Mercurial > repos > yufei-luo > s_mart
comparison commons/core/coord/test/Test_ConvCoord.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 import time | |
4 from commons.core.coord.ConvCoord import ConvCoord | |
5 from commons.core.utils.FileUtils import FileUtils | |
6 from commons.core.sql.DbFactory import DbFactory | |
7 from commons.core.coord.Map import Map | |
8 | |
9 class Test_ConvCoord( unittest.TestCase ): | |
10 | |
11 def setUp( self ): | |
12 self._i = ConvCoord() | |
13 self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() ) | |
14 self._inData = "dummyInData_%s" % ( self._uniqId ) | |
15 self._mapData = "dummyMapData_%s" % ( self._uniqId ) | |
16 self._expData = "dummyExpData_%s" % ( self._uniqId ) | |
17 self._obsData = "dummyObsData_%s" % ( self._uniqId ) | |
18 self._iDb = DbFactory.createInstance() | |
19 self._i._iDb = self._iDb | |
20 | |
21 def tearDown( self ): | |
22 self._iDb.close() | |
23 | |
24 #TODO: handle duplicated matchs for path | |
25 # def test_convCoordsChkToChrFromFile_duplicated_matchs( self ): | |
26 # dChunks2CoordMaps = {"chunk1": Map( "chunk1", "dmel_chr4", 760001, 960000 ), | |
27 # "chunk2": Map( "chunk2", "dmel_chr4", 950001, 1150000 ) } | |
28 # tmpPathFileName = "dummyPathCoordOnChr_%s" % self._uniqId | |
29 # self._writePathFileCoordOnChunk(tmpPathFileName) | |
30 # | |
31 # expPathFile = "dummyExpPathFile_%s" % self._uniqId | |
32 # self._writePathFileCoordOnChrWithOutDoublons(expPathFile) | |
33 # | |
34 # outTableName = self._i.convCoordsChkToChrFromFile(tmpPathFileName, "path", dChunks2CoordMaps) | |
35 # | |
36 # obsPathFile = "dummyObsPathFile_%s" % self._uniqId | |
37 # self._iDb.exportDataToFile(outTableName, obsPathFile) | |
38 # | |
39 # self.assertTrue(FileUtils.are2FilesIdentical(expPathFile, obsPathFile)) | |
40 # | |
41 # for f in [ expPathFile, obsPathFile, tmpPathFileName ]: | |
42 # os.remove( f ) | |
43 # self._iDb.dropTable(outTableName) | |
44 | |
45 #TODO: handle matchs out of chunk overlap ? For one side (=> path 128, remove path 152) ? For two sides (path 129, fusion with path 154) ? | |
46 # def test_convCoordsChkToChrFromFile_matchs_out_of_overlap( self ): | |
47 # dChunks2CoordMaps = {"chunk1": Map( "chunk1", "dmel_chr4", 760001, 960000 ), | |
48 # "chunk2": Map( "chunk2", "dmel_chr4", 950001, 1150000 ) } | |
49 # tmpPathFileName = "dummyPathCoordOnChr_%s" % self._uniqId | |
50 # self._writePathFileCoordOnChunk_outOfOverlap(tmpPathFileName) | |
51 # | |
52 # expPathFile = "dummyExpPathFile_%s" % self._uniqId | |
53 # self._writePathFileCoordOnChrWithOutDoublons_outOfOverlap(expPathFile) | |
54 # | |
55 # outTableName = self._i.convCoordsChkToChrFromFile(tmpPathFileName, "path", dChunks2CoordMaps) | |
56 # | |
57 # obsPathFile = "dummyObsPathFile_%s" % self._uniqId | |
58 # self._iDb.exportDataToFile(outTableName, obsPathFile) | |
59 # | |
60 # self.assertTrue(FileUtils.are2FilesIdentical(expPathFile, obsPathFile)) | |
