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1 import unittest
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2 import os
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3 from commons.core.utils.FileUtils import FileUtils
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4 from commons.core.sql.DbMySql import DbMySql
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5 from commons.tools.GFF3Maker import GFF3Maker
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6
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7 class Test_F_GFF3Maker(unittest.TestCase):
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8
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9 def setUp(self):
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10 self._projectName = "projectName"
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11 self._iDb = DbMySql()
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12 self._tablesFileName = "annotation_tables.txt"
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13 self._fastaFileName = "%s_chr.fa" % self._projectName
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14 self._fastaTableName = "%s_chr_seq" % self._projectName
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15 self._writeFastaFile(self._fastaFileName)
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16 self._iDb.createTable(self._fastaTableName, "seq", self._fastaFileName, True)
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17 self._inputFileName = "%s_chr_allTEs_nr_noSSR_join.pathOrSet" % self._projectName
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18 self._expGFFFileName = "explm_SuperContig_29_v2.gff3"
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19 self._obsGFFFileName = "lm_SuperContig_29_v2.gff3"
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20 self._obsGFFEmptyFileName = "lm_SuperContig_30_v2.gff3"
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21
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22 def tearDown(self):
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23 self._iDb.dropTable(self._fastaTableName)
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24 self._iDb.dropTable(self._inputTableName)
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25 self._iDb.close()
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26 os.remove(self._obsGFFFileName)
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27 os.remove(self._expGFFFileName)
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28 os.remove(self._fastaFileName)
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29 os.remove(self._tablesFileName)
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30 os.remove(self._inputFileName)
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31
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32 def test_run_as_script_path_with_seq_withAllFiles(self):
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33 self._writeTablesFile("path")
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34 self._writePathFile(self._inputFileName)
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35 self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName
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36 self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True)
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37 self._writeExpPathGFFFile(self._expGFFFileName)
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38 expGFFEmptyFileName = "explm_SuperContig_30_v2.gff3"
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39 self._writeExpEmptyPathGFFFileWithSeq(expGFFEmptyFileName)
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40
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41 cmd = "GFF3Maker.py -t %s -f %s -w -a -p"% (self._tablesFileName, self._fastaTableName)
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42 os.system(cmd)
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43
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44 self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName))
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45 self.assertTrue(FileUtils.are2FilesIdentical(expGFFEmptyFileName, self._obsGFFEmptyFileName))
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46
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47 os.remove(expGFFEmptyFileName)
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48 os.remove(self._obsGFFEmptyFileName)
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49
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50 def test_run_as_script_path_without_seq_withAllFiles(self):
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51 self._writeTablesFile("path")
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52 self._writePathFile(self._inputFileName)
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53 self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName
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54 self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True)
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55 self._writeExpPathGFFFile_without_seq(self._expGFFFileName)
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56 expGFFEmptyFileName = "explm_SuperContig_30_v2.gff3"
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57 self._writeExpEmptyPathGFFFile(expGFFEmptyFileName)
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58
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59 cmd = "GFF3Maker.py -t %s -f %s -a -p" % (self._tablesFileName, self._fastaTableName)
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60 os.system(cmd)
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61
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62 self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName))
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63 self.assertTrue(FileUtils.are2FilesIdentical(expGFFEmptyFileName, self._obsGFFEmptyFileName))
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64
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65 os.remove(expGFFEmptyFileName)
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66 os.remove(self._obsGFFEmptyFileName)
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67
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68 def test_run_without_seq(self):
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69 self._writeTablesFile("path")
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70 self._writePathFile(self._inputFileName)
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71 self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName
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72 self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True)
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73 self._writeExpPathGFFFile_without_seq(self._expGFFFileName)
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74
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75 iGFF3Maker = GFF3Maker()
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76 iGFF3Maker.setTablesFileName(self._tablesFileName)
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77 iGFF3Maker.setInFastaName(self._fastaTableName)
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78 iGFF3Maker.setAreMatchPartCompulsory(True)
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79 iGFF3Maker.run()
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80
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81 self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName))
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82 self.assertFalse(FileUtils.isRessourceExists(self._obsGFFEmptyFileName))
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83
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84 def test_run_without_seq_and_match_part_not_compulsory(self):
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85 self._writeTablesFile("path")
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86 self._writePathFile(self._inputFileName)
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87 self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName
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88 self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True)
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89 self._writeExpPathGFFFile_without_seq_and_match_part_not_comulsory(self._expGFFFileName)
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90
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91 iGFF3Maker = GFF3Maker()
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92 iGFF3Maker.setTablesFileName(self._tablesFileName)
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93 iGFF3Maker.setInFastaName(self._fastaTableName)
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94 iGFF3Maker.run()
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95
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96 self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName))
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97 self.assertFalse(FileUtils.isRessourceExists(self._obsGFFEmptyFileName))
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98
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99 def test_run_as_script_pathReversed(self):
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100 self._writeTablesFile("path")
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101 self._writePathFileReverse(self._inputFileName)
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102 self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName
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103 self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True)
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104 self._writeExpPathGFFFileReversed(self._expGFFFileName)
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105
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106 cmd = "GFF3Maker.py -t %s -f %s -w -p" % (self._tablesFileName, self._fastaTableName)
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107 os.system(cmd)
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108
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109 self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName))
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110 self.assertFalse(FileUtils.isRessourceExists(self._obsGFFEmptyFileName))
