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18
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1 import unittest
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2 import os
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3 from commons.core.utils.FileUtils import FileUtils
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4 from commons.launcher.LaunchPromer import LaunchPromer
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5
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6
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7 class Test_F_LaunchPromer(unittest.TestCase):
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8
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9 def setUp(self):
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10 self._queryFastaFileName = "query.fa"
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11 self._refFastaFileName = "ref.fa"
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12 self._writeInputFastaFiles()
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13 self._expDeltaFileName = "expPromer.delta"
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14 self._writeExpDeltaFile()
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15 self._obsDeltaFileName = "obsPromer.delta"
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16 self._obsCoordFileName= "obsPromer.coords"
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17 self._expCoordFileName= "expPromer.coords"
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18
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19 def tearDown(self):
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20 try:
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21 os.remove(self._queryFastaFileName)
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22 except:pass
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23 try:
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24 os.remove(self._refFastaFileName)
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25 except:pass
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26 try:
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27 os.remove(self._expDeltaFileName)
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28 except:pass
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29 try:
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30 os.remove(self._obsDeltaFileName)
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31 except:pass
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32
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33 def test_run(self):
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34 ilauncher = LaunchPromer(self._refFastaFileName, self._queryFastaFileName,"obsPromer",verbosity=1)
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35 ilauncher.run()
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36 self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName))
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37
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38 def test_run_as_script(self):
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39 cmd = 'LaunchPromer.py --query %s --ref %s --prefix %s' % (self._refFastaFileName, self._queryFastaFileName, "obsPromer")
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40 os.system(cmd)
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41 self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName))
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42
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43 def test_run_as_script_gencoords_output(self):
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44 self._writeExpGenCoordsFile()
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45 cmd = 'LaunchPromer.py --query %s --ref %s --prefix %s --gencoords' % (self._refFastaFileName, self._queryFastaFileName, "obsPromer")
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46 os.system(cmd)
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47 self.assertTrue(FileUtils.are2FilesIdentical(self._expCoordFileName, self._obsCoordFileName))
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48 os.remove(self._obsCoordFileName)
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49 os.remove(self._expCoordFileName)
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50
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51 def test_run_as_script_with_mincluster(self):
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52 cmd = 'LaunchPromer.py --query %s --ref %s --prefix %s --mincluster 30' % (self._refFastaFileName, self._queryFastaFileName, "obsPromer")
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53 os.system(cmd)
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54 self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName))
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55
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56 def test_run_as_script_showcoords_output(self):
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57 self._writeExpShowCoordsFile()
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58 cmd = 'LaunchPromer.py --query %s --ref %s --prefix %s --showcoords' % (self._refFastaFileName, self._queryFastaFileName, "obsPromer")
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59 os.system(cmd)
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60 self.assertTrue(FileUtils.are2FilesIdentical(self._expCoordFileName, self._obsCoordFileName))
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61 os.remove(self._obsCoordFileName)
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62 os.remove(self._expCoordFileName)
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63
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64 def _writeInputFastaFiles(self):
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65 InputFile = open(self._queryFastaFileName, 'w')
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66 InputFile.write('>Bovc-tA2:classI:SINE:SINE2/tRNA\n')
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67 InputFile.write('GGGCTTCCCTGGTAGCTCAGCTGGTAAAGAATCCGCCTGCAATGCAGGAGACCCCGGTTC\n')
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68 InputFile.write('GATTCCTGGGTCGGGAAGATCCCCTGGAGAAGGGATAGGCTACCCACTCCAGTATTCTTG\n')
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69 InputFile.write('GGCTTCCCTGGTGGCTCAGACGGTAAAGAATCCGCCTGCAATGCGGGAGACCTGGGTTCG\n')
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70 InputFile.write('ATCCCTGGGTTGGGAAGATCCCCTGGAGGAGGGCATGGCAACCCACTCCAGTATTCTTGC\n')
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71 InputFile.write('CTGGAGAATCCCCATGGACAGAGGAGCCTGGCGGGCTACAGTCCATGGGGTCGCAAAGAG\n')
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72 InputFile.write('TCGGACACGACTGAGCGACTAAGCACAGCACAG\n')
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73 InputFile.write('>SUSINE2:classI:SINE:SINE2/tRNA\n')
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74 InputFile.write('GGGAGTTCTCTGATGGCCTAGCGGGTTGAGGCTCCTGCGTTCTCACCGCTGTGGCTCTGG\n')
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75 InputFile.write('TTGCTGCTGTGCGGCGTAGGTTCAATCCCTGGCCCAGGAATTCCCACATACTGCCTGTGT\n')
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76 InputFile.write('GGCAAAAAAGAAAAAAAAAAAAAATACAAAAAAAAAAAAAACAAGAGAGAACCTGAAATA\n')
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77 InputFile.write('AACGTTGCAACTCTCATTNAAAAAAAAAAA\n')
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78 InputFile.write('>SINE1A_SS:classI:SINE:SINE2/tRNA\n')
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79 InputFile.write('GGGAGTTCTCTTGTGGCACAGCAGGTTAAGGATCCAGCGTTGTCACTGCAGTGGCTTGGG\n')
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80 InputFile.write('TCGCTGCTGTGGCACGGGTTCAATCCCTGGCCCAGGAACTTCCACATGCCACGGGCATGG\n')
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81 InputFile.write('CCAAAAAAAAA\n')