61 # | |
62 # for f in [ expPathFile, obsPathFile, tmpPathFileName ]: | |
63 # os.remove( f ) | |
64 # self._iDb.dropTable(outTableName) | |
65 | |
66 def test_mergeCoordsOnChunkOverlaps( self ): | |
67 dChunks2CoordMaps = { "chunk1": Map( "chunk1", "chromosome1", 1, 100 ), | |
68 "chunk2": Map( "chunk2", "chromosome1", 91, 190 ), | |
69 "chunk3": Map( "chunk3", "chromosome2", 1, 100 ) } | |
70 tmpPathTable = "dummyTmpPathTable" | |
71 linesToProcess = [ | |
72 "1" + "\t" + "chromosome1" + "\t" + "21" + "\t" + "37" + "\t" + "TE1" + "\t" + "1" + "\t" + "27" + "\t" + "8e-58" + "\t" + "30" + "\t" + "97.8" + "\n", # hit within the 1st chunk | |
73 "3" + "\t" + "chromosome1" + "\t" + "92" + "\t" + "99" + "\t" + "TE1" + "\t" + "1" + "\t" + "8" + "\t" + "8e-58" + "\t" + "11" + "\t" + "97.8" + "\n", # hit included within the chunk overlap, on the 2nd chunk | |
74 "2" + "\t" + "chromosome1" + "\t" + "92" + "\t" + "99" + "\t" + "TE1" + "\t" + "1" + "\t" + "8" + "\t" + "8e-58" + "\t" + "11" + "\t" + "97.8" + "\n", # hit included within the chunk overlap, on the 1st chunk | |
75 ] | |
76 FileUtils.writeLineListInFile( tmpPathTable, linesToProcess ) | |
77 self._iDb.createTable( tmpPathTable, "path", tmpPathTable, True) | |
78 os.remove( tmpPathTable ) | |
79 | |
80 expPathFile = "dummyExpPathFile" | |
81 linesToProcess = [ "1" + "\t" + "chromosome1" + "\t" + "21" + "\t" + "37" + "\t" + "TE1" + "\t" + "1" + "\t" + "27" + "\t" + "8e-58" + "\t" + "30" + "\t" + "97.8" + "\n", # hit within the 1st chunk | |
82 "2" + "\t" + "chromosome1" + "\t" + "92" + "\t" + "99" + "\t" + "TE1" + "\t" + "1" + "\t" + "8" + "\t" + "8e-58" + "\t" + "11" + "\t" + "97.8" + "\n", # hit included within the chunk overlap, on the 1st chunk | |
83 ] | |
84 FileUtils.writeLineListInFile( expPathFile, linesToProcess ) | |
85 | |
86 self._i.mergeCoordsOnChunkOverlaps( dChunks2CoordMaps, tmpPathTable) | |
87 | |
88 obsPathFile = "dummyObsPathFile" | |
89 self._iDb.exportDataToFile( tmpPathTable, obsPathFile ) | |
90 | |
91 self.assertTrue( FileUtils.are2FilesIdentical( expPathFile, obsPathFile ) ) | |
92 | |
93 for f in [ expPathFile, obsPathFile ]: | |
94 os.remove( f ) | |
95 self._iDb.dropTable( tmpPathTable ) | |
96 | |
97 def test_mergeCoordsOnChunkOverlaps_withConnectedMatches( self ): | |
98 dChunks2CoordMaps = { "chunk1": Map( "chunk1", "chromosome1", 1, 100 ), | |
99 "chunk2": Map( "chunk2", "chromosome1", 91, 190 ), | |
100 "chunk3": Map( "chunk3", "chromosome2", 1, 100 ) } | |
101 tmpPathTable = "dummyTmpPathTable" | |
102 linesToProcess = [ | |
103 "1" + "\t" + "chromosome1" + "\t" + "21" + "\t" + "37" + "\t" + "TE1" + "\t" + "1" + "\t" + "27" + "\t" + "8e-58" + "\t" + "30" + "\t" + "97.8" + "\n", # hit on the 1st chunk | |
104 "1" + "\t" + "chromosome1" + "\t" + "92" + "\t" + "99" + "\t" + "TE1" + "\t" + "28" + "\t" + "36" + "\t" + "8e-58" + "\t" + "10" + "\t" + "97.8" + "\n", # hit included within the chunk overlap, on the 1st chunk, connected to the previous | |