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111
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112 def test_run_as_script_set(self):
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113 self._writeTablesFile("set")
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114 self._writeSetFile(self._inputFileName)
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115 self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_set" % self._projectName
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116 self._iDb.createTable(self._inputTableName, "set", self._inputFileName, True)
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117 self._writeExpSetGFFFile(self._expGFFFileName)
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118
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119 cmd = "GFF3Maker.py -t %s -f %s -w -p " % (self._tablesFileName, self._fastaTableName)
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120 os.system(cmd)
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121
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122 self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName))
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123 self.assertFalse(FileUtils.isRessourceExists(self._obsGFFEmptyFileName))
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124
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125 def test_run_as_script_setReversed(self):
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126 self._writeTablesFile("set")
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127 self._writeSetFileReverse(self._inputFileName)
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128 self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_set" % self._projectName
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129 self._iDb.createTable(self._inputTableName, "set", self._inputFileName, True)
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130 self._writeExpSetGFFFileReversed(self._expGFFFileName)
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131
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132 cmd = "GFF3Maker.py -t %s -f %s -w -p " % (self._tablesFileName, self._fastaTableName)
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133 os.system(cmd)
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134
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135 self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName))
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136 self.assertFalse(FileUtils.isRessourceExists(self._obsGFFEmptyFileName))
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137
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138 def test_run_as_script_path_without_seq_withAllFilesWithClassif_headers_TEdenovo_step6_and_step8(self):
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139 self._writeTablesFile("path")
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140 self._writePathFile_withClassif(self._inputFileName)
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141 self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName
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142 self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True)
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143
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144 self._writeClassifFile("input.classif")
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145 inputClassifTableName = "%s_classif" % self._projectName
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146 self._iDb.createTable(inputClassifTableName, "classif", "input.classif", True)
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147
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148 self._expGFFFileName = "explm_SuperContig_30_v2.gff3"
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149 self._obsGFFFileName = "lm_SuperContig_30_v2.gff3"
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150 self._writeExpPathGFFFile_without_seq_withClassif(self._expGFFFileName)
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151
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152 cmd = "GFF3Maker.py -t %s -f %s -i %s -p" % (self._tablesFileName, self._fastaTableName, inputClassifTableName)
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153 os.system(cmd)
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154
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155 self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName))
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156
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157 os.remove("input.classif")
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158 os.remove("lm_SuperContig_29_v2.gff3")
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159 self._iDb.dropTable(inputClassifTableName)
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160
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161 def test_run_as_script_path_without_seq_withAllFilesWithTargetLength(self):
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162 fastaFileName = "genome.fa"
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163 self._writeFastaFileExtended(fastaFileName)
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164 self._iDb.createTable(self._fastaTableName, "seq", fastaFileName, True)
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165 os.remove(fastaFileName)
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166
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167 self._writeTablesFile_withTESeqTables("path")
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168
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169 self._writePathFile(self._inputFileName)
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170 self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName
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171 self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True)
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172
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173 inFileName2 = "%s_chr_bankBLRtx.path" % self._projectName
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174 self._writePathFile2(inFileName2)
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175 bankPathTableName = "%s_chr_bankBLRtx_path" % self._projectName
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176 self._iDb.createTable(bankPathTableName, "path", inFileName2, True)
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177 os.remove(inFileName2)
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178
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179 refTEsFastaFileName = "%s_refTEs.fa" % self._projectName
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180 self._writeRefTEsSeqFile(refTEsFastaFileName)
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181 refTESeqTableName = "%s_refTEs_seq" % self._projectName
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182 self._iDb.createTable(refTESeqTableName, "seq", refTEsFastaFileName, True)
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183 os.remove(refTEsFastaFileName)
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184
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185 bankBLRtxFastaFileName = "dummyRepbase.fa"
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186 self._writeBankBLRtxSeqFile(bankBLRtxFastaFileName)
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187 bankBLRtxTableName = "%s_bankBLRtx_nt_seq" % self._projectName
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188 self._iDb.createTable(bankBLRtxTableName, "seq", bankBLRtxFastaFileName, True)
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189 os.remove(bankBLRtxFastaFileName)
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190
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191 self._expGFFFileName = "explm_SuperContig_29_v2.gff3"
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192 expSeq2GFFFileName = "expChr1.gff3"
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193 self._obsGFFFileName = "lm_SuperContig_29_v2.gff3"
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194 obsSeq2GFFFileName = "chr1.gff3"
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195 self._writeExpPathGFFFile_without_seq_withTargetLength_seq1(self._expGFFFileName)
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196 self._writeExpPathGFFFile_without_seq_withTargetLength_seq2(expSeq2GFFFileName)
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197
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198 cmd = "GFF3Maker.py -t %s -f %s -p" % (self._tablesFileName, self._fastaTableName)
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199 os.system(cmd)
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200
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201 self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName))
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202 self.assertTrue(FileUtils.are2FilesIdentical(expSeq2GFFFileName, obsSeq2GFFFileName))
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203
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204 os.remove(expSeq2GFFFileName)
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205 os.remove(obsSeq2GFFFileName)
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206 self._iDb.dropTable(refTESeqTableName)
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207 self._iDb.dropTable(bankBLRtxTableName)
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208 self._iDb.dropTable(bankPathTableName)
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209
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210 def test_run_as_script_split_file_by_annotation_method(self):
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211 fastaFileName = "dummyDmelChr4.fa"
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212 self._writeFastaFile_DmelChr4(fastaFileName)
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213 self._iDb.createTable(self._fastaTableName, "seq", fastaFileName, True)
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214 os.remove(fastaFileName)
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215
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216 self._writeTablesFile_withTESeqTables("path")
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217
