Mercurial > repos > yufei-luo > s_mart

comparison commons/launcher/tests/Test_F_LaunchBlastclust.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 import unittest
2 import os
3 from commons.launcher.LaunchBlastclust import LaunchBlastclust
4 from commons.core.utils.FileUtils import FileUtils
5
6 class Test_F_LaunchBlastclust(unittest.TestCase):
7
8 def setUp(self):
9 self._inputFileName = "DmelChr4_LTRharvest_expected_with_default_params.fa"
10 os.symlink("%s/Tools/%s" % (os.environ["REPET_DATA"], self._inputFileName), self._inputFileName)
11 self._outputFileName = "%s_Blastclust.fa" % self._inputFileName
12 self._outBlastclustFileName = "%s_blastclust.txt" % self._inputFileName
13
14 def tearDown(self):
15 if os.path.exists(self._outputFileName):
16 os.remove(self._outputFileName)
17 if os.path.exists(self._outBlastclustFileName):
18 os.remove(self._outBlastclustFileName)
19 os.remove(self._inputFileName)
20
21 def test_run(self):
22 iLaunchBlastclust = LaunchBlastclust(self._inputFileName, clean = True)
23 iLaunchBlastclust.run()
24 expFileName = "%s/Tools/DmelChr4_LTRharvest_Blastclust_expected.fa" % os.environ["REPET_DATA"]
25 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
26
27 def test_run_with_tweaked_params(self):
28 iLaunchBlastclust = LaunchBlastclust(self._inputFileName, clean = True)
29 iLaunchBlastclust.setBothSequences("F")
30 iLaunchBlastclust.setIdentityThreshold(0)
31 iLaunchBlastclust.setIsBlastToMap()
32 iLaunchBlastclust.run()
33
34 faExpFileName = "%s/Tools/DmelChr4_LTRharvest_Blastclust_expected_with_tweaked_params.fa" % os.environ["REPET_DATA"]
35 mapExpFileName = "%s/Tools/DmelChr4_LTRharvest_Blastclust_expected_with_tweaked_params.map" % os.environ["REPET_DATA"]
36
37 self.assertTrue(FileUtils.are2FilesIdentical(faExpFileName, self._outputFileName))
38 self.assertTrue(FileUtils.are2FilesIdentical(mapExpFileName, "%s.map" % os.path.splitext(self._outputFileName)[0]))
39
40 os.remove("%s.map" % os.path.splitext(self._outputFileName)[0])
41
42 def test_run_with_header_options(self):
43 inFileName = "dummyHeaderForTEdenovo.fa"
44 expFileName = "expDummyHeaderForTEdenovo.fa"
45 self._writeInputFile_header_options(inFileName)
46 self._writeExpFile_header_options(expFileName)
47 obsFileName = "%s_Blastclust.fa" % inFileName
48
49 iLaunchBlastclust = LaunchBlastclust(inFileName, clean = True)
50 iLaunchBlastclust.setIsHeaderForTEdenovo(True)
51 iLaunchBlastclust.run()
52
53 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
54
55 os.remove(inFileName)
56 os.remove(expFileName)
57 os.remove(obsFileName)
58 os.remove("%s_blastclust.txt" % inFileName)
59
60 def test_run_as_script(self):
61 cmd = "LaunchBlastclust.py -i %s" % self._inputFileName
62 os.system(cmd)
63 expFileName = "%s/Tools/DmelChr4_LTRharvest_Blastclust_expected.fa" % os.environ["REPET_DATA"]
64 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, self._outputFileName))
65
66 def _writeInputFile_header_options(self, inFileName):
67 f = open(inFileName,"w")
68 f.write(">DTX-incomp_DmelChr4-B-R9-Map3_reversed\n")
69 f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n")
70 f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n")
71 f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n")
72 f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n")
73 f.write(">DTX-incomp_DmelChr4-B-R10-Map3_reversed\n")
74 f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n")
75 f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n")
76 f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n")
77 f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n")
78 f.write(">PotentialHostGene-chim_DmelChr4-B-R4-Map5_reversed\n")
79 f.write("TACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACGATTT\n")
80 f.write("TTTCGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAG\n")
81 f.write("AGCGGAGAGCGCTACAGCGAACAGCTCTTTTCAACGCATAAAGTGATAGCAGACAACTGT\n")
82 f.close()
83
84 def _writeExpFile_header_options(self, expFileName):
85 f = open(expFileName,"w")
86 f.write(">DTX-incomp_Blc1_DmelChr4-B-R9-Map3_reversed\n")
87 f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n")
88 f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n")
89 f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n")
90 f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n")
91 f.write(">DTX-incomp_Blc1_DmelChr4-B-R10-Map3_reversed\n")
92 f.write("CATTAGATTCAAGGCATCATGGATCAGCACATTTACACAGATATCCTGGAAAATGTGATG\n")
93 f.write("CTGCCATATGCCGGGGATGAAATGCCGTTGGTTTGGACATTTCAACAGGATAACGATTCA\n")
94 f.write("AAACACACGAGCAAGAAAGCTTGAAAGTGGTTTGAGCAGAAATCGATCCGAGTAATGAAA\n")
95 f.write("TGGCCTGCTCTGTCATCCGACTTGAATCCAATCGAAAACCTTTGGGCGGACGTGGAAAAA\n")
96 f.write(">PotentialHostGene-chim_Blc2_DmelChr4-B-R4-Map5_reversed\n")
97 f.write("TACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACGATTT\n")
98 f.write("TTTCGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAG\n")
99 f.write("AGCGGAGAGCGCTACAGCGAACAGCTCTTTTCAACGCATAAAGTGATAGCAGACAACTGT\n")
100 f.close()
101
102 if __name__ == "__main__":
103 unittest.main()