105 "2" + "\t" + "chromosome1" + "\t" + "92" + "\t" + "99" + "\t" + "TE1" + "\t" + "28" + "\t" + "36" + "\t" + "8e-58" + "\t" + "10" + "\t" + "97.8" + "\n", # hit included within the chunk overlap, on the 2nd chunk | |
106 "2" + "\t" + "chromosome1" + "\t" + "111" + "\t" + "120" + "\t" + "TE1" + "\t" + "37" + "\t" + "46" + "\t" + "8e-58" + "\t" + "15" + "\t" + "97.8" + "\n", # hit on the 2nd chunk, connected to the previous | |
107 ] | |
108 FileUtils.writeLineListInFile( tmpPathTable, linesToProcess ) | |
109 self._iDb.createTable( tmpPathTable, "path", tmpPathTable, True) | |
110 os.remove( tmpPathTable ) | |
111 | |
112 expPathFile = "dummyExpPathFile" | |
113 linesToProcess = [ "1" + "\t" + "chromosome1" + "\t" + "21" + "\t" + "37" + "\t" + "TE1" + "\t" + "1" + "\t" + "27" + "\t" + "8e-58" + "\t" + "30" + "\t" + "97.8" + "\n", # hit within the 1st chunk | |
114 "1" + "\t" + "chromosome1" + "\t" + "92" + "\t" + "99" + "\t" + "TE1" + "\t" + "28" + "\t" + "36" + "\t" + "8e-58" + "\t" + "10" + "\t" + "97.8" + "\n", # hit included within the chunk overlap, on the 1st chunk | |
115 "1" + "\t" + "chromosome1" + "\t" + "111" + "\t" + "120" + "\t" + "TE1" + "\t" + "37" + "\t" + "46" + "\t" + "8e-58" + "\t" + "15" + "\t" + "97.8" + "\n", # hit on the 2nd chunk, connected to the previous | |
116 ] | |
117 FileUtils.writeLineListInFile( expPathFile, linesToProcess ) | |
118 | |
119 self._i.mergeCoordsOnChunkOverlaps( dChunks2CoordMaps, tmpPathTable ) | |
120 | |
121 obsPathFile = "dummyObsPathFile" | |
122 self._iDb.exportDataToFile( tmpPathTable, obsPathFile ) | |
123 | |
124 self.assertTrue( FileUtils.are2FilesIdentical( expPathFile, obsPathFile ) ) | |
125 | |
126 for f in [ expPathFile, obsPathFile ]: | |
127 os.remove( f ) | |
128 self._iDb.dropTable( tmpPathTable ) | |
129 | |
130 def _writePathFileCoordOnChrWithOutDoublons(self, pathFileName): | |
131 file = open( pathFileName, "w" ) | |
132 file.write("123\tdmel_chr4\t868397\t868531\tMariner2_AG_1p:classII:TIR\t53\t97\t8e-19\t28\t35.56\n") | |
133 file.write("123\tdmel_chr4\t868545\t869120\tMariner2_AG_1p:classII:TIR\t102\t333\t8e-19\t87\t27.97\n") | |
134 file.write("124\tdmel_chr4\t819607\t819714\tLINER1-2_NVi_2p:classI:?\t502\t537\t3e-20\t30\t36.11\n") | |
135 file.write("124\tdmel_chr4\t819695\t820156\tLINER1-2_NVi_2p:classI:?\t533\t725\t3e-20\t90\t36.79\n") | |
136 file.write("125\tdmel_chr4\t953027\t953101\tCR1-8_AG_1p:classI:LINE\t470\t448\t1e-27\t11\t28.57\n") | |
137 file.write("126\tdmel_chr4\t862131\t862178\tTc1-1_TCa_1p:classII:TIR\t288\t274\t5e-29\t18\t52.5\n") | |
138 file.write("127\tdmel_chr4\t819520\t819606\tNotoAg1_2p:classI:?\t482\t508\t1e-13\t14\t30.61\n") | |
139 # file.write("128\tdmel_chr4\t953866\t953889\tCR1-19_HM_1p:classI:LINE\t898\t891\t5e-21\t4\t34.98\n") | |
140 # file.write("129\tdmel_chr4\t953866\t953889\tCR1-83_HM_1p:classI:LINE\t912\t905\t3e-21\t4\t34.62\n") | |
