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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.utils.FileUtils import FileUtils
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5 from commons.core.sql.DbMySql import DbMySql
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6
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7
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8 class Test_ConvCoordWithOverlaps( unittest.TestCase ):
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9 pass
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10
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11 # def setUp(self):
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12 # self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() )
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13 # self._mapFile = "map_file.map"
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14 # _MockMapFile( self._mapFile )
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15 # self._resultFile = "dummyObsFile_%s" % ( self._uniqId )
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16 # self._refFileToCompare = "dummyExpFile_%s" % ( self._uniqId )
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17 # self._configFileName = "dummyConfigFile_%s" % ( self._uniqId )
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18 # configF = open(self._configFileName, "w" )
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19 # configF.write( "[repet_env]\n" )
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20 # configF.write( "repet_host: %s\n" % ( os.environ["REPET_HOST"] ) )
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21 # configF.write( "repet_user: %s\n" % ( os.environ["REPET_USER"] ) )
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22 # configF.write( "repet_pw: %s\n" % ( os.environ["REPET_PW"] ) )
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23 # configF.write( "repet_db: %s\n" % ( os.environ["REPET_DB"] ) )
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24 # configF.write( "repet_port: %s\n" % ( os.environ["REPET_PORT"] ) )
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25 # configF.close()
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26 # self._db = DbMySql( cfgFileName = self._configFileName )
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27 #
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28 # def tearDown(self):
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29 # os.remove( self._mapFile )
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30 # os.remove( self._resultFile )
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31 # os.remove( self._refFileToCompare )
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32 # self._db.close()
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33 # self._uniqId = None
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34 #
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35 #
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36 # def test_run_TwoHitsOverlapOnFirstAndSecondChunks( self ):
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37 # file2Process = "two_hits_overlap_on_first_and_second_chunk.align"
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38 # linesToProcess = [ "chunk1" + "\t" + "95535" + "\t" + "95570" + "\t" + "sbj2" + "\t" + "125423" + "\t" + "125467" + "\t" + "7e-15" + "\t" + "82" + "\t" + "97.78" + "\n",
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39 # "chunk2" + "\t" + "5544" + "\t" + "5575" + "\t" + "sbj2" + "\t" + "125457" + "\t" + "133465" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n" ]
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40 # _MockAlignFile( file2Process, linesToProcess )
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41 #
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42 # convCoord = ConvCoord( file2Process, "q", self._mapFile, self._resultFile, "", 0, self._db )
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43 # convCoord.run()
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44 #
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45 # refLine = ["dmel_chr4" + "\t" + "95535" + "\t" + "95575" + "\t" + "sbj2" + "\t" + "125423" + "\t" + "133465" + "\t" + "2e-38" + "\t" + "83" + "\t" + "97.78" + "\n"]
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46 # _MockAlignFile( self._refFileToCompare, refLine )
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47 #
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48 # self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) )
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49 # os.remove( file2Process )
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50 #
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51 #
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52 # def test_run_ThreeHitsOverlapOnFirstAndSecondChunks( self ):
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53 # file2Process = "three_hits_overlap_on_first_and_second_chunk.align"
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54 # linesToProcess = [ "chunk1" + "\t" + "95535" + "\t" + "95570" + "\t" + "sbj2" + "\t" + "125423" + "\t" + "125467" + "\t" + "7e-15" + "\t" + "82" + "\t" + "97.78" + "\n",
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55 # "chunk2" + "\t" + "5544" + "\t" + "5575" + "\t" + "sbj2" + "\t" + "125457" + "\t" + "133465" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n"
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56 # "chunk2" + "\t" + "5540" + "\t" + "5573" + "\t" + "sbj2" + "\t" + "125454" + "\t" +"125750" + "\t" + "8e-58" + "\t" + "224" + "\t" + "86.43" + "\n" ]
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57 # _MockAlignFile( file2Process, linesToProcess )
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58 #
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59 # convCoord = ConvCoord( file2Process, "q", self._mapFile, self._resultFile, "", 0, self._db )
