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import os
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 FastqTest(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_build(self):
del self.fastq
if os.path.exists('{}.fxi'.format(gzip_fastq)):
os.remove('{}.fxi'.format(gzip_fastq))
fq = pyfastx.Fastq(gzip_fastq, build_index=False)
fq.build_index()
self.fastq = pyfastx.Fastq(gzip_fastq)
def test_fastq(self):
# test gzip format
self.assertEqual(pyfastx.gzip_check(gzip_fastq), self.fastq.is_gzip)
# test seq length
self.assertEqual(self.fastq.size, sum(self.bases.values()))
# test length
self.assertEqual(len(self.reads), len(self.fastq))
# test gc content
result = round(self.fastq.gc_content, 2)
expect = round((self.bases['G']+self.bases['C'])/(sum(self.bases.values()))*100, 2)
self.assertEqual(expect, result)
# test composition
self.assertEqual(self.fastq.composition, self.bases)
# test encoding type
self.assertEqual(['Sanger Phred+33', 'Illumina 1.8+ Phred+33', 'PacBio HiFi Phred+33'], self.fastq.encoding_type)
# test phred
self.assertEqual(self.fastq.phred, 33)
#test length
self.assertEqual(self.fastq.avglen, 150)
self.assertEqual(self.fastq.minlen, 150)
self.assertEqual(self.fastq.maxlen, 150)
#test quality
self.assertEqual(self.fastq.maxqual, 70)
self.assertEqual(self.fastq.minqual, 35)
def test_platform(self):
#test unknown
fqfile = 'test1.fq'
with open(fqfile, 'w') as fw:
fw.write("@read1\n")
fw.write("AAAAAAAAAA\n")
fw.write("+\n")
fw.write(" \n")
fq = pyfastx.Fastq(fqfile)
self.assertEqual(fq.encoding_type, ['Unknown'])
del fq
os.remove("{}.fxi".format(fqfile))
with open(fqfile, 'w') as fw:
fw.write("@read1\n")
qs = []
for i in range(59, 105):
qs.append(chr(i))
fw.write("{}\n".format('A'*len(qs)))
fw.write("+\n")
fw.write("{}\n".format(''.join(qs)))
fq = pyfastx.Fastq(fqfile)
self.assertIn("Solexa Solexa+64", fq.encoding_type)
del fq
os.remove("{}.fxi".format(fqfile))
with open(fqfile, 'w') as fw:
fw.write("@read1\n")
qs = []
for i in range(64, 105):
qs.append(chr(i))
fw.write("{}\n".format('A'*len(qs)))
fw.write("+\n")
fw.write("{}\n".format(''.join(qs)))
fq = pyfastx.Fastq(fqfile)
self.assertIn("Illumina 1.3+ Phred+64", fq.encoding_type)
del fq
os.remove("{}.fxi".format(fqfile))
with open(fqfile, 'w') as fw:
fw.write("@read1\n")
qs = []
for i in range(66, 105):
qs.append(chr(i))
fw.write("{}\n".format('A'*len(qs)))
fw.write("+\n")
fw.write("{}\n".format(''.join(qs)))
fq = pyfastx.Fastq(fqfile)
self.assertIn("Illumina 1.5+ Phred+64", fq.encoding_type)
del fq
os.remove("{}.fxi".format(fqfile))
os.remove(fqfile)
def test_negative(self):
read = self.fastq[-1]
self.assertEqual(read.name, self.reads[len(self.reads)-1][0])
def test_iter_object(self):
# test read iter
i = -1
for read in self.fastq:
i += 1
self.assertEqual(read.name, self.reads[i][0])
self.assertEqual(read.seq, self.reads[i][1])
self.assertEqual(read.qual, self.reads[i][2])
#test reference of read made from loop
for read in self.fastq:
break
expect = self.reads[0][1]
self.assertEqual(expect, read.seq)
self.assertEqual(expect, read.seq)
def test_iter_tuple(self):
i = -1
for name, seq, qual in pyfastx.Fastq(flat_fastq, build_index=False):
i += 1
self.assertEqual(name, self.reads[i][0])
self.assertEqual(seq, self.reads[i][1])
self.assertEqual(qual, self.reads[i][2])
def test_read_len(self):
lens = [len(it[1]) for it in self.reads.values()]
self.assertEqual(self.fastq.minlen, min(lens))
self.assertEqual(self.fastq.maxlen, min(lens))
def test_repr(self):
self.assertEqual(repr(self.fastq), "<Fastq> {} contains {} reads".format(gzip_fastq, len(self.reads)))
def test_full_name(self):
fq = pyfastx.Fastq(flat_fastq, build_index=False, full_name=True)
for name, _, _ in fq:
self.assertTrue(name, self.fastq[name.split()[0]].description)
def test_exception(self):
with self.assertRaises(FileExistsError):
_ = pyfastx.Fastq('a_fastq_file_not_exists')
with self.assertRaises(IndexError):
_ = self.fastq[len(self.fastq)]
with self.assertRaises(KeyError):
_ = self.fastq[int]
with self.assertRaises(KeyError):
_ = self.fastq['abc']
if __name__ == '__main__':
unittest.main()
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