141 file.write("150\tdmel_chr4\t971176\t971250\tTc1-1_TCa_1p:classII:TIR\t135\t109\t8e-32\t21\t41.57\n") | |
142 file.write("151\tdmel_chr4\t1066603\t1066698\tMARWOLEN1_1p:classII:TIR\t285\t320\t7e-25\t28\t41.67\n") | |
143 file.write("152\tdmel_chr4\t953866\t953889\tCR1-19_HM_1p:classI:LINE\t898\t891\t5e-21\t4\t34.98\n") | |
144 file.write("153\tdmel_chr4\t953951\t954343\tCR1-1_DWil_1p:classI:LINE\t127\t2\t4e-18\t92\t37.59\n") | |
145 file.write("154\tdmel_chr4\t953866\t953889\tCR1-83_HM_1p:classI:LINE\t912\t905\t3e-21\t4\t34.62\n") | |
146 file.write("155\tdmel_chr4\t953102\t953199\tCR1-1_DWil_2p:classI:LINE\t869\t837\t2e-26\t38\t57.89\n") | |
147 file.close() | |
148 | |
149 def _writePathFileCoordOnChunk(self, pathFileName): | |
150 pathFile = open( pathFileName, "w" ) | |
151 pathFile.write("123\tchunk1\t108397\t108531\tMariner2_AG_1p:classII:TIR\t53\t97\t8e-19\t28\t35.56\n") | |
152 pathFile.write("123\tchunk1\t108545\t109120\tMariner2_AG_1p:classII:TIR\t102\t333\t8e-19\t87\t27.97\n") | |
153 pathFile.write("124\tchunk1\t59607\t59714\tLINER1-2_NVi_2p:classI:?\t502\t537\t3e-20\t30\t36.11\n") | |
154 pathFile.write("124\tchunk1\t59695\t60156\tLINER1-2_NVi_2p:classI:?\t533\t725\t3e-20\t90\t36.79\n") | |
155 pathFile.write("125\tchunk1\t193027\t193101\tCR1-8_AG_1p:classI:LINE\t470\t448\t1e-27\t11\t28.57\n") | |
156 pathFile.write("126\tchunk1\t102131\t102178\tTc1-1_TCa_1p:classII:TIR\t288\t274\t5e-29\t18\t52.5\n") | |
157 pathFile.write("127\tchunk1\t59520\t59606\tNotoAg1_2p:classI:?\t482\t508\t1e-13\t14\t30.61\n") | |
158 pathFile.write("128\tchunk1\t193866\t193889\tCR1-19_HM_1p:classI:LINE\t898\t891\t5e-21\t4\t34.98\n") | |
159 pathFile.write("129\tchunk1\t193866\t193889\tCR1-83_HM_1p:classI:LINE\t912\t905\t3e-21\t4\t34.62\n") | |
160 pathFile.write("150\tchunk2\t21176\t21250\tTc1-1_TCa_1p:classII:TIR\t135\t109\t8e-32\t21\t41.57\n") | |
161 pathFile.write("151\tchunk2\t116603\t116698\tMARWOLEN1_1p:classII:TIR\t285\t320\t7e-25\t28\t41.67\n") | |
162 pathFile.write("152\tchunk2\t3866\t3889\tCR1-19_HM_1p:classI:LINE\t898\t891\t5e-21\t4\t34.98\n") | |
163 pathFile.write("153\tchunk2\t3951\t4343\tCR1-1_DWil_1p:classI:LINE\t127\t2\t4e-18\t92\t37.59\n") | |
164 pathFile.write("154\tchunk2\t3866\t3889\tCR1-83_HM_1p:classI:LINE\t912\t905\t3e-21\t4\t34.62\n") | |
165 pathFile.write("155\tchunk2\t3102\t3199\tCR1-1_DWil_2p:classI:LINE\t869\t837\t2e-26\t38\t57.89\n") | |
166 pathFile.close() | |
167 | |
168 # def _writePathFileCoordOnChunk_outOfOverlap(self, pathFileName): | |
169 # pathFile = open( pathFileName, "w" ) | |
170 # pathFile.write("123\tchunk1\t108397\t108531\tMariner2_AG_1p:classII:TIR\t53\t97\t8e-19\t28\t35.56\n") | |
171 # pathFile.write("123\tchunk1\t108545\t109120\tMariner2_AG_1p:classII:TIR\t102\t333\t8e-19\t87\t27.97\n") | |
172 # pathFile.write("124\tchunk1\t59607\t59714\tLINER1-2_NVi_2p:classI:?\t502\t537\t3e-20\t30\t36.11\n") | |
