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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.pyRepetUnit.profilesDB.ProfilesDB4Repet import ProfilesDB4Repet
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4 from commons.core.utils.FileUtils import FileUtils
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5
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6
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7 class Test_ProfilesDB4Repet(unittest.TestCase):
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8
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9 def setUp(self):
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10 self._inputDBFile = "./datas/dummy.hmm"
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11 self._expectedDBFile = "./datas/expected.hmm"
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12 self._outputDBFile = "./datas/output.hmm"
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13 self._profilesDB4Repet = ProfilesDB4Repet()
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14
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15 def tearDown(self):
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16 os.remove(self._expectedDBFile)
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17 os.remove(self._outputDBFile)
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18 os.remove(self._inputDBFile)
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19
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20 def testFormateProfilesDB4Repet(self):
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21 self._createHmmFile()
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22 self._createExpectedHmmFile()
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23 self._profilesDB4Repet.setInputFile(self._inputDBFile)
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24 self._profilesDB4Repet.setOutputFile(self._outputDBFile)
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25 self._profilesDB4Repet.run()
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26 self.assertTrue(FileUtils.are2FilesIdentical(self._expectedDBFile, self._outputDBFile))
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27
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28 def test_formateProfilesDB4Repet_GypsyDB(self):
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29 self._createHmmFile_GypsyDB()
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30 self._createExpectedHmmFile_GypsyDB()
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31 self._profilesDB4Repet.setInputFile(self._inputDBFile)
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32 self._profilesDB4Repet.setOutputFile(self._outputDBFile)
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33 self._profilesDB4Repet.run()
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34 self.assertTrue(FileUtils.are2FilesIdentical(self._expectedDBFile, self._outputDBFile))
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35
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36 def _createExpectedHmmFile(self):
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37 f = open(self._expectedDBFile, "w")
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38 f.write("HMMER2.0 [2.3.2]\n")
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39 f.write("NAME PF07582.4_AP_endonuc_2_N_APE_20.9\n")
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40 f.write("ACC PF07582.4\n")
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41 f.write("DESC AP endonuclease family 2 C terminus\n")
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42 f.write("LENG 84\n")
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43 f.write("ALPH Amino\n")
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44 f.write("RF no\n")
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45 f.write("CS yes\n")
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46 f.write("MAP yes\n")
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47 f.write("COM hmmbuild -A myhmms fn3.sto\n")
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48 f.write("COM hmmcalibrate myhmms\n")
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49 f.write("NSEQ 108\n")
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50 f.write("DATE Thu Jan 8 17:50:26 2009\n")
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51 f.write("CKSUM 6130\n")
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52 f.write("GA 20.9000 20.9000;\n")
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53 f.write("TC 21.2000 21.2000;\n")
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54 f.write("NC 20.8000 20.8000;\n")
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55 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n")
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56 f.write("NULT -4 -8455\n")
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57 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n")
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58 f.write("EVD -45.973442 0.237545\n")
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59 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n")
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60 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
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61 f.write("COM hmmcalibrate myhmms\n")
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62 f.write(" -13 * -6756\n")
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63 f.write(" 1 -1698 -4236 -5399 -847 -4220 -2885 -1259 -930 -2438 406 -3428 -4768 3631 -1835 -4773 -1187 -1331 -120 -4666 -1510 1\n")
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64 f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n")
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65 f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n")
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66 f.write("//\n")
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67 f.write("HMMER2.0 [2.3.2]\n")
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68 f.write("NAME PF01606.8_Arteri_env_ENV_25.0\n")
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69 f.write("ACC PF01606.8\n")
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70 f.write("DESC DESC Arterivirus envelope protein\n")
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71 f.write("LENG 123\n")
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72 f.write("ALPH Amino\n")
