def test_task_trim_galore_PE_exceptions():
## 2 inputs 1 output
passed= False
try:
tg= oxbs_qc_func.task_trim_galore(inFastq= ['test_data/mjb042_oxBS_R1.fastq.gz', 'test_data/mjb042_oxBS_R2.fastq.gz'], outFastq= ['fq1.fq.gz'], tmpdir= 'test_out', opts= '', path= '')
except oxbs_qc_func.TrimGaloreException:
passed= True
assert passed
## 1 inputs 2 output
passed= False
try:
tg= oxbs_qc_func.task_trim_galore(inFastq= ['test_data/mjb042_oxBS_R1.fastq.gz'], outFastq= ['fq1.fq.gz', 'fq2.fq.gz'], tmpdir= 'test_out', opts= '', path= '')
except oxbs_qc_func.TrimGaloreException:
passed= True
assert passed
## same input twice
passed= False
try:
tg= oxbs_qc_func.task_trim_galore(inFastq= ['test_data/mjb042_oxBS_R1.fastq.gz', 'test_data/mjb042_oxBS_R1.fastq.gz'], outFastq= ['fq1.fq.gz', 'fq2.fq.gz'], tmpdir= 'test_out', opts= '', path= '')
except oxbs_qc_func.TrimGaloreException:
passed= True
assert passed
## same Output twice
passed= False
try:
tg= oxbs_qc_func.task_trim_galore(inFastq= ['test_data/mjb042_oxBS_R1.fastq.gz', 'test_data/mjb042_oxBS_R2.fastq.gz'], outFastq= ['fq1.fq.gz', 'fq1.fq.gz'], tmpdir= 'test_out', opts= '', path= '')
except oxbs_qc_func.TrimGaloreException:
passed= True
assert passed
def test_task_trim_galore_PE_exceptions():
## 2 inputs 1 output
passed = False
try:
tg = oxbs_qc_func.task_trim_galore(inFastq=[
'test_data/mjb042_oxBS_R1.fastq.gz',
'test_data/mjb042_oxBS_R2.fastq.gz'
],
outFastq=['fq1.fq.gz'],
tmpdir='test_out',
opts='',
path='')
except oxbs_qc_func.TrimGaloreException:
passed = True
assert passed
## 1 inputs 2 output
passed = False
try:
tg = oxbs_qc_func.task_trim_galore(
inFastq=['test_data/mjb042_oxBS_R1.fastq.gz'],
outFastq=['fq1.fq.gz', 'fq2.fq.gz'],
tmpdir='test_out',
opts='',
path='')
except oxbs_qc_func.TrimGaloreException:
passed = True
assert passed
## same input twice
passed = False
try:
tg = oxbs_qc_func.task_trim_galore(inFastq=[
'test_data/mjb042_oxBS_R1.fastq.gz',
'test_data/mjb042_oxBS_R1.fastq.gz'
],
outFastq=['fq1.fq.gz', 'fq2.fq.gz'],
tmpdir='test_out',
opts='',
path='')
except oxbs_qc_func.TrimGaloreException:
passed = True
assert passed
## same Output twice
passed = False
try:
tg = oxbs_qc_func.task_trim_galore(inFastq=[
'test_data/mjb042_oxBS_R1.fastq.gz',
'test_data/mjb042_oxBS_R2.fastq.gz'
],
outFastq=['fq1.fq.gz', 'fq1.fq.gz'],
tmpdir='test_out',
opts='',
path='')
except oxbs_qc_func.TrimGaloreException:
passed = True
assert passed
def test_task_trim_galore_PE_1():
tg= oxbs_qc_func.task_trim_galore(inFastq= ['test_data/mjb042_oxBS_R1.fastq.gz', 'test_data/mjb042_oxBS_R2.fastq.gz'], outFastq= ['fq1.fq.gz', 'fq2.fq.gz'], tmpdir= 'test_out', opts= '-o test_out/trim_galore_pe1', path= '')
print(tg)
assert tg['fastq'][0] == 'test_out/trim_galore_pe1/fq1.fq.gz' ## Files are named as you expect
assert tg['fastq'][1] == 'test_out/trim_galore_pe1/fq2.fq.gz'
assert os.path.exists(tg['fastq'][0]) ## Files do exist
assert os.path.exists(tg['fastq'][1])
def test_task_trim_galore_SE():
passed= False
try:
tg= oxbs_qc_func.task_trim_galore(inFastq= ['test_data/mjb042_oxBS_R1.fastq.gz'], outFastq= ['bla/fq1.fq.gz'], tmpdir= 'test_out', opts= '-o test_out/trim_galore', path= '')
except oxbs_qc_func.TrimGaloreException:
"outFastq has path attached"
passed= True
assert passed
def test_task_trim_galore_SE_4():
tg = oxbs_qc_func.task_trim_galore(
inFastq=['test_data/mjb042_oxBS_R1.txt.gz'],
