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import os
import gzip
import random
import pyfastx
import unittest
join = os.path.join
data_dir = join(os.path.dirname(os.path.abspath(__file__)), 'data')
gzip_fastq = join(data_dir, 'test.fq.gz')
flat_fastq = join(data_dir, 'test.fq')
class ReadTest(unittest.TestCase):
def setUp(self):
self.fastq = pyfastx.Fastq(gzip_fastq)
#reload index
self.fastq = pyfastx.Fastq(gzip_fastq)
#flat fastq
self.flatq = pyfastx.Fastq(flat_fastq)
self.reads = {}
self.bases = {'A': 0, 'T': 0, 'G': 0, 'C':0, 'N':0}
i = 0
c = -1
with open(flat_fastq) as fh:
for line in fh:
i += 1
if i % 4 == 1:
c += 1
self.reads[c] = [line[1:].strip().split()[0], 0, 0]
elif i % 4 == 2:
self.reads[c][1] = line.strip()
self.bases['A'] += line.count('A')
self.bases['T'] += line.count('T')
self.bases['G'] += line.count('G')
self.bases['C'] += line.count('C')
self.bases['N'] += line.count('N')
elif i % 4 == 0:
self.reads[c][2] = line.strip()
def tearDown(self):
del self.fastq
del self.flatq
if os.path.exists('{}.fxi'.format(gzip_fastq)):
os.remove('{}.fxi'.format(gzip_fastq))
if os.path.exists('{}.fxi'.format(flat_fastq)):
os.remove('{}.fxi'.format(flat_fastq))
def get_random_read(self):
return random.randint(0, len(self.fastq)-1)
def test_repr(self):
idx = self.get_random_read()
read = self.flatq[idx]
read1 = self.reads[idx]
self.assertEqual(repr(read), "<Read> {} with length of {}".format(read1[0], len(read1[1])))
def test_read(self):
idx = self.get_random_read()
result = self.fastq[idx]
expect = self.reads[idx]
del result
result = self.fastq[idx]
read0 = self.flatq[idx]
# test length
self.assertEqual(len(result), len(expect[1]))
# test name
self.assertEqual(result.name, expect[0])
# test str
self.assertEqual(str(result), expect[1])
# test seq
self.assertEqual(result.seq, expect[1])
self.assertEqual(read0.seq, expect[1])
# test quality
self.assertEqual(result.qual, expect[2])
self.assertEqual(read0.qual, expect[2])
# test quality integer
self.assertEqual(result.quali, [ord(b)-33 for b in expect[2]])
result = self.fastq[expect[0]]
# test subscript
self.assertEqual(result.seq, expect[1])
# test contain
self.assertTrue(result.name in self.fastq)
def test_read_seq(self):
#test reverse
idx = self.get_random_read()
result = self.fastq[idx]
expect = self.reads[idx][1]
self.assertEqual(result.reverse, expect[::-1])
#test complement
complement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A', 'N':'N'}
expect1 = ''.join(complement.get(b) for b in expect)
self.assertEqual(result.complement, expect1)
#test antisense
expect2 = ''.join(complement.get(b) for b in reversed(expect))
self.assertEqual(result.antisense, expect2)
def test_read_description(self):
idx = self.get_random_read()
read = self.fastq[idx]
i = -1
with open(flat_fastq) as fh:
for line in fh:
if line[0] == '@':
i += 1
if i == idx:
break
self.assertEqual(line.strip(), read.description)
read = self.flatq[idx]
self.assertEqual(line.strip(), read.description)
def test_read_raw(self):
idx = self.get_random_read()
read = self.fastq[idx]
lines = []
with gzip.open(gzip_fastq, 'rb') as fh:
for line in fh:
line = line.decode()
if line.startswith('@{}'.format(read.name)):
lines.append(line)
continue
if lines:
if line[0] == '@':
break
lines.append(line)
self.assertEqual(''.join(lines), read.raw)
idx = self.get_random_read()
read = self.flatq[idx]
lines = []
with open(flat_fastq, 'rb') as fh:
for line in fh:
line = line.decode()
if line.startswith('@{}'.format(read.name)):
lines.append(line)
continue
if lines:
if line[0] == '@':
break
lines.append(line)
self.assertEqual(''.join(lines), read.raw)
if __name__ == '__main__':
unittest.main()
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