raises(SystemExit), redirect_stderr():
execute_cli([
'-a', 'XX', '--paired-output', 'out.fastq',
datapath('paired.1.fastq')
])
def test_missing_file():
with raises(SystemExit), redirect_stderr():
execute_cli(['-a', 'XX', '--paired-output', 'out.fastq', datapath('paired.1.fastq')])
def test_qualfile_only():
with raises(SystemExit), redirect_stderr():
execute_cli(['-sq', datapath('E3M.qual')])
def test_two_fastqs():
with raises(SystemExit), redirect_stderr():
execute_cli(['-pe1', datapath('paired.1.fastq'), '-pe2', datapath('paired.2.fastq')])
def test_no_args():
with redirect_stderr():
assert execute_cli() != 0
def test_qualfile_only():
with raises(SystemExit), redirect_stderr():
execute_cli(['-sq', datapath('E3M.qual')])
def test_E3M():
'''Read the E3M dataset'''
# not really colorspace, but a fasta/qual file pair
execute_cli(['-o', '/dev/null', '-se', datapath("E3M.fasta"), '-sq', datapath("E3M.qual")])
def test_no_args():
with redirect_stderr():
assert execute_cli() != 0
def test_no_trimming():
# make sure that this doesn't divide by zero
execute_cli(['-a', 'XXXXX', '-A', 'XXXXX', '-o', '/dev/null', '-p', '/dev/null', '-pe1', datapath('paired.1.fastq'), '-pe2', datapath('paired.2.fastq')])