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218 self._writePathFile_refTEs_annotation(self._inputFileName)
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219 self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName
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220 self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True)
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221
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222 inFileName2 = "%s_chr_bankBLRtx.path" % self._projectName
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223 self._writePathFile_bankBLRtx_annotation(inFileName2)
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224 bankPathTableName = "%s_chr_bankBLRtx_path" % self._projectName
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225 self._iDb.createTable(bankPathTableName, "path", inFileName2, True)
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226 os.remove(inFileName2)
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227
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228 refTEsFastaFileName = "%s_refTEs.fa" % self._projectName
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229 self._writeRefTEsSeqFile(refTEsFastaFileName)
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230 refTESeqTableName = "%s_refTEs_seq" % self._projectName
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231 self._iDb.createTable(refTESeqTableName, "seq", refTEsFastaFileName, True)
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232 os.remove(refTEsFastaFileName)
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233
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234 bankBLRtxFastaFileName = "dummyRepbase.fa"
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235 self._writeBankBLRtxSeqFile(bankBLRtxFastaFileName)
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236 bankBLRtxTableName = "%s_bankBLRtx_nt_seq" % self._projectName
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237 self._iDb.createTable(bankBLRtxTableName, "seq", bankBLRtxFastaFileName, True)
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238 os.remove(bankBLRtxFastaFileName)
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239
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240 self._expGFFFileName = "expdmel_chr4_Annot1.gff3"
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241 expGFFFileName2 = "expdmel_chr1_Annot1.gff3"
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242 expGFFFileName3 = "expdmel_chr4_Annot2.gff3"
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243 self._obsGFFFileName = "dmel_chr4_Annot1.gff3"
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244 obsGFFFileName2 = "dmel_chr1_Annot1.gff3"
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245 obsGFFFileName3 = "dmel_chr4_Annot2.gff3"
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246 self._writeExpPathGFFFile_split_file1(self._expGFFFileName)
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247 self._writeExpPathGFFFile_split_file2(expGFFFileName2)
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248 self._writeExpPathGFFFile_split_file3(expGFFFileName3)
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249
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250 cmd = "GFF3Maker.py -t %s -f %s -s -p" % (self._tablesFileName, self._fastaTableName)
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251 os.system(cmd)
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252
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253 self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName))
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254 self.assertTrue(FileUtils.are2FilesIdentical(expGFFFileName2, obsGFFFileName2))
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255 self.assertTrue(FileUtils.are2FilesIdentical(expGFFFileName3, obsGFFFileName3))
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256
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257 os.remove(expGFFFileName2)
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258 os.remove(expGFFFileName3)
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259 os.remove(obsGFFFileName2)
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260 os.remove(obsGFFFileName3)
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261 self._iDb.dropTable(refTESeqTableName)
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262 self._iDb.dropTable(bankBLRtxTableName)
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263 self._iDb.dropTable(bankPathTableName)
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264
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265 def test_run_path_without_seq_withAllFilesWithClassif_headers_TEdenovo_step6_and_step8_withIdenticalMatches(self):
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266 self._writeTablesFile("path")
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267 self._writePathFile_withClassif_withIdenticalMatches(self._inputFileName)
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268 self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName
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269 self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True)
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270
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271 self._writeClassifFile("input.classif")
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272 inputClassifTableName = "%s_classif" % self._projectName
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273 self._iDb.createTable(inputClassifTableName, "classif", "input.classif", True)
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274
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275 self._expGFFFileName = "explm_SuperContig_30_v2.gff3"
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276 self._obsGFFFileName = "lm_SuperContig_30_v2.gff3"
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277 self._writeExpPathGFFFile_without_seq_withClassif_withIdenticalMatches(self._expGFFFileName)
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278
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279 iGFF3Maker = GFF3Maker()
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280 iGFF3Maker.setTablesFileName(self._tablesFileName)
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281 iGFF3Maker.setInFastaName(self._fastaTableName)
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282 iGFF3Maker.setClassifTable(inputClassifTableName)
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283 iGFF3Maker.setDoMergeIdenticalMatches(True)
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284 iGFF3Maker.setAreMatchPartCompulsory(True)
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285 iGFF3Maker.run()
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286
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287 self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName))
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288
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289 os.remove("input.classif")
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290 os.remove("lm_SuperContig_29_v2.gff3")
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291 self._iDb.dropTable(inputClassifTableName)
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292
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293 def test_run_as_script_path_without_seq_withAllFilesWithClassif_headers_TEdenovo_step6_and_step8_withIdenticalMatches(self):
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294 self._writeTablesFile("path")
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295 self._writePathFile_withClassif_withIdenticalMatches(self._inputFileName)
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296 self._inputTableName = "%s_chr_allTEs_nr_noSSR_join_path" % self._projectName
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297 self._iDb.createTable(self._inputTableName, "path", self._inputFileName, True)
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298
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299 self._writeClassifFile("input.classif")
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300 inputClassifTableName = "%s_classif" % self._projectName
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301 self._iDb.createTable(inputClassifTableName, "classif", "input.classif", True)
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302
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303 self._expGFFFileName = "explm_SuperContig_30_v2.gff3"
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304 self._obsGFFFileName = "lm_SuperContig_30_v2.gff3"
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305 self._writeExpPathGFFFile_without_seq_withClassif_withIdenticalMatches(self._expGFFFileName)
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306
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307 cmd = "GFF3Maker.py -t %s -f %s -i %s -m -p" % (self._tablesFileName, self._fastaTableName, inputClassifTableName)
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308 os.system(cmd)
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309
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310 self.assertTrue(FileUtils.are2FilesIdentical(self._expGFFFileName, self._obsGFFFileName))
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311
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312 os.remove("input.classif")
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313 os.remove("lm_SuperContig_29_v2.gff3")
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314 self._iDb.dropTable(inputClassifTableName)
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315
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316 def _writeRefTEsSeqFile(self, inFileName):
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317 with open(inFileName, "w") as f:
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318 f.write(">DTX-incomp_DmelChr4-L-B1-Map3\n")
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319 f.write("ATCGATCGTT\n")
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320 f.write(">DTX-incomp_DmelChr4-B-P0.0-Map3\n")
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321 f.write("GCTAGCTA\n")
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322
