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18
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1 #!/usr/bin/env python
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2
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3 """
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4 This program takes a query directory as input,
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5 then launches Blaster and/or Matcher on each file in it,
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6 finally results are optionally gathered in a single file.
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7 """
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8
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9 import os
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10 import sys
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11 import getopt
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12 import logging
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13 import glob
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14 import ConfigParser
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15
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16 from pyRepet.launcher.programLauncher import programLauncher
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17 from pyRepet.launcher import Launcher
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18 from pyRepet.sql.RepetJobMySQL import RepetJob
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19 from commons.core.coord.Align import Align
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20
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21
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22 def help():
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23 print
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24 print "usage: %s [ options ]" % ( sys.argv[0].split("/")[-1] )
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25 print "options:"
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26 print " -h: this help"
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27 print " -g: name of the group identifier (same for all the jobs)"
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28 print " -q: name of the query directory"
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29 print " -S: suffix in the query directory (default='*.fa' for Blaster, '*.align' for Matcher)"
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30 print " -s: absolute path to the subject databank"
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31 print " -Q: resources needed on the cluster)"
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32 print " -d: absolute path to the temporary directory"
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33 print " -m: mix of Blaster and/or Matcher"
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34 print " 1: launch Blaster only"
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35 print " 2: launch Matcher only (on '*.align' query files)"
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36 print " 3: launch Blaster+Matcher in the same job"
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37 print " -B: parameters for Blaster (e.g. \"-a -n tblastx\")"
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38 print " -M: parameters for Matcher (e.g. \"-j\")"
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39 print " -Z: collect all the results into a single file"
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40 print " align (after Blaster)"
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41 print " path/tab (after Matcher)"
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42 print " -C: configuration file from TEdenovo or TEannot pipeline"
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43 print " -t: name of the table recording the jobs (default=jobs)"
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44 print " -p: absolute path to project directory (if jobs management via files)"
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45 print " -c: clean (remove job launch files and job stdout)"
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46 print " -v: verbose (default=0/1/2)"
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47 print
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48
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49
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50 def filterRedundantMatches( inFile, outFile ):
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51 """
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52 When a pairwise alignment is launched ~ all-by-all (ie one batch against all chunks),
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53 one filters the redundant matches. For instance we keep 'chunk3-1-100-chunk7-11-110-...'
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54 and we discards 'chunk7-11-110-chunk3-1-100-...'.
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55 Also we keep 'chunk5-1-100-chunk5-11-110-...' and we discards
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56 'chunk5-11-110-chunk5-1-100-...'.
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57 For this of course the results need to be sorted by query, on plus strand,
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58 and in ascending coordinates (always the case with Blaster).
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59 """
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60 inFileHandler = open( inFile, "r" )
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61 outFileHandler = open( outFile, "w" )
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62 iAlign = Align()
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63 countMatches = 0
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64 tick = 100000
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65 while True:
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66 line = inFileHandler.readline()
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67 if line == "":
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68 break
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69 countMatches += 1
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70 iAlign.setFromString( line )
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71 if "chunk" not in iAlign.range_query.seqname \
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72 or "chunk" not in iAlign.range_subject.seqname:
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73 print "ERROR: 'chunk' not in seqname"
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74 sys.exit(1)
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75 if int(iAlign.range_query.seqname.split("chunk")[1]) < int(iAlign.range_subject.seqname.split("chunk")[1]):
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76 iAlign.write( outFileHandler )
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77 elif int(iAlign.range_query.seqname.split("chunk")[1]) == int(iAlign.range_subject.seqname.split("chunk")[1]):
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78 if iAlign.range_query.getMin() < iAlign.range_subject.getMin():
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79 iAlign.write( outFileHandler )
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80 if countMatches % tick == 0: # need to free buffer frequently as file can be big
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81 outFileHandler.flush()
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82 os.fsync( outFileHandler.fileno() )
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83 inFileHandler.close()
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84 outFileHandler.close()
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85
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86
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87 def runCollect( groupid, collect, allByAll ):
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88 """
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89 Gather the results of each job in a single job and adapt path ID if necessary.
