Mercurial > repos > yufei-luo > s_mart

comparison smart_toolShed/SMART/Java/Python/ncList/test/Test_F_NCList.py @ 0:e0f8dcca02ed

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:e0f8dcca02ed
1 import os
2 import unittest
3 import struct
4 from SMART.Java.Python.ncList.NCList import NCList
5 from SMART.Java.Python.misc import Utils
6 from commons.core.utils.FileUtils import FileUtils
7 from SMART.Java.Python.ncList.test.MockFindOverlapsWithSeveralIntervals import *
8 from commons.core.parsing.GffParser import GffParser
9 from SMART.Java.Python.ncList.FileSorter import FileSorter
10
11 class Test_F_NCList(unittest.TestCase):
12
13 def setUp(self):
14 self._inputGff3FileName = 'sortedFile.gff3'
15 self._sortedFileName = 'sortedFile.pkl'
16 self._expHFileName = 'expH.bin'
17 self._expLFileName = 'expL.bin'
18 self._obsHFileName = 'H.bin'
19 self._obsLFileName = 'L.bin'
20 self._addressFileName = 'address.txt'
21 self._writeGFF3File(self._inputGff3FileName)
22 self._ncList = NCList(0)
23 self._ncList.setChromosome("chr1")
24
25 def tearDown(self):
26 return
27 for fileName in (self._inputGff3FileName, self._sortedFileName, self._expHFileName, self._expLFileName, self._obsHFileName, self._obsLFileName, self._addressFileName):
28 if os.path.exists(fileName):
29 os.remove(fileName)
30
31 def _sortAndBuild(self):
32 parser = GffParser(self._inputGff3FileName)
33 fs = FileSorter(parser, 0)
34 fs.setOutputFileName(self._sortedFileName)
35 fs.sort()
36 self._ncList.setFileName(self._sortedFileName)
37 self._ncList.setNbElements(parser.getNbTranscripts())
38 self._ncList.buildLists()
39
40 def test_run_with_one_elementSubList(self):
41 iMock = MockFindOverlapsWithOneInterval()
42 iMock.write(self._inputGff3FileName)
43 self._sortAndBuild()
44 self._writeExpHFile_one_elementSubList()
45 self._writeExpLFile_one_elementSubList()
46 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName))
47 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName))
48
49 def test_case1(self):
50 iMock = MockFindOverlapsWithServeralIntervals_case1()
51 iMock.write(self._inputGff3FileName)
52 self._sortAndBuild()
53 self._writeExpHFileCase1()
54 self._writeExpLFileCase1()
55 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName))
56 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName))
57
58 def test_case2(self):
59 iMock = MockFindOverlapsWithServeralIntervals_case2()
60 iMock.write(self._inputGff3FileName)
61 self._sortAndBuild()
62 self._writeExpHFileCase2()
63 self._writeExpLFileCase2()
64 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName))
65 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName))
66
67 def test_case3(self):
68 iMock = MockFindOverlapsWithServeralIntervals_case3()
69 iMock.write(self._inputGff3FileName)
70 self._sortAndBuild()
71 self._writeExpHFileCase3()
72 self._writeExpLFileCase3()
73 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName))
74 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName))
75
76 def test_case4_5(self):
77 iMock = MockFindOverlapsWithServeralIntervals_case4_5()
78 iMock.write(self._inputGff3FileName)
79 self._sortAndBuild()
80 self._writeExpHFileCase4_5()
81 self._writeExpLFileCase4_5()
82 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName))
83 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName))
84
85 def test_case6_7(self):
86 iMock = MockFindOverlapsWithServeralIntervals_case6_7()
87 iMock.write(self._inputGff3FileName)
88 self._sortAndBuild()
89 self._writeExpHFileCase6_7()
90 self._writeExpLFileCase6_7()
