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18
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1 import os
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2 import unittest
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3 from commons.core.utils.FileUtils import FileUtils
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4 from commons.tools.MergeMatchsFiles import MergeMatchsFiles
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5
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6
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7 class Test_F_MergeMatchsFiles(unittest.TestCase):
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8
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9 def test_run_set(self):
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10 inFileName1 = "test1.set"
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11 inFileName2 = "test2.set"
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12 self._writeSetFiles(inFileName1, inFileName2)
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13 iMMF = MergeMatchsFiles("set", "out")
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14 iMMF.run()
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15 obsFileName = "out.set"
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16 expFileName = "exp.set"
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17 self._writeExpSetFile(expFileName)
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18 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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19 os.remove(expFileName)
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20 os.remove(obsFileName)
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21
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22 def test_run_align(self):
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23 inFileName1 = "test1.align"
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24 inFileName2 = "test2.align"
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25 self._writeAlignFiles(inFileName1, inFileName2)
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26 iMMF = MergeMatchsFiles("align", "out")
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27 iMMF.run()
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28 obsFileName = "out.align"
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29 expFileName = "exp.align"
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30 self._writeExpAlignFile(expFileName)
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31 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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32 os.remove(expFileName)
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33 os.remove(obsFileName)
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34
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35 def test_run_align_allByAll(self):
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36 inFileName1 = "test1.align"
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37 inFileName2 = "test2.align"
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38 self._writeAlignFiles(inFileName1, inFileName2)
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39 iMMF = MergeMatchsFiles("align", "out", True)
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40 iMMF.run()
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41 obsFileName = "out.align"
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42 expFileName = "exp.align"
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43 self._writeExpAlignFile_allByAll(expFileName)
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44 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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45 os.remove(expFileName)
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46 os.remove(obsFileName)
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47
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48 def test_run_path(self):
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49 inFileName1 = "test1.path"
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50 inFileName2 = "test2.path"
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51 self._writePathFiles(inFileName1, inFileName2)
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52 iMMF = MergeMatchsFiles("path", "out")
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53 iMMF.run()
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54 obsFileName = "out.path"
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55 expFileName = "exp.path"
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56 self._writeExpPathFile(expFileName)
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57 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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58 os.remove(expFileName)
