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1 # Copyright INRA (Institut National de la Recherche Agronomique)
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2 # http://www.inra.fr
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3 # http://urgi.versailles.inra.fr
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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29 # knowledge of the CeCILL license and that you accept its terms.
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30
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31
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32 class Utils_for_T_FastaUtils( object ):
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33
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34 def _createFastaFile_for_empty_file(fileName):
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35 f = open(fileName, 'w')
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36 f.write("")
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37 f.close()
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38
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39 _createFastaFile_for_empty_file = staticmethod ( _createFastaFile_for_empty_file )
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40
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41
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42 def _createFastaFile_one_sequence(fileName):
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43 f = open(fileName, 'w')
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44 f.write(">seq 1\n")
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45 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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46 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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47 f.write("ATATTCG\n")
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48 f.close()
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49
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50 _createFastaFile_one_sequence = staticmethod ( _createFastaFile_one_sequence )
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51
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52
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53 def createFastaFile_twoSequences( fileName ):
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54 f = open( fileName, "w" )
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55 f.write( ">seq 1\n" )
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56 f.write( "ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n" )
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57 f.write( "ATATTCG\n" )
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58 f.write( ">seq 2\n" )
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59 f.write( "ATATTCTTTCATCGATCGATCGGCGGCTATATGCTAGTGACGAAGCTAGTGTGAGTAGTA\n" )
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60 f.write( "ATATTCG\n" )
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61 f.close()
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62
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63 createFastaFile_twoSequences = staticmethod ( createFastaFile_twoSequences )
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64
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65
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66 def createFastaFile_seq_1( fileName ):
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67 f = open( fileName, "w" )
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68 f.write( ">seq 1\n" )
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69 f.write( "ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n" )
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70 f.write( "ATATTCG\n" )
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71 f.close()
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72
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73 createFastaFile_seq_1 = staticmethod( createFastaFile_seq_1 )
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74
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75
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76 def createFastaFile_seq_2( fileName ):
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77 f = open( fileName, "w" )
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78 f.write( ">seq 2\n" )
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79 f.write( "ATATTCTTTCATCGATCGATCGGCGGCTATATGCTAGTGACGAAGCTAGTGTGAGTAGTA\n" )
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80 f.write( "ATATTCG\n" )
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81 f.close()
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82
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83 createFastaFile_seq_2 = staticmethod( createFastaFile_seq_2 )
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84
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85
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86 def _createFastaFile_sequence_without_header(fileName):
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87 f = open(fileName, 'w')
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88 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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89 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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90 f.write("ATATTCG\n")
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91 f.close()
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92
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93 _createFastaFile_sequence_without_header = staticmethod ( _createFastaFile_sequence_without_header )
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94
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95
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96 def _createFastaFile_four_sequences(fileName):
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97 f = open(fileName, 'w')
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98 f.write(">seq 1\n")
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99 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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100 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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101 f.write("ATATTCG\n")
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102 f.write(">seq 2\n")
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103 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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104 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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105 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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106 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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107 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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108 f.write("ATATTCG\n")
