Mercurial > repos > yufei-luo > s_mart

annotate 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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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 import unittest
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2 import os
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3 import time
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4 from commons.core.coord.ConvCoord import ConvCoord
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5 from commons.core.utils.FileUtils import FileUtils
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6 from commons.core.sql.DbFactory import DbFactory
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7 from commons.core.coord.Map import Map
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8
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9 class Test_ConvCoord( unittest.TestCase ):
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11 def setUp( self ):
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12 self._i = ConvCoord()
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13 self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() )
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14 self._inData = "dummyInData_%s" % ( self._uniqId )
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15 self._mapData = "dummyMapData_%s" % ( self._uniqId )
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16 self._expData = "dummyExpData_%s" % ( self._uniqId )
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17 self._obsData = "dummyObsData_%s" % ( self._uniqId )
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18 self._iDb = DbFactory.createInstance()
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19 self._i._iDb = self._iDb
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20
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21 def tearDown( self ):
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22 self._iDb.close()
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23
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24 #TODO: handle duplicated matchs for path
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25 # def test_convCoordsChkToChrFromFile_duplicated_matchs( self ):
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26 # dChunks2CoordMaps = {"chunk1": Map( "chunk1", "dmel_chr4", 760001, 960000 ),
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27 # "chunk2": Map( "chunk2", "dmel_chr4", 950001, 1150000 ) }
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28 # tmpPathFileName = "dummyPathCoordOnChr_%s" % self._uniqId
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29 # self._writePathFileCoordOnChunk(tmpPathFileName)
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30 #
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31 # expPathFile = "dummyExpPathFile_%s" % self._uniqId
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32 # self._writePathFileCoordOnChrWithOutDoublons(expPathFile)
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33 #
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34 # outTableName = self._i.convCoordsChkToChrFromFile(tmpPathFileName, "path", dChunks2CoordMaps)
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35 #
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36 # obsPathFile = "dummyObsPathFile_%s" % self._uniqId
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37 # self._iDb.exportDataToFile(outTableName, obsPathFile)
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38 #
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39 # self.assertTrue(FileUtils.are2FilesIdentical(expPathFile, obsPathFile))
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40 #
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41 # for f in [ expPathFile, obsPathFile, tmpPathFileName ]:
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42 # os.remove( f )
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43 # self._iDb.dropTable(outTableName)
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44
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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) ?
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46 # def test_convCoordsChkToChrFromFile_matchs_out_of_overlap( self ):
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47 # dChunks2CoordMaps = {"chunk1": Map( "chunk1", "dmel_chr4", 760001, 960000 ),
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48 # "chunk2": Map( "chunk2", "dmel_chr4", 950001, 1150000 ) }
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49 # tmpPathFileName = "dummyPathCoordOnChr_%s" % self._uniqId
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50 # self._writePathFileCoordOnChunk_outOfOverlap(tmpPathFileName)
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51 #
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52 # expPathFile = "dummyExpPathFile_%s" % self._uniqId
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53 # self._writePathFileCoordOnChrWithOutDoublons_outOfOverlap(expPathFile)
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54 #
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55 # outTableName = self._i.convCoordsChkToChrFromFile(tmpPathFileName, "path", dChunks2CoordMaps)
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56 #
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57 # obsPathFile = "dummyObsPathFile_%s" % self._uniqId
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58 # self._iDb.exportDataToFile(outTableName, obsPathFile)
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59 #
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60 # self.assertTrue(FileUtils.are2FilesIdentical(expPathFile, obsPathFile))
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61 #
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62 # for f in [ expPathFile, obsPathFile, tmpPathFileName ]:
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63 # os.remove( f )
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64 # self._iDb.dropTable(outTableName)
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65