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59 os.remove(obsFileName)
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60
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61 def test_run_tab(self):
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62 inFileName1 = "test1.tab"
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63 inFileName2 = "test2.tab"
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64 self._writeTabFiles(inFileName1, inFileName2)
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65 iMMF = MergeMatchsFiles("tab", "out")
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66 iMMF.run()
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67 obsFileName = "out.tab"
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68 expFileName = "exp.tab"
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69 self._writeExpTabFile(expFileName)
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70 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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71 os.remove(expFileName)
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72 os.remove(obsFileName)
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73
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74 def _writeSetFiles(self, fileName1, fileName2):
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75 f = open(fileName1, "w")
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76 f.write("1\t(TCTAT)3\tchunk006\t295\t309\n")
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77 f.write("2\t(A)33\tchunk006\t679\t711\n")
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78 f.write("3\t(G)16\tchunk006\t731\t746\n")
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79 f.write("4\t(GAG)9\tchunk006\t903\t929\n")
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80 f.write("5\t(GGAGGG)4\tchunk006\t905\t929\n")
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81 f.close()
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82 f = open(fileName2, "w")
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83 f.write("1\t(CCACT)3\tchunk011\t101\t116\n")
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84 f.write("2\t(TATATA)7\tchunk011\t316\t357\n")
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85 f.write("3\t(AT)22\tchunk011\t323\t366\n")
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86 f.close()
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87
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88 def _writeExpSetFile(self, fileName):
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89 f = open(fileName, "w")
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90 f.write("1\t(TCTAT)3\tchunk006\t295\t309\n")
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91 f.write("2\t(A)33\tchunk006\t679\t711\n")
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92 f.write("3\t(G)16\tchunk006\t731\t746\n")
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93 f.write("4\t(GAG)9\tchunk006\t903\t929\n")
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94 f.write("5\t(GGAGGG)4\tchunk006\t905\t929\n")
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95 f.write("6\t(CCACT)3\tchunk011\t101\t116\n")
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96 f.write("7\t(TATATA)7\tchunk011\t316\t357\n")
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97 f.write("8\t(AT)22\tchunk011\t323\t366\n")
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98 f.close()
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99
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100 def _writeAlignFiles(self, fileName1, fileName2):
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101 f = open(fileName1, "w")
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102 f.write("chunk1\t25601\t27800\tchunk1\t52250\t54450\t0\t4244\t99.36\n")
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103 f.write("chunk1\t27791\t28620\tchunk1\t55918\t56749\t0\t1588\t99.16\n")
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104 f.write("chunk1\t28618\t32380\tchunk1\t56794\t60572\t0\t7299\t99.29\n")
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105 f.write("chunk1\t28692\t30872\tchunk1\t49901\t52081\t0\t4260\t99.63\n")
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106 f.write("chunk1\t32216\t34275\tchunk1\t52084\t54143\t0\t4012\t99.56\n")
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107 f.write("chunk1\t41016\t45652\tchunk1\t55918\t60572\t0\t8942\t99.18\n")
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108 f.write("chunk1\t41964\t44144\tchunk1\t49901\t52081\t0\t4252\t99.59\n")
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109 f.write("chunk1\t46237\t46863\tchunk1\t73980\t74625\t0\t837\t91.36\n")
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110 f.write("chunk1\t46330\t46860\tchunk1\t54981\t54450\t0\t841\t95.11\n")