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90 """
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91 if verbose > 0:
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92 print "concatenate the results of each job"; sys.stdout.flush()
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93
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94 # retrieve the list of the files
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95 lFiles = glob.glob( "*.%s" % ( collect ) )
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96 lFiles.sort()
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97
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98 # concatenate all the individual files
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99 if os.path.exists( "%s.%s_tmp" % ( groupid, collect ) ):
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100 os.remove( "%s.%s_tmp" % ( groupid, collect ) )
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101 for resFile in lFiles:
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102 prg = "cat"
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103 cmd = prg
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104 cmd += " %s >> %s.%s_tmp" % ( resFile, groupid, collect )
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105 pL.launch( prg, cmd )
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106 if clean == True:
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107 prg = "rm"
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108 cmd = prg
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109 cmd += " -f %s" % ( resFile )
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110 pL.launch( prg, cmd )
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111
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112 if os.path.exists( "%s.%s" % ( groupid, collect ) ):
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113 os.remove( "%s.%s" % ( groupid, collect ) )
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114
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115 if collect == "align":
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116 if not allByAll:
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117 os.system( "mv %s.%s_tmp %s.%s" % ( groupid, collect, groupid, collect ) )
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118 else:
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119 filterRedundantMatches( "%s.%s_tmp" % ( groupid, collect ),
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120 "%s.%s" % ( groupid, collect ) )
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121
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122 # adapt the path IDs if necessary
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123 elif collect == "path":
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124 prg = os.environ["REPET_PATH"] + "/bin/"
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125 if os.path.exists( prg + "pathnum2id" ):
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126 prg += "pathnum2id"
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127 cmd = prg
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128 cmd += " -i %s.path_tmp" % ( groupid )
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129 cmd += " -o %s.path" % ( groupid )
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130 cmd += " -v %i" % ( verbose - 1 )
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131 pL.launch( prg, cmd )
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132 else:
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133 prg += "pathnum2id.py"
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134 cmd = prg
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135 cmd += " -i %s.path_tmp" % ( groupid )
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136 cmd += " -o %s.path" % ( groupid )
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137 pL.launch( prg, cmd )
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138
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139 elif collect == "tab":
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140 prg = os.environ["REPET_PATH"] + "/bin/"
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141 if os.path.exists( prg + "tabnum2id" ):
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142 prg += "tabnum2id"
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143 cmd = prg
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144 cmd += " -i %s.tab_tmp" % ( groupid )
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145 cmd += " -o %s.tab" % ( groupid )
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146 cmd += " -v %i" % ( verbose - 1 )
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147 pL.launch( prg, cmd )
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148 else:
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149 prg += "tabnum2id.py"
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150 cmd = prg
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151 cmd += " -i %s.tab_tmp" % ( groupid )
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152 cmd += " -o %s.tab" % ( groupid )
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153 pL.launch( prg, cmd )
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154
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155 if clean == True:
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156 os.remove( "%s.%s_tmp" % ( groupid, collect ) )
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157
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158
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159 def main():
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160 """
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161 This program takes a query directory as input,
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162 then launches Blaster and/or Matcher on each file in it,
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163 finally results are optionally gathered in a single file.