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73 f.write("RF no\n")
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74 f.write("CS yes\n")
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75 f.write("MAP yes\n")
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76 f.write("COM hmmbuild -A myhmms fn3.sto\n")
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77 f.write("COM hmmcalibrate myhmms\n")
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78 f.write("NSEQ 108\n")
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79 f.write("DATE Thu Jan 8 17:50:26 2009\n")
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80 f.write("CKSUM 6130\n")
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81 f.write("GA 21.0000 25.0000;\n")
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82 f.write("TC 306.0000 406.0000;\n")
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83 f.write("NC 10.3000 11.3000;\n")
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84 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n")
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85 f.write("NULT -4 -8455\n")
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86 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n")
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87 f.write("EVD -45.973442 0.237545\n")
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88 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n")
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89 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
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90 f.write("COM hmmcalibrate myhmms\n")
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91 f.write(" -13 * -6756\n")
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92 f.write(" 1 -1698 -4236 -5399 -847 -4220 -2885 -1259 -930 -2438 406 -3428 -4768 3631 -1835 -4773 -1187 -1331 -120 -4666 -1510 1\n")
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93 f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n")
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94 f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n")
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95 f.write("//\n")
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96 f.write("HMMER2.0 [2.3.2]\n")
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97 f.write("NAME PF01606.8_Dummy_name_OTHER_25.0\n")
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98 f.write("ACC PF01606.8\n")
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99 f.write("DESC Dummy Description\n")
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100 f.write("LENG 123\n")
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101 f.write("ALPH Amino\n")
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102 f.write("RF no\n")
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103 f.write("CS yes\n")
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104 f.write("MAP yes\n")
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105 f.write("COM hmmbuild -A myhmms fn3.sto\n")
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106 f.write("COM hmmcalibrate myhmms\n")
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107 f.write("NSEQ 108\n")
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108 f.write("DATE Thu Jan 8 17:50:26 2009\n")
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109 f.write("CKSUM 6130\n")
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110 f.write("GA 21.0000 25.0000;\n")
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111 f.write("TC 306.0000 406.0000;\n")
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112 f.write("NC 10.3000 11.3000;\n")
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113 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n")
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114 f.write("NULT -4 -8455\n")
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115 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n")
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116 f.write("EVD -45.973442 0.237545\n")
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117 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n")
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118 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
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119 f.write("COM hmmcalibrate myhmms\n")
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120 f.write(" -13 * -6756\n")
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121 f.write(" 1 -1698 -4236 -5399 -847 -4220 -2885 -1259 -930 -2438 406 -3428 -4768 3631 -1835 -4773 -1187 -1331 -120 -4666 -1510 1\n")
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122 f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n")
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123 f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n")
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124 f.write("//\n")
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125 f.close()
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126
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127 def _createHmmFile(self):
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128 f = open(self._inputDBFile, "w")
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129 f.write("HMMER2.0 [2.3.2]\n")
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130 f.write("NAME AP_endonuc_2_N\n")
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131 f.write("ACC PF07582.4\n")
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132 f.write("DESC AP endonuclease family 2 C terminus\n")
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133 f.write("LENG 84\n")
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134 f.write("ALPH Amino\n")
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135 f.write("RF no\n")
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136 f.write("CS yes\n")
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137 f.write("MAP yes\n")
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138 f.write("COM hmmbuild -A myhmms fn3.sto\n")
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139 f.write("COM hmmcalibrate myhmms\n")
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140 f.write("NSEQ 108\n")
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141 f.write("DATE Thu Jan 8 17:50:26 2009\n")