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111 f.write("chunk1\t46861\t48962\tchunk1\t52349\t54450\t0\t4103\t99.62\n")
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112 f.write("chunk1\t48953\t50000\tchunk1\t55918\t56967\t0\t2036\t99.52\n")
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113 f.write("chunk1\t49901\t52081\tchunk1\t28692\t30872\t0\t4260\t99.63\n")
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114 f.write("chunk1\t49901\t52081\tchunk1\t41964\t44144\t0\t4252\t99.59\n")
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115 f.write("chunk1\t52084\t54143\tchunk1\t32216\t34275\t0\t4012\t99.56\n")
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116 f.write("chunk1\t52250\t54450\tchunk1\t25601\t27800\t0\t4244\t99.36\n")
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117 f.write("chunk1\t52349\t54450\tchunk1\t46861\t48962\t0\t4103\t99.62\n")
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118 f.write("chunk1\t54450\t54980\tchunk1\t74622\t74091\t0\t769\t93.63\n")
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119 f.write("chunk1\t54450\t54981\tchunk1\t46860\t46330\t0\t841\t95.11\n")
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120 f.write("chunk1\t55918\t56749\tchunk1\t27791\t28620\t0\t1588\t99.16\n")
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121 f.write("chunk1\t55918\t56967\tchunk1\t48953\t50000\t0\t2036\t99.52\n")
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122 f.write("chunk1\t55918\t60572\tchunk1\t41016\t45652\t0\t8942\t99.18\n")
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123 f.write("chunk1\t56794\t60572\tchunk1\t28618\t32380\t0\t7299\t99.29\n")
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124 f.write("chunk1\t73980\t74625\tchunk1\t46237\t46863\t0\t837\t91.36\n")
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125 f.write("chunk1\t74091\t74622\tchunk1\t54980\t54450\t0\t769\t93.63\n")
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126 f.write("chunk1\t99211\t99791\tchunk1\t164000\t164577\t0\t767\t91.74\n")
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127 f.write("chunk1\t101527\t102429\tchunk1\t167161\t168059\t0\t1074\t90.14\n")
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128 f.write("chunk1\t164000\t164577\tchunk1\t99211\t99791\t0\t767\t91.74\n")
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129 f.write("chunk1\t167161\t168059\tchunk1\t101527\t102429\t0\t1074\t90.14\n")
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130 f.write("chunk1\t46330\t46862\tchunk6\t2564\t3101\t0\t835\t94.8\n")
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131 f.write("chunk1\t46372\t46862\tchunk6\t5328\t4837\t0\t753\t94.51\n")
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132 f.write("chunk1\t54450\t54915\tchunk6\t4839\t5304\t0\t749\t95.28\n")
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133 f.write("chunk1\t54450\t55021\tchunk6\t3099\t2524\t0\t878\t94.27\n")
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134 f.write("chunk1\t54600\t55021\tchunk6\t25505\t25926\t0\t638\t94.08\n")
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135 f.write("chunk1\t74091\t74624\tchunk6\t2565\t3101\t0\t898\t96.48\n")
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136 f.write("chunk1\t74132\t74624\tchunk6\t5328\t4837\t0\t763\t94.95\n")
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137 f.close()
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138 f = open(fileName2, "w")
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139 f.write("chunk6\t2524\t3099\tchunk1\t55021\t54450\t0\t878\t94.27\n")
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140 f.write("chunk6\t2564\t3101\tchunk1\t46330\t46862\t0\t835\t94.8\n")
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141 f.write("chunk6\t2565\t3101\tchunk1\t74091\t74624\t0\t898\t96.48\n")
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142 f.write("chunk6\t4837\t5328\tchunk1\t46862\t46372\t0\t753\t94.51\n")
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143 f.write("chunk6\t4837\t5328\tchunk1\t74624\t74132\t0\t763\t94.95\n")
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144 f.write("chunk6\t4839\t5304\tchunk1\t54450\t54915\t0\t749\t95.28\n")
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145 f.write("chunk6\t25505\t25926\tchunk1\t54600\t55021\t0\t638\t94.08\n")
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146 f.write("chunk6\t1998\t2948\tchunk6\t26450\t25506\t0\t1758\t98.42\n")
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147 f.write("chunk6\t2606\t3101\tchunk6\t5328\t4837\t0\t815\t95.77\n")
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148 f.write("chunk6\t4837\t5328\tchunk6\t3101\t2606\t0\t815\t95.77\n")
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149 f.write("chunk6\t25506\t26450\tchunk6\t2948\t1998\t0\t1758\t98.42\n")