outFastq=['fq1.txt'],
tmpdir='test_out',
opts='-o test_out/trim_galore_4 --dont_gzip',
path='')
print(tg)
assert tg['fastq'][0] == 'test_out/trim_galore_4/fq1.txt'
assert os.path.exists(tg['fastq'][0])
def test_task_trim_galore_PE_3():
tg= oxbs_qc_func.task_trim_galore(inFastq= ['test_data/mjb042_oxBS_R1.txt', 'test_data/mjb042_oxBS_R2.txt'], outFastq= ['fq1.txt', 'fq2.txt'], tmpdir= 'test_out', opts= '-o test_out/trim_galore_pe3', path= '')
print(tg)
assert tg['fastq'][0] == 'test_out/trim_galore_pe3/fq1.txt' ## Files are named as you expect
assert tg['fastq'][1] == 'test_out/trim_galore_pe3/fq2.txt'
for x in tg['fastq']:
assert os.path.exists(x) ## files do exist
for x in tg['report']:
assert os.path.exists(x) ## Reports do exist
assert len(os.listdir('test_out/trim_galore_pe3/')) == 4
def test_task_trim_galore_SE_1():
tg = oxbs_qc_func.task_trim_galore(
inFastq=['test_data/mjb042_oxBS_R1.fastq.gz'],
outFastq=['fq1.fq.gz'],
tmpdir='test_out',
opts='-o test_out/trim_galore_1',
path='')
print(tg)
assert tg['fastq'][0] == 'test_out/trim_galore_1/fq1.fq.gz'
assert os.path.exists(tg['fastq'][0])
assert os.path.exists(
'test_out/trim_galore_1/mjb042_oxBS_R1.fastq.gz_trimming_report.txt')
def test_task_trim_galore_SE():
passed = False
try:
tg = oxbs_qc_func.task_trim_galore(
inFastq=['test_data/mjb042_oxBS_R1.fastq.gz'],
outFastq=['bla/fq1.fq.gz'],
tmpdir='test_out',
opts='-o test_out/trim_galore',
path='')
except oxbs_qc_func.TrimGaloreException:
"outFastq has path attached"
passed = True
assert passed
def test_task_trim_galore_PE_1():
tg = oxbs_qc_func.task_trim_galore(inFastq=[
'test_data/mjb042_oxBS_R1.fastq.gz',
'test_data/mjb042_oxBS_R2.fastq.gz'
],
outFastq=['fq1.fq.gz', 'fq2.fq.gz'],
tmpdir='test_out',
opts='-o test_out/trim_galore_pe1',
path='')
print(tg)
assert tg['fastq'][
0] == 'test_out/trim_galore_pe1/fq1.fq.gz' ## Files are named as you expect
assert tg['fastq'][1] == 'test_out/trim_galore_pe1/fq2.fq.gz'
assert os.path.exists(tg['fastq'][0]) ## Files do exist
assert os.path.exists(tg['fastq'][1])
def test_task_trim_galore_PE_3():
tg = oxbs_qc_func.task_trim_galore(inFastq=[
'test_data/mjb042_oxBS_R1.txt', 'test_data/mjb042_oxBS_R2.txt'
],
outFastq=['fq1.txt', 'fq2.txt'],
tmpdir='test_out',
opts='-o test_out/trim_galore_pe3',
path='')
print(tg)
assert tg['fastq'][
0] == 'test_out/trim_galore_pe3/fq1.txt' ## Files are named as you expect
assert tg['fastq'][1] == 'test_out/trim_galore_pe3/fq2.txt'
for x in tg['fastq']:
assert os.path.exists(x) ## files do exist
for x in tg['report']:
assert os.path.exists(x) ## Reports do exist
assert len(os.listdir('test_out/trim_galore_pe3/')) == 4
def test_task_trim_galore_SE_4():
tg= oxbs_qc_func.task_trim_galore(inFastq= ['test_data/mjb042_oxBS_R1.txt.gz'], outFastq= ['fq1.txt'], tmpdir= 'test_out', opts= '-o test_out/trim_galore_4 --dont_gzip', path= '')
print(tg)
assert tg['fastq'][0] == 'test_out/trim_galore_4/fq1.txt'
assert os.path.exists(tg['fastq'][0])
def test_task_trim_galore_SE_1():
tg= oxbs_qc_func.task_trim_galore(inFastq= ['test_data/mjb042_oxBS_R1.fastq.gz'], outFastq= ['fq1.fq.gz'], tmpdir= 'test_out', opts= '-o test_out/trim_galore_1', path= '')
print(tg)
assert tg['fastq'][0] == 'test_out/trim_galore_1/fq1.fq.gz'
assert os.path.exists(tg['fastq'][0])
assert os.path.exists('test_out/trim_galore_1/mjb042_oxBS_R1.fastq.gz_trimming_report.txt')