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109 f.write(">seq 3\n")
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110 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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111 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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112 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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113 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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114 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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115 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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116 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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117 f.write("ATATTCG\n")
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118 f.write(">seq 4\n")
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119 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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120 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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121 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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122 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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123 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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124 f.write("ATATTCG\n")
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125 f.close()
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126
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127 _createFastaFile_four_sequences = staticmethod ( _createFastaFile_four_sequences )
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128
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129
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130 def _createFastaFile_three_sequences(fileName):
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131 f = open(fileName, 'w')
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132 f.write(">seq 1\n")
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133 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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134 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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135 f.write("ATATTCG\n")
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136 f.write(">seq 2\n")
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137 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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138 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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139 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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140 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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141 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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142 f.write("ATATTCG\n")
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143 f.write(">seq 4\n")
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144 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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145 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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146 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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147 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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148 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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149 f.write("ATATTCG\n")
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150 f.close()
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151
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152 _createFastaFile_three_sequences = staticmethod ( _createFastaFile_three_sequences )
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153
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154
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155 # ------------------ for dbSplit ---------------- #
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156
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157 def _createBatch1_two_sequences(inFileName):
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158 f = open(inFileName, 'w')
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159 f.write(">seq 1\n")
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160 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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161 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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162 f.write("ATATTCG\n")
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163 f.write(">seq 2\n")
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164 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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165 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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166 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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167 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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168 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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169 f.write("ATATTCG\n")
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170 f.close()
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171
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172 _createBatch1_two_sequences = staticmethod ( _createBatch1_two_sequences )
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173
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174
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175 def _createBatch2_two_sequences(inFileName):
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176 f = open(inFileName, 'w')
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177 f.write(">seq 3\n")