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66 def test_mergeCoordsOnChunkOverlaps( self ):
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67 dChunks2CoordMaps = { "chunk1": Map( "chunk1", "chromosome1", 1, 100 ),
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68 "chunk2": Map( "chunk2", "chromosome1", 91, 190 ),
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69 "chunk3": Map( "chunk3", "chromosome2", 1, 100 ) }
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70 tmpPathTable = "dummyTmpPathTable"
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71 linesToProcess = [
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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
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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
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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
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75 ]
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76 FileUtils.writeLineListInFile( tmpPathTable, linesToProcess )
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77 self._iDb.createTable( tmpPathTable, "path", tmpPathTable, True)
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78 os.remove( tmpPathTable )
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79
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80 expPathFile = "dummyExpPathFile"
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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
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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
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83 ]
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84 FileUtils.writeLineListInFile( expPathFile, linesToProcess )
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85
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86 self._i.mergeCoordsOnChunkOverlaps( dChunks2CoordMaps, tmpPathTable)
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87
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88 obsPathFile = "dummyObsPathFile"
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89 self._iDb.exportDataToFile( tmpPathTable, obsPathFile )
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90
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91 self.assertTrue( FileUtils.are2FilesIdentical( expPathFile, obsPathFile ) )
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92
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93 for f in [ expPathFile, obsPathFile ]:
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94 os.remove( f )
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95 self._iDb.dropTable( tmpPathTable )
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96
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97 def test_mergeCoordsOnChunkOverlaps_withConnectedMatches( self ):
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98 dChunks2CoordMaps = { "chunk1": Map( "chunk1", "chromosome1", 1, 100 ),
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99 "chunk2": Map( "chunk2", "chromosome1", 91, 190 ),
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100 "chunk3": Map( "chunk3", "chromosome2", 1, 100 ) }
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101 tmpPathTable = "dummyTmpPathTable"
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102 linesToProcess = [
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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
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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
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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
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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
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107 ]
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108 FileUtils.writeLineListInFile( tmpPathTable, linesToProcess )
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109 self._iDb.createTable( tmpPathTable, "path", tmpPathTable, True)
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110 os.remove( tmpPathTable )
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111
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112 expPathFile = "dummyExpPathFile"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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116 ]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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117 FileUtils.writeLineListInFile( expPathFile, linesToProcess )
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118
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119 self._i.mergeCoordsOnChunkOverlaps( dChunks2CoordMaps, tmpPathTable )
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120
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121 obsPathFile = "dummyObsPathFile"
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122 self._iDb.exportDataToFile( tmpPathTable, obsPathFile )
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123
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124 self.assertTrue( FileUtils.are2FilesIdentical( expPathFile, obsPathFile ) )
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125
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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126 for f in [ expPathFile, obsPathFile ]:
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127 os.remove( f )
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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128 self._iDb.dropTable( tmpPathTable )
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129
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130 def _writePathFileCoordOnChrWithOutDoublons(self, pathFileName):
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131 file = open( pathFileName, "w" )
