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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.LaunchNucmer import LaunchNucmer
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5
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6 class Test_F_LaunchNucmer(unittest.TestCase):
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7
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8 def setUp(self):
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9 self._queryFastaFileName = "query.fa"
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10 self._refFastaFileName = "ref.fa"
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11 self._writeInputFastaFiles()
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12 self._expDeltaFileName = "expNucmer.delta"
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13 self._writeExpDeltaFile()
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14 self._obsDeltaFileName = "obsNucmer.delta"
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15 self._obsCoordFileName= "obsNucmer.coords"
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16 self._expCoordFileName= "expNucmer.coords"
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17
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18 def tearDown(self):
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19 try:
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20 os.remove(self._queryFastaFileName)
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21 except:pass
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22 try:
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23 os.remove(self._refFastaFileName)
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24 except:pass
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25 try:
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26 os.remove(self._expDeltaFileName)
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27 except:pass
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28 try:
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29 os.remove(self._obsDeltaFileName)
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30 except:pass
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31
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32 def test_run(self):
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33 ilauncher = LaunchNucmer(self._refFastaFileName, self._queryFastaFileName,"obsNucmer",verbosity=1)
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34 ilauncher.run()
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35 self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName))
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36
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37 def test_run_as_script(self):
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38 cmd = 'LaunchNucmer.py --query %s --ref %s --prefix %s' % (self._refFastaFileName, self._queryFastaFileName, "obsNucmer")
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39 os.system(cmd)
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40 self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName))
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41
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42 def test_run_as_script_gencoords_output(self):
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43 self._writeExpGenCoordsFile()
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44 cmd = 'LaunchNucmer.py --query %s --ref %s --prefix %s --gencoords' % (self._refFastaFileName, self._queryFastaFileName, "obsNucmer")
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45 os.system(cmd)
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46 self.assertTrue(FileUtils.are2FilesIdentical(self._expCoordFileName, self._obsCoordFileName))
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47 os.remove(self._obsCoordFileName)
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48 os.remove(self._expCoordFileName)
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49
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50 def test_run_as_script_with_mincluster(self):
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51 cmd = 'LaunchNucmer.py --query %s --ref %s --prefix %s --mincluster 30' % (self._refFastaFileName, self._queryFastaFileName, "obsNucmer")
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52 os.system(cmd)
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53 self.assertTrue(FileUtils.are2FilesIdentical(self._expDeltaFileName, self._obsDeltaFileName))
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54
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55 def test_run_as_script_showcoords_output(self):
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56 self._writeExpShowCoordsFile()
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57 cmd = 'LaunchNucmer.py --query %s --ref %s --prefix %s --showcoords' % (self._refFastaFileName, self._queryFastaFileName, "obsNucmer")
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58 os.system(cmd)
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59 self.assertTrue(FileUtils.are2FilesIdentical(self._expCoordFileName, self._obsCoordFileName))