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178 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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179 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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180 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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181 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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182 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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183 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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184 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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185 f.write("ATATTCG\n")
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186 f.write(">seq 4\n")
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187 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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188 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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189 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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190 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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191 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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192 f.write("ATATTCG\n")
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193 f.close()
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194
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195 _createBatch2_two_sequences = staticmethod ( _createBatch2_two_sequences )
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196
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197
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198 def _createBatch1_three_sequences(inFileName):
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199 f = open(inFileName, 'w')
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200 f.write(">seq 1\n")
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201 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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202 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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203 f.write("ATATTCG\n")
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204 f.write(">seq 2\n")
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205 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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206 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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207 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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208 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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209 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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210 f.write("ATATTCG\n")
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211 f.write(">seq 3\n")
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212 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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213 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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214 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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215 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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216 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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217 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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218 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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219 f.write("ATATTCG\n")
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220 f.close()
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221
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222 _createBatch1_three_sequences = staticmethod ( _createBatch1_three_sequences )
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223
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224
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225 def _createBatch2_one_sequence(inFileName):
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226 f = open(inFileName, 'w')
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227 f.write(">seq 4\n")
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228 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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229 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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230 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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231 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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232 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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233 f.write("ATATTCG\n")
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234 f.close()
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235
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236 _createBatch2_one_sequence = staticmethod ( _createBatch2_one_sequence )
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237
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238
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239 def _createFastaFile_ten_sequences(fileName):
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240 f = open(fileName, 'w')
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241 f.write(">seq 1\n")
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242 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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243 f.write(">seq 2\n")
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244 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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245 f.write(">seq 3\n")
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246 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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247 f.write(">seq 4\n")
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248 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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249 f.write(">seq 5\n")
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250 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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251 f.write(">seq 6\n")
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252 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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253 f.write(">seq 7\n")