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132 file.write("123\tdmel_chr4\t868397\t868531\tMariner2_AG_1p:classII:TIR\t53\t97\t8e-19\t28\t35.56\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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133 file.write("123\tdmel_chr4\t868545\t869120\tMariner2_AG_1p:classII:TIR\t102\t333\t8e-19\t87\t27.97\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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134 file.write("124\tdmel_chr4\t819607\t819714\tLINER1-2_NVi_2p:classI:?\t502\t537\t3e-20\t30\t36.11\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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135 file.write("124\tdmel_chr4\t819695\t820156\tLINER1-2_NVi_2p:classI:?\t533\t725\t3e-20\t90\t36.79\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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136 file.write("125\tdmel_chr4\t953027\t953101\tCR1-8_AG_1p:classI:LINE\t470\t448\t1e-27\t11\t28.57\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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137 file.write("126\tdmel_chr4\t862131\t862178\tTc1-1_TCa_1p:classII:TIR\t288\t274\t5e-29\t18\t52.5\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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138 file.write("127\tdmel_chr4\t819520\t819606\tNotoAg1_2p:classI:?\t482\t508\t1e-13\t14\t30.61\n")
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139 # file.write("128\tdmel_chr4\t953866\t953889\tCR1-19_HM_1p:classI:LINE\t898\t891\t5e-21\t4\t34.98\n")
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140 # file.write("129\tdmel_chr4\t953866\t953889\tCR1-83_HM_1p:classI:LINE\t912\t905\t3e-21\t4\t34.62\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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141 file.write("150\tdmel_chr4\t971176\t971250\tTc1-1_TCa_1p:classII:TIR\t135\t109\t8e-32\t21\t41.57\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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142 file.write("151\tdmel_chr4\t1066603\t1066698\tMARWOLEN1_1p:classII:TIR\t285\t320\t7e-25\t28\t41.67\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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143 file.write("152\tdmel_chr4\t953866\t953889\tCR1-19_HM_1p:classI:LINE\t898\t891\t5e-21\t4\t34.98\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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144 file.write("153\tdmel_chr4\t953951\t954343\tCR1-1_DWil_1p:classI:LINE\t127\t2\t4e-18\t92\t37.59\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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145 file.write("154\tdmel_chr4\t953866\t953889\tCR1-83_HM_1p:classI:LINE\t912\t905\t3e-21\t4\t34.62\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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146 file.write("155\tdmel_chr4\t953102\t953199\tCR1-1_DWil_2p:classI:LINE\t869\t837\t2e-26\t38\t57.89\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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147 file.close()
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148
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149 def _writePathFileCoordOnChunk(self, pathFileName):
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150 pathFile = open( pathFileName, "w" )
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151 pathFile.write("123\tchunk1\t108397\t108531\tMariner2_AG_1p:classII:TIR\t53\t97\t8e-19\t28\t35.56\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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152 pathFile.write("123\tchunk1\t108545\t109120\tMariner2_AG_1p:classII:TIR\t102\t333\t8e-19\t87\t27.97\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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153 pathFile.write("124\tchunk1\t59607\t59714\tLINER1-2_NVi_2p:classI:?\t502\t537\t3e-20\t30\t36.11\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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154 pathFile.write("124\tchunk1\t59695\t60156\tLINER1-2_NVi_2p:classI:?\t533\t725\t3e-20\t90\t36.79\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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155 pathFile.write("125\tchunk1\t193027\t193101\tCR1-8_AG_1p:classI:LINE\t470\t448\t1e-27\t11\t28.57\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
156 pathFile.write("126\tchunk1\t102131\t102178\tTc1-1_TCa_1p:classII:TIR\t288\t274\t5e-29\t18\t52.5\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
157 pathFile.write("127\tchunk1\t59520\t59606\tNotoAg1_2p:classI:?\t482\t508\t1e-13\t14\t30.61\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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158 pathFile.write("128\tchunk1\t193866\t193889\tCR1-19_HM_1p:classI:LINE\t898\t891\t5e-21\t4\t34.98\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
159 pathFile.write("129\tchunk1\t193866\t193889\tCR1-83_HM_1p:classI:LINE\t912\t905\t3e-21\t4\t34.62\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
160 pathFile.write("150\tchunk2\t21176\t21250\tTc1-1_TCa_1p:classII:TIR\t135\t109\t8e-32\t21\t41.57\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
161 pathFile.write("151\tchunk2\t116603\t116698\tMARWOLEN1_1p:classII:TIR\t285\t320\t7e-25\t28\t41.67\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
162 pathFile.write("152\tchunk2\t3866\t3889\tCR1-19_HM_1p:classI:LINE\t898\t891\t5e-21\t4\t34.98\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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163 pathFile.write("153\tchunk2\t3951\t4343\tCR1-1_DWil_1p:classI:LINE\t127\t2\t4e-18\t92\t37.59\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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164 pathFile.write("154\tchunk2\t3866\t3889\tCR1-83_HM_1p:classI:LINE\t912\t905\t3e-21\t4\t34.62\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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165 pathFile.write("155\tchunk2\t3102\t3199\tCR1-1_DWil_2p:classI:LINE\t869\t837\t2e-26\t38\t57.89\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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166 pathFile.close()
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167
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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168 # def _writePathFileCoordOnChunk_outOfOverlap(self, pathFileName):
