Mercurial > repos > yufei-luo > s_mart

comparison commons/launcher/tests/Test_F_LaunchMatcher.py @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
1 from commons.core.utils.FileUtils import FileUtils
2 import unittest
3 import os
4 import subprocess
5 from commons.launcher.LaunchMatcher import LaunchMatcher
6
7 class Test_F_LaunchMatcher(unittest.TestCase):
8
9 def setUp(self):
10 self._inFileName = "DmelChr4.align"
11 self._fastaFileName = "DmelChr4.fa"
12 inFilePath = "%s/Tools/%s" % (os.environ["REPET_DATA"], self._inFileName)
13 inFastaPath = "%s/Tools/%s" % (os.environ["REPET_DATA"], self._fastaFileName)
14 try:
15 os.remove(self._inFileName)
16 except:
17 pass
18 os.symlink(inFilePath, self._inFileName)
19 os.symlink(inFastaPath, self._fastaFileName)
20 self._iLaunchMatcher = LaunchMatcher(align=self._inFileName, queryFileName=self._fastaFileName, subjectFileName=self._fastaFileName, doJoin=True, evalue="1e-20", keepConflict=True)
21 self._iLaunchMatcher.setVerbosity(2)
22
23 def tearDown(self):
24 try:
25 FileUtils.removeFilesByPattern("%s*" % self._inFileName)
26 os.remove(self._fastaFileName)
27 except:
28 pass
29
30 def test_run_as_class_1_file(self):
31 expPathFileName = "%s/Tools/DmelChr4.align.match.path" % os.environ["REPET_DATA"]
32 expTabFileName = "%s/Tools/DmelChr4.align.match.tab" % os.environ["REPET_DATA"]
33
34 obsPathFileName = "%s.match.path" % self._inFileName
35 obsTabFileName = "%s.match.tab" % self._inFileName
36
37 self._iLaunchMatcher.run()
38
39 self.assertTrue(FileUtils.are2FilesIdentical(expPathFileName, obsPathFileName))
40 self.assertTrue(FileUtils.are2FilesIdentical(expTabFileName, obsTabFileName))
41
42 def test_run_as_script(self):
43 expPathFileName = "%s/Tools/DmelChr4.align.match.path" % os.environ["REPET_DATA"]
44 expTabFileName = "%s/Tools/DmelChr4.align.match.tab" % os.environ["REPET_DATA"]
45
46 cmd = "LaunchMatcher.py "
47 cmd += "-a %s " % self._inFileName
48 cmd += "-q %s " % self._fastaFileName
49 cmd += "-s %s " % self._fastaFileName
50 cmd += "-o DmelChr4.align "
51 cmd += "-j "
52 cmd += "-k "
53 cmd += "-e 1e-20 "
54 process = subprocess.Popen(cmd, shell = True)
55 process.communicate()
56 obsPathFileName = "%s.match.path" % self._inFileName
57 obsTabFileName = "%s.match.tab" % self._inFileName
58
59 self.assertTrue(FileUtils.are2FilesIdentical(expPathFileName, obsPathFileName))
60 self.assertTrue(FileUtils.are2FilesIdentical(expTabFileName, obsTabFileName))
61
62 if __name__ == "__main__":
63 unittest.main()