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254 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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255 f.write(">seq 8\n")
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256 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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257 f.write(">seq 9\n")
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258 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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259 f.write(">seq 10\n")
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260 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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261 f.close()
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262
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263 _createFastaFile_ten_sequences = staticmethod ( _createFastaFile_ten_sequences )
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264
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265
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266 def _createBatch_one_small_sequence(fileName, seqName):
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267 f = open(fileName, 'w')
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268 f.write(">" +seqName + "\n")
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269 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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270 f.close()
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271
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272 _createBatch_one_small_sequence = staticmethod ( _createBatch_one_small_sequence )
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273
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274
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275 # ------------------ for dbChunks ------------------- #
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276
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277 def _createFastaFile_big_sequence(fileName):
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278 f = open(fileName, 'w')
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279 f.write(">sequence\n")
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280 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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281 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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282 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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283 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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284 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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285 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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286 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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287 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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288 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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289 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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290 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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291 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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292 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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293 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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294 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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295 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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296 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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297 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
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298 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
299 f.write("ATATTCG\n")
|
|
300 f.close()
|
|
301
|
|
302 _createFastaFile_big_sequence = staticmethod ( _createFastaFile_big_sequence )
|
|
303
|
|
304
|
|
305 def _createFastaFile_of_Chunks(fileName):
|
|
306 f = open(fileName, 'w')
|
|
307 f.write('>chunk01\n')
|
|
308 f.write('ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n')
|
|
309 f.write('>chunk02\n')
|
|
310 f.write('GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n')
|
|
311 f.write('>chunk03\n')
|
|
312 f.write('GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n')
|
|
313 f.write('>chunk04\n')
|
|
314 f.write('ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n')
|
|
315 f.write('>chunk05\n')
|
|
316 f.write('CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGAT\n')
|
|
317 f.write('>chunk06\n')
|
|
318 f.write('ATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGC\n')
|
|
319 f.write('>chunk07\n')
|
|
320 f.write('ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n')
|
|
321 f.write('>chunk08\n')
|
|
322 f.write('GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n')
|
|
323 f.write('>chunk09\n')
|
|
324 f.write('GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n')
|
|
325 f.write('>chunk10\n')
|
|
326 f.write('ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n')
|
|
327 f.write('>chunk11\n')
|
|
328 f.write('CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGAT\n')
|
|
329 f.write('>chunk12\n')
|
|
330 f.write('ATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGC\n')
|
|
331 f.write('>chunk13\n')
|
|
332 f.write('ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n')
|
|
333 f.write('>chunk14\n')
|
|
334 f.write('GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n')
|
|
335 f.write('>chunk15\n')
|
|
336 f.write('GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n')
|
|
337 f.write('>chunk16\n')
|
|
338 f.write('ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n')
|
|
339 f.write('>chunk17\n')
|
|
340 f.write('CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGAT\n')
|
|
341 f.write('>chunk18\n')
|
|
342 f.write('ATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGC\n')
|
|
343 f.write('>chunk19\n')
|
|
344 f.write('ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n')
|
|
345 f.write('>chunk20\n')
|
|
346 f.write('GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n')
|
|
347 f.write('>chunk21\n')
|
|
348 f.write('GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n')
|
|
349 f.write('>chunk22\n')
|
|
350 f.write('ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n')
|
|
351 f.write('>chunk23\n')
|
|
352 f.write('CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCG\n')
|
|
353 f.close()