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323 def _writeBankBLRtxSeqFile(self, inFileName):
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324 with open(inFileName, "w") as f:
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325 f.write(">PROTOP_B:classII:TIR\n")
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326 f.write("ATCGATCGTT\n")
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327 f.write(">DMRT1C:classI:?\n")
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328 f.write("GCTAGCTA\n")
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329 f.write(">BATUMI_I:classI:LTR_retrotransposon\n")
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330 f.write("GCTAATGGCATA\n")
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331
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332 def _writeExpPathGFFFile_without_seq_withTargetLength_seq1(self, inFileName):
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333 with open(inFileName, "w") as f:
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334 f.write("##gff-version 3\n")
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335 f.write("##sequence-region lm_SuperContig_29_v2 1 120\n")
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336 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t193781\t194212\t0.0\t-\t.\tID=ms1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 85 228;TargetLength=10;Identity=30.56\n")
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337 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t193781\t194212\t1e-40\t-\t.\tID=mp1-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Parent=ms1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 85 228;Identity=30.56\n")
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338 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t192832\t193704\t0.0\t-\t.\tID=ms2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 229 522;TargetLength=10;Identity=23.99\n")
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339 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t192832\t193704\t1e-40\t-\t.\tID=mp2-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Parent=ms2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 229 522;Identity=23.99\n")
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340 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t78031\t78588\t0.0\t+\t.\tID=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;TargetLength=8\n")
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341 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78031\t78080\t3e-21\t+\t.\tID=mp3-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;Identity=30.89\n")
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342 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78588\t3e-21\t+\t.\tID=mp3-2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;Identity=30.89\n")
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343
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344 def _writeExpPathGFFFile_without_seq_withTargetLength_seq2(self, inFileName):
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345 with open(inFileName, "w") as f:
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346 f.write("##gff-version 3\n")
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347 f.write("##sequence-region chr1 1 18\n")
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348 f.write("chr1\tprojectName_REPET_TEs\tmatch\t1\t100\t0.0\t-\t.\tID=ms1_chr1_PROTOP_B:classII:TIR;Target=PROTOP_B:classII:TIR 85 228;TargetLength=10;Identity=30.56\n")
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349 f.write("chr1\tprojectName_REPET_TEs\tmatch_part\t1\t100\t1e-20\t-\t.\tID=mp1-1_chr1_PROTOP_B:classII:TIR;Parent=ms1_chr1_PROTOP_B:classII:TIR;Target=PROTOP_B:classII:TIR 85 228;Identity=30.56\n")
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350 f.write("chr1\tprojectName_REPET_TEs\tmatch\t100\t1000\t0.0\t-\t.\tID=ms2_chr1_DMRT1C:classI:?;Target=DMRT1C:classI:? 85 228;TargetLength=8;Identity=30.56\n")
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351 f.write("chr1\tprojectName_REPET_TEs\tmatch_part\t100\t1000\t1e-30\t-\t.\tID=mp2-1_chr1_DMRT1C:classI:?;Parent=ms2_chr1_DMRT1C:classI:?;Target=DMRT1C:classI:? 85 228;Identity=30.56\n")
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352
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353 def _writeExpPathGFFFile_split_file1(self, inFileName):
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354 with open(inFileName, 'w') as f:
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355 f.write("##gff-version 3\n")
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356 f.write("##sequence-region dmel_chr4 1 18\n")
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357 f.write("dmel_chr4\t%s_REPET_TEs\tmatch\t4630\t4889\t0.0\t+\t.\tID=ms21_dmel_chr4_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 232 512;TargetLength=8\n" % self._projectName)
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358 f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4630\t4704\t0.0\t+\t.\tID=mp21-1_dmel_chr4_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms21_dmel_chr4_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 232 312;Identity=84.4417\n" % self._projectName)
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|
359 f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4837\t4889\t0.0\t+\t.\tID=mp21-2_dmel_chr4_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms21_dmel_chr4_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 456 512;Identity=84.4417\n" % self._projectName)
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|
|
360 f.write("dmel_chr4\t%s_REPET_TEs\tmatch\t4364\t4611\t0.0\t+\t.\tID=ms6_dmel_chr4_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 854 1150;TargetLength=10;Identity=91.24\n" % self._projectName)
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|
|
361 f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4364\t4611\t0.0\t+\t.\tID=mp6-1_dmel_chr4_DTX-incomp_DmelChr4-L-B1-Map3;Parent=ms6_dmel_chr4_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 854 1150;Identity=91.24\n" % self._projectName)
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|
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362
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|
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363 def _writeExpPathGFFFile_split_file2(self, inFileName):
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|
|
364 with open(inFileName, 'w') as f:
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|
|
365 f.write("##gff-version 3\n")
|
|
|
366 f.write("##sequence-region dmel_chr1 1 25\n")
|
|
|
367 f.write("dmel_chr1\t%s_REPET_TEs\tmatch\t4364\t4611\t0.0\t+\t.\tID=ms35_dmel_chr1_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 854 1150;TargetLength=10;Identity=91.24\n" % self._projectName)
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|
|
368 f.write("dmel_chr1\t%s_REPET_TEs\tmatch_part\t4364\t4611\t0.0\t+\t.\tID=mp35-1_dmel_chr1_DTX-incomp_DmelChr4-L-B1-Map3;Parent=ms35_dmel_chr1_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 854 1150;Identity=91.24\n" % self._projectName)
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|
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369
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|
|
370 def _writeExpPathGFFFile_split_file3(self, inFileName):
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|
|
371 with open(inFileName, 'w') as f:
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|
|
372 f.write("##gff-version 3\n")
|
|
|
373 f.write("##sequence-region dmel_chr4 1 18\n")
|
|
|
374 f.write("dmel_chr4\t%s_REPET_TEs\tmatch\t3143\t4364\t0.0\t-\t.\tID=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 24 2206;TargetLength=8\n" % self._projectName)
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|
|
375 f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t3143\t3361\t0.0\t-\t.\tID=mp66-1_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 1988 2206;Identity=89.7202\n" % self._projectName)
|
|
|
376 f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t3345\t3410\t0.0\t-\t.\tID=mp66-2_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 1654 1719;Identity=54.55\n" % self._projectName)
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|
|
377 f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t3448\t3572\t0.0\t-\t.\tID=mp66-3_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 1495 1619;Identity=77.3433\n" % self._projectName)
|
|
|
378 f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t3564\t3693\t0.0\t-\t.\tID=mp66-4_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 1380 1509;Identity=83.7306\n" % self._projectName)
|
|
|
379 f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t3705\t3857\t0.0\t-\t.\tID=mp66-5_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 539 691;Identity=84.5762\n" % self._projectName)
|
|
|
380 f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t3861\t3992\t0.0\t-\t.\tID=mp66-6_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 403 534;Identity=67.1422\n" % self._projectName)
|
|
|
381 f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t3985\t4106\t0.0\t-\t.\tID=mp66-7_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 290 411;Identity=76.612\n" % self._projectName)
|
|
|
382 f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4102\t4248\t0.0\t-\t.\tID=mp66-8_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 139 285;Identity=75.3027\n" % self._projectName)
|
|
|
383 f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4236\t4364\t0.0\t-\t.\tID=mp66-9_dmel_chr4_DMRT1C:classI:?;Parent=ms66_dmel_chr4_DMRT1C:classI:?;Target=DMRT1C:classI:? 24 152;Identity=66.6657\n" % self._projectName)
|
|
|
384 f.write("dmel_chr4\t%s_REPET_TEs\tmatch\t4412\t4889\t0.0\t-\t.\tID=ms27_dmel_chr4_PROTOP_B:classII:TIR;Target=PROTOP_B:classII:TIR 553 1082;TargetLength=10\n" % self._projectName)
|
|
|
385 f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4412\t4501\t5e-108\t-\t.\tID=mp27-1_dmel_chr4_PROTOP_B:classII:TIR;Parent=ms27_dmel_chr4_PROTOP_B:classII:TIR;Target=PROTOP_B:classII:TIR 993 1082;Identity=91.3066\n" % self._projectName)
|
|
|
386 f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4483\t4652\t9e-146\t-\t.\tID=mp27-2_dmel_chr4_PROTOP_B:classII:TIR;Parent=ms27_dmel_chr4_PROTOP_B:classII:TIR;Target=PROTOP_B:classII:TIR 821 990;Identity=86.5572\n" % self._projectName)