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150 f.write("chunk6\t95526\t96047\tchunk6\t115678\t116199\t0\t688\t92.19\n")
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151 f.write("chunk6\t115678\t116199\tchunk6\t95526\t96047\t0\t688\t92.19\n")
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152 f.close()
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153
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154 def _writeExpAlignFile_allByAll(self, fileName):
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155 f = open(fileName, "w")
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156 f.write("chunk1\t25601\t27800\tchunk1\t52250\t54450\t0\t4244\t99.360000\n")
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157 f.write("chunk1\t27791\t28620\tchunk1\t55918\t56749\t0\t1588\t99.160000\n")
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158 f.write("chunk1\t28618\t32380\tchunk1\t56794\t60572\t0\t7299\t99.290000\n")
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159 f.write("chunk1\t28692\t30872\tchunk1\t49901\t52081\t0\t4260\t99.630000\n")
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160 f.write("chunk1\t32216\t34275\tchunk1\t52084\t54143\t0\t4012\t99.560000\n")
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161 f.write("chunk1\t41016\t45652\tchunk1\t55918\t60572\t0\t8942\t99.180000\n")
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162 f.write("chunk1\t41964\t44144\tchunk1\t49901\t52081\t0\t4252\t99.590000\n")
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163 f.write("chunk1\t46237\t46863\tchunk1\t73980\t74625\t0\t837\t91.360000\n")
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164 f.write("chunk1\t46330\t46860\tchunk1\t54981\t54450\t0\t841\t95.110000\n")
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165 f.write("chunk1\t46861\t48962\tchunk1\t52349\t54450\t0\t4103\t99.620000\n")
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166 f.write("chunk1\t48953\t50000\tchunk1\t55918\t56967\t0\t2036\t99.520000\n")
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167 f.write("chunk1\t54450\t54980\tchunk1\t74622\t74091\t0\t769\t93.630000\n")
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168 f.write("chunk1\t99211\t99791\tchunk1\t164000\t164577\t0\t767\t91.740000\n")
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169 f.write("chunk1\t101527\t102429\tchunk1\t167161\t168059\t0\t1074\t90.140000\n")
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170 f.write("chunk1\t46330\t46862\tchunk6\t2564\t3101\t0\t835\t94.800000\n")
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171 f.write("chunk1\t46372\t46862\tchunk6\t5328\t4837\t0\t753\t94.510000\n")
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172 f.write("chunk1\t54450\t54915\tchunk6\t4839\t5304\t0\t749\t95.280000\n")
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173 f.write("chunk1\t54450\t55021\tchunk6\t3099\t2524\t0\t878\t94.270000\n")
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174 f.write("chunk1\t54600\t55021\tchunk6\t25505\t25926\t0\t638\t94.080000\n")
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175 f.write("chunk1\t74091\t74624\tchunk6\t2565\t3101\t0\t898\t96.480000\n")
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176 f.write("chunk1\t74132\t74624\tchunk6\t5328\t4837\t0\t763\t94.950000\n")
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177 f.write("chunk6\t1998\t2948\tchunk6\t26450\t25506\t0\t1758\t98.420000\n")
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178 f.write("chunk6\t2606\t3101\tchunk6\t5328\t4837\t0\t815\t95.770000\n")
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179 f.write("chunk6\t95526\t96047\tchunk6\t115678\t116199\t0\t688\t92.190000\n")
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180 f.close()
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181
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182 def _writeExpAlignFile(self, fileName):
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183 f = open(fileName, "w")
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184 f.write("chunk1\t25601\t27800\tchunk1\t52250\t54450\t0\t4244\t99.36\n")
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185 f.write("chunk1\t27791\t28620\tchunk1\t55918\t56749\t0\t1588\t99.16\n")
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186 f.write("chunk1\t28618\t32380\tchunk1\t56794\t60572\t0\t7299\t99.29\n")
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187 f.write("chunk1\t28692\t30872\tchunk1\t49901\t52081\t0\t4260\t99.63\n")
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188 f.write("chunk1\t32216\t34275\tchunk1\t52084\t54143\t0\t4012\t99.56\n")
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189 f.write("chunk1\t41016\t45652\tchunk1\t55918\t60572\t0\t8942\t99.18\n")