|
|
354
|
|
355 _createFastaFile_of_Chunks = staticmethod ( _createFastaFile_of_Chunks )
|
|
356
|
|
357
|
|
358 def _createMapFile_of_Chunks(fileName):
|
|
359 f = open(fileName, 'w')
|
|
360 f.write("chunk01\tsequence\t1\t60\n")
|
|
361 f.write("chunk02\tsequence\t51\t110\n")
|
|
362 f.write("chunk03\tsequence\t101\t160\n")
|
|
363 f.write("chunk04\tsequence\t151\t210\n")
|
|
364 f.write("chunk05\tsequence\t201\t260\n")
|
|
365 f.write("chunk06\tsequence\t251\t310\n")
|
|
366 f.write("chunk07\tsequence\t301\t360\n")
|
|
367 f.write("chunk08\tsequence\t351\t410\n")
|
|
368 f.write("chunk09\tsequence\t401\t460\n")
|
|
369 f.write("chunk10\tsequence\t451\t510\n")
|
|
370 f.write("chunk11\tsequence\t501\t560\n")
|
|
371 f.write("chunk12\tsequence\t551\t610\n")
|
|
372 f.write("chunk13\tsequence\t601\t660\n")
|
|
373 f.write("chunk14\tsequence\t651\t710\n")
|
|
374 f.write("chunk15\tsequence\t701\t760\n")
|
|
375 f.write("chunk16\tsequence\t751\t810\n")
|
|
376 f.write("chunk17\tsequence\t801\t860\n")
|
|
377 f.write("chunk18\tsequence\t851\t910\n")
|
|
378 f.write("chunk19\tsequence\t901\t960\n")
|
|
379 f.write("chunk20\tsequence\t951\t1010\n")
|
|
380 f.write("chunk21\tsequence\t1001\t1060\n")
|
|
381 f.write("chunk22\tsequence\t1051\t1110\n")
|
|
382 f.write("chunk23\tsequence\t1101\t1147\n")
|
|
383 f.close()
|
|
384
|
|
385 _createMapFile_of_Chunks = staticmethod ( _createMapFile_of_Chunks )
|
|
386
|
|
387
|
|
388 def _createFastaFile_of_cut(fileName):
|
|
389 f = open(fileName, 'w')
|
|
390 f.write(">1 sequence {Cut} 1..60\n")
|
|
391 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
392 f.write(">2 sequence {Cut} 51..110\n")
|
|
393 f.write("GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n")
|
|
394 f.write(">3 sequence {Cut} 101..160\n")
|
|
395 f.write("GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n")
|
|
396 f.write(">4 sequence {Cut} 151..210\n")
|
|
397 f.write("ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n")
|
|
398 f.write(">5 sequence {Cut} 201..260\n")
|
|
399 f.write("CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGAT\n")
|
|
400 f.write(">6 sequence {Cut} 251..310\n")
|
|
401 f.write("ATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGC\n")
|
|
402 f.write(">7 sequence {Cut} 301..360\n")
|
|
403 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
404 f.write(">8 sequence {Cut} 351..410\n")
|
|
405 f.write("GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n")
|
|
406 f.write(">9 sequence {Cut} 401..460\n")
|
|
407 f.write("GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n")
|
|
408 f.write(">10 sequence {Cut} 451..510\n")
|
|
409 f.write("ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n")
|
|
410 f.write(">11 sequence {Cut} 501..560\n")
|
|
411 f.write("CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGAT\n")
|
|
412 f.write(">12 sequence {Cut} 551..610\n")
|
|
413 f.write("ATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGC\n")
|
|
414 f.write(">13 sequence {Cut} 601..660\n")
|
|
415 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
416 f.write(">14 sequence {Cut} 651..710\n")
|
|
417 f.write("GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n")
|
|
418 f.write(">15 sequence {Cut} 701..760\n")
|
|
419 f.write("GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n")
|
|
420 f.write(">16 sequence {Cut} 751..810\n")
|
|
421 f.write("ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n")
|
|
422 f.write(">17 sequence {Cut} 801..860\n")
|
|
423 f.write("CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGAT\n")
|
|
424 f.write(">18 sequence {Cut} 851..910\n")
|
|
425 f.write("ATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGC\n")
|
|
426 f.write(">19 sequence {Cut} 901..960\n")
|
|
427 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
428 f.write(">20 sequence {Cut} 951..1010\n")
|
|
429 f.write("GTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGT\n")
|
|
430 f.write(">21 sequence {Cut} 1001..1060\n")
|
|
431 f.write("GCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCA\n")
|
|
432 f.write(">22 sequence {Cut} 1051..1110\n")
|
|
433 f.write("ATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCGCGCATCGATCGATCGGCGGCTAT\n")
|
|
434 f.write(">23 sequence {Cut} 1101..1147\n")
|
|
435 f.write("CGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTAATATTCG\n")
|
|
436 f.close()
|
|
437
|
|
438 _createFastaFile_of_cut = staticmethod ( _createFastaFile_of_cut )
|
|
439
|
|
440
|
|
441 def _createFastaFile_of_Nstretch(fileName):
|
|
442 f = open(fileName, 'w')
|
|
443 f.write("")
|
|
444 f.close()
|
|
445
|
|
446 _createFastaFile_of_Nstretch = staticmethod ( _createFastaFile_of_Nstretch )
|
|
447
|
|
448
|
|
449 # ------------------ for splitSeqPerCluster ------------------- #
|
|
450
|
|
451 def _createFastaFile_of_four_sequences_with_specific_header(inFileName):
|
|
452 f = open(inFileName, 'w')
|
|
453 f.write(">ReconCluster1Mb155 chunk183 {Fragment} 1..5506\n")
|
|
454 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
455 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
456 f.write("ATATTCG\n")
|
|
457 f.write(">MbQ3Gr2Cl0 chunk440 {Fragment} 2678..3645\n")
|
|
458 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
459 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
460 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
461 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
462 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
463 f.write("ATATTCG\n")
|
|
464 f.write(">MbS2Gr2Cl0 chunk622 {Fragment} 104..1078\n")
|
|
465 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
466 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
467 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
468 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
469 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
470 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
471 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
472 f.write("ATATTCG\n")
|
|
473 f.write(">PilerCluster3.574Mb796 chunk0117 {Fragment} 51582..50819\n")
|
|
474 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
475 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
476 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
477 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
478 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
479 f.write("ATATTCG\n")
|
|
480 f.close()
|
|
481
|
|
482 _createFastaFile_of_four_sequences_with_specific_header = staticmethod ( _createFastaFile_of_four_sequences_with_specific_header )
|
|
483
|
|
484
|
|
485 def _createFastaFile_of_four_sequences_with_specific_header_shuffle(inFileName):
|
|
486 f = open(inFileName, 'w')
|
|
487 f.write(">MbQ3Gr2Cl0 chunk440 {Fragment} 2678..3645\n")
|
|
488 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
489 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
490 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