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142 f.write("CKSUM 6130\n")
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143 f.write("GA 20.9000 20.9000;\n")
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144 f.write("TC 21.2000 21.2000;\n")
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145 f.write("NC 20.8000 20.8000;\n")
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146 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n")
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147 f.write("NULT -4 -8455\n")
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148 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n")
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149 f.write("EVD -45.973442 0.237545\n")
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150 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n")
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151 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
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152 f.write("COM hmmcalibrate myhmms\n")
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153 f.write(" -13 * -6756\n")
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154 f.write(" 1 -1698 -4236 -5399 -847 -4220 -2885 -1259 -930 -2438 406 -3428 -4768 3631 -1835 -4773 -1187 -1331 -120 -4666 -1510 1\n")
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155 f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n")
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156 f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n")
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157 f.write("//\n")
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158 f.write("HMMER2.0 [2.3.2]\n")
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159 f.write("NAME Arteri_env\n")
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160 f.write("ACC PF01606.8\n")
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161 f.write("DESC DESC Arterivirus envelope protein\n")
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162 f.write("LENG 123\n")
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163 f.write("ALPH Amino\n")
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164 f.write("RF no\n")
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165 f.write("CS yes\n")
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166 f.write("MAP yes\n")
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167 f.write("COM hmmbuild -A myhmms fn3.sto\n")
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168 f.write("COM hmmcalibrate myhmms\n")
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169 f.write("NSEQ 108\n")
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170 f.write("DATE Thu Jan 8 17:50:26 2009\n")
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171 f.write("CKSUM 6130\n")
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172 f.write("GA 21.0000 25.0000;\n")
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173 f.write("TC 306.0000 406.0000;\n")
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174 f.write("NC 10.3000 11.3000;\n")
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175 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n")
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176 f.write("NULT -4 -8455\n")
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177 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n")
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178 f.write("EVD -45.973442 0.237545\n")
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179 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n")
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180 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
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181 f.write("COM hmmcalibrate myhmms\n")
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182 f.write(" -13 * -6756\n")
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183 f.write(" 1 -1698 -4236 -5399 -847 -4220 -2885 -1259 -930 -2438 406 -3428 -4768 3631 -1835 -4773 -1187 -1331 -120 -4666 -1510 1\n")
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184 f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n")
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185 f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n")
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186 f.write("//\n")
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187 f.write("HMMER2.0 [2.3.2]\n")
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188 f.write("NAME Dummy_name\n")
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189 f.write("ACC PF01606.8\n")
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190 f.write("DESC Dummy Description\n")
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191 f.write("LENG 123\n")
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192 f.write("ALPH Amino\n")
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193 f.write("RF no\n")
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194 f.write("CS yes\n")
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195 f.write("MAP yes\n")
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196 f.write("COM hmmbuild -A myhmms fn3.sto\n")
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197 f.write("COM hmmcalibrate myhmms\n")
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198 f.write("NSEQ 108\n")
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199 f.write("DATE Thu Jan 8 17:50:26 2009\n")
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200 f.write("CKSUM 6130\n")
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201 f.write("GA 21.0000 25.0000;\n")
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202 f.write("TC 306.0000 406.0000;\n")
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203 f.write("NC 10.3000 11.3000;\n")
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204 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 \n")
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205 f.write("NULT -4 -8455\n")
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206 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 \n")
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207 f.write("EVD -45.973442 0.237545\n")
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208 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y \n")
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209 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