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190 f.write("chunk1\t41964\t44144\tchunk1\t49901\t52081\t0\t4252\t99.59\n")
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191 f.write("chunk1\t46237\t46863\tchunk1\t73980\t74625\t0\t837\t91.36\n")
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192 f.write("chunk1\t46330\t46860\tchunk1\t54981\t54450\t0\t841\t95.11\n")
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193 f.write("chunk1\t46861\t48962\tchunk1\t52349\t54450\t0\t4103\t99.62\n")
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194 f.write("chunk1\t48953\t50000\tchunk1\t55918\t56967\t0\t2036\t99.52\n")
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195 f.write("chunk1\t49901\t52081\tchunk1\t28692\t30872\t0\t4260\t99.63\n")
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196 f.write("chunk1\t49901\t52081\tchunk1\t41964\t44144\t0\t4252\t99.59\n")
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197 f.write("chunk1\t52084\t54143\tchunk1\t32216\t34275\t0\t4012\t99.56\n")
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198 f.write("chunk1\t52250\t54450\tchunk1\t25601\t27800\t0\t4244\t99.36\n")
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199 f.write("chunk1\t52349\t54450\tchunk1\t46861\t48962\t0\t4103\t99.62\n")
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200 f.write("chunk1\t54450\t54980\tchunk1\t74622\t74091\t0\t769\t93.63\n")
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201 f.write("chunk1\t54450\t54981\tchunk1\t46860\t46330\t0\t841\t95.11\n")
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202 f.write("chunk1\t55918\t56749\tchunk1\t27791\t28620\t0\t1588\t99.16\n")
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203 f.write("chunk1\t55918\t56967\tchunk1\t48953\t50000\t0\t2036\t99.52\n")
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204 f.write("chunk1\t55918\t60572\tchunk1\t41016\t45652\t0\t8942\t99.18\n")
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205 f.write("chunk1\t56794\t60572\tchunk1\t28618\t32380\t0\t7299\t99.29\n")
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206 f.write("chunk1\t73980\t74625\tchunk1\t46237\t46863\t0\t837\t91.36\n")
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207 f.write("chunk1\t74091\t74622\tchunk1\t54980\t54450\t0\t769\t93.63\n")
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208 f.write("chunk1\t99211\t99791\tchunk1\t164000\t164577\t0\t767\t91.74\n")
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209 f.write("chunk1\t101527\t102429\tchunk1\t167161\t168059\t0\t1074\t90.14\n")
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210 f.write("chunk1\t164000\t164577\tchunk1\t99211\t99791\t0\t767\t91.74\n")
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211 f.write("chunk1\t167161\t168059\tchunk1\t101527\t102429\t0\t1074\t90.14\n")
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212 f.write("chunk1\t46330\t46862\tchunk6\t2564\t3101\t0\t835\t94.8\n")
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213 f.write("chunk1\t46372\t46862\tchunk6\t5328\t4837\t0\t753\t94.51\n")
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214 f.write("chunk1\t54450\t54915\tchunk6\t4839\t5304\t0\t749\t95.28\n")
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215 f.write("chunk1\t54450\t55021\tchunk6\t3099\t2524\t0\t878\t94.27\n")
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216 f.write("chunk1\t54600\t55021\tchunk6\t25505\t25926\t0\t638\t94.08\n")
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217 f.write("chunk1\t74091\t74624\tchunk6\t2565\t3101\t0\t898\t96.48\n")
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218 f.write("chunk1\t74132\t74624\tchunk6\t5328\t4837\t0\t763\t94.95\n")
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219 f.write("chunk6\t2524\t3099\tchunk1\t55021\t54450\t0\t878\t94.27\n")
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220 f.write("chunk6\t2564\t3101\tchunk1\t46330\t46862\t0\t835\t94.8\n")
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221 f.write("chunk6\t2565\t3101\tchunk1\t74091\t74624\t0\t898\t96.48\n")
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222 f.write("chunk6\t4837\t5328\tchunk1\t46862\t46372\t0\t753\t94.51\n")
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223 f.write("chunk6\t4837\t5328\tchunk1\t74624\t74132\t0\t763\t94.95\n")
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224 f.write("chunk6\t4839\t5304\tchunk1\t54450\t54915\t0\t749\t95.28\n")
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225 f.write("chunk6\t25505\t25926\tchunk1\t54600\t55021\t0\t638\t94.08\n")
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226 f.write("chunk6\t1998\t2948\tchunk6\t26450\t25506\t0\t1758\t98.42\n")
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227 f.write("chunk6\t2606\t3101\tchunk6\t5328\t4837\t0\t815\t95.77\n")
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228 f.write("chunk6\t4837\t5328\tchunk6\t3101\t2606\t0\t815\t95.77\n")