491 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
492 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
493 f.write("ATATTCG\n")
|
|
494 f.write(">ReconCluster1Mb155 chunk183 {Fragment} 1..5506\n")
|
|
495 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
496 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
497 f.write("ATATTCG\n")
|
|
498 f.write(">MbS2Gr2Cl0 chunk622 {Fragment} 104..1078\n")
|
|
499 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
500 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
501 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
502 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
503 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
504 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
505 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
506 f.write("ATATTCG\n")
|
|
507 f.write(">PilerCluster3.574Mb796 chunk0117 {Fragment} 51582..50819\n")
|
|
508 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
509 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
510 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
511 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
512 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
513 f.write("ATATTCG\n")
|
|
514 f.close()
|
|
515
|
|
516 _createFastaFile_of_four_sequences_with_specific_header_shuffle = staticmethod ( _createFastaFile_of_four_sequences_with_specific_header_shuffle )
|
|
517
|
|
518
|
|
519 def _createFastaFile_of_four_sequences_with_specific_header_in_same_cluster(inFileName):
|
|
520 f = open(inFileName, 'w')
|
|
521 f.write(">ReconCluster1Mb155 chunk1 {Fragment} 1..5506\n")
|
|
522 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
523 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
524 f.write("ATATTCG\n")
|
|
525 f.write(">ReconCluster1Mb155 chunk2 {Fragment} 1..5506\n")
|
|
526 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
527 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
528 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
529 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
530 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
531 f.write("ATATTCG\n")
|
|
532 f.write(">ReconCluster1Mb155 chunk3 {Fragment} 1..5506\n")
|
|
533 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
534 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
535 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
536 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
537 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
538 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
539 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
540 f.write("ATATTCG\n")
|
|
541 f.write(">ReconCluster1Mb155 chunk4 {Fragment} 1..5506\n")
|
|
542 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
543 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
544 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
545 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
546 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
547 f.write("ATATTCG\n")
|
|
548 f.close()
|
|
549
|
|
550 _createFastaFile_of_four_sequences_with_specific_header_in_same_cluster = staticmethod ( _createFastaFile_of_four_sequences_with_specific_header_in_same_cluster )
|
|
551
|
|
552
|
|
553 def _createFastaFile_of_first_cluster_result(inFileName):
|
|
554 f = open(inFileName, 'w')
|
|
555 f.write(">ReconCluster1Mb155 chunk183 {Fragment} 1..5506\n")
|
|
556 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
557 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
558 f.write("ATATTCG\n")
|
|
559 f.close()
|
|
560
|
|
561 _createFastaFile_of_first_cluster_result = staticmethod ( _createFastaFile_of_first_cluster_result )
|
|
562
|
|
563
|
|
564 def _createFastaFile_of_second_cluster_result(inFileName):
|
|
565 f = open(inFileName, 'w')
|
|
566 f.write(">MbQ3Gr2Cl0 chunk440 {Fragment} 2678..3645\n")
|
|
567 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
568 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
569 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
570 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
571 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
572 f.write("ATATTCG\n")
|
|
573 f.write(">MbS2Gr2Cl0 chunk622 {Fragment} 104..1078\n")
|
|
574 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
575 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
576 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
577 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
578 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
579 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
580 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
581 f.write("ATATTCG\n")
|
|
582 f.close()
|
|
583
|
|
584 _createFastaFile_of_second_cluster_result = staticmethod ( _createFastaFile_of_second_cluster_result )
|
|
585
|
|
586
|
|
587 def _createFastaFile_of_third_cluster_result(inFileName):
|
|
588 f = open(inFileName, 'w')
|
|
589 f.write(">PilerCluster3.574Mb796 chunk0117 {Fragment} 51582..50819\n")
|
|
590 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
591 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
592 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
593 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
594 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
595 f.write("ATATTCG\n")
|
|
596 f.close()
|
|
597
|
|
598 _createFastaFile_of_third_cluster_result = staticmethod ( _createFastaFile_of_third_cluster_result )
|
|
599
|
|
600
|
|
601 def _createFastaFile_of_first_cluster_result_with_simplify_header(inFileName):
|
|
602 f = open(inFileName, 'w')
|
|
603 f.write(">Piler_Cluster1_Seq155\n")
|
|
604 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
605 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
606 f.write("ATATTCG\n")
|
|
607 f.close()
|
|
608
|
|
609 _createFastaFile_of_first_cluster_result_with_simplify_header = staticmethod ( _createFastaFile_of_first_cluster_result_with_simplify_header )
|
|
610
|
|
611
|
|
612 def _createFastaFile_of_second_cluster_result_with_simplify_header(inFileName):
|
|
613 f = open(inFileName, 'w')
|
|
614 f.write(">Piler_Cluster2_Seq3\n")
|
|
615 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
616 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
617 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
618 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
619 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
620 f.write("ATATTCG\n")
|
|
621 f.write(">Piler_Cluster2_Seq2\n")
|
|
622 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
623 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
624 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
625 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
626 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
627 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