|
|
|
387 f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4672\t4775\t9e-146\t-\t.\tID=mp27-3_dmel_chr4_PROTOP_B:classII:TIR;Parent=ms27_dmel_chr4_PROTOP_B:classII:TIR;Target=PROTOP_B:classII:TIR 684 787;Identity=88.8013\n" % self._projectName)
|
|
|
388 f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4782\t4889\t9e-141\t-\t.\tID=mp27-4_dmel_chr4_PROTOP_B:classII:TIR;Parent=ms27_dmel_chr4_PROTOP_B:classII:TIR;Target=PROTOP_B:classII:TIR 553 661;Identity=53.7067\n" % self._projectName)
|
|
|
389 f.write("dmel_chr4\t%s_REPET_TEs\tmatch\t4917\t5195\t0.0\t+\t.\tID=ms141_dmel_chr4_BATUMI_I:classI:LTR_retrotransposon;Target=BATUMI_I:classI:LTR_retrotransposon 7030 7303;TargetLength=12\n" % self._projectName)
|
|
|
390 f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4917\t5007\t2e-144\t+\t.\tID=mp141-1_dmel_chr4_BATUMI_I:classI:LTR_retrotransposon;Parent=ms141_dmel_chr4_BATUMI_I:classI:LTR_retrotransposon;Target=BATUMI_I:classI:LTR_retrotransposon 7030 7120;Identity=94.1756\n" % self._projectName)
|
|
|
391 f.write("dmel_chr4\t%s_REPET_TEs\tmatch_part\t4976\t5195\t2e-144\t+\t.\tID=mp141-2_dmel_chr4_BATUMI_I:classI:LTR_retrotransposon;Parent=ms141_dmel_chr4_BATUMI_I:classI:LTR_retrotransposon;Target=BATUMI_I:classI:LTR_retrotransposon 7087 7303;Identity=82.2343\n" % self._projectName)
|
|
|
392
|
|
|
393 def _writeClassifFile(self, inputFileName):
|
|
|
394 f = open(inputFileName, "w")
|
|
|
395 f.write("PotentialHostGene-chim_fTest05105818-B-G11-Map20\t1240\t+\tPotentialChimeric\tNA\tPotentialHostGene\tNA\tCI=100; coding=(HG_BLRn: FBtr0089196_Dmel_r4.3: 95.65%); other=(TE_BLRtx: PROTOP:classII:TIR: 12.03%, PROTOP_A:classII:TIR: 49.14%; TermRepeats: termTIR: 49; SSRCoverage=0.25<0.75)\n")
|
|
|
396 f.write("DTX-comp-chim_fTest05105818-B-G7-Map3_reversed\t1944\t-\tPotentialChimeric\tII\tTIR\tcomplete\tCI=33; coding=(TE_BLRtx: PROTOP:classII:TIR: 12.77%, PROTOP_A:classII:TIR: 25.16%, PROTOP_A:classII:TIR: 100.00%); struct=(TElength: <700bps; TermRepeats: termTIR: 844); other=(HG_BLRn: FBtr0089196_Dmel_r4.3: 29.48%; SSRCoverage=0.24<0.75)\n")
|
|
|
397 f.write("DTX-incomp_fTest05105818-B-G9-Map3_reversed\t1590\t-\tok\tII\tTIR\tincomplete\tCI=33; coding=(TE_BLRtx: PROTOP:classII:TIR: 10.92%, PROTOP:classII:TIR: 11.03%, PROTOP_A:classII:TIR: 55.20%); struct=(TElength: >700bps); other=(HG_BLRn: FBtr0089196_Dmel_r4.3: 35.60%; SSRCoverage=0.21<0.75)\n")
|
|
|
398 f.write("DTX-incomp_fTest05105818-B-P0.0-Map3\t1042\t.\tok\tII\tTIR\tincomplete\tCI=50; coding=(TE_BLRtx: PROTOP:classII:TIR: 17.39%, PROTOP_A:classII:TIR: 22.17%); struct=(TElength: >700bps; TermRepeats: termTIR: 50); other=(HG_BLRn: FBtr0089196_Dmel_r4.3: 47.22%; SSRCoverage=0.25<0.75)\n")
|
|
|
399 f.write("DTX-comp_fTest05105818-B-P1.0-Map9_reversed\t1137\t-\tok\tII\tTIR\tcomplete\tCI=50; coding=(TE_BLRtx: PROTOP:classII:TIR: 6.70%, PROTOP_A:classII:TIR: 66.43%, PROTOP_B:classII:TIR: 6.42%); struct=(TElength: >700bps; TermRepeats: termTIR: 52); other=(HG_BLRn: FBtr0089196_Dmel_r4.3: 51.19%; SSRCoverage=0.22<0.75)\n")
|
|
|
400 f.write("RLX-incomp_fTest05105818-B-R12-Map3_reversed\t2284\t-\tok\tI\tLTR\tincomplete\tCI=28; coding=(TE_BLRtx: ROOA_I:classI:LTR_retrotransposon: 27.57%, ROOA_LTR:classI:LTR_retrotransposon: 94.56%; TE_BLRx: BEL11_AGp:classI:LTR_retrotransposon: 19.47%, BEL2-I_Dmoj_1p:classI:LTR_retrotransposon: 11.49%); struct=(TElength: >700bps); other=(SSRCoverage=0.07<0.75)\n")
|
|
|
401 f.write("DTX-incomp_fTest05105818-B-R19-Map4\t705\t+\tok\tII\tTIR\tincomplete\tCI=66; coding=(TE_BLRtx: TC1-2_DM:classII:TIR: 42.70%; TE_BLRx: TC1-2_DMp:classII:TIR: 41.18%); struct=(TElength: >700bps); other=(SSRCoverage=0.14<0.75)\n")
|
|
|
402 f.write("DHX-incomp_fTest05105818-B-R1-Map4\t2367\t.\tok\tII\tHelitron\tincomplete\tCI=20; coding=(TE_BLRtx: DNAREP1_DM:classII:Helitron: 17.00%, DNAREP1_DYak:classII:Helitron: 9.08%); struct=(TElength: >700bps); other=(HG_BLRn: FBtr0089179_Dmel_r4.3: 13.52%; SSRCoverage=0.18<0.75)\n")
|
|
|
403 f.write("noCat_fTest05105818-B-R2-Map6\t4638\t.\tok\tnoCat\tnoCat\tNA\tCI=NA; coding=(HG_BLRn: FBtr0089179_Dmel_r4.3: 73.65%); struct=(SSRCoverage=0.05<0.75)\n")
|
|
|
404 f.write("PotentialHostGene-chim_fTest05105818-B-R4-Map5_reversed\t1067\t-\tPotentialChimeric\tNA\tPotentialHostGene\tNA\tCI=100; coding=(HG_BLRn: FBtr0089196_Dmel_r4.3: 99.91%); other=(TE_BLRtx: PROTOP:classII:TIR: 13.06%, PROTOP_A:classII:TIR: 37.47%; SSRCoverage=0.27<0.75)\n")
|
|
|
405 f.write("DTX-incomp_fTest05105818-B-R9-Map3_reversed\t714\t-\tok\tII\tTIR\tincomplete\tCI=66; coding=(TE_BLRtx: TC1_DM:classII:TIR: 40.88%; TE_BLRx: Tc1-1_TCa_1p:classII:TIR: 30.18%, Tc1-3_FR_1p:classII:TIR: 9.97%); struct=(TElength: >700bps); other=(SSRCoverage=0.08<0.75)\n")
|
|
|
406 f.close()
|
|
|
407
|
|
|
408 def _writePathFile_withClassif(self,inFileName):
|
|
|
409 f = open(inFileName,'w')
|
|
|
410 f.write('1\tlm_SuperContig_29_v2\t193781\t194212\t1nc550_030\t228\t85\t1e-40\t84\t30.56\n')
|
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411 f.write('2\tlm_SuperContig_29_v2\t192832\t193704\t1nc550_030\t522\t229\t1e-40\t106\t23.99\n')
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412 f.write('3\tlm_SuperContig_30_v2\t78081\t78088\tDHX-incomp_Blc1_fTest05105818-B-R1-Map4\t19\t209\t3e-21\t101\t30.89\n')
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413 f.write('3\tlm_SuperContig_30_v2\t78089\t78588\tDHX-incomp_Blc1_fTest05105818-B-R1-Map4\t150\t350\t3e-22\t101\t35.89\n')
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414 f.write('4\tlm_SuperContig_30_v2\t88031\t88080\tDTX-incomp_fTest05105818-B-G1-Map3\t370\t420\t3e-23\t101\t31.89\n')
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415 f.write('5\tlm_SuperContig_30_v2\t108588\t108081\tDTX-incomp_fTest05105818-B-G9-Map3_reversed\t590\t820\t3e-24\t101\t32.89\n')
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416 f.write('6\tlm_SuperContig_30_v2\t118081\t118588\tPotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed\t154\t289\t3e-25\t101\t33.89\n')
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417 f.write('7\tlm_SuperContig_30_v2\t288031\t288080\tnoCat_Blc22_fTest05105818-B-R2-Map6\t1900\t2090\t3e-26\t101\t34.89\n')
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418 f.close()
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419
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420 def _writeExpPathGFFFile_without_seq_withClassif(self, inFileName):
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421 f = open(inFileName, 'w')
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422 f.write("##gff-version 3\n")
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423 f.write("##sequence-region lm_SuperContig_30_v2 1 120\n")
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424 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t78081\t78588\t0.0\t+\t.\tID=ms3_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 19 350;TargetDescription=CI:20 coding:(TE_BLRtx: DNAREP1_DM:classII:Helitron: 17.00% | DNAREP1_DYak:classII:Helitron: 9.08%) struct:(TElength: >700bps) other:(HG_BLRn: FBtr0089179_Dmel_r4.3: 13.52% SSRCoverage:0.18<0.75)\n")
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425 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78088\t3e-21\t+\t.\tID=mp3-1_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Parent=ms3_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 19 209;Identity=30.89\n")
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426 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t78089\t78588\t3e-22\t+\t.\tID=mp3-2_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Parent=ms3_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 150 350;Identity=35.89\n")
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427
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428 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t88031\t88080\t0.0\t+\t.\tID=ms4_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Target=DTX-incomp_fTest05105818-B-G1-Map3 370 420;Identity=31.89\n")
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429 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t88031\t88080\t3e-23\t+\t.\tID=mp4-1_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Parent=ms4_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Target=DTX-incomp_fTest05105818-B-G1-Map3 370 420;Identity=31.89\n")
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430
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431 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t108081\t108588\t0.0\t-\t.\tID=ms5_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G9-Map3_reversed;Target=DTX-incomp_fTest05105818-B-G9-Map3_reversed 590 820;TargetDescription=CI:33 coding:(TE_BLRtx: PROTOP:classII:TIR: 10.92% | PROTOP:classII:TIR: 11.03% | PROTOP_A:classII:TIR: 55.20%) struct:(TElength: >700bps) other:(HG_BLRn: FBtr0089196_Dmel_r4.3: 35.60% SSRCoverage:0.21<0.75);Identity=32.89\n")
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432 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t108081\t108588\t3e-24\t-\t.\tID=mp5-1_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G9-Map3_reversed;Parent=ms5_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G9-Map3_reversed;Target=DTX-incomp_fTest05105818-B-G9-Map3_reversed 590 820;Identity=32.89\n")
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433
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434 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t118081\t118588\t0.0\t+\t.\tID=ms6_lm_SuperContig_30_v2_PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed;Target=PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed 154 289;TargetDescription=CI:100 coding:(HG_BLRn: FBtr0089196_Dmel_r4.3: 99.91%) other:(TE_BLRtx: PROTOP:classII:TIR: 13.06% | PROTOP_A:classII:TIR: 37.47% SSRCoverage:0.27<0.75);Identity=33.89\n")
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435 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t118081\t118588\t3e-25\t+\t.\tID=mp6-1_lm_SuperContig_30_v2_PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed;Parent=ms6_lm_SuperContig_30_v2_PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed;Target=PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed 154 289;Identity=33.89\n")
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436