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169 # pathFile = open( pathFileName, "w" )
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170 # pathFile.write("123\tchunk1\t108397\t108531\tMariner2_AG_1p:classII:TIR\t53\t97\t8e-19\t28\t35.56\n")
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171 # pathFile.write("123\tchunk1\t108545\t109120\tMariner2_AG_1p:classII:TIR\t102\t333\t8e-19\t87\t27.97\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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172 # pathFile.write("124\tchunk1\t59607\t59714\tLINER1-2_NVi_2p:classI:?\t502\t537\t3e-20\t30\t36.11\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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173 # pathFile.write("124\tchunk1\t59695\t60156\tLINER1-2_NVi_2p:classI:?\t533\t725\t3e-20\t90\t36.79\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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174 # pathFile.write("125\tchunk1\t193027\t193101\tCR1-8_AG_1p:classI:LINE\t470\t448\t1e-27\t11\t28.57\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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175 # pathFile.write("126\tchunk1\t102131\t102178\tTc1-1_TCa_1p:classII:TIR\t288\t274\t5e-29\t18\t52.5\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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176 # pathFile.write("127\tchunk1\t59520\t59606\tNotoAg1_2p:classI:?\t482\t508\t1e-13\t14\t30.61\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
177 # pathFile.write("128\tchunk1\t183866\t193889\tCR1-19_HM_1p:classI:LINE\t898\t1891\t5e-21\t4\t34.98\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
178 # pathFile.write("129\tchunk1\t183866\t200000\tCR1-83_HM_1p:classI:LINE\t912\t905\t3e-21\t4\t34.62\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
179 # pathFile.write("150\tchunk2\t21176\t21250\tTc1-1_TCa_1p:classII:TIR\t135\t109\t8e-32\t21\t41.57\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
180 # pathFile.write("151\tchunk2\t116603\t116698\tMARWOLEN1_1p:classII:TIR\t285\t320\t7e-25\t28\t41.67\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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diff changeset
181 # pathFile.write("152\tchunk2\t1\t3889\tCR1-19_HM_1p:classI:LINE\t898\t1891\t5e-21\t4\t34.98\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
182 # pathFile.write("153\tchunk2\t3951\t4343\tCR1-1_DWil_1p:classI:LINE\t127\t2\t4e-18\t92\t37.59\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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183 # pathFile.write("154\tchunk2\t1\t13889\tCR1-83_HM_1p:classI:LINE\t912\t905\t3e-21\t4\t34.62\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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184 # pathFile.write("155\tchunk2\t3102\t3199\tCR1-1_DWil_2p:classI:LINE\t869\t837\t2e-26\t38\t57.89\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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185 # pathFile.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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186 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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187 # def _writePathFileCoordOnChrWithOutDoublons_outOfOverlap(self, pathFileName):
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188 # file = open( pathFileName, "w" )
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189 # file.write("123\tdmel_chr4\t868397\t868531\tMariner2_AG_1p:classII:TIR\t53\t97\t8e-19\t28\t35.56\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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190 # file.write("123\tdmel_chr4\t868545\t869120\tMariner2_AG_1p:classII:TIR\t102\t333\t8e-19\t87\t27.97\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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191 # file.write("124\tdmel_chr4\t819607\t819714\tLINER1-2_NVi_2p:classI:?\t502\t537\t3e-20\t30\t36.11\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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192 # file.write("124\tdmel_chr4\t819695\t820156\tLINER1-2_NVi_2p:classI:?\t533\t725\t3e-20\t90\t36.79\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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193 # file.write("125\tdmel_chr4\t953027\t953101\tCR1-8_AG_1p:classI:LINE\t470\t448\t1e-27\t11\t28.57\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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194 # file.write("126\tdmel_chr4\t862131\t862178\tTc1-1_TCa_1p:classII:TIR\t288\t274\t5e-29\t18\t52.5\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
195 # file.write("127\tdmel_chr4\t819520\t819606\tNotoAg1_2p:classI:?\t482\t508\t1e-13\t14\t30.61\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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diff changeset
196 # file.write("128\tdmel_chr4\t943866\t953889\tCR1-19_HM_1p:classI:LINE\t898\t1891\t5e-21\t4\t34.98\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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197 # file.write("129\tdmel_chr4\t943866\t963889\tCR1-83_HM_1p:classI:LINE\t912\t905\t3e-21\t4\t34.62\n")
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198 # file.write("150\tdmel_chr4\t971176\t971250\tTc1-1_TCa_1p:classII:TIR\t135\t109\t8e-32\t21\t41.57\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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199 # file.write("151\tdmel_chr4\t1066603\t1066698\tMARWOLEN1_1p:classII:TIR\t285\t320\t7e-25\t28\t41.67\n")
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200 # file.write("153\tdmel_chr4\t953951\t954343\tCR1-1_DWil_1p:classI:LINE\t127\t2\t4e-18\t92\t37.59\n")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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201 # file.write("155\tdmel_chr4\t953102\t953199\tCR1-1_DWil_2p:classI:LINE\t869\t837\t2e-26\t38\t57.89\n")
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202 # file.close()
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203
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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204 if __name__ == "__main__":
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205 unittest.main()