Mercurial > repos > yufei-luo > s_mart

comparison smart_toolShed/commons/core/coord/test/Test_ConvCoord.py @ 0:e0f8dcca02ed

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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
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-1:000000000000 0:e0f8dcca02ed
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()