Mercurial > repos > yufei-luo > s_mart
comparison commons/core/parsing/test/Test_pilerTAToGrouperMap.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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5:ea3082881bf8 | 6:769e306b7933 |
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1 import unittest | |
2 import os | |
3 from commons.core.parsing.PilerTAToGrouperMap import PilerTAToGrouperMap | |
4 from commons.core.utils.FileUtils import FileUtils | |
5 | |
6 class Test_pilerTAToGrouperMap(unittest.TestCase): | |
7 | |
8 def setUp(self): | |
9 self._inputGffFileName = "input.gff" | |
10 self._inputPYRFileName = "input_pyr.gff" | |
11 self._inputMOTIFFileName = "input_motif.gff" | |
12 | |
13 self._obsOutFileName = "output.info" | |
14 self._obsGrouperFileName = "input_motif.gff.grp" | |
15 self._obsGrpMapFileName = "input_motif.gff.grp.map" | |
16 | |
17 self._expOutFileName = "exp_output.info" | |
18 self._expGrouperFileName = "exp_motif.gff.grp" | |
19 self._expGrpMapFileName = "exp_motif.gff.grp.map" | |
20 | |
21 def tearDown(self): | |
22 os.remove(self._inputGffFileName) | |
23 os.remove(self._inputPYRFileName) | |
24 os.remove(self._inputMOTIFFileName) | |
25 | |
26 os.remove(self._obsOutFileName) | |
27 os.remove(self._obsGrouperFileName) | |
28 os.remove(self._obsGrpMapFileName) | |
29 | |
30 os.remove(self._expOutFileName) | |
31 os.remove(self._expGrouperFileName) | |
32 os.remove(self._expGrpMapFileName) | |
33 | |
34 def testRun(self): | |
35 self._writePilerTAFilePYR(self._inputPYRFileName) | |
36 self._writePilerTAFileMOTIF(self._inputMOTIFFileName) | |
37 self._writePilerTAGff(self._inputGffFileName) | |
38 | |
39 self._writeExpOutputFile(self._expOutFileName) | |
40 self._writeExpGrouperFile(self._expGrouperFileName) | |
41 self._writeExpGrouperMapFile(self._expGrpMapFileName) | |
42 | |
43 iPilerTAToGrouperMap = PilerTAToGrouperMap(self._inputGffFileName, self._inputPYRFileName,self._inputMOTIFFileName, self._obsOutFileName) | |
44 iPilerTAToGrouperMap.run() | |
45 | |
46 self.assertTrue(FileUtils.are2FilesIdentical(self._expOutFileName, self._obsOutFileName)) | |
47 self.assertTrue(FileUtils.are2FilesIdentical(self._expGrouperFileName, self._obsGrouperFileName)) | |
48 self.assertTrue(FileUtils.are2FilesIdentical(self._expGrpMapFileName, self._obsGrpMapFileName)) | |
49 | |
50 | |
51 def _writePilerTAGff(self, fileName): | |
52 f = open(fileName, "w") | |
53 f.write("chunk21\tpiler\thit\t155146\t156020\t0\t+\t.\tTarget chunk21 150519 151392 ; Pile 510 ; Pyramid 0\n") | |
54 f.write("chunk21\tpiler\thit\t154790\t156023\t0\t+\t.\tTarget chunk21 150519 151751 ; Pile 510 ; Pyramid 0\n") | |
55 f.write("chunk21\tpiler\thit\t154078\t156023\t0\t+\t.\tTarget chunk21 150519 152463 ; Pile 510 ; Pyramid 0\n") | |
56 f.write("chunk21\tpiler\thit\t154256\t156023\t0\t+\t.\tTarget chunk21 150519 152285 ; Pile 510 ; Pyramid 0\n") | |
