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18
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1 """
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2 Launch Blaster and then Matcher to compare the input sequences with known TEs via blastn and record the results into a MySQL table.
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3 """
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4
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5 import os
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6 import ConfigParser
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7 from commons.core.utils.FileUtils import FileUtils
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8 from commons.core.LoggerFactory import LoggerFactory
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9
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10 LOG_DEPTH = "repet.tools"
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11
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12 class RepbaseBLRnForClassifierStep1( object ):
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13
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14 """
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15 Launch Blaster and then Matcher to compare the input sequences with known TEs via blastn and record the results into a MySQL table.
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16
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17 @param inFileName: name of the input fasta file
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18 @type inFileName: string
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19
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20 @param launch_1: generic command at the beginning of a specific command
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21 @type launch_1: string
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22
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23 @param launch_2: generic command at the end of a specific command
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24 @type launch_2: string
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25
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26 @return: all the commands to run the job
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27 @rtype: string
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28
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29 @param cDir: current directory (where to retrieve the result files)
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30 @ype cDir: string
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31
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32 @param tmpDir: temporary directory (where the job will run)
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33 @type tmpDir: string
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34
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35 @param configFileName: configuration file name
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36 @type configFileName: string
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37
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38 @param logger: a logger Instance
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39 @type logger: logger
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40
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41 @param verbose: verbose(0/1/2)
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42 @type verbose: int
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43
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44 @param pL: program launcher
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45 @type pL: programLauncher Instance
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46
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47 @param project: project name
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48 @type project: string
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49
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50 """
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51
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52 def __init__(self, inFileName, launch_1, launch_2, cDir, tmpDir, configFileName, verbose, pL, project):
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53 """
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54 Constructor
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55 """
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56 self._inFileName = inFileName
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57 self._launch_1 = launch_1
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58 self._launch_2 = launch_2
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59 self._cDir = cDir
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60 self._tmpDir = tmpDir
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61 self._verbose = verbose
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62 self._pL = pL
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63 self._project = project
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64 self._fileUtils = FileUtils()
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65 self._config = ConfigParser.ConfigParser()
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66 self._configFileName = configFileName
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67 self._config.readfp( open(self._configFileName) )
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68 self._bank = self._config.get("detect_features","TE_nucl_bank")
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69 self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbose)
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70
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71 def formatRepbase_ntIfNecessary( self ):
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72 """
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73 Format Repbase (make 'cut' files).
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74 """
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75 if not os.path.exists( "%s_cut" % ( self._bank ) ):
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76 self._log.debug("prepare bank '%s'..." % ( self._bank ))
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77 prg = os.environ["REPET_PATH"] + "/bin/blaster"
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78 cmd = prg
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79 cmd += " -s %s" % ( self._bank )
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80 cmd += " -n blastn"
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81 if self._config.get("detect_features","wublast") == "yes":
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82 cmd += " -W"
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83 cmd += " -r"
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84 cmd += " -P"
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85 self._pL.launch( prg, cmd )
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86 os.system( "rm -f %s-blastn-*.param" % ( self._bank ) )
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87
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88 def createCmdToLaunch( self ):
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89 cmd = self._launch_1 + os.environ["REPET_PATH"] + "/bin/blaster"
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90 cmd += " -q %s" % ( self._inFileName )
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91 cmd += " -s %s/%s" % ( self._cDir, self._bank )
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92 cmd += " -B %s_BLRn_%s" % ( self._inFileName, self._bank )
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93 cmd += " -n blastn"
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94 if self._config.get("detect_features","wublast") == "yes":
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95 cmd += " -W"
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96 cmd += " -r"
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97 cmd += " -v 1"
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98 cmd += self._launch_2
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99
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100 cmd += "if not os.path.exists( \"%s/%s_BLRn_%s.param\" ):\n" % ( self._cDir, self._inFileName, self._bank )
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101 cmd += "\tos.system( \"mv %s_BLRn_%s.param %s\" )\n" % ( self._inFileName, self._bank, self._cDir )
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102 cmd += "if os.path.exists( \"%s_cut\" ):\n" % ( self._inFileName )