91 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName))
92 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName))
93
94 def test_case8(self):
95 iMock = MockFindOverlapsWithServeralIntervals_case8()
96 iMock.write(self._inputGff3FileName)
97 self._sortAndBuild()
98 self._writeExpHFileCase8()
99 self._writeExpLFileCase8()
100 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName))
101 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName))
102
103 def test_case9(self):
104 iMock = MockFindOverlapsWithServeralIntervals_case9()
105 iMock.write(self._inputGff3FileName)
106 self._sortAndBuild()
107 self._writeExpHFileCase9()
108 self._writeExpLFileCase9()
109 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName))
110 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName))
111
112 def test_case10(self):
113 iMock = MockFindOverlapsWithServeralIntervals_case10()
114 iMock.write(self._inputGff3FileName)
115 self._sortAndBuild()
116 self._writeExpHFileCase10()
117 self._writeExpLFileCase10()
118 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName))
119 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName))
120
121 def test_case11(self):
122 iMock = MockFindOverlapsWithServeralIntervals_case11()
123 iMock.write(self._inputGff3FileName)
124 self._sortAndBuild()
125 self._writeExpHFileCase11()
126 self._writeExpLFileCase11()
127 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName))
128 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName))
129
130 def test_case12(self):
131 iMock = MockFindOverlapsWithServeralIntervals_case12()
132 iMock.write(self._inputGff3FileName)
133 self._sortAndBuild()
134 self._writeExpHFileCase12()
135 self._writeExpLFileCase12()
136 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName))
137 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName))
138
139 def _writeGFF3File(self, fileName):
140 f = open(fileName, "w")
141 f.write("chr1\ttest\ttest2.1\t9\t1000\t1001\t+\t.\tID=test2.1;Name=test2.1\n")
142 f.write("chr1\ttest\ttest2.2\t50\t350\t301\t+\t.\tID=test2.2;Name=test2.2\n")
143 f.write("chr1\ttest\ttest2.3\t100\t600\t501\t+\t.\tID=test2.3;Name=test2.3\n")
144 f.write("chr1\ttest\ttest2.4\t200\t450\t251\t+\t.\tID=test2.4;Name=test2.4\n")
145 f.write("chr1\ttest\ttest2.5\t700\t950\t251\t+\t.\tID=test2.5;Name=test2.5\n")
146 f.write("chr1\ttest\ttest2.6\t800\t900\t101\t+\t.\tID=test2.6;Name=test2.6\n")
147 f.write("chr1\ttest\ttest2.7\t1200\t1300\t101\t+\t.\tID=test2.7;Name=test2.7\n")
148 f.close()
149
150 def _writeBinFile(self, fileName, elements):
151 handle = open(fileName, "wb")
152 for element in elements:
153 handle.write(struct.pack('l', element))
154 handle.close()
155
156 def _writeExpHFile(self, HFileName):
157 list = [0, 2, 48, 3, -1, -1, -1, -1, 120, 1, 144, 1, -1, -1, -1, -1]
158 H = open(HFileName, 'wb')
159
160 for item in list:
161 item = struct.pack('l', item)
162 H.write(item)
163 H.close()
164
165 def _writeExpHFile_with_empty_SubParentDict(self, HFileName):
166 list = [0, 1, -1, -1]
167 H = open(HFileName, 'wb')
168
169 for item in list:
170 item = struct.pack('l', item)
171 H.write(item)
172 H.close()
173
174 def _writeExpHFile_one_elementSubList(self):
175 elements = [0, 1]
176 self._writeBinFile(self._expHFileName, elements)
177
178 def _writeExpHFileCase1(self):
179 elements = [0, 2, 2, 3, 5, 1, 6, 1]
180 self._writeBinFile(self._expHFileName, elements)
181
182 def _writeExpHFileCase2(self):
183 elements = [0, 2, 2, 1, 3, 1, 4, 1]
184 self._writeBinFile(self._expHFileName, elements)
185
186 def _writeExpHFileCase3(self):