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229 f.write("chunk6\t25506\t26450\tchunk6\t2948\t1998\t0\t1758\t98.42\n")
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230 f.write("chunk6\t95526\t96047\tchunk6\t115678\t116199\t0\t688\t92.19\n")
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231 f.write("chunk6\t115678\t116199\tchunk6\t95526\t96047\t0\t688\t92.19\n")
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232 f.close()
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233
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234 def _writePathFiles(self, fileName1, fileName2):
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235 f = open(fileName1, "w")
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236 f.write("1\tchunk001\t11046\t11071\tAT_rich#Low_complexity\t166\t141\t0.0\t9\t34.62\n")
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237 f.write("2\tchunk001\t11050\t11074\tAT_rich#Low_complexity\t161\t137\t0.0\t14\t56.0\n")
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238 f.write("3\tchunk001\t17216\t17266\tAT_rich#Low_complexity\t144\t194\t0.0\t14\t29.41\n")
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239 f.write("4\tchunk001\t17736\t17766\tAT_rich#Low_complexity\t118\t148\t0.0\t6\t22.58\n")
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240 f.write("5\tchunk001\t18723\t18758\tAT_rich#Low_complexity\t110\t145\t0.0\t5\t13.89\n")
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241 f.write("6\tchunk001\t20024\t20073\tAT_rich#Low_complexity\t125\t174\t0.0\t13\t26.0\n")
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242 f.write("7\tchunk002\t12855\t12882\tAT_rich#Low_complexity\t131\t158\t0.0\t13\t46.43\n")
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243 f.write("8\tchunk002\t20736\t20771\tAT_rich#Low_complexity\t135\t170\t0.0\t12\t36.11\n")
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244 f.close()
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245 f = open(fileName2, "w")
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246 f.write("1\tchunk006\t12114\t12143\tAT_rich#Low_complexity\t146\t117\t0.0\t6\t20.0\n")
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247 f.write("2\tchunk006\t25538\t25574\tAT_rich#Low_complexity\t128\t164\t0.0\t14\t37.84\n")
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248 f.write("3\tchunk006\t25794\t25818\tAT_rich#Low_complexity\t162\t138\t0.0\t15\t60.0\n")
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249 f.write("4\tchunk006\t28373\t28403\tAT_rich#Low_complexity\t135\t165\t0.0\t17\t54.84\n")
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250 f.write("5\tchunk006\t29180\t29201\tAT_rich#Low_complexity\t163\t142\t0.0\t14\t68.18\n")
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251 f.write("6\tchunk006\t33773\t33825\tAT_rich#Low_complexity\t142\t194\t0.0\t11\t22.64\n")
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252 f.close()
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253
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254 def _writeExpPathFile(self, fileName):
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255 f = open(fileName, "w")
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256 f.write("1\tchunk001\t11046\t11071\tAT_rich#Low_complexity\t166\t141\t0.0\t9\t34.62\n")
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257 f.write("2\tchunk001\t11050\t11074\tAT_rich#Low_complexity\t161\t137\t0.0\t14\t56.0\n")
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258 f.write("3\tchunk001\t17216\t17266\tAT_rich#Low_complexity\t144\t194\t0.0\t14\t29.41\n")
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259 f.write("4\tchunk001\t17736\t17766\tAT_rich#Low_complexity\t118\t148\t0.0\t6\t22.58\n")
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260 f.write("5\tchunk001\t18723\t18758\tAT_rich#Low_complexity\t110\t145\t0.0\t5\t13.89\n")
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261 f.write("6\tchunk001\t20024\t20073\tAT_rich#Low_complexity\t125\t174\t0.0\t13\t26.0\n")
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262 f.write("7\tchunk002\t12855\t12882\tAT_rich#Low_complexity\t131\t158\t0.0\t13\t46.43\n")
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263 f.write("8\tchunk002\t20736\t20771\tAT_rich#Low_complexity\t135\t170\t0.0\t12\t36.11\n")
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264 f.write("9\tchunk006\t12114\t12143\tAT_rich#Low_complexity\t146\t117\t0.0\t6\t20.0\n")
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265 f.write("10\tchunk006\t25538\t25574\tAT_rich#Low_complexity\t128\t164\t0.0\t14\t37.84\n")
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266 f.write("11\tchunk006\t25794\t25818\tAT_rich#Low_complexity\t162\t138\t0.0\t15\t60.0\n")