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437 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t288031\t288080\t0.0\t+\t.\tID=ms7_lm_SuperContig_30_v2_noCat_Blc22_fTest05105818-B-R2-Map6;Target=noCat_Blc22_fTest05105818-B-R2-Map6 1900 2090;TargetDescription=CI:NA coding:(HG_BLRn: FBtr0089179_Dmel_r4.3: 73.65%) struct:(SSRCoverage:0.05<0.75);Identity=34.89\n")
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438 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t288031\t288080\t3e-26\t+\t.\tID=mp7-1_lm_SuperContig_30_v2_noCat_Blc22_fTest05105818-B-R2-Map6;Parent=ms7_lm_SuperContig_30_v2_noCat_Blc22_fTest05105818-B-R2-Map6;Target=noCat_Blc22_fTest05105818-B-R2-Map6 1900 2090;Identity=34.89\n")
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439
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440 f.close()
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441
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442 def _writePathFile_withClassif_withIdenticalMatches(self,inFileName):
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443 f = open(inFileName,'w')
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444 f.write('1\tlm_SuperContig_29_v2\t193781\t194212\t1nc550_030\t228\t85\t1e-40\t84\t30.56\n')
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445 f.write('2\tlm_SuperContig_29_v2\t192832\t193704\t1nc550_030\t522\t229\t1e-40\t106\t23.99\n')
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446 f.write('3\tlm_SuperContig_30_v2\t78081\t78088\tDHX-incomp_Blc1_fTest05105818-B-R1-Map4\t19\t209\t3e-21\t101\t30.89\n')
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447 f.write('3\tlm_SuperContig_30_v2\t78089\t78588\tDHX-incomp_Blc1_fTest05105818-B-R1-Map4\t150\t350\t3e-22\t101\t35.89\n')
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448 f.write('4\tlm_SuperContig_30_v2\t88031\t88080\tDTX-incomp_fTest05105818-B-G1-Map3\t370\t420\t3e-23\t101\t31.89\n')
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449 f.write('5\tlm_SuperContig_30_v2\t108588\t108081\tDTX-incomp_fTest05105818-B-G9-Map3_reversed\t590\t820\t3e-24\t101\t32.89\n')
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450 f.write('6\tlm_SuperContig_30_v2\t118081\t118588\tPotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed\t154\t289\t3e-25\t101\t33.89\n')
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451
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452 f.write('7\tlm_SuperContig_30_v2\t288031\t288080\tnoCat_Blc22_fTest05105818-B-R2-Map6\t1900\t2090\t3e-26\t101\t34.89\n')
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453 f.write('8\tlm_SuperContig_30_v2\t288031\t288080\tDTX-incomp_fTest05105818-B-P0.0-Map3\t100\t190\t3e-26\t101\t39.89\n')
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454 f.write('9\tlm_SuperContig_30_v2\t288031\t288080\tRLX-incomp_fTest05105818-B-R12-Map3_reversed\t1100\t1290\t3e-26\t101\t40.89\n')
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455 f.write('10\tlm_SuperContig_30_v2\t288031\t288080\tPotentialHostGene-chim_fTest05105818-B-G11-Map20\t990\t1890\t3e-26\t101\t38.09\n')
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456
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457 f.write('11\tlm_SuperContig_30_v2\t288031\t288080\tDTX-incomp_fTest05105818-B-G1-Map3\t990\t1890\t3e-26\t301\t38.09\n')
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458
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459 f.write('12\tlm_SuperContig_30_v2\t388031\t388080\tDHX-incomp_Blc1_fTest05105818-B-R1-Map4\t19\t209\t3e-21\t101\t30.89\n')
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460 f.write('12\tlm_SuperContig_30_v2\t388081\t388380\tDHX-incomp_Blc1_fTest05105818-B-R1-Map4\t150\t350\t3e-22\t101\t35.89\n')
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461
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462 f.write('13\tlm_SuperContig_30_v2\t388031\t388080\tDTX-incomp_fTest05105818-B-P0.0-Map3\t119\t309\t3e-21\t101\t30.89\n')
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463 f.write('13\tlm_SuperContig_30_v2\t388081\t388380\tDTX-incomp_fTest05105818-B-P0.0-Map3\t250\t450\t3e-22\t101\t35.89\n')
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464 f.close()
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465
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466 def _writeExpPathGFFFile_without_seq_withClassif_withIdenticalMatches(self, inFileName):
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467 f = open(inFileName, 'w')
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468 f.write("##gff-version 3\n")
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469 f.write("##sequence-region lm_SuperContig_30_v2 1 120\n")
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470 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t78081\t78588\t0.0\t+\t.\tID=ms3_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 19 350;TargetDescription=CI:20 coding:(TE_BLRtx: DNAREP1_DM:classII:Helitron: 17.00% | DNAREP1_DYak:classII:Helitron: 9.08%) struct:(TElength: >700bps) other:(HG_BLRn: FBtr0089179_Dmel_r4.3: 13.52% SSRCoverage:0.18<0.75)\n")
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471 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78088\t3e-21\t+\t.\tID=mp3-1_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Parent=ms3_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 19 209;Identity=30.89\n")
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472 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t78089\t78588\t3e-22\t+\t.\tID=mp3-2_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Parent=ms3_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 150 350;Identity=35.89\n")
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473
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474 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t88031\t88080\t0.0\t+\t.\tID=ms4_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Target=DTX-incomp_fTest05105818-B-G1-Map3 370 420;Identity=31.89\n")
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475 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t88031\t88080\t3e-23\t+\t.\tID=mp4-1_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Parent=ms4_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Target=DTX-incomp_fTest05105818-B-G1-Map3 370 420;Identity=31.89\n")
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476
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477 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t108081\t108588\t0.0\t-\t.\tID=ms5_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G9-Map3_reversed;Target=DTX-incomp_fTest05105818-B-G9-Map3_reversed 590 820;TargetDescription=CI:33 coding:(TE_BLRtx: PROTOP:classII:TIR: 10.92% | PROTOP:classII:TIR: 11.03% | PROTOP_A:classII:TIR: 55.20%) struct:(TElength: >700bps) other:(HG_BLRn: FBtr0089196_Dmel_r4.3: 35.60% SSRCoverage:0.21<0.75);Identity=32.89\n")
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478 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t108081\t108588\t3e-24\t-\t.\tID=mp5-1_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G9-Map3_reversed;Parent=ms5_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G9-Map3_reversed;Target=DTX-incomp_fTest05105818-B-G9-Map3_reversed 590 820;Identity=32.89\n")
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|
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479
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|
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480 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t118081\t118588\t0.0\t+\t.\tID=ms6_lm_SuperContig_30_v2_PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed;Target=PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed 154 289;TargetDescription=CI:100 coding:(HG_BLRn: FBtr0089196_Dmel_r4.3: 99.91%) other:(TE_BLRtx: PROTOP:classII:TIR: 13.06% | PROTOP_A:classII:TIR: 37.47% SSRCoverage:0.27<0.75);Identity=33.89\n")
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481 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t118081\t118588\t3e-25\t+\t.\tID=mp6-1_lm_SuperContig_30_v2_PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed;Parent=ms6_lm_SuperContig_30_v2_PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed;Target=PotentialHostGene-chim_Blc6_fTest05105818-B-R4-Map5_reversed 154 289;Identity=33.89\n")
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482
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|
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483 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t288031\t288080\t0.0\t+\t.\tID=ms10_lm_SuperContig_30_v2_PotentialHostGene-chim_fTest05105818-B-G11-Map20;Target=PotentialHostGene-chim_fTest05105818-B-G11-Map20 990 1890;OtherTargets=RLX-incomp_fTest05105818-B-R12-Map3_reversed 1100 1290, DTX-incomp_fTest05105818-B-P0.0-Map3 100 190, noCat_Blc22_fTest05105818-B-R2-Map6 1900 2090\n")
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484 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t288031\t288080\t3e-26\t+\t.\tID=mp10-1_lm_SuperContig_30_v2_PotentialHostGene-chim_fTest05105818-B-G11-Map20;Parent=ms10_lm_SuperContig_30_v2_PotentialHostGene-chim_fTest05105818-B-G11-Map20;Target=PotentialHostGene-chim_fTest05105818-B-G11-Map20 990 1890\n")
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485
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486 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t288031\t288080\t0.0\t+\t.\tID=ms11_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Target=DTX-incomp_fTest05105818-B-G1-Map3 990 1890;Identity=38.09\n")
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487 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t288031\t288080\t3e-26\t+\t.\tID=mp11-1_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Parent=ms11_lm_SuperContig_30_v2_DTX-incomp_fTest05105818-B-G1-Map3;Target=DTX-incomp_fTest05105818-B-G1-Map3 990 1890;Identity=38.09\n")
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488
|
|
|
489 #TODO:
|
|
|
490 #Should this case really occur : If merging multiple match-parts, the current behaviour needs to be fixed to get correct subject start/end coordinates
|
|
|
491 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch\t388031\t388380\t0.0\t+\t.\tID=ms12_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 19 350;OtherTargets=DTX-incomp_fTest05105818-B-P0.0-Map3 119 309\n")
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|