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210 f.write("COM hmmcalibrate myhmms\n")
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211 f.write(" -13 * -6756\n")
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212 f.write(" 1 -1698 -4236 -5399 -847 -4220 -2885 -1259 -930 -2438 406 -3428 -4768 3631 -1835 -4773 -1187 -1331 -120 -4666 -1510 1\n")
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213 f.write(" - -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251 \n")
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214 f.write(" C -144 -3400 -12951 -19 -6286 -701 -1378 -13 * \n")
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215 f.write("//\n")
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216 f.close()
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217
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218 def _createExpectedHmmFile_GypsyDB(self):
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219 f = open(self._expectedDBFile, "w")
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220 f.write("HMMER2.0 [2.3.2]\n")
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221 f.write("NAME _AP_17_6_AP_NA\n")
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222 f.write("LENG 97\n")
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223 f.write("ALPH Amino\n")
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224 f.write("RF no\n")
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225 f.write("CS no\n")
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226 f.write("MAP yes\n")
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227 f.write("COM hmmbuild output/AP_17_6.hmm input/AP_17_6.sto\n")
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228 f.write("COM hmmcalibrate output/AP_17_6.hmm\n")
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229 f.write("NSEQ 7\n")
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230 f.write("DATE Tue Nov 3 12:11:06 2009\n")
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231 f.write("CKSUM 7992\n")
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232 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n")
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233 f.write("NULT -4 -8455\n")
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234 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n")
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235 f.write("EVD -62.517647 0.206604\n")
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236 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n")
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237 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
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238 f.write(" -193 * -2999\n")
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239 f.write("1 -2855 -2358 -5336 -4935 -1676 -5061 -4339 3600 -4729 809 -490 -4773 -4645 -4163 -4574 -4431 -2811 -4 -3348 -3185 1\n")
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240 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
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241 f.write("- -9 -7942 -8984 -894 -1115 -701 -1378 -193 *\n")
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242 f.write("2 -3852 -3208 -4863 -4900 -13 -4670 -1533 -2120 -4409 1711 -1558 -3673 -4546 -3569 -4004 -4001 -3768 -2552 -797 4153 97\n")
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243 f.write("- * * * * * * * * * * * * * * * * * * * *\n")
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244 f.write("- * * * * * * * * 0 \n")
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245 f.write("//\n")
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246 f.write("HMMER2.0 [2.3.2]\n")
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247 f.write("NAME _ENV_athila_ENV_NA\n")
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248 f.write("LENG 647\n")
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249 f.write("ALPH Amino\n")
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250 f.write("RF no\n")
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251 f.write("CS no\n")
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252 f.write("MAP yes\n")
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253 f.write("COM hmmbuild -f ENV_athila.hmm ENV_athila.txt\n")
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254 f.write("COM hmmcalibrate ENV_athila.hmm\n")
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255 f.write("NSEQ 3\n")
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256 f.write("DATE Fri Sep 9 13:24:44 2005\n")
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257 f.write("CKSUM 3522\n")
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258 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n")
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259 f.write("NULT -4 -8455\n")
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260 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n")
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261 f.write("EVD -12.496953 0.641902\n")
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262 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n")
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263 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
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264 f.write(" -576 * -1603\n")
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265 f.write("1 -995 -1009 -2161 -1884 -298 -2046 -1336 348 -1429 591 4179 -1738 -2255 -1394 -1460 -1476 -1060 98 -1303 -906 1\n")
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266 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
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267 f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -1576 -10335\n")
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268 f.write("2 95 -518 -873 -904 -1785 -691 -984 -1664 -955 -1934 -1254 -652 -1327 -861 -1134 2815 -243 -1070 -2024 -1564 2\n")
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269 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
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270 f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -10911 -10334\n")
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271 f.write("//\n")
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272 f.write("HMMER2.0 [2.3.2]\n")