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82 InputFile.write('>SINE2-1_Pca:classI:SINE:SINE2/tRNA\n')
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83 InputFile.write('GGGCAGTGGTGGTTCAGTGGTAGAATTCTTGCCTTCCATGCGGGAGACCCGGGTTCGATT\n')
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84 InputFile.write('CCCGGCCAGTGCACCTCATGCGCAGCCACCACCCGTCTGTCAGTGGAGGCTTGCGTGTTG\n')
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85 InputFile.write('CTGTGATGCTGAACAGGTTTCAGCGGAGCTTCCAGACTAAGACGGACTAGGAAGAAAGGC\n')
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86 InputFile.write('CTGGCGATCTACTTCTGAAAATCAGCCAATGAAAACCCTGTGGATCACAGTGGTCTGATC\n')
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87 InputFile.write('TGCAACTGATCATGGGGATGGCGCAGGACCGGGCAGCGTTTTGTTCTATTGTGCATGGGG\n')
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88 InputFile.write('TCGCCATGAGTCGGGCCGACTCGATGGCAGCTAACAACAA\n')
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89 InputFile.write('>SINE_FR2:classI:SINE:?\n')
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90 InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
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91 InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
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92 InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
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93 InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
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94 InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
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95 InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCGCGACCCTCAGTGGAGGAA\n')
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96 InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n')
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97 InputFile.write('>SINEC1B2_CF:classI:SINE:?\n')
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98 InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
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99 InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
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100 InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAATAA\n')
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101 InputFile.write('>ALPINE1:classI:SINE:SINE2/tRNA\n')
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102 InputFile.write('GGGGAGGGTATAGCTCAGTGGTAGAGCGCATGCTTAGCATGCACGAGGTCCTGGGTTCAA\n')
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103 InputFile.write('TCCCCAGTACCTCCATTAAAAATAAATAAATAAATAAACCTAATTACCTCCCCCACCAAA\n')
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104 InputFile.write('AAAAAAA\n')
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105 InputFile.close()
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106
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107 InputFile = open(self._refFastaFileName, 'w')
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108 InputFile.write('>SINE_FR2:classI:SINE:?\n')
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109 InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
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110 InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
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111 InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
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112 InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
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113 InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
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114 InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCG\n')
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115 InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n')
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116 InputFile.write('>SINEC1B2_CF:classI:SINE:?\n')
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117 InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
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118 InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
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119 InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAA\n')
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120 InputFile.close()
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121
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122 def _writeExpDeltaFile(self):
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123 with open(self._expDeltaFileName, 'w') as f:
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124 f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName)))
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125 f.write('PROMER\n')
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126 f.write('>SINE_FR2:classI:SINE:? SINE_FR2:classI:SINE:? 389 371\n')
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127 f.write('1 387 1 369 6 6 10\n')
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128 f.write('115\n')
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129 f.write('1\n')
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130 f.write('1\n')
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131 f.write('1\n')
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132 f.write('1\n')
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133 f.write('1\n')
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134 f.write('0\n')
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135 f.write('2 388 2 370 6 6 8\n')
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136 f.write('115\n')
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137 f.write('1\n')
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138 f.write('1\n')
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139 f.write('1\n')
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140 f.write('1\n')
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141 f.write('1\n')
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142 f.write('0\n')
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143 f.write('3 389 3 371 6 6 16\n')
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144 f.write('115\n')
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145 f.write('1\n')
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146 f.write('1\n')
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147 f.write('1\n')
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148 f.write('1\n')
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149 f.write('1\n')
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150 f.write('0\n')
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151 f.write('388 2 370 2 6 6 6\n')
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152 f.write('10\n')
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153 f.write('1\n')
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154 f.write('1\n')
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155 f.write('1\n')
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156 f.write('1\n')
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157 f.write('1\n')
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158 f.write('0\n')
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159 f.write('387 1 369 1 6 6 5\n')
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160 f.write('10\n')
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161 f.write('1\n')
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162 f.write('1\n')
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163 f.write('1\n')
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164 f.write('1\n')
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165 f.write('1\n')
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166 f.write('0\n')