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164 """
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165
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166 groupid = ""
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167 queryDir = ""
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168 patternSuffix = ""
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169 subjectBank = ""
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170 queue = ""
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171 tmpDir = ""
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172 mix = ""
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173 paramBlaster = ""
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174 paramMatcher = ""
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175 collect = ""
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176 configFileName = ""
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177 jobTable = "jobs"
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178 projectDir = ""
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179 global clean
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180 clean = False
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181 global verbose
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182 verbose = 0
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183 allByAll = False
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184
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185 try:
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186 opts, args = getopt.getopt(sys.argv[1:],"hg:q:S:s:Q:d:m:B:M:Z:C:t:p:cv:")
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187 except getopt.GetoptError, err:
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188 print str(err)
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189 help()
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190 sys.exit(1)
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191 for o,a in opts:
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192 if o == "-h":
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193 help()
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194 sys.exit(0)
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195 elif o == "-g":
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196 groupid = a
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197 elif o == "-q":
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198 queryDir = a
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199 if queryDir[-1] == "/":
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200 queryDir = queryDir[:-1]
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201 elif o == "-S":
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202 patternSuffix = a
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203 elif o == "-s":
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204 subjectBank = a
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205 elif o == "-Q":
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206 queue = a
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207 elif o == "-d":
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208 tmpDir = a
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209 if tmpDir[-1] == "/":
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210 tmpDir = tmpDir[:-1]
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211 elif o == "-m":
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212 mix = a
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213 elif o == "-B":
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214 paramBlaster = a
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215 elif o == "-M":
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216 paramMatcher = a
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217 elif o == "-C":
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218 configFileName = a
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219 elif o == "-Z":
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220 collect = a
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221 elif o == "-t":
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222 jobTable = a
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223 elif o == "-p":
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224 projectDir = a
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225 elif o == "-c":
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226 clean = True
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227 elif o == "-v":
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228 verbose = int(a)
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229
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230 if groupid == "":
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231 print "ERROR: missing group identifier (-g)"
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232 help()
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233 sys.exit(1)
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234
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235 if queryDir == "":
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236 print "ERROR: missing query directory (-q)"
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237 help()
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238 sys.exit(1)
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239
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240 if mix in [ "1", "3" ] and subjectBank == "":
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241 print "ERROR: missing subject bank for Blaster"
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242 sys.exit(1)
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243
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244 if os.environ["REPET_JOBS"] == "files" and projectDir == "":
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245 print "ERROR: missing compulsory options for jobs management via files"
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246 help()
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247 sys.exit(1)
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248
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249 if not os.path.exists( queryDir ):
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250 print "ERROR: can't find query directory '%s'" % ( queryDir )
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251 sys.exit(1)
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252
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253 if verbose > 0:
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254 print "START %s" % ( sys.argv[0].split("/")[-1] )
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255 sys.stdout.flush()
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256
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257
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258 logFileName = "%s_pid%s.log" % ( groupid, os.getpid() )
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259 handler = logging.FileHandler( logFileName )
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260 formatter = logging.Formatter( "%(asctime)s %(levelname)s: %(message)s" )
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261 handler.setFormatter( formatter )
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262 logging.getLogger('').addHandler( handler )
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263 logging.getLogger('').setLevel( logging.DEBUG )
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264 logging.info( "started" )
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265