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103 cmd += "\tos.system( \"rm -f %s_cut*\" )\n" % ( self._inFileName )
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104 cmd += "if os.path.exists( \"%s.Nstretch.map\" ):\n" % ( self._inFileName )
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105 cmd += "\tos.remove( \"%s.Nstretch.map\" )\n" % ( self._inFileName )
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106 cmd += "if os.path.exists( \"%s_BLRn_%s.raw\" ):\n" % ( self._inFileName, self._bank )
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107 cmd += "\tos.remove( \"%s_BLRn_%s.raw\" )\n" % ( self._inFileName, self._bank )
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108 cmd += "if os.path.exists( \"%s_BLRn_%s.seq_treated\" ):\n" % ( self._inFileName, self._bank )
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109 cmd += "\tos.remove( \"%s_BLRn_%s.seq_treated\" )\n" % ( self._inFileName, self._bank )
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110
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111 cmd += self._launch_1
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112 cmd += os.environ["REPET_PATH"] + "/bin/matcher"
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113 cmd += " -m %s_BLRn_%s.align" % ( self._inFileName, self._bank )
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114 cmd += " -q %s" % ( self._inFileName )
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115 cmd += " -s %s/%s" % ( self._cDir, self._bank )
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116 cmd += " -j"
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117 cmd += " -v 1"
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118 cmd += self._launch_2
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119
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120 cmd += "if not os.path.exists( \"%s/%s_BLRn_%s.align.clean_match.path\" ):\n" % ( self._cDir, self._inFileName, self._bank )
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121 cmd += "\tos.system( \"mv %s_BLRn_%s.align.clean_match.path %s\" )\n" % ( self._inFileName, self._bank, self._cDir )
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122 cmd += "if not os.path.exists( \"%s/%s_BLRn_%s.align.clean_match.param\" ):\n" % ( self._cDir, self._inFileName, self._bank )
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123 cmd += "\tos.system( \"mv %s_BLRn_%s.align.clean_match.param %s\" )\n" % ( self._inFileName, self._bank, self._cDir )
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124 cmd += "if os.path.exists( \"%s_BLRn_%s.align\" ):\n" % ( self._inFileName, self._bank )
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125 cmd += "\tos.remove( \"%s_BLRn_%s.align\" )\n" % ( self._inFileName, self._bank )
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126 cmd += "if os.path.exists( \"%s_BLRn_%s.align.clean_match.fa\" ):\n" % ( self._inFileName, self._bank )
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127 cmd += "\tos.remove( \"%s_BLRn_%s.align.clean_match.fa\" )\n" % ( self._inFileName, self._bank )
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128 cmd += "if os.path.exists( \"%s_BLRn_%s.align.clean_match.map\" ):\n" % ( self._inFileName, self._bank )
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129 cmd += "\tos.remove( \"%s_BLRn_%s.align.clean_match.map\" )\n" % ( self._inFileName, self._bank )
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130 cmd += "if os.path.exists( \"%s_BLRn_%s.align.clean_match.tab\" ):\n" % ( self._inFileName, self._bank )
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131 cmd += "\tos.remove( \"%s_BLRn_%s.align.clean_match.tab\" )\n" % ( self._inFileName, self._bank )
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132
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133 if self._tmpDir != self._cDir:
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134 cmd += "if os.path.exists( \"%s\" ):\n" % ( self._bank )
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135 cmd += "\tos.remove( \"%s\" )\n" % ( self._bank )
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136
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137 return cmd
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138
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139 def collectRepbaseBLRn( self ):
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140 """
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141 Concatenate the outputs of blastn, adapt the ID and load the results into a table.
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142 """
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143 bankFull = self._bank
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144 bankPath, bank = os.path.split( bankFull )
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145 self._concatPathFile(bank)
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146 self._adaptIDInPathFile(bank)
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147 self._loadPathFileInTable(bank)
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148 self._findAndRemoveUselessFiles(bank)
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149
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150 def _concatPathFile(self, bank):
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151 FileUtils.catFilesByPattern("../batch_*.fa_BLRn_%s.align.clean_match.path" % bank,
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152 "%s_BLRn_%s.align.clean_match.path.tmp" % (self._project, bank))
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153
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154 def _adaptIDInPathFile(self, bank):
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155 if os.path.exists(os.environ["REPET_PATH"] + "/bin/pathnum2id"):
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156 prg = os.environ["REPET_PATH"] + "/bin/pathnum2id"
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157 cmd = prg
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158 cmd += " -i %s_BLRn_%s.align.clean_match.path.tmp" % (self._project, bank)
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159 cmd += " -o %s_BLRn_%s.align.clean_match.path" % (self._project, bank)
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160 cmd += " -v %i" % (self._verbose - 1)
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161 self._pL.launch(prg, cmd)
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162 else:
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163 prg = os.environ["REPET_PATH"] + "/bin/pathnum2id.py"
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164 cmd = prg
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165 cmd += " -i %s_BLRn_%s.align.clean_match.path.tmp" % (self._project, bank)
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166 cmd += " -o %s_BLRn_%s.align.clean_match.path" % (self._project, bank)
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167 self._pL.launch(prg, cmd)
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168
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169 def _loadPathFileInTable(self, bank):
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170 prg = os.environ["REPET_PATH"] + "/bin/srptCreateTable.py"
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171 cmd = prg
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172 cmd += " -f %s_BLRn_%s.align.clean_match.path" % (self._project, bank)
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173 cmd += " -n %s_TE_BLRn_path" % (self._project)
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174 cmd += " -t path"
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175 cmd += " -c ../%s" % (self._configFileName)
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176 self._pL.launch(prg, cmd)
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177
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178 def _findAndRemoveUselessFiles(self, bank):
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179 prg = "find"
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180 cmd = prg
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181 cmd += " .. -name \"batch_*.fa_BLRn_%s.*\" -exec rm {} \;" % (bank)
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182 self._pL.launch(prg, cmd)
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183 prg = "rm"
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184 cmd = prg
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185 cmd += " %s_BLRn_%s.align.clean_match.path.tmp" % (self._project, bank)
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186 self._pL.launch(prg, cmd)
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