Mercurial > repos > yufei-luo > s_mart

comparison commons/tools/tests/Test_F_LaunchBlaster.py @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 from commons.core.utils.FileUtils import FileUtils
2 import unittest
3 import os
4 import glob
5 from commons.tools.LaunchBlaster import LaunchBlaster
6
7 class Test_F_LaunchBlaster(unittest.TestCase):
8
9 def setUp(self):
10 self._inFileName = "DmelChr4.fa"
11 inFilePath = "%s/Tools/%s" % (os.environ["REPET_DATA"], self._inFileName)
12 try:
13 os.remove(self._inFileName)
14 except:
15 pass
16 os.symlink(inFilePath, self._inFileName)
17 self._iLaunchBlaster = LaunchBlaster(self._inFileName)
18 self._iLaunchBlaster.setDoAllByall(True)
19 self._iLaunchBlaster.setVerbosity(4)
20
21 def tearDown(self):
22 try:
23 FileUtils.removeFilesByPattern("%s*" % self._inFileName)
24 os.remove("formatdb.log")
25 except:
26 pass
27
28 def test_run_as_class_1_file(self):
29 expFileName = "%s/Tools/DmelChr4.align" % os.environ["REPET_DATA"]
30 obsFileName = "%s.align" % self._inFileName
31
32 self._iLaunchBlaster.run()
33
34 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
35
36 def test_run_as_class_1_file_changed_params(self):
37 expFileName = "DmelChr4.align"
38 with open(expFileName, "w") as fh:
39 fh.write("dmel_chr4\t691910\t692326\tdmel_chr4\t700019\t700435\t0\t827\t100\n")
40 obsFileName = "%s.align" % self._inFileName
41
42 self._iLaunchBlaster.setIdentity(100)
43 self._iLaunchBlaster.setCPU(4)
44 self._iLaunchBlaster.setDoClean(True)
45 self._iLaunchBlaster.run()
46
47 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
48 os.remove(expFileName)
49 self.assertTrue(glob.glob("*fa_cut*") == [])
50 self.assertTrue(glob.glob("*Nstretch*") == [])
51 self.assertTrue(glob.glob("*seq_treated*") == [])
52 self.assertTrue(glob.glob("*.log") == [])
53
54 def test_run_as_script_1bank_1file(self):
55 inputFileName = "chunks.fa"
56 with open(inputFileName, "w") as f:
57 f.write(">chunk1\n")
58 f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n")
59 f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n")
60 expFileName = "exp.align"
61 with open(expFileName, "w") as f:
62 f.write("chunk1\t1\t120\tdmel_chr4\t1\t120\t2e-64\t238\t100\n")
63 obsFileName = "%s.align" % inputFileName
64
65 cmd = "LaunchBlaster.py -q %s -s %s -e 0.1 -a" % (inputFileName, self._inFileName)
66 os.system(cmd)
67
68 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
69 FileUtils.removeFilesByPattern("%s*" % inputFileName)
70 os.remove(expFileName)
71
72 def test_run_as_script_1bank_1file_withoutABA(self):
73 queryFileName = "chunks.fa"
74 with open(queryFileName, "w") as f:
75 f.write(">chunk1\n")
76 f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n")
77 f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n")
78 subjectFileName = "genome.fa"
79 with open(subjectFileName, "w") as f:
80 f.write(">chunk1\n")
81 f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n")
82 f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n")
83 f.write(">chunk2\n")
84 f.write("GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC\n")
85 f.write("GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT\n")
86 expFileName = "exp.align"
87 with open(expFileName, "w") as f:
88 f.write("chunk1\t1\t120\tchunk1\t1\t120\t4e-68\t238\t100\n")
89 f.write("chunk1\t1\t120\tchunk2\t1\t120\t4e-68\t238\t100\n")
90 obsFileName = "%s.align" % queryFileName
91
92 cmd = "LaunchBlaster.py -q %s -s %s -e 0.1" % (queryFileName, subjectFileName)
93 os.system(cmd)
94
95 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
96 FileUtils.removeFilesByPattern("%s*" % queryFileName)
97 FileUtils.removeFilesByPattern("%s*" % subjectFileName)
98 os.remove(expFileName)
99
100 if __name__ == "__main__":
101 unittest.main()