1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
|
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 FastxTest(unittest.TestCase):
def setUp(self):
self.fastq = pyfastx.Fastq(gzip_fastq)
with open(flat_fastq) as fh:
self.keys = [line.split()[0][1:] for line in fh if line[0] == '@']
self.count = len(self.keys)
def tearDown(self):
del self.fastq
if os.path.exists('{}.fxi'.format(gzip_fastq)):
os.remove('{}.fxi'.format(gzip_fastq))
def get_random_index(self):
return random.randint(0, self.count-1)
def test_fastq_key(self):
#test for repr
keys = self.fastq.keys()
self.assertEqual(repr(keys), "<FastqKeys> contains {} keys".format(self.count))
#test for lenth
self.assertEqual(self.count, len(keys))
#test for iter
for i, k in enumerate(keys):
self.assertEqual(self.keys[i], k)
#test random access
idx = self.get_random_index()
self.assertEqual(self.keys[idx], keys[idx])
#test contain
idx = self.get_random_index()
self.assertTrue(self.keys[idx] in keys)
#test negative index
neg = (self.count - idx) * -1
self.assertEqual(self.keys[neg], keys[neg])
def test_exception(self):
with self.assertRaises(IndexError):
_ = self.keys[self.count*2]
|