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266
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267 if configFileName != "":
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268 if not os.path.exists( configFileName ):
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269 print "ERROR: configuration file '%s' doesn't exist" % ( configFileName )
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270 sys.exit(1)
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271 config = ConfigParser.ConfigParser()
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272 config.readfp( open(configFileName) )
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273 host = config.get("repet_env","repet_host")
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274 user = config.get("repet_env","repet_user")
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275 passwd = config.get("repet_env","repet_pw")
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276 dbname = config.get("repet_env","repet_db")
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277 else:
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278 host = os.environ["REPET_HOST"]
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279 user = os.environ["REPET_USER"]
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280 passwd = os.environ["REPET_PW"]
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281 dbname = os.environ["REPET_DB"]
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282
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283 if os.environ["REPET_JOBS"] == "files":
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284 jobdb = RepetJob( dbname = projectDir + "/" + os.environ["REPET_DB"] )
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285 elif os.environ["REPET_JOBS"] == "MySQL":
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286 jobdb = RepetJob( user, host, passwd, dbname )
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287 else:
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288 print "ERROR: REPET_JOBS is '%s'" % ( os.environ["REPET_JOBS"] )
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289 sys.exit(1)
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290
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291
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292 currentDir = os.getcwd()
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293 if tmpDir == "":
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294 tmpDir = currentDir
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295
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296 global pL
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297 pL = programLauncher()
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298
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299 if "-a" in paramBlaster:
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300 allByAll = True
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301
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302
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303 # if Blaster will be launched, prepare the subject data if necessary
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304 if mix != "2" and not os.path.exists( "%s_cut" % ( subjectBank ) ):
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305 if verbose > 0:
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306 print "prepare subject bank '%s'..." % ( subjectBank.split("/")[-1] )
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307 sys.stdout.flush()
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308 prg = "blaster"
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309 cmd = prg
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310 cmd += " -q %s" % ( subjectBank )
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311 cmd += " %s" % ( paramBlaster )
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312 cmd += " -P"
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313 pL.launch( prg, cmd )
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314
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315
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316 # launch Blaster only (on '*.fa' in queryDir)
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317 if mix == "1":
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318 launcher = Launcher.BlasterLauncher( jobdb, queryDir, subjectBank, paramBlaster, currentDir, tmpDir, jobTable, queue, groupid, "Blaster" )
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319 if patternSuffix == "":
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320 patternSuffix = "*.fa"
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321 launcher.run( patternSuffix, verbose )
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322 if clean == True:
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323 launcher.clean()
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324
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325 # launch Matcher only (on '*.align' in queryDir; don't use '-q' or '-s', only '-m')
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326 elif mix == "2":
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327 launcher = Launcher.MatcherLauncher( jobdb, queryDir, subjectBank, paramMatcher, currentDir, tmpDir, jobTable, queue, groupid, "Matcher" )
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328 if patternSuffix == "":
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329 patternSuffix = "*.align"
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330 launcher.run( patternSuffix, verbose )
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331 if clean == True:
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332 launcher.clean()
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333
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334 # launch Blaster+Matcher (on '*.fa' in queryDir)
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335 elif mix == "3":
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336 launcher = Launcher.Launcher( jobdb, queryDir, subjectBank, paramBlaster, currentDir, tmpDir, jobTable, queue, groupid, "BlasterMatcher" )
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337 launcher.beginRun()
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338 if patternSuffix == "":
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339 patternSuffix = "*.fa"
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340 lFaFiles = glob.glob( queryDir + "/" + patternSuffix )
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341 if len(lFaFiles) == 0:
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342 print "ERROR: query directory '%s' is empty of suffix '%s'" % ( queryDir, patternSuffix )
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343 sys.exit(1)
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344 count = 0
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345 for inFaName in lFaFiles:
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346 count += 1
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347 launcher.acronyme = "BlasterMatcher_%i" % ( count )
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348 launcher.job.jobname = launcher.acronyme
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349 prefix = os.path.basename( inFaName )
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350 cmd_start = ""
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351 cmd_start += "if not os.path.exists( \"" + prefix + "\" ):\n"
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352 cmd_start += "\tos.system( \"cp " + inFaName + " .\" )\n"