187 elements = [0, 2, 2, 1, 3, 1, 4, 2]
188 self._writeBinFile(self._expHFileName, elements)
189
190 def _writeExpHFileCase4_5(self):
191 elements = [0, 1, 1, 1, 2, 1]
192 self._writeBinFile(self._expHFileName, elements)
193
194 def _writeExpHFileCase6_7(self):
195 elements = [0, 1, 1, 4]
196 self._writeBinFile(self._expHFileName, elements)
197
198 def _writeExpHFileCase8(self):
199 elements = [0, 1, 1, 2]
200 self._writeBinFile(self._expHFileName, elements)
201
202 def _writeExpHFileCase9(self):
203 elements = [0, 2, 2, 1]
204 self._writeBinFile(self._expHFileName, elements)
205
206 def _writeExpHFileCase10(self):
207 elements = [0, 3, 3, 3]
208 self._writeBinFile(self._expHFileName, elements)
209
210 def _writeExpHFileCase11(self):
211 elements = [0, 2, 2, 2, 4, 2]
212 self._writeBinFile(self._expHFileName, elements)
213
214 def _writeExpHFileCase12(self):
215 elements = [0, 1, 1, 3, 4, 1]
216 self._writeBinFile(self._expHFileName, elements)
217
218 def _writeExpLFile_one_elementSubList(self):
219 elements = [0, 1000, 0, -1, -1]
220 self._writeBinFile(self._expLFileName, elements)
221
222 def _writeExpLFileCase1(self):
223 elements = [ 0, 1000, 0, 1, -1, \
224 1200, 1300, 2345, -1, -1, \
225 50, 350, 391, -1, 0, \
226 100, 600, 781, 2, 0, \
227 700, 950, 1563, 3, 0, \
228 200, 450, 1172, -1, 3, \
229 800, 900, 1954, -1, 4]
230 self._writeBinFile(self._expLFileName, elements)
231
232 def _writeExpLFileCase2(self):
233 elements = [ 0, 500, 0, 1, -1, \
234 900, 1200, 1561, -1, -1, \
235 50, 450, 389, 2, 0, \
236 100, 400, 779, 3, 2, \
237 100, 200, 1170, -1, 3]
238 self._writeBinFile(self._expLFileName, elements)
239
240 def _writeExpLFileCase3(self):
241 elements = [ 0, 500, 0, 1, -1, \
242 800, 1000, 1952, -1, -1, \
243 50, 450, 389, 2, 0, \
244 100, 400, 779, 3, 2, \
245 100, 200, 1170, -1, 3, \
246 300, 400, 1561, -1, 3]
247 self._writeBinFile(self._expLFileName, elements)
248
249 def _writeExpLFileCase4_5(self):
250 elements = [ 0, 1000, 0, 1, -1, \
251 200, 800, 391, 2, 0, \
252 400, 600, 782, -1, 1]
253 self._writeBinFile(self._expLFileName, elements)
254
255 def _writeExpLFileCase6_7(self):
256 elements = [ 0, 1000, 0, 1, -1, \
257 100, 300, 391, -1, 0, \
258 400, 500, 782, -1, 0, \
259 510, 520, 1173, -1, 0, \
260 850, 950, 1563, -1, 0]
261 self._writeBinFile(self._expLFileName, elements)
262
263 def _writeExpLFileCase8(self):
264 elements = [ 0, 1000, 0, 1, -1, \
265 100, 200, 391, -1, 0, \
266 300, 400, 782, -1, 0]
267 self._writeBinFile(self._expLFileName, elements)
268
269 def _writeExpLFileCase9(self):
270 elements = [ 0, 1000, 0, 1, -1, \
271 800, 1200, 782, -1, -1, \
272 600, 700, 391, -1, 0]
273 self._writeBinFile(self._expLFileName, elements)
274
275 def _writeExpLFileCase10(self):
276 elements = [ 0, 1000, 0, 1, -1, \
277 1200, 1300, 1576, -1, -1, \
278 1400, 1500, 1972, -1, -1, \
279 100, 200, 394, -1, 0, \
280 300, 400, 788, -1, 0, \
281 500, 600, 1182, -1, 0]
282 self._writeBinFile(self._expLFileName, elements)
283
284 def _writeExpLFileCase11(self):
285 elements = [ 0, 500, 0, 1, -1, \
286 700, 900, 1180, 2, -1, \
287 100, 200, 392, -1, 0, \
288 300, 400, 786, -1, 0, \
289 710, 720, 1574, -1, 1, \
290 740, 750, 1967, -1, 1]
291 self._writeBinFile(self._expLFileName, elements)
292
293 def _writeExpLFileCase12(self):
294 elements = [ 0, 1400, 0, 1, -1, \
295 300, 500, 368, 2, 0, \
296 800, 1100, 1106, -1, 0, \
297 1200, 1300, 1476, -1, 0, \
298 300, 500, 737, -1, 1]
299 self._writeBinFile(self._expLFileName, elements)
300
301 if __name__ == "__main__":
302 unittest.main()