492 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t388031\t388080\t3e-21\t+\t.\tID=mp12-1_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Parent=ms12_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 19 209\n")
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493 f.write("lm_SuperContig_30_v2\tprojectName_REPET_TEs\tmatch_part\t388081\t388380\t3e-22\t+\t.\tID=mp12-2_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Parent=ms12_lm_SuperContig_30_v2_DHX-incomp_Blc1_fTest05105818-B-R1-Map4;Target=DHX-incomp_Blc1_fTest05105818-B-R1-Map4 150 350\n")
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494 f.close()
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|
495
|
|
|
496 def _writeTablesFile_withTESeqTables(self, tableType):
|
|
|
497 tableFile = open( self._tablesFileName, "w" )
|
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|
498 string = "%s_REPET_TEs\t%s\t%s_chr_allTEs_nr_noSSR_join_%s\t%s_refTEs_seq\n" % (self._projectName, tableType, self._projectName, tableType, self._projectName)
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|
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499 tableFile.write(string)
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|
|
500 string = "%s_REPET_TEs\t%s\t%s_chr_bankBLRtx_%s\t%s_bankBLRtx_nt_seq\n" % (self._projectName, tableType, self._projectName, tableType, self._projectName)
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|
|
501 tableFile.write(string)
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|
|
502 tableFile.close()
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503
|
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|
504 def _writeTablesFile(self, tableType):
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|
505 tableFile = open( self._tablesFileName, "w" )
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|
506 string = "%s_REPET_TEs\t%s\t%s_chr_allTEs_nr_noSSR_join_%s\n" % (self._projectName, tableType, self._projectName, tableType)
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|
|
507 tableFile.write(string)
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|
|
508 tableFile.close()
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|
|
509
|
|
|
510 def _writePathFile(self,inFileName):
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|
511 f = open(inFileName,'w')
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|
|
512 f.write('1\tlm_SuperContig_29_v2\t193781\t194212\tDTX-incomp_DmelChr4-L-B1-Map3\t228\t85\t1e-40\t84\t30.56\n')
|
|
|
513 f.write('2\tlm_SuperContig_29_v2\t192832\t193704\tDTX-incomp_DmelChr4-L-B1-Map3\t522\t229\t1e-40\t106\t23.99\n')
|
|
|
514 f.write('3\tlm_SuperContig_29_v2\t78031\t78080\tDTX-incomp_DmelChr4-B-P0.0-Map3\t19\t209\t3e-21\t101\t30.89\n')
|
|
|
515 f.write('3\tlm_SuperContig_29_v2\t78081\t78588\tDTX-incomp_DmelChr4-B-P0.0-Map3\t19\t209\t3e-21\t101\t30.89\n')
|
|
|
516 f.close()
|
|
|
517
|
|
|
518 def _writePathFile2(self,inFileName):
|
|
|
519 f = open(inFileName,'w')
|
|
|
520 f.write('1\tchr1\t1\t100\tPROTOP_B:classII:TIR\t228\t85\t1e-20\t84\t30.56\n')
|
|
|
521 f.write('2\tchr1\t100\t1000\tDMRT1C:classI:?\t228\t85\t1e-30\t84\t30.56\n')
|
|
|
522 f.close()
|
|
|
523
|
|
|
524 def _writePathFile_refTEs_annotation(self,inFileName):
|
|
|
525 f = open(inFileName,'w')
|
|
|
526 f.write('6\tdmel_chr4\t4364\t4611\tDTX-incomp_DmelChr4-L-B1-Map3\t854\t1150\t0\t1475\t91.24\n')
|
|
|
527 f.write('21\tdmel_chr4\t4630\t4704\tDTX-incomp_DmelChr4-B-P0.0-Map3\t232\t312\t0\t65\t84.4417\n')
|
|
|
528 f.write('21\tdmel_chr4\t4837\t4889\tDTX-incomp_DmelChr4-B-P0.0-Map3\t456\t512\t0\t46\t84.4417\n')
|
|
|
529 f.write('35\tdmel_chr1\t4364\t4611\tDTX-incomp_DmelChr4-L-B1-Map3\t854\t1150\t0\t1475\t91.24\n')
|
|
|
530 f.close()
|
|
|
531
|
|
|
532 def _writePathFile_bankBLRtx_annotation(self,inFileName):
|
|
|
533 f = open(inFileName, 'w')
|
|
|
534 f.write('27\tdmel_chr4\t4412\t4501\tPROTOP_B:classII:TIR\t1082\t993\t5e-108\t702\t91.3066\n')
|
|
|
535 f.write('27\tdmel_chr4\t4483\t4652\tPROTOP_B:classII:TIR\t990\t821\t9e-146\t707\t86.5572\n')
|
|
|
536 f.write('27\tdmel_chr4\t4672\t4775\tPROTOP_B:classII:TIR\t787\t684\t9e-146\t707\t88.8013\n')
|
|
|
537 f.write('27\tdmel_chr4\t4782\t4889\tPROTOP_B:classII:TIR\t661\t553\t9e-141\t356\t53.7067\n')
|
|
|
538 f.write('66\tdmel_chr4\t3143\t3361\tDMRT1C:classI:?\t2206\t1988\t0\t1878\t89.7202\n')
|
|
|
539 f.write('66\tdmel_chr4\t3345\t3410\tDMRT1C:classI:?\t1719\t1654\t0\t313\t54.55\n')
|
|
|
540 f.write('66\tdmel_chr4\t3448\t3572\tDMRT1C:classI:?\t1619\t1495\t0\t1252\t77.3433\n')
|
|
|
541 f.write('66\tdmel_chr4\t3564\t3693\tDMRT1C:classI:?\t1509\t1380\t0\t1565\t83.7306\n')
|
|
|
542 f.write('66\tdmel_chr4\t3705\t3857\tDMRT1C:classI:?\t691\t539\t0\t1252\t84.5762\n')
|
|
|
543 f.write('66\tdmel_chr4\t3861\t3992\tDMRT1C:classI:?\t534\t403\t0\t1565\t67.1422\n')
|
|
|
544 f.write('66\tdmel_chr4\t3985\t4106\tDMRT1C:classI:?\t411\t290\t0\t1252\t76.612\n')
|
|
|
545 f.write('66\tdmel_chr4\t4102\t4248\tDMRT1C:classI:?\t285\t139\t0\t1565\t75.3027\n')
|
|
|
546 f.write('66\tdmel_chr4\t4236\t4364\tDMRT1C:classI:?\t152\t24\t0\t1565\t66.6657\n')
|
|
|
547 f.write('141\tdmel_chr4\t4917\t5007\tBATUMI_I:classI:LTR_retrotransposon\t7030\t7120\t2e-144\t984\t94.1756\n')
|
|
|
548 f.write('141\tdmel_chr4\t4976\t5195\tBATUMI_I:classI:LTR_retrotransposon\t7087\t7303\t2e-144\t2098\t82.2343\n')
|
|
|
549 f.close()
|
|
|
550
|
|
|
551 def _writePathFileReverse(self,inFileName):
|
|
|
552 f = open(inFileName,'w')
|
|
|
553 f.write('1\tlm_SuperContig_29_v2\t193781\t194212\t1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein)\t228\t85\t1e-40\t84\t30.56\n')
|
|
|
554 f.write('2\tlm_SuperContig_29_v2\t192832\t193704\t1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein)\t522\t229\t1e-40\t106\t23.99\n')
|
|
|
555 f.write('3\tlm_SuperContig_29_v2\t78080\t78031\txnc164_090 related to multidrug resistance protein\t19\t209\t3e-21\t101\t30.89\n')
|
|
|
556 f.write('3\tlm_SuperContig_29_v2\t78588\t78081\txnc164_090 related to multidrug resistance protein\t19\t209\t3e-21\t101\t30.89\n')
|
|
|
557 f.close()
|
|
|
558
|
|
|
559 def _writeSetFile(self,inFileName):
|
|
|
560 f = open(inFileName,'w')
|
|
|
561 f.write('1\tset1\tlm_SuperContig_29_v2\t193781\t194212\n')
|
|
|
562 f.write('2\tset2\tlm_SuperContig_29_v2\t192832\t193704\n')
|
|
|
563 f.write('3\tset3\tlm_SuperContig_29_v2\t78031\t78080\n')
|
|
|
564 f.write('3\tset3\tlm_SuperContig_29_v2\t78081\t78588\n')
|
|
|
565 f.close()
|
|
|
566
|
|
|
567 def _writeSetFileReverse(self,inFileName):
|
|
|
568 f = open(inFileName,'w')
|
|
|
569 f.write('1\tset1\tlm_SuperContig_29_v2\t193781\t194212\n')
|
|
|
570 f.write('2\tset2\tlm_SuperContig_29_v2\t192832\t193704\n')
|
|
|
571 f.write('3\tset3\tlm_SuperContig_29_v2\t78080\t78031\n')
|
|
|
572 f.write('3\tset3\tlm_SuperContig_29_v2\t78588\t78081\n')
|
|
|
573 f.close()
|
|
|
574
|
|
|
575 def _writeExpEmptyPathGFFFile(self, inFileName):
|
|
|
576 f = open(inFileName, 'w')
|
|
|
577 f.write("##gff-version 3\n")
|
|
|
578 f.write("##sequence-region lm_SuperContig_30_v2 1 120\n")
|
|
|
579 f.close()
|
|
|
580
|
|
|
581 def _writeExpPathGFFFile(self, inFileName):
|
|
|
582 f = open(inFileName, 'w')
|
|
|
583 f.write("##gff-version 3\n")
|
|
|
584 f.write("##sequence-region lm_SuperContig_29_v2 1 120\n")
|
|
|
585 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t193781\t194212\t0.0\t-\t.\tID=ms1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 85 228;Identity=30.56\n")
|
|
|
586 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t193781\t194212\t1e-40\t-\t.\tID=mp1-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Parent=ms1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 85 228;Identity=30.56\n")
|
|
|
587 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t192832\t193704\t0.0\t-\t.\tID=ms2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 229 522;Identity=23.99\n")
|
|
|
588 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t192832\t193704\t1e-40\t-\t.\tID=mp2-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Parent=ms2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 229 522;Identity=23.99\n")
|
|
|
589 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t78031\t78588\t0.0\t+\t.\tID=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209\n")
|
|
|
590 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78031\t78080\t3e-21\t+\t.\tID=mp3-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;Identity=30.89\n")
|
|
|
591 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78588\t3e-21\t+\t.\tID=mp3-2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;Identity=30.89\n")
|
|
|
592 f.write("##FASTA\n")
|
|
|
593 self._writeSeq1(f)
|
|
|
594 f.close()
|
|
|
595
|
|
|
596 def _writeExpEmptyPathGFFFileWithSeq(self, inFileName):
|
|
|
597 f = open(inFileName, 'w')
|
|
|
598 f.write("##gff-version 3\n")
|
|
|
599 f.write("##sequence-region lm_SuperContig_30_v2 1 120\n")
|
|
|
600 f.write("##FASTA\n")
|
|
|
601 self._writeSeq2(f)
|
|
|
602 f.close()
|
|
|
603
|
|
|
604 def _writeExpPathGFFFile_without_seq(self, inFileName):
|
|
|
605 f = open(inFileName, 'w')
|
|
|
606 f.write("##gff-version 3\n")
|
|
|
607 f.write("##sequence-region lm_SuperContig_29_v2 1 120\n")
|
|
|
608 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t193781\t194212\t0.0\t-\t.\tID=ms1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 85 228;Identity=30.56\n")
|
|
|
609 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t193781\t194212\t1e-40\t-\t.\tID=mp1-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Parent=ms1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 85 228;Identity=30.56\n")
|
|
|
610 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t192832\t193704\t0.0\t-\t.\tID=ms2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 229 522;Identity=23.99\n")
|
|
|
611 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t192832\t193704\t1e-40\t-\t.\tID=mp2-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Parent=ms2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 229 522;Identity=23.99\n")
|
|
|
612 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t78031\t78588\t0.0\t+\t.\tID=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209\n")
|
|
|
613 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78031\t78080\t3e-21\t+\t.\tID=mp3-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;Identity=30.89\n")
|
|
|
614 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78588\t3e-21\t+\t.\tID=mp3-2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;Identity=30.89\n")
|
|
|