628 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
629 f.write("ATATTCG\n")
|
|
630 f.close()
|
|
631
|
|
632 _createFastaFile_of_second_cluster_result_with_simplify_header = staticmethod ( _createFastaFile_of_second_cluster_result_with_simplify_header )
|
|
633
|
|
634
|
|
635 def _createFastaFile_of_third_cluster_result_with_simplify_header(inFileName):
|
|
636 f = open(inFileName, 'w')
|
|
637 f.write(">Piler_Cluster3.574_Seq796\n")
|
|
638 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
639 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
640 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
641 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
642 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
643 f.write("ATATTCG\n")
|
|
644 f.close()
|
|
645
|
|
646 _createFastaFile_of_third_cluster_result_with_simplify_header = staticmethod ( _createFastaFile_of_third_cluster_result_with_simplify_header )
|
|
647
|
|
648 # ---------------------------------- #
|
|
649
|
|
650 def _createPatternFile(fileName):
|
|
651 f = open(fileName, 'w')
|
|
652 f.write('seq 3\n')
|
|
653 f.write('f\n')
|
|
654 f.write('s.q 1\n')
|
|
655 f.write('q 8\n')
|
|
656
|
|
657 _createPatternFile = staticmethod ( _createPatternFile )
|
|
658
|
|
659
|
|
660 def _createResult_of_dbLengthFilter_sup(inFileName):
|
|
661 f = open(inFileName, 'w')
|
|
662 f.write(">seq 2\n")
|
|
663 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
664 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
665 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
666 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
667 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
668 f.write("ATATTCG\n")
|
|
669 f.write(">seq 3\n")
|
|
670 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
671 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
672 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
673 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
674 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
675 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
676 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
677 f.write("ATATTCG\n")
|
|
678 f.write(">seq 4\n")
|
|
679 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
680 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
681 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
682 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
683 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
684 f.write("ATATTCG\n")
|
|
685 f.close()
|
|
686
|
|
687 _createResult_of_dbLengthFilter_sup = staticmethod ( _createResult_of_dbLengthFilter_sup )
|
|
688
|
|
689
|
|
690 def _createFastaFile_four_sequences_for_header_filtering(fileName):
|
|
691 f = open(fileName, 'w')
|
|
692 f.write(">seq1_HostGene\n")
|
|
693 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
694 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
695 f.write("ATATTCG\n")
|
|
696 f.write(">seq2_SSR\n")
|
|
697 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
698 f.write("ATATTCG\n")
|
|
699 f.write(">seq3_Map2_NoCat\n")
|
|
700 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
701 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
702 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
703 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
704 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
705 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
706 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
707 f.write("ATATTCG\n")
|
|
708 f.write(">seq4_confused\n")
|
|
709 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
710 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
711 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
712 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
713 f.write("ATATTCGCGCATCGATCGATCGGCGGCTATATGCTAGTCAGCTAGCTAGTGTGAGTAGTA\n")
|
|
714 f.write("ATATTCG\n")
|
|
715 f.close()
|
|
716
|
|
717 _createFastaFile_four_sequences_for_header_filtering = staticmethod ( _createFastaFile_four_sequences_for_header_filtering )
|
|
718
|
|
719
|
|
720 def _createFastaFile_three_sequences_with_ORFs(fileName):
|
|
721 f = open(fileName, 'w')
|
|
722 f.write(">Mivi_sl_Blaster_Grouper_1_Map_3\n")
|
|
723 f.write("TACAGTCAAACCTGAGAAAATTTATATCGCCCAATCTTATACCTGGCAAAATTTATGGAC\n")
|
|
724 f.write("TTTTCAATCTCCCGACTTTTTTGGCTGACAGAACCTGTCCAATCTTATACCTTATAATTT\n")
|
|
725 f.write("ATGGGTTTACAGGTCAAATTATAAGATAAGAGAGAGCCGGAAATGAGCGATTGATCAGGA\n")
|
|
726 f.write("ATTGGCCTCTCCTTCGGCGTTCTTGTTGACGAGCCGCCTGCTGGAACAGTCCGAAATGCC\n")
|
|
727 f.write("CCGAAACAGCCGAGAAGCGAGCACAGTAGAGCAAAGGCGGCGGTTGACACGTTGACAGGC\n")
|
|
728 f.write("TATTAGTCGCGACGTGCTTCTCTCTCCTCTTCCGCCGACAACGACGCCGAAATGAACATC\n")
|
|
729 f.write("TTCACAATTCGAGAAGCCCTCATCAGAAATTCCTCTTCATATCATCATGGTCTCATTCCC\n")
|
|
730 f.write("TTCCCGGAATTCAACTGCTGGCGCCACGCTCAAATCTTGTCTGATCGCAAGAACAAAGGA\n")
|
|
731 f.write("TCGACCGACCATACACCTCTTCCCAACGGTCGCGGGCCTCTCGATGGCGATCGCGGCATC\n")
|
|
732 f.write("ATCAACGCGATGAACGCTCTGAAGACGGCGAACGATGAGCTGGTCGAAAAGGGGATAGTT\n")
|
|
733 f.write("ACGAGCAACGAGAAGATGAGTATCCACTTTCTCGTCGATGTGGAGGAGGAGAACCTTGCT\n")
|
|
734 f.write("GGTGGGGCTGAAATGACCGATCAGGAGATTGTGGACCTGGTCATTGCCGAAGAGTTGGAG\n")
|
|
735 f.write("GAGAATTGCGAGGGAGAAGGAGGAGAGGAGGAAGCGGAGATAGAGCTCCGACCGGCGGAG\n")
|
|
736 f.write("CGAACGACGCTGAAGGAGGCAATCTCAGCGCTTGATGTTTTCCTTAGGTTTGCTATGAAT\n")
|
|
737 f.write("GGGTACTCAGGTCCAACGGATTTGATTTCTTTTGAGGACGAGGCTAGGAGGATTCGCAGG\n")
|
|
738 f.write("ACTCTTGTTGCCGAGCAGGATGCCGCGAGGATTCAGACGACAATGACTTCGTATTTCCAG\n")
|
|
739 f.write("CGTCAGTAG\n")
|
|
740 f.write(">Mivi_sl_Blaster_Grouper_2_Map_3\n")
|
|
741 f.write("TACAGTCAGACCTGAGAAAATTTATATCGCCCAATCTTATACCTGTCAAAATTTATGGAC\n")
|
|
742 f.write("TTTTCAATCTCCCGACTTTTTTGGCTGACAGAACCTGTCCAATCTTATACCTTATAATTT\n")
|
|
743 f.write("ATGGGTTTACAGGTCAAATTATAAGATAAGAGAGAGCCGGAAATGAGCGATTGATCAGGA\n")
|
|
744 f.write("ATTGGCCTCTCCTTCGGCGTTCTTGTTGACGAGCCGCCTGCTGGAAGAGTCCGAAATGCC\n")
|
|
745 f.write("CCGAAACAGCCAAGAAGCGAGCACAGTAGAGCAAAGGCGGCGGTTGACACGTTGACAGGC\n")
|
|
746 f.write("TAGTCGCGACGTGCTTCTCTCTCCTCTTCCGCCGACAACGACGCCGAAATGAACATCTTC\n")
|
|
747 f.write("ACAATCCGAGAAGCCCTCATCAGAAATTCCTCTTCATATCATCATGGTCTCATTCCCTTC\n")
|
|
748 f.write("CCGGAATTCAACTGCTGGCGCCACGCTCAAATCTTGTCTGATCGCAAGAACAAAGGATCG\n")
|
|
749 f.write("ACCGACCATACACCTCTTCCCAACGGTCGCGGGCCTCTCGATGGCGATCGCGGCATCATC\n")
|
|
750 f.write("AACGCGATGAACGCTCTGAAGACGGCGAACGATGAGCTGGTCGAAAAGGGGATAGTTACG\n")
|
|
751 f.write("AGCAACGAGAAGATGAGTATCCACTTTCTCGTCGATGTGGAGGAGGAGAACCTTGCTGGT\n")
|
|
752 f.write("GGGGCTGAAATGACCGATCAGGAGATTGTGGACCTGGGGTCATTGCCGAAGAGTTGGAGG\n")
|
|
753 f.write("AGAATTGCGAGGGAGAACTTGAAGGAGGAGAGGAGGAAGCGGAGATAGAGCTCCGACCGG\n")
|
|
754 f.write("CGGAGCGAACGACGCTGAAGGAGGCAATCTCAGCGCTTGGTGTTTTCCTTAGGTTTGCTA\n")
|
|
755 f.write("TGAATGGGTACTCAGGTCCAACGAATTTGATTTCTTTTGAGGACGAGGCTAGGAGGATTC\n")
|
|
756 f.write("GCAGGACTCTTGTTGCCGAGCAGGATGCCGCGAGGATTCAGACGACAATGACTTCGTATT\n")
