|
18
|
1 import unittest
|
|
|
2 import os, glob
|
|
|
3
|
|
|
4
|
|
|
5 class Test_F_qualToFastq(unittest.TestCase):
|
|
|
6
|
|
|
7 def setUp(self):
|
|
|
8 self.fastaFileName = "file.fasta"
|
|
|
9 self.qualFileName = "file.qual"
|
|
|
10 self.outputFileName = "outputFile.fastq"
|
|
|
11
|
|
|
12 def tearDown(self):
|
|
|
13 for fileRoot in (self.fastaFileName, self.qualFileName, self.outputFileName):
|
|
|
14 for file in glob.glob("%s*" % (fileRoot)):
|
|
|
15 os.remove(file)
|
|
|
16
|
|
|
17 def test_run_simple(self):
|
|
|
18 handle = open(self.fastaFileName, "w")
|
|
|
19 handle.write(">test1\n")
|
|
|
20 handle.write("AAAAAA")
|
|
|
21 handle.close()
|
|
|
22 handle = open(self.qualFileName, "w")
|
|
|
23 handle.write(">test1\n")
|
|
|
24 handle.write("32\t32\t32\t32\t32\t32")
|
|
|
25 handle.close()
|
|
|
26 os.system("python ../qualToFastq.py -f %s -q %s -o %s -v 0" % (self.fastaFileName, self.qualFileName, self.outputFileName))
|
|
|
27 handle = open(self.outputFileName)
|
|
|
28 lines = handle.readlines()
|
|
|
29 self.assertEquals(len(lines), 4)
|
|
|
30 self.assertEquals(lines[0], "@test1\n")
|
|
|
31 self.assertEquals(lines[1], "AAAAAA\n")
|
|
|
32 self.assertEquals(lines[2], "+\n")
|
|
|
33 self.assertEquals(lines[3], "AAAAAA\n")
|
|
|
34
|
|
|
35
|
|
|
36 if __name__ == "__main__":
|
|
|
37 unittest.main()
|
|
|
38
|