615 f.close()
|
|
|
616
|
|
|
617 def _writeExpPathGFFFile_without_seq_and_match_part_not_comulsory(self, inFileName):
|
|
|
618 f = open(inFileName, 'w')
|
|
|
619 f.write("##gff-version 3\n")
|
|
|
620 f.write("##sequence-region lm_SuperContig_29_v2 1 120\n")
|
|
|
621 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t193781\t194212\t0.0\t-\t.\tID=ms1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 85 228;Identity=30.56\n")
|
|
|
622 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t192832\t193704\t0.0\t-\t.\tID=ms2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-L-B1-Map3;Target=DTX-incomp_DmelChr4-L-B1-Map3 229 522;Identity=23.99\n")
|
|
|
623 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t78031\t78588\t0.0\t+\t.\tID=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209\n")
|
|
|
624 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78031\t78080\t3e-21\t+\t.\tID=mp3-1_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;Identity=30.89\n")
|
|
|
625 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78588\t3e-21\t+\t.\tID=mp3-2_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Parent=ms3_lm_SuperContig_29_v2_DTX-incomp_DmelChr4-B-P0.0-Map3;Target=DTX-incomp_DmelChr4-B-P0.0-Map3 19 209;Identity=30.89\n")
|
|
|
626 f.close()
|
|
|
627
|
|
|
628 def _writeExpPathGFFFileReversed(self, inFileName):
|
|
|
629 f = open(inFileName, 'w')
|
|
|
630 f.write("##gff-version 3\n")
|
|
|
631 f.write("##sequence-region lm_SuperContig_29_v2 1 120\n")
|
|
|
632 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t193781\t194212\t0.0\t-\t.\tID=ms1_lm_SuperContig_29_v2_1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein);Target=1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein) 85 228;Identity=30.56\n")
|
|
|
633 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t193781\t194212\t1e-40\t-\t.\tID=mp1-1_lm_SuperContig_29_v2_1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein);Parent=ms1_lm_SuperContig_29_v2_1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein);Target=1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein) 85 228;Identity=30.56\n")
|
|
|
634 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t192832\t193704\t0.0\t-\t.\tID=ms2_lm_SuperContig_29_v2_1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein);Target=1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein) 229 522;Identity=23.99\n")
|
|
|
635 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t192832\t193704\t1e-40\t-\t.\tID=mp2-1_lm_SuperContig_29_v2_1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein);Parent=ms2_lm_SuperContig_29_v2_1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein);Target=1nc550_030 related to putative multidrug transporter Mfs1.1 (major facilitator family protein) 229 522;Identity=23.99\n")
|
|
|
636 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t78031\t78588\t0.0\t-\t.\tID=ms3_lm_SuperContig_29_v2_xnc164_090 related to multidrug resistance protein;Target=xnc164_090 related to multidrug resistance protein 19 209\n")
|
|
|
637 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78031\t78080\t3e-21\t-\t.\tID=mp3-1_lm_SuperContig_29_v2_xnc164_090 related to multidrug resistance protein;Parent=ms3_lm_SuperContig_29_v2_xnc164_090 related to multidrug resistance protein;Target=xnc164_090 related to multidrug resistance protein 19 209;Identity=30.89\n")
|
|
|
638 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78588\t3e-21\t-\t.\tID=mp3-2_lm_SuperContig_29_v2_xnc164_090 related to multidrug resistance protein;Parent=ms3_lm_SuperContig_29_v2_xnc164_090 related to multidrug resistance protein;Target=xnc164_090 related to multidrug resistance protein 19 209;Identity=30.89\n")
|
|
|
639 f.write("##FASTA\n")
|
|
|
640 self._writeSeq1(f)
|
|
|
641 f.close()
|
|
|
642
|
|
|
643 def _writeExpSetGFFFile(self, inFileName):
|
|
|
644 f = open(inFileName, 'w')
|
|
|
645 f.write("##gff-version 3\n")
|
|
|
646 f.write("##sequence-region lm_SuperContig_29_v2 1 120\n")
|
|
|
647 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t193781\t194212\t0.0\t+\t.\tID=ms1_lm_SuperContig_29_v2_set1;Target=set1 1 432\n")
|
|
|
648 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t193781\t194212\t0.0\t+\t.\tID=mp1-1_lm_SuperContig_29_v2_set1;Parent=ms1_lm_SuperContig_29_v2_set1;Target=set1 1 432\n")
|
|
|
649 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t192832\t193704\t0.0\t+\t.\tID=ms2_lm_SuperContig_29_v2_set2;Target=set2 1 873\n")
|
|
|
650 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t192832\t193704\t0.0\t+\t.\tID=mp2-1_lm_SuperContig_29_v2_set2;Parent=ms2_lm_SuperContig_29_v2_set2;Target=set2 1 873\n")
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651 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t78031\t78588\t0.0\t+\t.\tID=ms3_lm_SuperContig_29_v2_set3;Target=set3 1 558\n")
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652 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78031\t78080\t0.0\t+\t.\tID=mp3-1_lm_SuperContig_29_v2_set3;Parent=ms3_lm_SuperContig_29_v2_set3;Target=set3 1 50\n")
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653 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78588\t0.0\t+\t.\tID=mp3-2_lm_SuperContig_29_v2_set3;Parent=ms3_lm_SuperContig_29_v2_set3;Target=set3 1 508\n")
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654 f.write("##FASTA\n")
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655 self._writeSeq1(f)
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656 f.close()
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657
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658 def _writeExpSetGFFFileReversed(self, inFileName):
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659 f = open(inFileName, 'w')
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660 f.write("##gff-version 3\n")
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661 f.write("##sequence-region lm_SuperContig_29_v2 1 120\n")
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662 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t193781\t194212\t0.0\t+\t.\tID=ms1_lm_SuperContig_29_v2_set1;Target=set1 1 432\n")
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663 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t193781\t194212\t0.0\t+\t.\tID=mp1-1_lm_SuperContig_29_v2_set1;Parent=ms1_lm_SuperContig_29_v2_set1;Target=set1 1 432\n")
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664 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t192832\t193704\t0.0\t+\t.\tID=ms2_lm_SuperContig_29_v2_set2;Target=set2 1 873\n")
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665 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t192832\t193704\t0.0\t+\t.\tID=mp2-1_lm_SuperContig_29_v2_set2;Parent=ms2_lm_SuperContig_29_v2_set2;Target=set2 1 873\n")
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666 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch\t78031\t78588\t0.0\t-\t.\tID=ms3_lm_SuperContig_29_v2_set3;Target=set3 1 558\n")
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667 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78031\t78080\t0.0\t-\t.\tID=mp3-1_lm_SuperContig_29_v2_set3;Parent=ms3_lm_SuperContig_29_v2_set3;Target=set3 1 50\n")
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668 f.write("lm_SuperContig_29_v2\tprojectName_REPET_TEs\tmatch_part\t78081\t78588\t0.0\t-\t.\tID=mp3-2_lm_SuperContig_29_v2_set3;Parent=ms3_lm_SuperContig_29_v2_set3;Target=set3 1 508\n")
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669 f.write("##FASTA\n")
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670 self._writeSeq1(f)
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671 f.close()
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672
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673 def _writeFastaFile(self, inFileName):
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674 f = open(inFileName,'w')
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675 self._writeSeq2(f)
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676 self._writeSeq1(f)
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677 f.close()
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678
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679 def _writeFastaFileExtended(self, inFileName):
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680 f = open(inFileName,'w')
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681 self._writeSeq2(f)
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682 self._writeSeq1(f)
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683 f.write(">chr1\n")
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684 f.write("CTAAGCTGCGCTATGTAG\n")
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685 f.close()
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686
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687 def _writeSeq1(self, f):
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688 f.write('>lm_SuperContig_29_v2\n')
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689 f.write('CCTAGACAATTAATTATAATAATTAATAAACTATTAGGCTAGTAGTAGGTAATAATAAAA\n')
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690 f.write('GGATTACTACTAAGCTGCGCTATGTAGATATTTAAAACATGTGGCTTAGGCAAGAGTATA\n')
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|
691
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692 def _writeSeq2(self, f):
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693 f.write('>lm_SuperContig_30_v2\n')
|
|
|
694 f.write('TGTTCATATTCATAGGATGGAGCTAGTAAGCGATGTCGGCTTAGCTCATCCACATGAATG\n')
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695 f.write('CAGGAATCATGAAGGGTACGACTGTTCGTCGATTAAAGAGCTACACGAGCTGGGTTAAAT\n')
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696
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|
|
697 def _writeFastaFile_DmelChr4(self, inFileName):
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698 f = open(inFileName,'w')
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699 f.write(">dmel_chr4\n")
|
|
|
700 f.write("CTAAGCTGCGCTATGTAG\n")
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701 f.write(">dmel_chr1\n")
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|
|
702 f.write("CGTAACGCTAGCGCTTATAGTGAGC\n")
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|
|
703 f.close()
|
|
|
704
|
|
|
705
|
|
|
706 if __name__ == "__main__":
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|
|
707 unittest.main() |
