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
|
'''
compile_test.py - check pyximport functionality with pysam
==========================================================
test script for checking if compilation against
pysam and tabix works.
'''
# clean up previous compilation
import os
import unittest
import pysam
from TestUtils import BAM_DATADIR, TABIX_DATADIR
try:
os.unlink('tests/_compile_test.c')
os.unlink('tests/_compile_test.pyxbldc')
except OSError:
pass
import pyximport
pyximport.install(build_in_temp=False)
import _compile_test
class BAMTest(unittest.TestCase):
input_filename = os.path.join(BAM_DATADIR, "ex1.bam")
def testCount(self):
nread = _compile_test.testCountBAM(
pysam.Samfile(self.input_filename))
self.assertEqual(nread, 3270)
class GTFTest(unittest.TestCase):
input_filename = os.path.join(TABIX_DATADIR, "example.gtf.gz")
def testCount(self):
nread = _compile_test.testCountGTF(
pysam.Tabixfile(self.input_filename))
self.assertEqual(nread, 237)
if __name__ == "__main__":
unittest.main()
|