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273 f.write("NAME _ENVathila_OTHER_NA\n")
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274 f.write("LENG 647\n")
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275 f.write("ALPH Amino\n")
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276 f.write("RF no\n")
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277 f.write("CS no\n")
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278 f.write("MAP yes\n")
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279 f.write("COM hmmbuild -f ENV_athila.hmm ENV_athila.txt\n")
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280 f.write("COM hmmcalibrate ENV_athila.hmm\n")
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281 f.write("NSEQ 3\n")
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282 f.write("DATE Fri Sep 9 13:24:44 2005\n")
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283 f.write("CKSUM 3522\n")
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284 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n")
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285 f.write("NULT -4 -8455\n")
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286 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n")
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287 f.write("EVD -12.496953 0.641902\n")
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288 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n")
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289 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
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290 f.write(" -576 * -1603\n")
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291 f.write("1 -995 -1009 -2161 -1884 -298 -2046 -1336 348 -1429 591 4179 -1738 -2255 -1394 -1460 -1476 -1060 98 -1303 -906 1\n")
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292 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
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293 f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -1576 -10335\n")
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294 f.write("2 95 -518 -873 -904 -1785 -691 -984 -1664 -955 -1934 -1254 -652 -1327 -861 -1134 2815 -243 -1070 -2024 -1564 2\n")
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295 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
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296 f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -10911 -10334\n")
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297 f.write("//\n")
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298 f.write("HMMER2.0 [2.3.2]\n")
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299 f.write("NAME _MOV_cavemovirus_OTHER_NA\n")
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300 f.write("LENG 302\n")
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301 f.write("ALPH Amino\n")
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302 f.write("RF no\n")
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303 f.write("CS no\n")
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304 f.write("MAP yes\n")
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305 f.write("COM hmmbuild output/MOV_cavemovirus.hmm input/MOV_cavemovirus.sto\n")
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306 f.write("COM hmmcalibrate output/MOV_cavemovirus.hmm\n")
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307 f.write("NSEQ 2\n")
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308 f.write("DATE Tue Nov 3 11:25:12 2009\n")
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309 f.write("CKSUM 1918\n")
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310 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n")
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311 f.write("NULT -4 -8455\n")
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312 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n")
|
|
|
313 f.write("EVD -135.876633 0.154850\n")
|
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314 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n")
|
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315 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
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|
316 f.write(" -585 * -1585\n")
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|
317 f.write("1 -1028 -1686 -800 -442 -2171 -1521 -263 -1873 3103 -1859 -1251 -547 -1750 74 599 -1004 -972 -1620 -1812 -1528 5\n")
|
|
|
318 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
|
|
|
319 f.write("- -33 -6045 -7087 -894 -1115 -701 -1378 -585 *\n")
|
|
|
320 f.write("2 -1016 -805 -2637 -2367 -591 -2470 -1853 3039 -2040 329 346 -2180 -2589 -1943 -2070 -1879 -1051 1184 -1698 -1261 6\n")
|
|
|
321 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
|
|
|
322 f.write("- -33 -6045 -7087 -894 -1115 -701 -1378 * *\n")
|
|
|
323 f.write("3 -1016 -805 -2637 -2367 -591 -2470 -1853 3039 -2040 329 346 -2180 -2589 -1943 -2070 -1879 -1051 1184 -1698 -1261 7\n")
|
|
|
324 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
|
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|
325 f.write("- -33 -6045 -7087 -894 -1115 -701 -1378 * *\n")
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326 f.write("//\n")
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|
327 f.close()
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328
|
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329 def _createHmmFile_GypsyDB(self):
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330 f = open(self._inputDBFile, "w")
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331 f.write("HMMER2.0 [2.3.2]\n")
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332 f.write("NAME AP_17_6\n")
|
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|
333 f.write("LENG 97\n")
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|
334 f.write("ALPH Amino\n")
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|
335 f.write("RF no\n")
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|
336 f.write("CS no\n")
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|
337 f.write("MAP yes\n")
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|
338 f.write("COM hmmbuild output/AP_17_6.hmm input/AP_17_6.sto\n")
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339 f.write("COM hmmcalibrate output/AP_17_6.hmm\n")
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340 f.write("NSEQ 7\n")
