Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/test/Test_F_trimSequences.py @ 18:94ab73e8a190

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
parents
children
comparison
equal deleted inserted replaced
17:b0e8584489e6 18:94ab73e8a190
1 import unittest, os, os.path
2 from SMART.Java.Python.misc import Utils
3 SMART_PATH = os.environ["REPET_PATH"] + "/SMART"
4
5 class Test_F_trimSequences(unittest.TestCase):
6
7 def setUp(self):
8 self._expOutputFileName = "expOutputFile.fasta"
9 self._obsOutputFileName = "obsOutputFile.mfa"
10 self._inputFileName = "inputFile.fasta"
11
12 def tearDown(self):
13 for fileName in (self._expOutputFileName, self._obsOutputFileName, self._inputFileName):
14 if os.path.exists(fileName):
15 os.remove(fileName)
16
17 def test_simple(self):
18 expOutputFile = open(self._expOutputFileName, "w")
19 expOutputFile.write(">sequence1\nTTGCATAGCGCTACGTA\n")
20 expOutputFile.close()
21 inputFile = open(self._inputFileName, "w")
22 inputFile.write(">sequence1\nAGCTCGGGTATTGCATAGCGCTACGTACCCTTTATATC\n")
23 inputFile.close()
24 os.system("python %s/Java/Python/trimSequences.py -i %s -f fasta -3 CCCTTTATATC -5 AGCTCGGGTA -o %s -v 0" % (SMART_PATH, self._inputFileName, self._obsOutputFileName))
25 self.assertTrue(Utils.diff(self._expOutputFileName, self._obsOutputFileName))
26
27 if __name__ == "__main__":
28 unittest.main()