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60 os.remove(self._obsCoordFileName)
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61 os.remove(self._expCoordFileName)
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62
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63 def _writeInputFastaFiles(self):
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64 InputFile = open(self._queryFastaFileName, 'w')
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65 InputFile.write('>Bovc-tA2:classI:SINE:SINE2/tRNA\n')
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66 InputFile.write('GGGCTTCCCTGGTAGCTCAGCTGGTAAAGAATCCGCCTGCAATGCAGGAGACCCCGGTTC\n')
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67 InputFile.write('GATTCCTGGGTCGGGAAGATCCCCTGGAGAAGGGATAGGCTACCCACTCCAGTATTCTTG\n')
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68 InputFile.write('GGCTTCCCTGGTGGCTCAGACGGTAAAGAATCCGCCTGCAATGCGGGAGACCTGGGTTCG\n')
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69 InputFile.write('ATCCCTGGGTTGGGAAGATCCCCTGGAGGAGGGCATGGCAACCCACTCCAGTATTCTTGC\n')
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70 InputFile.write('CTGGAGAATCCCCATGGACAGAGGAGCCTGGCGGGCTACAGTCCATGGGGTCGCAAAGAG\n')
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71 InputFile.write('TCGGACACGACTGAGCGACTAAGCACAGCACAG\n')
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72 InputFile.write('>SUSINE2:classI:SINE:SINE2/tRNA\n')
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73 InputFile.write('GGGAGTTCTCTGATGGCCTAGCGGGTTGAGGCTCCTGCGTTCTCACCGCTGTGGCTCTGG\n')
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74 InputFile.write('TTGCTGCTGTGCGGCGTAGGTTCAATCCCTGGCCCAGGAATTCCCACATACTGCCTGTGT\n')
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75 InputFile.write('GGCAAAAAAGAAAAAAAAAAAAAATACAAAAAAAAAAAAAACAAGAGAGAACCTGAAATA\n')
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76 InputFile.write('AACGTTGCAACTCTCATTNAAAAAAAAAAA\n')
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77 InputFile.write('>SINE1A_SS:classI:SINE:SINE2/tRNA\n')
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78 InputFile.write('GGGAGTTCTCTTGTGGCACAGCAGGTTAAGGATCCAGCGTTGTCACTGCAGTGGCTTGGG\n')
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79 InputFile.write('TCGCTGCTGTGGCACGGGTTCAATCCCTGGCCCAGGAACTTCCACATGCCACGGGCATGG\n')
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80 InputFile.write('CCAAAAAAAAA\n')
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81 InputFile.write('>SINE2-1_Pca:classI:SINE:SINE2/tRNA\n')
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82 InputFile.write('GGGCAGTGGTGGTTCAGTGGTAGAATTCTTGCCTTCCATGCGGGAGACCCGGGTTCGATT\n')
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83 InputFile.write('CCCGGCCAGTGCACCTCATGCGCAGCCACCACCCGTCTGTCAGTGGAGGCTTGCGTGTTG\n')
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84 InputFile.write('CTGTGATGCTGAACAGGTTTCAGCGGAGCTTCCAGACTAAGACGGACTAGGAAGAAAGGC\n')
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85 InputFile.write('CTGGCGATCTACTTCTGAAAATCAGCCAATGAAAACCCTGTGGATCACAGTGGTCTGATC\n')
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86 InputFile.write('TGCAACTGATCATGGGGATGGCGCAGGACCGGGCAGCGTTTTGTTCTATTGTGCATGGGG\n')
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87 InputFile.write('TCGCCATGAGTCGGGCCGACTCGATGGCAGCTAACAACAA\n')
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88 InputFile.write('>SINE_FR2:classI:SINE:?\n')
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89 InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
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90 InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
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91 InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
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92 InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
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93 InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
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94 InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCGCGACCCTCAGTGGAGGAA\n')
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95 InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n')
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96 InputFile.write('>SINEC1B2_CF:classI:SINE:?\n')
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97 InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
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98 InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
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99 InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAATAA\n')
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100 InputFile.write('>ALPINE1:classI:SINE:SINE2/tRNA\n')
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101 InputFile.write('GGGGAGGGTATAGCTCAGTGGTAGAGCGCATGCTTAGCATGCACGAGGTCCTGGGTTCAA\n')
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102 InputFile.write('TCCCCAGTACCTCCATTAAAAATAAATAAATAAATAAACCTAATTACCTCCCCCACCAAA\n')
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103 InputFile.write('AAAAAAA\n')
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104 InputFile.close()