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|
|
341 f.write("DATE Tue Nov 3 12:11:06 2009\n")
|
|
|
342 f.write("CKSUM 7992\n")
|
|
|
343 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n")
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344 f.write("NULT -4 -8455\n")
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345 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n")
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346 f.write("EVD -62.517647 0.206604\n")
|
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347 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n")
|
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|
348 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
|
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349 f.write(" -193 * -2999\n")
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350 f.write("1 -2855 -2358 -5336 -4935 -1676 -5061 -4339 3600 -4729 809 -490 -4773 -4645 -4163 -4574 -4431 -2811 -4 -3348 -3185 1\n")
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351 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
|
|
|
352 f.write("- -9 -7942 -8984 -894 -1115 -701 -1378 -193 *\n")
|
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|
353 f.write("2 -3852 -3208 -4863 -4900 -13 -4670 -1533 -2120 -4409 1711 -1558 -3673 -4546 -3569 -4004 -4001 -3768 -2552 -797 4153 97\n")
|
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354 f.write("- * * * * * * * * * * * * * * * * * * * *\n")
|
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|
355 f.write("- * * * * * * * * 0 \n")
|
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356 f.write("//\n")
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|
357 f.write("HMMER2.0 [2.3.2]\n")
|
|
|
358 f.write("NAME ENV_athila\n")
|
|
|
359 f.write("LENG 647\n")
|
|
|
360 f.write("ALPH Amino\n")
|
|
|
361 f.write("RF no\n")
|
|
|
362 f.write("CS no\n")
|
|
|
363 f.write("MAP yes\n")
|
|
|
364 f.write("COM hmmbuild -f ENV_athila.hmm ENV_athila.txt\n")
|
|
|
365 f.write("COM hmmcalibrate ENV_athila.hmm\n")
|
|
|
366 f.write("NSEQ 3\n")
|
|
|
367 f.write("DATE Fri Sep 9 13:24:44 2005\n")
|
|
|
368 f.write("CKSUM 3522\n")
|
|
|
369 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n")
|
|
|
370 f.write("NULT -4 -8455\n")
|
|
|
371 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n")
|
|
|
372 f.write("EVD -12.496953 0.641902\n")
|
|
|
373 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n")
|
|
|
374 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
|
|
|
375 f.write(" -576 * -1603\n")
|
|
|
376 f.write("1 -995 -1009 -2161 -1884 -298 -2046 -1336 348 -1429 591 4179 -1738 -2255 -1394 -1460 -1476 -1060 98 -1303 -906 1\n")
|
|
|
377 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
|
|
|
378 f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -1576 -10335\n")
|
|
|
379 f.write("2 95 -518 -873 -904 -1785 -691 -984 -1664 -955 -1934 -1254 -652 -1327 -861 -1134 2815 -243 -1070 -2024 -1564 2\n")
|
|
|
380 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
|
|
|
381 f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -10911 -10334\n")
|
|
|
382 f.write("//\n")
|
|
|
383 f.write("HMMER2.0 [2.3.2]\n")
|
|
|
384 f.write("NAME ENVathila\n")
|
|
|
385 f.write("LENG 647\n")
|
|
|
386 f.write("ALPH Amino\n")
|
|
|
387 f.write("RF no\n")
|
|
|
388 f.write("CS no\n")
|
|
|
389 f.write("MAP yes\n")
|
|
|
390 f.write("COM hmmbuild -f ENV_athila.hmm ENV_athila.txt\n")
|
|
|
391 f.write("COM hmmcalibrate ENV_athila.hmm\n")
|
|
|
392 f.write("NSEQ 3\n")
|
|
|
393 f.write("DATE Fri Sep 9 13:24:44 2005\n")
|
|
|
394 f.write("CKSUM 3522\n")
|
|
|
395 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n")
|
|
|
396 f.write("NULT -4 -8455\n")
|
|
|
397 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n")
|
|
|
398 f.write("EVD -12.496953 0.641902\n")
|
|
|
399 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n")
|
|
|
400 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
|
|
|
401 f.write(" -576 * -1603\n")
|
|
|
402 f.write("1 -995 -1009 -2161 -1884 -298 -2046 -1336 348 -1429 591 4179 -1738 -2255 -1394 -1460 -1476 -1060 98 -1303 -906 1\n")
|
|
|
403 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
|
|
|
404 f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -1576 -10335\n")
|
|
|
405 f.write("2 95 -518 -873 -904 -1785 -691 -984 -1664 -955 -1934 -1254 -652 -1327 -861 -1134 2815 -243 -1070 -2024 -1564 2\n")
|
|
|
406 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
|
|
|
407 f.write("- -33 -6075 -7117 -894 -1115 -701 -1378 -10911 -10334\n")
|
|
|
408 f.write("//\n")
|
|
|
409 f.write("HMMER2.0 [2.3.2]\n")
|
|
|
410 f.write("NAME MOV_cavemovirus\n")
|
|
|
411 f.write("LENG 302\n")
|
|
|
412 f.write("ALPH Amino\n")
|
|
|
413 f.write("RF no\n")
|
|
|
414 f.write("CS no\n")
|
|
|
415 f.write("MAP yes\n")
|
|
|
416 f.write("COM hmmbuild output/MOV_cavemovirus.hmm input/MOV_cavemovirus.sto\n")
|
|
|
417 f.write("COM hmmcalibrate output/MOV_cavemovirus.hmm\n")
|
|
|
418 f.write("NSEQ 2\n")
|
|
|
419 f.write("DATE Tue Nov 3 11:25:12 2009\n")
|
|
|
420 f.write("CKSUM 1918\n")
|
|
|
421 f.write("XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4\n")
|
|
|
422 f.write("NULT -4 -8455\n")
|
|
|
423 f.write("NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644\n")
|
|
|
424 f.write("EVD -135.876633 0.154850\n")
|
|
|
425 f.write("HMM A C D E F G H I K L M N P Q R S T V W Y\n")
|
|
|
426 f.write(" m->m m->i m->d i->m i->i d->m d->d b->m m->e\n")
|
|
|
427 f.write(" -585 * -1585\n")
|
|
|
428 f.write("1 -1028 -1686 -800 -442 -2171 -1521 -263 -1873 3103 -1859 -1251 -547 -1750 74 599 -1004 -972 -1620 -1812 -1528 5\n")
|
|
|
429 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
|
|
|
430 f.write("- -33 -6045 -7087 -894 -1115 -701 -1378 -585 *\n")
|
|
|
431 f.write("2 -1016 -805 -2637 -2367 -591 -2470 -1853 3039 -2040 329 346 -2180 -2589 -1943 -2070 -1879 -1051 1184 -1698 -1261 6\n")
|
|
|
432 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
|
|
|
433 f.write("- -33 -6045 -7087 -894 -1115 -701 -1378 * *\n")
|
|
|
434 f.write("3 -1016 -805 -2637 -2367 -591 -2470 -1853 3039 -2040 329 346 -2180 -2589 -1943 -2070 -1879 -1051 1184 -1698 -1261 7\n")
|
|
|
435 f.write("- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249\n")
|
|
|
436 f.write("- -33 -6045 -7087 -894 -1115 -701 -1378 * *\n")
|
|
|
437 f.write("//\n")
|
|
|
438 f.close()
|
|
|
439
|
|
|
440
|
|
|
441 if __name__ == "__main__":
|
|
|
442 unittest.main() |