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60 # convCoord.run()
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61 #
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62 # refLine = ["dmel_chr4" + "\t" + "95535" + "\t" + "95575" + "\t" + "sbj2" + "\t" + "125423" + "\t" + "133465" + "\t" + "8e-58" + "\t" + "224" + "\t" + "97.78" + "\n"]
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63 # _MockAlignFile( self._refFileToCompare, refLine )
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64 #
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65 # self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) )
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66 # os.remove( file2Process )
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67 #
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68 #
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69 # def test_run_HitsOnDifferentStrandsAndDifferentSubjects( self ):
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70 # file2Process = "hits_on_different_strands_and_different_subjects.align"
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71 # linesToProcess = [ "chunk1" + "\t" + "95535" + "\t" + "95570" + "\t" + "sbj2" + "\t" + "125423" + "\t" + "125467" + "\t" + "7e-15" + "\t" + "82" + "\t" + "97.78" + "\n",
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72 # "chunk2" + "\t" + "5575" + "\t" + "5544" + "\t" + "sbj2" + "\t" + "125457" + "\t" + "133465" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n",
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73 # "chunk2" + "\t" + "5540" + "\t" + "5573" + "\t" + "sbj3" + "\t" + "125454" + "\t" +"125750" + "\t" + "8e-58" + "\t" + "224" + "\t" + "86.43" + "\n" ]
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74 # _MockAlignFile( file2Process, linesToProcess )
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75 #
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76 # convCoord = ConvCoord( file2Process, "q", self._mapFile, self._resultFile, "", 0, self._db )
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77 # convCoord.run()
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78 #
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79 # refLine = ["dmel_chr4" + "\t" + "95535" + "\t" + "95570" + "\t" + "sbj2" + "\t" + "125423" + "\t" + "125467" + "\t" + "7e-15" + "\t" + "82" + "\t" + "97.78" + "\n",
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80 # "dmel_chr4" + "\t" + "95544" + "\t" + "95575" + "\t" + "sbj2" + "\t" + "133465" + "\t" + "125457" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n",
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81 # "dmel_chr4" + "\t" + "95540" + "\t" + "95573" + "\t" + "sbj3" + "\t" + "125454" + "\t" +"125750" + "\t" + "8e-58" + "\t" + "224" + "\t" + "86.43" + "\n" ]
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82 # _MockAlignFile( self._refFileToCompare, refLine )
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83 #
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84 # self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) )
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85 # os.remove( file2Process )
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86 #
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87 #
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88 # def test_run_TwoHitsOnChunksOnlyAndOnOverlap( self ):
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89 # file2Process = "two_hits_on_chunks_only_and_on_overlap.align"
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90 # linesToProcess = [ "chunk2" + "\t" + "85000" + "\t" + "95000" + "\t" + "sbj2" + "\t" + "125457" + "\t" + "133465" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n",
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91 # "chunk3" + "\t" + "1000" + "\t" +" 5000" + "\t" + "sbj2" + "\t" + "125454" + "\t" + "125750" + "\t" + "8e-58" + "\t" + "224" + "\t" + "86.43" + "\n" ]
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92 # _MockAlignFile( file2Process, linesToProcess )
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93 #
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94 # convCoord = ConvCoord( file2Process, "q", self._mapFile, self._resultFile, "", 0, self._db )
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95 # convCoord.run()
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96 #
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97 # refLine = ["dmel_chr4" + "\t" + "175000"+ "\t" + "185000"+ "\t" + "sbj2"+ "\t" + "125454"+ "\t" + "133465"+ "\t" + "8e-58"+ "\t" + "224"+ "\t" + "86.43"+"\n"]
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98 # _MockAlignFile( self._refFileToCompare, refLine )
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99 #
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100 # self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) )
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101 # os.remove( file2Process )
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102 #
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103 #
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104 # def test_run_TwoHitsOnChunks_And_OnOverlap_OnReverseStrand_ForSubject( self ):
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105 # file2Process = "two_hits_on_chunks_and_on_overlap_on_reverse_strand_for_subject.align"
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106 # linesToProcess = [ "chunk2" + "\t" + "85000" + "\t" + "95000" + "\t" + "sbj2" + "\t" + "133465" + "\t" + "125457" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n",
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107 # "chunk3" + "\t" + "1000" + "\t" + "5000" + "\t" + "sbj2" + "\t" + "125750" + "\t" + "125454" + "\t" + "8e-58" + "\t" + "224" + "\t" + "86.43" + "\n" ]
