def test_demultiplex():
multiout = os.path.join(os.path.dirname(__file__), 'data',
'tmp-demulti.{name}.fasta')
params = [
'-a',
'first=AATTTCAGGAATT',
'-a',
'second=GTTCTCTAGTTCT',
'-o',
multiout,
'-se',
datapath('twoadapters.fasta'),
]
command = get_command('trim')
result = command.execute(params)
assert isinstance(result, tuple)
assert len(result) == 2
assert result[0] == 0
assert files_equal(cutpath('twoadapters.first.fasta'),
multiout.format(name='first'))
assert files_equal(cutpath('twoadapters.second.fasta'),
multiout.format(name='second'))
assert files_equal(cutpath('twoadapters.unknown.fasta'),
multiout.format(name='unknown'))
os.remove(multiout.format(name='first'))
os.remove(multiout.format(name='second'))
os.remove(multiout.format(name='unknown'))
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 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_demultiplex():
multiout = os.path.join(os.path.dirname(__file__), 'data', 'tmp-demulti.{name}.fasta')
params = ['-a', 'first=AATTTCAGGAATT', '-a', 'second=GTTCTCTAGTTCT', '-o', multiout, '-se', datapath('twoadapters.fasta')]
command = get_command('trim')
result = command.execute(params)
assert isinstance(result, tuple)
assert len(result) == 2
assert result[0] == 0
assert files_equal(cutpath('twoadapters.first.fasta'), multiout.format(name='first'))
assert files_equal(cutpath('twoadapters.second.fasta'), multiout.format(name='second'))
assert files_equal(cutpath('twoadapters.unknown.fasta'), multiout.format(name='unknown'))
os.remove(multiout.format(name='first'))
os.remove(multiout.format(name='second'))
os.remove(multiout.format(name='unknown'))
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 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 run(
params,
expected,
inpath=None,
inpath2=None,
qualfile=None,
interleaved_input=False,
interleaved_output=False,
sra_accn=None,
):
if type(params) is str:
params = params.split()
with temporary_path(expected) as tmp_fastaq:
if sra_accn:
params += ['-sra', sra_accn]
elif interleaved_input:
params += ['-l', inpath]
elif inpath2:
params += ['-pe1', datapath(inpath)]
params += ['-pe2', datapath(inpath2)]
else:
params += ['-se', datapath(inpath)]
if qualfile:
params += ['-sq', datapath(qualfile)]
if interleaved_output:
params += ['-L', tmp_fastaq]
else:
params += ['-o', tmp_fastaq] # TODO not parallelizable
# print(params)
command = get_command('trim')
retcode, summary = command.execute(params)
assert summary is not None
assert isinstance(summary, dict)
if 'exception' in summary and summary['exception'] is not None:
assert retcode != 0
err = summary['exception']
traceback.print_exception(*err['details'])
raise Exception("Unexpected error: {}".format(err['message']))
else:
assert retcode == 0
# TODO redirect standard output
assert os.path.exists(tmp_fastaq)
assert files_equal(cutpath(expected), tmp_fastaq)
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')
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')
def run(
params, expected, inpath=None, inpath2=None, qualfile=None,
interleaved_input=False, interleaved_output=False, sra_accn=None):
if type(params) is str:
params = params.split()
with temporary_path(expected) as tmp_fastaq:
if sra_accn:
params += ['-sra', sra_accn]
elif interleaved_input:
params += ['-l', inpath]
elif inpath2:
params += ['-pe1', datapath(inpath)]
params += ['-pe2', datapath(inpath2)]
else:
params += ['-se', datapath(inpath)]
if qualfile:
params += ['-sq', datapath(qualfile)]
if interleaved_output:
params += ['-L', tmp_fastaq]
else:
params += ['-o', tmp_fastaq] # TODO not parallelizable
#print(params)
command = get_command('trim')
retcode, summary = command.execute(params)
assert summary is not None
assert isinstance(summary, dict)
if 'exception' in summary and summary['exception'] is not None:
assert retcode != 0
err = summary['exception']
traceback.print_exception(*err['details'])
raise Exception("Unexpected error: {}".format(err['message']))
else:
assert retcode == 0
# TODO redirect standard output
assert os.path.exists(tmp_fastaq)
assert files_equal(cutpath(expected), tmp_fastaq)