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167 f.write('389 3 371 3 6 6 4\n')
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168 f.write('11\n')
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169 f.write('1\n')
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170 f.write('1\n')
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171 f.write('1\n')
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172 f.write('1\n')
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173 f.write('1\n')
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174 f.write('0\n')
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175 f.write('>SINEC1B2_CF:classI:SINE:? SINEC1B2_CF:classI:SINE:? 164 161\n')
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176 f.write('1 159 1 159 0 0 2\n')
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177 f.write('0\n')
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178 f.write('3 161 3 161 0 0 2\n')
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179 f.write('0\n')
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180 f.write('161 3 161 3 0 0 0\n')
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181 f.write('0\n')
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182 f.write('160 2 160 2 0 0 2\n')
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183 f.write('0\n')
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184 f.write('159 1 159 1 0 0 4\n')
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185 f.write('0\n')
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186 f.write('2 160 2 160 0 0 4\n')
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187 f.write('0\n')
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188
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189
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190
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191
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192 def _writeExpGenCoordsFile(self):
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193 with open(self._expCoordFileName, 'w') as f:
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194 f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName)))
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195 f.write('PROMER\n\n')
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196 f.write(' [S1] [E1] | [S2] [E2] | [LEN 1] [LEN 2] | [% IDY] [% SIM] [% STP] | [FRM] [TAGS]\n')
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197 f.write('==============================================================================================================\n')
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198 f.write(' 1 159 | 1 159 | 159 159 | 100.00 100.00 1.89 | 1 1 SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
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199 f.write(' 2 160 | 2 160 | 159 159 | 100.00 100.00 3.77 | 2 2 SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
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200 f.write(' 3 161 | 3 161 | 159 159 | 100.00 100.00 1.89 | 3 3 SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
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201 f.write(' 159 1 | 159 1 | 159 159 | 100.00 100.00 3.77 | -3 -3 SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
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202 f.write(' 160 2 | 160 2 | 159 159 | 100.00 100.00 1.89 | -2 -2 SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
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203 f.write(' 161 3 | 161 3 | 159 159 | 100.00 100.00 0.00 | -1 -1 SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
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204 f.write(' 1 387 | 1 369 | 387 369 | 95.35 95.35 3.88 | 1 1 SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
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205 f.write(' 2 388 | 2 370 | 387 369 | 95.35 95.35 3.10 | 2 2 SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
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206 f.write(' 3 389 | 3 371 | 387 369 | 95.35 95.35 6.20 | 3 3 SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
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207 f.write(' 387 1 | 369 1 | 387 369 | 95.35 95.35 1.94 | -3 -3 SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
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208 f.write(' 388 2 | 370 2 | 387 369 | 95.35 95.35 2.33 | -2 -2 SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
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209 f.write(' 389 3 | 371 3 | 387 369 | 95.35 95.35 1.55 | -1 -1 SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
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210
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211
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212 def _writeExpShowCoordsFile(self):
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213 with open(self._expCoordFileName, 'w') as f:
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214 f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName)))
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215 f.write('PROMER\n\n')
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216 f.write('[S1]\t[E1]\t[S2]\t[E2]\t[LEN 1]\t[LEN 2]\t[% IDY]\t[% SIM]\t[% STP]\t[LEN R]\t[LEN Q]\t[COV R]\t[COV Q]\t[FRM]\t[TAGS]\n')
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217 f.write('1\t159\t1\t159\t159\t159\t100.00\t100.00\t1.89\t164\t161\t96.95\t98.76\t1\t1\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
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218 f.write('2\t160\t2\t160\t159\t159\t100.00\t100.00\t3.77\t164\t161\t96.95\t98.76\t2\t2\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
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219 f.write('3\t161\t3\t161\t159\t159\t100.00\t100.00\t1.89\t164\t161\t96.95\t98.76\t3\t3\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
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220 f.write('159\t1\t159\t1\t159\t159\t100.00\t100.00\t3.77\t164\t161\t96.95\t98.76\t-3\t-3\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
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221 f.write('160\t2\t160\t2\t159\t159\t100.00\t100.00\t1.89\t164\t161\t96.95\t98.76\t-2\t-2\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
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222 f.write('161\t3\t161\t3\t159\t159\t100.00\t100.00\t0.00\t164\t161\t96.95\t98.76\t-1\t-1\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
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223 f.write('1\t387\t1\t369\t387\t369\t95.35\t95.35\t3.88\t389\t371\t99.49\t99.46\t1\t1\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
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224 f.write('2\t388\t2\t370\t387\t369\t95.35\t95.35\t3.10\t389\t371\t99.49\t99.46\t2\t2\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
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225 f.write('3\t389\t3\t371\t387\t369\t95.35\t95.35\t6.20\t389\t371\t99.49\t99.46\t3\t3\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
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226 f.write('387\t1\t369\t1\t387\t369\t95.35\t95.35\t1.94\t389\t371\t99.49\t99.46\t-3\t-3\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
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227 f.write('388\t2\t370\t2\t387\t369\t95.35\t95.35\t2.33\t389\t371\t99.49\t99.46\t-2\t-2\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
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228 f.write('389\t3\t371\t3\t387\t369\t95.35\t95.35\t1.55\t389\t371\t99.49\t99.46\t-1\t-1\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
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229
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230 if __name__ == "__main__":
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231 unittest.main() |