57 f.write("chunk21\tpiler\thit\t154434\t156023\t0\t+\t.\tTarget chunk21 150519 152107 ; Pile 510 ; Pyramid 0\n") | |
58 f.close() | |
59 | |
60 def _writePilerTAFilePYR(self, fileName): | |
61 f = open(fileName, "w") | |
62 f.write("chunk21\tpiler\tpyramid\t150519\t156023\t0\t.\t.\tPyramidIndex 0\n") | |
63 f.write("chunk21\tpiler\tpyramid\t150519\t156023\t0\t.\t.\tPyramidIndex 1\n") | |
64 f.write("chunk21\tpiler\tpyramid\t165574\t174424\t0\t.\t.\tPyramidIndex 2\n") | |
65 f.write("chunk21\tpiler\tpyramid\t166301\t174424\t0\t.\t.\tPyramidIndex 3\n") | |
66 f.write("chunk21\tpiler\tpyramid\t168967\t174424\t0\t.\t.\tPyramidIndex 4\n") | |
67 f.write("chunk21\tpiler\tpyramid\t170215\t174424\t0\t.\t.\tPyramidIndex 5\n") | |
68 f.close() | |
69 | |
70 def _writePilerTAFileMOTIF(self, fileName): | |
71 f = open(fileName, "w") | |
72 f.write("chunk21\tpiler\ttandemmotif\t155843\t156020\t0\t.\t.\tTarget chunk21 151215 151392 ; Pyramid 0\n") | |
73 f.write("chunk21\tpiler\ttandemmotif\t151215\t151392\t0\t.\t.\tTarget chunk21 155843 156020 ; Pyramid 0\n") | |
74 f.write("chunk21\tpiler\ttandemmotif\t151574\t151751\t0\t.\t.\tTarget chunk21 155843 156020 ; Pyramid 0\n") | |
75 f.write("chunk21\tpiler\ttandemmotif\t152286\t152463\t0\t.\t.\tTarget chunk21 155843 156020 ; Pyramid 0\n") | |
76 f.write("chunk21\tpiler\ttandemmotif\t152108\t152285\t0\t.\t.\tTarget chunk21 155843 156020 ; Pyramid 0\n") | |
77 f.close() | |
78 | |
79 def _writeExpOutputFile(self, fileName): | |
80 f = open(fileName, "w") | |
81 f.write("Pile 510\tPyramid 0\n") | |
82 f.write("\tPyramid 1\n") | |
83 f.write("\tPyramid 2\n") | |
84 f.write("\tPyramid 3\n") | |
85 f.write("\tPyramid 4\n") | |
86 f.write("\tPyramid 5\n") | |
87 f.close() | |
88 | |
89 def _writeExpGrouperFile(self, fileName): | |
90 f = open(fileName, "w") | |
91 f.write("MbS1Gr0Cl510\tchunk21\tpiler\ttandemmotif\t155843\t156020\t0\t.\t.\tTarget chunk21 151215 151392 \tPile 510\tPyramid 0\n") | |
92 f.write("MbS2Gr0Cl510\tchunk21\tpiler\ttandemmotif\t151215\t151392\t0\t.\t.\tTarget chunk21 155843 156020 \tPile 510\tPyramid 0\n") | |
93 f.write("MbS3Gr0Cl510\tchunk21\tpiler\ttandemmotif\t151574\t151751\t0\t.\t.\tTarget chunk21 155843 156020 \tPile 510\tPyramid 0\n") | |
94 f.write("MbS4Gr0Cl510\tchunk21\tpiler\ttandemmotif\t152286\t152463\t0\t.\t.\tTarget chunk21 155843 156020 \tPile 510\tPyramid 0\n") | |
95 f.write("MbS5Gr0Cl510\tchunk21\tpiler\ttandemmotif\t152108\t152285\t0\t.\t.\tTarget chunk21 155843 156020 \tPile 510\tPyramid 0\n") | |
96 f.close() | |
97 | |
98 def _writeExpGrouperMapFile(self, fileName): | |
99 f = open(fileName, "w") | |
100 f.write("MbS1Gr0Cl510\tchunk21\t155843\t156020\n") | |
101 f.write("MbS2Gr0Cl510\tchunk21\t151215\t151392\n") | |
102 f.write("MbS3Gr0Cl510\tchunk21\t151574\t151751\n") | |
103 f.write("MbS4Gr0Cl510\tchunk21\t152286\t152463\n") | |
104 f.write("MbS5Gr0Cl510\tchunk21\t152108\t152285\n") | |
105 f.close() | |
106 | |
107 if __name__ == "__main__": | |
108 unittest.main() |