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108 # _MockAlignFile( file2Process, linesToProcess )
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109 #
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110 # convCoord = ConvCoord( file2Process, "q", self._mapFile, self._resultFile, "", 0, self._db )
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111 # convCoord.run()
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112 #
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113 # refLine = ["dmel_chr4" + "\t" + "175000"+ "\t" + "185000" + "\t" + "sbj2"+ "\t" + "133465" + "\t" + "125454" + "\t" + "8e-58"+ "\t" + "224"+ "\t" + "86.43"+"\n"]
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114 # _MockAlignFile( self._refFileToCompare, refLine )
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115 #
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116 # self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) )
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117 # os.remove( file2Process )
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118 #
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119 #
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120 # def test_run_ThreeHitsAllByAllWithTwoHitsWithinAChunkOverlap( self ):
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121 # file2Process = "dummyAlignFile_%s" % ( self._uniqId )
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122 # linesToProcess = [ "chunk1"+"\t"+"192"+"\t"+"197"+"\t"+"chunk2"+"\t"+"2"+"\t"+"7"+"\t"+"8e-58"+"\t"+"11"+"\t"+"97.8"+"\n",
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123 # "chunk1"+"\t"+"192"+"\t"+"197"+"\t"+"chunk2"+"\t"+"51"+"\t"+"56"+"\t"+"8e-58"+"\t"+"11"+"\t"+"97.8"+"\n",
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124 # "chunk2"+"\t"+"2"+"\t"+"7"+"\t"+"chunk2"+"\t"+"51"+"\t"+"56"+"\t"+"8e-58"+"\t"+"11"+"\t"+"97.8"+"\n" ]
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125 # _MockAlignFile( file2Process, linesToProcess )
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126 #
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127 # mapFileName = "dummyMapFile_%s" % ( self._uniqId )
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128 # mapF = open( mapFileName, "w" )
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129 # mapF.write( "chunk1\tdmel_chr4\t1\t200\n" )
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130 # mapF.write( "chunk2\tdmel_chr4\t191\t390\n" )
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131 # mapF.close()
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132 #
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133 # convCoord = ConvCoord( file2Process, "qs", mapFileName, self._resultFile, "", 0, self._db )
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134 # convCoord.run()
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135 #
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136 # refLine = [ "dmel_chr4"+"\t"+"192"+"\t"+"197"+"\t"+"dmel_chr4"+"\t"+"241"+"\t"+"246"+"\t"+"8e-58"+"\t"+"11"+"\t"+"97.8"+"\n" ]
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137 # _MockAlignFile( self._refFileToCompare, refLine )
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138 #
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139 # self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) )
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140 # os.remove( file2Process )
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141 # os.remove( mapFileName )
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142 #
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143 #
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144 #class _MockAlignFile:
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145 #
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146 # def __init__(self, fileName, lines):
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147 # alignF = open(fileName, "w");
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148 # for line in lines:
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149 # alignF.write(line)
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150 # alignF.close
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151 #
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152 #
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153 #class _MockMapFile:
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154 #
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155 # def __init__ (self, fileName):
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156 # mapF = open(fileName, "w")
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157 # line1 = "chunk1" + '\t' + "dmel_chr4" + '\t' + "1" + '\t'+ "100000" + "\n"
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158 # line2 = "chunk2" + '\t' + "dmel_chr4" + '\t' + "90001" + '\t'+ "190000" + "\n"
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159 # line3 = "chunk3" + '\t' + "dmel_chr4" + '\t' + "180001" + '\t' + "280000" + "\n"
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160 # mapF.write(line1)
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161 # mapF.write(line2)
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162 # mapF.write(line3)
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163 # mapF.close
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164
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165
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166 test_suite = unittest.TestSuite()
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167 test_suite.addTest( unittest.makeSuite( Test_ConvCoordWithOverlaps ) )
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168 if __name__ == "__main__":
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169 unittest.TextTestRunner(verbosity=2).run( test_suite )
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