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105
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106 InputFile = open(self._refFastaFileName, 'w')
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107 InputFile.write('>SINE_FR2:classI:SINE:?\n')
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108 InputFile.write('GGGCGGCACGGTGGTGTGGTGGTTAGCACTGTTGCCTCACAGCAAGAAGGCCCCGGGTTC\n')
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109 InputFile.write('GATCCCCGGTTGGGACTGAGGCTGGGGACTTTCTGTGTGGAGTTTGCATGTTCTCCCTGT\n')
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110 InputFile.write('GCCTGCGTGGGTTCTCTCCGGGTACTCCGGCTTCCTCCCACAGTCCAAAGACATGCATGA\n')
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111 InputFile.write('TTGGGGATTAGGCTAATTGGAAACTCTAAAATTGCCCGTAGGTGTGAGTGTGAGAGAGAA\n')
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112 InputFile.write('TGGTTGTTTGTCTATATGTGTTAGCCCTGCGATTGACTGGCGTCCAGTCCAGGGTGTACC\n')
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113 InputFile.write('CTGCCTCCGCCCATTGTGCTGGGATAGGCTCCAGTCCCCCCG\n')
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114 InputFile.write('CAAGCGGTAGAAAGTGAGTGAGTGAGTGA\n')
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115 InputFile.write('>SINEC1B2_CF:classI:SINE:?\n')
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116 InputFile.write('GGGCAGCCTGGGTGGCTCAGCGGTTTAGCGCCTGCCTTTGGCCCAGGGCGTGATCCTGGA\n')
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117 InputFile.write('GACCCGGGATCGAGTCCCACATCGGGCTCCCTGCATGGAGCCTGCTTCTCCCTCTGCCTG\n')
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118 InputFile.write('TGTCTCTGCCTCTCTCTCTCTCTGTGTCTCTCATGAATAAA\n')
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119 InputFile.close()
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120
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121 def _writeExpDeltaFile(self):
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122 f = open(self._expDeltaFileName, 'w')
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123 f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName)))
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124 f.write('NUCMER\n')
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125 f.write('>SINE_FR2:classI:SINE:? SINE_FR2:classI:SINE:? 389 371\n')
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126 f.write('1 343 1 343 0 0 0\n')
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127 f.write('0\n')
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128 f.write('>SINEC1B2_CF:classI:SINE:? SINEC1B2_CF:classI:SINE:? 164 161\n')
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129 f.write('1 161 1 161 0 0 0\n')
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130 f.write('0\n')
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131 f.close()
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132
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133 def _writeExpGenCoordsFile(self):
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134 f = open(self._expCoordFileName, 'w')
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135 f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName)))
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136 f.write('NUCMER\n\n')
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137 f.write(' [S1] [E1] | [S2] [E2] | [LEN 1] [LEN 2] | [% IDY] | [TAGS]\n')
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138 f.write('=====================================================================================\n')
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139 f.write(' 1 161 | 1 161 | 161 161 | 100.00 | SINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
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140 f.write(' 1 343 | 1 343 | 343 343 | 100.00 | SINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
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141 f.close()
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142
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143 def _writeExpShowCoordsFile(self):
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144 f = open(self._expCoordFileName, 'w')
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145 f.write("%s %s\n" %(os.path.abspath(self._queryFastaFileName), os.path.abspath(self._refFastaFileName)))
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146 f.write('NUCMER\n\n')
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147 f.write('[S1]\t[E1]\t[S2]\t[E2]\t[LEN 1]\t[LEN 2]\t[% IDY]\t[LEN R]\t[LEN Q]\t[COV R]\t[COV Q]\t[FRM]\t[TAGS]\n')
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148 f.write('1\t161\t1\t161\t161\t161\t100.00\t164\t161\t98.17\t100.00\t1\t1\tSINEC1B2_CF:classI:SINE:?\tSINEC1B2_CF:classI:SINE:?\n')
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149 f.write('1\t343\t1\t343\t343\t343\t100.00\t389\t371\t88.17\t92.45\t1\t1\tSINE_FR2:classI:SINE:?\tSINE_FR2:classI:SINE:?\n')
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150 f.close()
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151
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152 if __name__ == "__main__":
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153 unittest.main() |