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267 f.write("12\tchunk006\t28373\t28403\tAT_rich#Low_complexity\t135\t165\t0.0\t17\t54.84\n")
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268 f.write("13\tchunk006\t29180\t29201\tAT_rich#Low_complexity\t163\t142\t0.0\t14\t68.18\n")
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269 f.write("14\tchunk006\t33773\t33825\tAT_rich#Low_complexity\t142\t194\t0.0\t11\t22.64\n")
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270 f.close()
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271
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272 def _writeTabFiles(self, fileName1, fileName2):
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273 f = open(fileName1, "w")
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274 f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n")
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275 f.write("DmelChr4_bench_Blaster_Grouper_1_Map_3\t2\t542\t541\t0.998155\t0.32473\tTC1_DM:ClassII:TIR:Tc1-Mariner\t1\t543\t543\t0.32593\t1.4e-93\t984\t87.541\t1\n")
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276 f.write("DmelChr4_bench_Blaster_Grouper_2_Map_8\t2\t517\t516\t0.998066\t0.115179\tPROTOP:ClassII:TIR:P\t530\t16\t515\t0.114955\t1.2e-79\t928\t95.2118\t2\n")
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277 f.write("DmelChr4_bench_Blaster_Grouper_3_Map_20\t5\t598\t594\t0.978583\t0.537557\tPROTOP_A:ClassII:TIR:P\t572\t1\t572\t0.517647\t3e-93\t1048\t97.6307\t3\n")
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278 f.write("DmelChr4_bench_Blaster_Grouper_4_Map_3\t5\t534\t530\t0.992509\t0.479638\tPROTOP_A:ClassII:TIR:P\t1105\t576\t530\t0.479638\t2.9e-87\t1828\t98.4848\t4\n")
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279 f.write("DmelChr4_bench_Blaster_Grouper_5_Map_3\t5\t704\t700\t0.994318\t0.425791\tTC1-2_DM:ClassII:TIR:Tc1-Mariner\t1644\t945\t700\t0.425791\t7.3e-120\t1228\t98.1349\t5\n")
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280 f.close()
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281 f = open(fileName2, "w")
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282 f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n")
|
|
|
283 f.write("DmelChr4_bench_Blaster_Grouper_5_Map_3\t274\t702\t429\t0.609375\t1.26176\tTC1-2_DMp:ClassII:TIR:Tc1-Mariner\t340\t198\t143\t0.420588\t5e-74\t265\t98.6014\t1\n")
|
|
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284 f.write("DmelChr4_bench_Blaster_Recon_12_Map_3\t311\t374\t64\t0.028021\t0.0359349\tBEL-27_AA-I_1p:ClassI:LTR:Bel-Pao\t605\t582\t24\t0.0134756\t6.3e-17\t11\t30.8511\t2\n")
|
|
|
285 f.write("DmelChr4_bench_Blaster_Recon_12_Map_3\t1472\t1552\t81\t0.0354641\t0.0463918\tBEL-76_AA-I_1p:ClassI:LTR:Bel-Pao\t79\t52\t28\t0.0160367\t1e-13\t8\t27.7778\t3\n")
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286 f.close()
|
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|
287
|
|
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288 def _writeExpTabFile(self, fileName):
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289 f = open(fileName, "w")
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290 f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n")
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|
|
291 f.write("DmelChr4_bench_Blaster_Grouper_1_Map_3\t2\t542\t541\t0.998155\t0.32473\tTC1_DM:ClassII:TIR:Tc1-Mariner\t1\t543\t543\t0.32593\t1.4e-93\t984\t87.541\t1\n")
|
|
|
292 f.write("DmelChr4_bench_Blaster_Grouper_2_Map_8\t2\t517\t516\t0.998066\t0.115179\tPROTOP:ClassII:TIR:P\t530\t16\t515\t0.114955\t1.2e-79\t928\t95.2118\t2\n")
|
|
|
293 f.write("DmelChr4_bench_Blaster_Grouper_3_Map_20\t5\t598\t594\t0.978583\t0.537557\tPROTOP_A:ClassII:TIR:P\t572\t1\t572\t0.517647\t3e-93\t1048\t97.6307\t3\n")
|
|
|
294 f.write("DmelChr4_bench_Blaster_Grouper_4_Map_3\t5\t534\t530\t0.992509\t0.479638\tPROTOP_A:ClassII:TIR:P\t1105\t576\t530\t0.479638\t2.9e-87\t1828\t98.4848\t4\n")
|
|
|
295 f.write("DmelChr4_bench_Blaster_Grouper_5_Map_3\t5\t704\t700\t0.994318\t0.425791\tTC1-2_DM:ClassII:TIR:Tc1-Mariner\t1644\t945\t700\t0.425791\t7.3e-120\t1228\t98.1349\t5\n")
|
|
|
296 f.write("DmelChr4_bench_Blaster_Grouper_5_Map_3\t274\t702\t429\t0.609375\t1.26176\tTC1-2_DMp:ClassII:TIR:Tc1-Mariner\t340\t198\t143\t0.420588\t5e-74\t265\t98.6014\t6\n")
|
|
|
297 f.write("DmelChr4_bench_Blaster_Recon_12_Map_3\t311\t374\t64\t0.028021\t0.0359349\tBEL-27_AA-I_1p:ClassI:LTR:Bel-Pao\t605\t582\t24\t0.0134756\t6.3e-17\t11\t30.8511\t7\n")
|
|
|
298 f.write("DmelChr4_bench_Blaster_Recon_12_Map_3\t1472\t1552\t81\t0.0354641\t0.0463918\tBEL-76_AA-I_1p:ClassI:LTR:Bel-Pao\t79\t52\t28\t0.0160367\t1e-13\t8\t27.7778\t8\n")
|
|
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299 f.close()
|
|
|
300
|
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|
301 if __name__ == "__main__":
|
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302 unittest.main() |