|
|
757 f.write("TCCAGCGTCAGTAGGTCAAGATATTTTTTCTTGGAGCTTTCATAACTTGTTAGATGTCAT\n")
|
|
758 f.write("CATGCCTCAGTAGAGGCCGTACATTGGCTGCAATTCAGTAATTCGGGCCTTCTGAATTTC\n")
|
|
759 f.write("CTCCCCCTCAAAAGTCAATGTATCGACTCAAACGATGCACGAAAATTCTTGATTTGATGT\n")
|
|
760 f.write("AGGAAGCTCAAAAACGGAGTTTCAGGTCATAATGTAGTGATCTGAAGCCGAACTCTCCAA\n")
|
|
761 f.write("GCTTATACCTGTCTTAATTTATGGGAAAATCCGTCCACCGAAAATATAAATTTTCTCAGG\n")
|
|
762 f.write("TCTGACTGTA\n")
|
|
763 f.write(">Mivi_sl_Blaster_Grouper_3_Map_3\n")
|
|
764 f.write("CAACACAAAGATAAGGCACCTTCATCCAGTGGCTCGCACGAACTTTCAATTGCAAGTCGT\n")
|
|
765 f.write("TGGCGTGCGCTGGGCGGGATCAAAACCGGGTCTGGGAGTCGCGTAACCCACTGGAGCAAG\n")
|
|
766 f.write("TAGGTGGTAGCCTGGACTGACAACGTGGACGTCAGCGACTTGAAATAGGTATTCGCGGCT\n")
|
|
767 f.write("TTCGTGGTCGGTGTACCCCTGTGTGTCCGGCATCGGCTGTCCAGAGTCGCCAGCCTGCCC\n")
|
|
768 f.write("GGTGCGAATGTGGGGGGCAGTCTCGGTCGCGCACGTGCGATGTCCCTCTCCCCACACGGG\n")
|
|
769 f.write("CCTGTCGGCTGCGGCTAACGGCCCCTGCAATGAGTCCTATCGACAGAAGTCCACCCAAGC\n")
|
|
770 f.write("TCAGCCTTCCCTCCACCAACACCAACATCGCAAGCCTCTCAAAAATTCACATCTCTTACA\n")
|
|
771 f.write("TCCCCTCGAAACACCCACTAAATGGATCCCTACCCTATCACTTGGCGGCAGTACTAGTAG\n")
|
|
772 f.write("CACGGGCCCAACTTCGACGGATCTCGAACGGACTTCCCACGGGTTCTCGGTGTGCAAGCG\n")
|
|
773 f.write("TCTCAGGTCAAGGTTTTGGTTGGTGGGCTTTCTGGGTGTGCAAAGGGGATTATTATAGAG\n")
|
|
774 f.write("GGAAGAAGAAGAAGGATGGGACCAGGGAGGCAGAGACGTGCGGGGTCAGGTTGATGGGGG\n")
|
|
775 f.write("AAGGTCGTGGAAGCGAAGAACGAGAGGCGAGCTTGTCGTTTGAGGAGAAAGGGGCCTCGC\n")
|
|
776 f.write("TGCCTGCAGAGAAAGGCGGTAAGTTGACCGGCGCAAAGTTATCATGAGACCGTAGCTCAG\n")
|
|
777 f.write("TATCGTTTCCTGTCGAGGGCATGGGTTACAGTCCGTCGAACTATGCGCGAGATCATCTGG\n")
|
|
778 f.write("TAGTAAAGAATCCCGCCGCCACTGACCAGATCTCCTGTGTCCTCTCAGCTCTCACAAAAC\n")
|
|
779 f.write("CTAGAAAAGCTTCGCATGGAGCCAAACGAATACTCCAATCCGACATTGAGCAAGACCCTT\n")
|
|
780 f.write("CCCTCTCGCCTCATAGGAACGAAACGGCCCATCTTCGAAGGGACAACTCTCTGTCGGCCG\n")
|
|
781 f.write("AGGAGATGACTTTTCTGACCGAGCGTAAGAGGAGATCGCACAGAGTCAGGGGTTGGTCGA\n")
|
|
782 f.write("GCTTTTGGGATTGGAGGAAGGGGGAGAGATTGATGAACGAGACGTCCCAATAGTGAGTCG\n")
|
|
783 f.write("CTCCGCACTGGAGCAATGATGGCAAACCGTGGAGTTGAAGAGTCTTGAACGCTATCAGAT\n")
|
|
784 f.write("CGGGCTAGGAGGGTCGGGAGGCGGTTGAATGCGTGCCAACCTTGGCTTCCTGTCAACGAT\n")
|
|
785 f.write("CCTCGCCTTTCAAGAGCTCGATCTATGGCAGTTGTTGACCTACACAGCGGGGGTATCCGG\n")
|
|
786 f.write("GTCCTGTTGGGCTCTGGCGAGTTTATATACGCTACCGATCGCACGTCCGCTCACACCATC\n")
|
|
787 f.write("CATCACTCAACGCCGCTGCGGTGATTGAGCACTTTATGTCCGTCTCAGGGGATCACCGTC\n")
|
|
788 f.write("TGAGTACAAAATCGGTCAACCGAGTCAGGGAGGCACACGGAGGGTACCAATCGCTTTTCG\n")
|
|
789 f.write("GACCTTTGATTTCAAAGTCTAAGAACAGTCAAAAGATCTGTAGTGAGTACAGACCACTGA\n")
|
|
790 f.write("CCCTCACTTGAGTAGATATTGACACTGACGAAGATCGCTACACTGCGGGCCTTGACAGTG\n")
|
|
791 f.write("ATTGATCTGTACTCGACACTGGTCTCATCGTACTTCTGGATGATGCCCAGAAAAGATGGG\n")
|
|
792 f.write("AAGGATCAGGTTGATCCGTATGTACCCCTGCGTCGGCTCGTGAGGTCCAGAGAGGGTCAT\n")
|
|
793 f.write("TCCACTGACTGTCCCGAACCCCCCCTGGCTGATCGTCAGCGCCTCGATGAAATGGTCGCG\n")
|
|
794 f.write("CGCGTACGATAATGCGGGCCTGGCTCACGGATGCGCGCCTTTCCCTATCGTCAGTCACGC\n")
|
|
795 f.write("AAATGTAGGCTTCCATCTGGAACGCTGCTTGATGGCCTAAGAATGGGCCGTCACGGAACA\n")
|
|
796 f.write("GCTCACCGCCTGCAGACACGAACGGCCGTGGCGGTCATGGAAGGATCTGAACGTGTCGCC\n")
|
|
797 f.write("CCATACGATTGACGAAGAGATGTAAGCTCCCTTGGTA\n")
|
|
798 f.close()
|
|
799
|
|
800 _createFastaFile_three_sequences_with_ORFs = staticmethod ( _createFastaFile_three_sequences_with_ORFs )
|
|
801
|
|
802
|
|
803 def _createFastaFile_three_sequences_with_ORFs_expected(fileName):
|
|
804 f = open(fileName, 'w')
|
|
805 f.write("ORF|1|662\tMivi_sl_Blaster_Grouper_1_Map_3\t307\t969\n")
|
|
806 f.write("ORF|-3|254\tMivi_sl_Blaster_Grouper_1_Map_3\t793\t539\n")
|
|
807 f.write("ORF|2|197\tMivi_sl_Blaster_Grouper_1_Map_3\t356\t553\n")
|
|
808 f.write("ORF|3|176\tMivi_sl_Blaster_Grouper_1_Map_3\t288\t464\n")
|
|
809 f.write("ORF|-1|176\tMivi_sl_Blaster_Grouper_1_Map_3\t786\t610\n")
|
|
810 f.write("ORF|3|143\tMivi_sl_Blaster_Grouper_1_Map_3\t672\t815\n")
|
|
811 f.write("ORF|1|131\tMivi_sl_Blaster_Grouper_1_Map_3\t175\t306\n")
|
|
812 f.write("ORF|-2|131\tMivi_sl_Blaster_Grouper_1_Map_3\t797\t666\n")
|
|
813 f.write("ORF|2|128\tMivi_sl_Blaster_Grouper_1_Map_3\t167\t295\n")
|
|
814 f.write("ORF|-2|119\tMivi_sl_Blaster_Grouper_1_Map_3\t242\t123\n")
|
|
815 f.write("ORF|1|464\tMivi_sl_Blaster_Grouper_2_Map_3\t304\t768\n")
|
|
816 f.write("ORF|3|305\tMivi_sl_Blaster_Grouper_2_Map_3\t669\t974\n")
|
|
817 f.write("ORF|-3|251\tMivi_sl_Blaster_Grouper_2_Map_3\t1094\t843\n")
|
|
818 f.write("ORF|-2|245\tMivi_sl_Blaster_Grouper_2_Map_3\t531\t286\n")
|
|
819 f.write("ORF|-3|224\tMivi_sl_Blaster_Grouper_2_Map_3\t791\t567\n")
|
|
820 f.write("ORF|-2|215\tMivi_sl_Blaster_Grouper_2_Map_3\t1098\t883\n")
|
|
821 f.write("ORF|2|197\tMivi_sl_Blaster_Grouper_2_Map_3\t353\t550\n")
|
|
822 f.write("ORF|3|173\tMivi_sl_Blaster_Grouper_2_Map_3\t288\t461\n")
|
|
823 f.write("ORF|-1|173\tMivi_sl_Blaster_Grouper_2_Map_3\t1087\t914\n")
|
|
824 f.write("ORF|-1|143\tMivi_sl_Blaster_Grouper_2_Map_3\t310\t167\n")
|
|
825 f.write("ORF|3|626\tMivi_sl_Blaster_Grouper_3_Map_3\t141\t767\n")
|
|
826 f.write("ORF|2|434\tMivi_sl_Blaster_Grouper_3_Map_3\t164\t598\n")
|
|
827 f.write("ORF|3|365\tMivi_sl_Blaster_Grouper_3_Map_3\t768\t1133\n")
|
|
828 f.write("ORF|-3|359\tMivi_sl_Blaster_Grouper_3_Map_3\t1514\t1155\n")
|
|
829 f.write("ORF|-1|320\tMivi_sl_Blaster_Grouper_3_Map_3\t1879\t1559\n")
|
|
830 f.write("ORF|3|272\tMivi_sl_Blaster_Grouper_3_Map_3\t1299\t1571\n")
|
|
831 f.write("ORF|-2|248\tMivi_sl_Blaster_Grouper_3_Map_3\t1503\t1255\n")
|
|
832 f.write("ORF|1|236\tMivi_sl_Blaster_Grouper_3_Map_3\t1576\t1812\n")
|
|
833 f.write("ORF|-1|227\tMivi_sl_Blaster_Grouper_3_Map_3\t1423\t1196\n")
|
|
834 f.write("ORF|-3|227\tMivi_sl_Blaster_Grouper_3_Map_3\t368\t141\n")
|
|
835 f.close()
|
|
836
|
|
837 _createFastaFile_three_sequences_with_ORFs_expected = staticmethod ( _createFastaFile_three_sequences_with_ORFs_expected )
|
|
838
|
|
839
|
|
840 def _createLinkFile_four_sequences_with_new_headers(fileName):
|
|
841 f = open(fileName, 'w')
|
|
842 f.write("seq 1\tReconCluster1Mb155 chunk183 {Fragment} 1..5506\t1\t127\n")
|
|
843 f.write("seq 2\tMbQ3Gr2Cl0 chunk440 {Fragment} 2678..3645\t1\t307\n")
|
|
844 f.write("seq 3\tMbS2Gr2Cl0 chunk622 {Fragment} 104..1078\t1\t427\n")
|
|
845 f.write("seq 4\tPilerCluster3.574Mb796 chunk0117 {Fragment} 51582..50819\t1\t307\n")
|
|
846
|
|
847 _createLinkFile_four_sequences_with_new_headers = staticmethod ( _createLinkFile_four_sequences_with_new_headers )
|
|
848
|
|
849
|
|
850 def _createLinkFile_four_sequences_same_headers(fileName):
|
|
851 f = open(fileName, 'w')
|
|
852 f.write("seq 1\tseq 1\t1\t127\n")
|
|
853 f.write("seq 2\tseq 2\t1\t307\n")
|
|
854 f.write("seq 3\tseq 3\t1\t427\n")
|
|
855 f.write("seq 4\tseq 4\t1\t307\n")
|
|
856
|
|
857 _createLinkFile_four_sequences_same_headers = staticmethod ( _createLinkFile_four_sequences_same_headers )
|