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353 launchB = ""
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354 launchB += "blaster"
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355 launchB += " -q %s" % ( prefix )
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356 launchB += " -s %s" % ( subjectBank )
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357 launchB += " -B %s" % ( prefix )
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358 if paramBlaster != "":
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359 launchB += " %s" % ( paramBlaster )
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360 cleanB = ""
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361 cleanB += "if not os.path.exists( \"%s/%s.param\" ):\n" % ( currentDir, prefix )
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362 cleanB += "\tos.system( \"mv %s.param %s\" )\n" % ( prefix, currentDir )
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363 cleanB += "if os.path.exists( \"" + prefix + ".Nstretch.map\" ):\n"
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364 cleanB += "\tos.remove( \"" + prefix + ".Nstretch.map\" )\n"
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365 cleanB += "if os.path.exists( \"" + prefix + "_cut\" ):\n"
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366 cleanB += "\tos.system( \"rm -f " + prefix + "_cut*\" )\n"
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367 cleanB += "if os.path.exists( \"" + prefix + ".raw\" ):\n"
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368 cleanB += "\tos.remove( \"" + prefix + ".raw\" )\n"
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369 cleanB += "if os.path.exists( \"" + prefix + ".seq_treated\" ):\n"
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370 cleanB += "\tos.remove( \"" + prefix + ".seq_treated\" )\n"
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371 launchM = ""
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372 launchM += os.environ["REPET_PATH"] + "/bin/matcher"
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373 launchM += " -m %s.align" % ( prefix )
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374 launchM += " -q %s" % ( prefix )
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375 launchM += " -s %s" % ( subjectBank )
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376 if paramMatcher != "":
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377 launchM += " %s" % ( paramMatcher )
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378 cleanM = ""
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379 s = ""
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380 if "-a" in paramMatcher:
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381 s = "match"
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382 else:
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383 s = "clean_match"
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384 if collect == "path":
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385 cleanM += "if not os.path.exists( \"%s/%s.align.%s.path\" ):\n" % ( currentDir, prefix, s )
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386 cleanM += "\tos.system( \"mv %s.align.%s.path %s\" )\n" % ( prefix, s, currentDir )
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387 cleanM += "if os.path.exists( \"" + prefix + ".align."+s+".tab\" ):\n"
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388 cleanM += "\tos.remove( \"" + prefix + ".align."+s+".tab\" )\n"
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389 elif collect == "tab":
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390 cleanM += "if not os.path.exists( \"%s/%s.align.%s.tab\" ):\n" % ( currentDir, prefix, s )
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391 cleanM += "\tos.system( \"mv %s.align.%s.tab %s\" )\n" % ( prefix, s, currentDir )
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392 cleanM += "if os.path.exists( \"" + prefix + ".align."+s+".path\" ):\n"
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393 cleanM += "\tos.remove( \"" + prefix + ".align."+s+".path\" )\n"
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394 cleanM += "if not os.path.exists( \"%s/%s.align.%s.param\" ):\n" % ( currentDir, prefix, s )
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395 cleanM += "\tos.system( \"mv %s.align.%s.param %s\" )\n" % ( prefix, s, currentDir )
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396 if tmpDir != currentDir:
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397 cleanM += "if os.path.exists( \"%s\" ):\n" % ( prefix )
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398 cleanM += "\tos.remove( \"%s\" )\n" % ( prefix )
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399 if clean == True:
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400 cleanM += "if os.path.exists( \"" + prefix + ".align\" ):\n"
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401 cleanM += "\tos.remove( \"" + prefix + ".align\" )\n"
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402 else:
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403 cleanM += "if not os.path.exists( \"%s/%s.align\" ):\n" % ( currentDir, prefix )
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404 cleanM += "\tos.system( \"mv %s.align %s\" )\n" % ( prefix, currentDir )
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405 cleanM += "if os.path.exists( \"" + prefix + ".align."+s+".fa\" ):\n"
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406 cleanM += "\tos.remove( \"" + prefix + ".align."+s+".fa\" )\n"
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407 cleanM += "if os.path.exists( \"" + prefix + ".align."+s+".map\" ):\n"
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408 cleanM += "\tos.remove( \"" + prefix + ".align."+s+".map\" )\n"
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409 cmd_start += "print \"" + launchB + "\"; sys.stdout.flush()\n"
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410 cmd_start += "log = os.system( \"" + launchB + "\" )\n"
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411 cmd_start += "if log != 0:\n"
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412 cmd_start += launcher.cmd_test( launcher.job, "error", loop=1 )
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413 cmd_start += "\tsys.exit(1)\n"
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414 cmd_start += cleanB
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415 cmd_start += "print \"" + launchM + "\"; sys.stdout.flush()\n"
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416 cmd_start += "log = os.system( \"" + launchM + "\" )\n"
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|
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417 cmd_start += cleanM
|
|
|
418 launcher.runSingleJob( cmd_start )
|
|
|
419 launcher.acronyme = "BlasterMatcher"
|
|
|
420 launcher._nbJobs = count
|
|
|
421 launcher.endRun()
|
|
|
422 if clean == True:
|
|
|
423 launcher.clean( "BlasterMatcher_*" )
|
|
|
424
|
|
|
425 else:
|
|
|
426 print "ERROR: option '-m %s' not recognized" % ( mix )
|
|
|
427 sys.exit(1)
|
|
|
428
|
|
|
429
|
|
|
430 if collect != "":
|
|
|
431 if collect in [ "align", "path", "tab" ]:
|
|
|
432 runCollect( groupid, collect, allByAll )
|
|
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433 else:
|
|
|
434 print "ERROR: collect '%s' not implemented" % ( collect )
|
|
|
435 sys.exit(1)
|
|
|
436
|
|
|
437
|
|
|
438 logging.info( "finished" )
|
|
|
439
|
|
|
440 if verbose > 0:
|
|
|
441 print "END %s" % ( sys.argv[0].split("/")[-1] )
|
|
|
442 sys.stdout.flush()
|
|
|
443
|
|
|
444 return 0
|
|
|
445
|
|
|
446
|
|
|
447 if __name__ == "__main__":
|
|
|
448 main()
|