173 # pathFile.write("124\tchunk1\t59695\t60156\tLINER1-2_NVi_2p:classI:?\t533\t725\t3e-20\t90\t36.79\n") | |
174 # pathFile.write("125\tchunk1\t193027\t193101\tCR1-8_AG_1p:classI:LINE\t470\t448\t1e-27\t11\t28.57\n") | |
175 # pathFile.write("126\tchunk1\t102131\t102178\tTc1-1_TCa_1p:classII:TIR\t288\t274\t5e-29\t18\t52.5\n") | |
176 # pathFile.write("127\tchunk1\t59520\t59606\tNotoAg1_2p:classI:?\t482\t508\t1e-13\t14\t30.61\n") | |
177 # pathFile.write("128\tchunk1\t183866\t193889\tCR1-19_HM_1p:classI:LINE\t898\t1891\t5e-21\t4\t34.98\n") | |
178 # pathFile.write("129\tchunk1\t183866\t200000\tCR1-83_HM_1p:classI:LINE\t912\t905\t3e-21\t4\t34.62\n") | |
179 # pathFile.write("150\tchunk2\t21176\t21250\tTc1-1_TCa_1p:classII:TIR\t135\t109\t8e-32\t21\t41.57\n") | |
180 # pathFile.write("151\tchunk2\t116603\t116698\tMARWOLEN1_1p:classII:TIR\t285\t320\t7e-25\t28\t41.67\n") | |
181 # pathFile.write("152\tchunk2\t1\t3889\tCR1-19_HM_1p:classI:LINE\t898\t1891\t5e-21\t4\t34.98\n") | |
182 # pathFile.write("153\tchunk2\t3951\t4343\tCR1-1_DWil_1p:classI:LINE\t127\t2\t4e-18\t92\t37.59\n") | |
183 # pathFile.write("154\tchunk2\t1\t13889\tCR1-83_HM_1p:classI:LINE\t912\t905\t3e-21\t4\t34.62\n") | |
184 # pathFile.write("155\tchunk2\t3102\t3199\tCR1-1_DWil_2p:classI:LINE\t869\t837\t2e-26\t38\t57.89\n") | |
185 # pathFile.close() | |
186 # | |
187 # def _writePathFileCoordOnChrWithOutDoublons_outOfOverlap(self, pathFileName): | |
188 # file = open( pathFileName, "w" ) | |
189 # file.write("123\tdmel_chr4\t868397\t868531\tMariner2_AG_1p:classII:TIR\t53\t97\t8e-19\t28\t35.56\n") | |
190 # file.write("123\tdmel_chr4\t868545\t869120\tMariner2_AG_1p:classII:TIR\t102\t333\t8e-19\t87\t27.97\n") | |
191 # file.write("124\tdmel_chr4\t819607\t819714\tLINER1-2_NVi_2p:classI:?\t502\t537\t3e-20\t30\t36.11\n") | |
192 # file.write("124\tdmel_chr4\t819695\t820156\tLINER1-2_NVi_2p:classI:?\t533\t725\t3e-20\t90\t36.79\n") | |
193 # file.write("125\tdmel_chr4\t953027\t953101\tCR1-8_AG_1p:classI:LINE\t470\t448\t1e-27\t11\t28.57\n") | |
194 # file.write("126\tdmel_chr4\t862131\t862178\tTc1-1_TCa_1p:classII:TIR\t288\t274\t5e-29\t18\t52.5\n") | |
195 # file.write("127\tdmel_chr4\t819520\t819606\tNotoAg1_2p:classI:?\t482\t508\t1e-13\t14\t30.61\n") | |
196 # file.write("128\tdmel_chr4\t943866\t953889\tCR1-19_HM_1p:classI:LINE\t898\t1891\t5e-21\t4\t34.98\n") | |
197 # file.write("129\tdmel_chr4\t943866\t963889\tCR1-83_HM_1p:classI:LINE\t912\t905\t3e-21\t4\t34.62\n") | |
198 # file.write("150\tdmel_chr4\t971176\t971250\tTc1-1_TCa_1p:classII:TIR\t135\t109\t8e-32\t21\t41.57\n") | |
199 # file.write("151\tdmel_chr4\t1066603\t1066698\tMARWOLEN1_1p:classII:TIR\t285\t320\t7e-25\t28\t41.67\n") | |
200 # file.write("153\tdmel_chr4\t953951\t954343\tCR1-1_DWil_1p:classI:LINE\t127\t2\t4e-18\t92\t37.59\n") | |
201 # file.write("155\tdmel_chr4\t953102\t953199\tCR1-1_DWil_2p:classI:LINE\t869\t837\t2e-26\t38\t57.89\n") | |
202 # file.close() | |
203 | |
204 if __name__ == "__main__": | |
205 unittest.main() |