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1 #!/usr/bin/env python
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2
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3 import user, os, sys, getopt, ConfigParser
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4 from os import listdir
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5
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6 def setup_env():
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7 if "REPET_PATH" in os.environ.keys():
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8 sys.path.append( os.environ["REPET_PATH"] )
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9 else:
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10 print "*** Error: no environment variable REPET_PATH ***"
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11 sys.exit(1)
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12 setup_env()
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13
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14 from pyRepet.sql.RepetDBMySQL import *
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15 from pyRepet.gamexml.Xml_writer import *
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16 from pyRepet.gamexml.computational import *
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17
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18 #------------------------------------------------------------------------------
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19
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20 def help():
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21
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22 print ""
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23 print "usage:",sys.argv[0],"[options]"
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24 print "options:"
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25 print " -h: this help"
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26 print " -f: fasta file (required to generate new '.gamexml' files)"
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27 print " -n: annotation tier_name"
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28 print " -g: gamexml file (for Apollo). If it's not mentionned, all '.gamexml' files will be updated with the result file"
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29 print " -l: light gameXML file (without sequence)"
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30 print " -r: result files (require -n)"
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31 print " -R: reverse the query and subject of Blaster results"
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32 print " -s: tier_name of an annotation to remove from a gameXML file"
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33 print " -t: file of table name to use to create the gamexml files (tier name 'tab' format 'tab' table name)"
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34 print " -c: configuration file from TEdenovo or TEannot pipeline"
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35 print " -H: MySQL host (if no configuration file)"
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36 print " -U: MySQL user (if no configuration file)"
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37 print " -P: MySQL password (if no configuration file)"
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38 print " -D: MySQL database (if no configuration file)"
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39 print " -v: verbose (default=0/1/2)"
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40 print ""
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41
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42 #------------------------------------------------------------------------------
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43
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44 def automatisation( result_file, tier_name, reverse, comput ):
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45
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46 if verbose > 1:
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47 print "Auto update"; sys.stdout.flush()
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48 writer = Xml_writer()
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49 file_liste = []
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50 liste_comp = []
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51 liste_comp = listdir('./')
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52
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53 if result_file != "":
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54 for j in liste_comp:
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55 if writer.file_in_keys( j, comput ):
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56 file_liste = file_liste + [j]
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57
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58 for i in file_liste:
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59 writer.update_gamexml( i, result_file, tier_name, comput )
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60
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61 else:
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62 for j in liste_comp:
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63 if j.find( "gamexml" ) != -1:
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64 writer.parse_gamexml( j )
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65 writer.verif_name_prog( tier_name )
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66 writer.write( j )
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67 if verbose > 1:
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68 print tier_name + " program from " +j +" removed"
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69
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70 #------------------------------------------------------------------------------
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71
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72 def main():
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73
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74 f_result = ""
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75 f_gamexml = ""
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76 f_fasta = ""
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77 f_table = ""
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78 tier_name = ""
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79 substract_name = ""
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80 no_seq = 0
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81 configFileName = ""
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82 host = ""
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83 user = ""
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84 passwd = ""
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85 dbname = ""
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86 verbose = 0
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87
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88 try:
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89 options,arguments=getopt.getopt(sys.argv[1:],"hn:f:g:r:s:lRt:c:H:U:P:D:v:",["help","tier_name=","fasta","gamexml","result","substract_program","light","reverse_result","table"])
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90 except getopt.GetoptError:
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91 help()
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92 sys.exit(1)
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93 if options == []:
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94 help()
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95 sys.exit(1)
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96 for o,a in options:
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97 if o == "-h" or o == "--help":
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98 help()
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99 sys.exit(0)
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100 elif o == "-f" or o == "--fasta":
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101 f_fasta = a
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102 elif o == "-g" or o == "--gamexml":
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103 f_gamexml = a
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104 elif o == "-n" or o == "--tier_name":
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105 tier_name = a
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106 elif o == "-r" or o == "--result":
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107 f_result = a
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108 elif o == "-s" or o == "--subtract_program":
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109 substract_name = a
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110 elif o == "-l" or o == "--light":
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111 no_seq = 1
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112 elif o == "-R" or o == "--reverse_result":
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113 writer.set_reverse()
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114 elif o == "-t" or o == "--table":
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115 f_table = a
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116 elif o == "-c":
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117 configFileName = a
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118 elif o == "-H":
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119 host = a
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120 elif o == "-U":
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121 user = a
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122 elif o == "-P":
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123 passwd = a
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124 elif o == "-D":
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125 dbname = a
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126 elif o == "-v":
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127 verbose = int(a)
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128
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129 if tier_name == "" and substract_name == "" and f_result != "":
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130 print "*** Error: option -n required"
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131 help()
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132 sys.exit(1)
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133
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134 if f_fasta == "" and f_gamexml == "":
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135 print "*** Error: options -g or -f required"
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136 help()
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137 sys.exit(1)
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138
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139 if substract_name!="" and f_result!="" :
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140 print "Error: option -s and -r together"
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141 help()
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142 sys.exit(1)
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143
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144
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145 if verbose > 0:
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146 print "\nbeginning of %s" % (sys.argv[0].split("/")[-1])
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147 sys.stdout.flush()
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148
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149 if configFileName != "":
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150 config = ConfigParser.ConfigParser()
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151 config.readfp( open(configFileName) )
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152 host = config.get("repet_env","repet_host")
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153 user = config.get("repet_env","repet_user")
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154 passwd = config.get("repet_env","repet_pw")
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155 dbname = config.get("repet_env","repet_db")
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156
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157 if host == "" and os.environ.get( "REPET_HOST" ) != None:
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158 host = os.environ.get( "REPET_HOST" )
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159 if user == "" and os.environ.get( "REPET_USER" ) != None:
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160 user = os.environ.get( "REPET_USER" )
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161 if passwd == "" and os.environ.get( "REPET_PW" ) != None:
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162 passwd = os.environ.get( "REPET_PW" )
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163 if dbname == "" and os.environ.get( "REPET_DB" ) != None:
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164 dbname = os.environ.get( "REPET_DB" )
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165
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166 writer = Xml_writer()
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167
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168 # create the dico
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169 comput = computational()
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170
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171 # create all the ".gamexml" files (option '-f')
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172 if f_fasta != "":
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173 writer.create_gamexml( f_fasta, f_result, tier_name, comput, no_seq )
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174
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175 #
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176 if f_result != "":
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177 if f_gamexml != "":
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178 key = ".".join( f_gamexml.split(".")[:-1] )
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179 else:
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180 key = ""
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181 format = writer.find_type_file( f_result )
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182 resFile = open( f_result )
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183 if format == "path":
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184 comput.load_dico_path_from_file( key, f_result )
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185
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186 if f_table != "":
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187 if verbose > 1:
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188 print "parsing file %s... " % ( f_gamexml ); sys.stdout.flush()
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189 writer.parse_gamexml( f_gamexml )
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190
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191 if f_gamexml != "":
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192 ## key=".".join(f_gamexml.split(".")[:-1])
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193 key = f_gamexml.split(".")[0]
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194 else:
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195 key = ""
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196
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197 tfile = open( f_table )
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198 lines = tfile.readlines()
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199 for l in lines:
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200 if l[0] == "#":
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201 continue
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202 tok = l.split()
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203 #print tok
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204 if len(tok) == 0:
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205 break
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206 tier_name = tok[0]
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207 format = tok[1]
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208 table = tok[2]
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209 alias = ""
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210 if verbose > 1:
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211 print "table: " + table + " (format=" + format + ")"
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212 if len(tok) > 3:
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213 alias = tok[3]
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214 if verbose > 1:
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215 print " alias=" + alias
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216
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217 if host == "" or user == "" or passwd == "" or dbname == "":
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218 print "*** Error: missing information about MySQL connection"
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219 sys.exit(1)
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220 db = RepetDB( user, host, passwd, dbname )
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221
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222 if format == "path":
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223 comput.load_dico_path_from_table( db, key, table, alias )
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224 writer.update_gamexml_comput( tier_name, comput )
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225 elif format == "rpath":
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226 comput.load_dico_rpath_from_table( db, key, table, alias )
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227 elif format == "ipath":
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228 comput.load_dico_ipath_from_table( db, key, table, alias )
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229 writer.update_gamexml_comput( tier_name, comput )
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230 elif format == "align":
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231 comput.load_dico_align_from_table( db, key, table, alias )
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232 writer.update_gamexml_comput( tier_name, comput )
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233 elif format == "map":
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234 comput.load_dico_map_from_table( db, key, table, alias )
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235 writer.update_gamexml_comput( tier_name, comput )
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236 elif format == "rmap":
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237 comput.load_dico_rmap_from_table( db, key, table, alias )
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238 writer.update_gamexml_comput( tier_name, comput )
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239 elif format == "set":
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240 comput.load_dico_set_from_table( db, key, table, alias )
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241 writer.update_gamexml_comput( tier_name, comput )
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242 elif format == "annot":
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243 comput.load_dico_annot_from_table( db, key, table, alias )
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244 writer.update_gamexml_annot( table, comput )
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245 elif format == "annot_set":
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246 comput.load_dico_annotset_from_table( db, key, table, alias )
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247 writer.update_gamexml_annot( table, comput )
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248 else:
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249 print "*** Error: unknown format '%s'" % ( format )
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250 sys.exit(1)
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251 writer.write(f_gamexml)
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252
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253 db.close()
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254
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255 #
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256 if f_gamexml == "" and f_result != "" and f_fasta == "":
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257 automatisation( f_result, tier_name, writer.get_reverse(), comput )
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258
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259 # update a ".gamexml" file (options '-g' and '-t')
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260 if f_gamexml != "" and f_result != "":
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261 writer.update_gamexml( f_gamexml, f_result, tier_name, comput )
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262
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263 # remove a comput
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264 if substract_name != "" and tier_name == "":
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265 if f_gamexml != "":
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266 writer.parse_gamexml( f_gamexml )
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267 writer.verif_name_prog( substract_name )
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268 writer.write( f_gamexml )
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269 if verbose > 1:
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270 print substract_name + " program from " + f_gamexml +" removed"
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271 else:
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272 automatisation( "", substract_name, 0, None )
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273
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274 if verbose > 0:
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275 print "%s finished successfully\n" % (sys.argv[0].split("/")[-1])
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276 sys.stdout.flush()
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277
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278 return 0
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279
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280 #------------------------------------------------------------------------------
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281
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282 if __name__ == '__main__':
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283 main()
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