def test_trim_fastq_exception():
passed = False
try:
oxbs_qc_func.trim_fastq('test_data/mjb042_oxBS_R1.txt', -1,
'mjb042_oxBS_R1.fq') ### Invalid -1
except oxbs_qc_func.TrimFastqException:
passed = True
assert passed
passed = False
try:
x = oxbs_qc_func.trim_fastq(
'test_data/mjb042_oxBS_R1.txt.gz', 1,
'test_data/mjb042_oxBS_R1.txt.gz') ## input == output
except oxbs_qc_func.TrimFastqException:
passed = True
assert passed
passed = False
try:
x = oxbs_qc_func.trim_fastq(
'test_data/mjb042_oxBS_R1.txt.gz', 1,
'/nonsense/mjb042_oxBS_R1.txt.gz') ## output dir does not exists
except oxbs_qc_func.TrimFastqException:
passed = True
assert passed
def test_trim_fastq_exception():
passed= False
try:
oxbs_qc_func.trim_fastq('test_data/mjb042_oxBS_R1.txt', -1, 'mjb042_oxBS_R1.fq') ### Invalid -1
except oxbs_qc_func.TrimFastqException:
passed= True
assert passed
passed= False
try:
x= oxbs_qc_func.trim_fastq('test_data/mjb042_oxBS_R1.txt.gz', 1, 'test_data/mjb042_oxBS_R1.txt.gz') ## input == output
except oxbs_qc_func.TrimFastqException:
passed= True
assert passed
passed= False
try:
x= oxbs_qc_func.trim_fastq('test_data/mjb042_oxBS_R1.txt.gz', 1, '/nonsense/mjb042_oxBS_R1.txt.gz') ## output dir does not exists
except oxbs_qc_func.TrimFastqException:
passed= True
assert passed
def test_trim_fastq_1():
try:
os.makedirs('test_out')
except OSError:
pass
xout= oxbs_qc_func.trim_fastq('test_data/mjb042_oxBS_R1.txt.gz', 20, 'test_out/mjb042_oxBS_R1.fq')
assert xout
assert os.path.exists('test_out/mjb042_oxBS_R1.fq.gz') ## Note .gz included!
## Same number of lines in input and output
tfq= gzip.open('test_out/mjb042_oxBS_R1.fq.gz').readlines()
fq= gzip.open('test_data/mjb042_oxBS_R1.txt.gz').readlines()
assert len(tfq) == len(fq)
## Lenght of read AND quality == 20
read_quality_qlen= [len(tfq[x].strip()) for x in range(1, 100, 2)]
assert set(read_quality_qlen) == set([20])
def test_trim_fastq_1():
try:
os.makedirs('test_out')
except OSError:
pass
xout = oxbs_qc_func.trim_fastq('test_data/mjb042_oxBS_R1.txt.gz', 20,
'test_out/mjb042_oxBS_R1.fq')
assert xout
assert os.path.exists(
'test_out/mjb042_oxBS_R1.fq.gz') ## Note .gz included!
## Same number of lines in input and output
tfq = gzip.open('test_out/mjb042_oxBS_R1.fq.gz').readlines()
fq = gzip.open('test_data/mjb042_oxBS_R1.txt.gz').readlines()
assert len(tfq) == len(fq)
## Lenght of read AND quality == 20
read_quality_qlen = [len(tfq[x].strip()) for x in range(1, 100, 2)]
assert set(read_quality_qlen) == set([20])
