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1 #!/usr/bin/env python
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2
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3 import os
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4 import sys
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5 import getopt
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6 import exceptions
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7
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8 if not os.environ.has_key( "REPET_PATH" ):
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9 print "ERROR: no environment variable REPET_PATH"
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10 sys.exit(1)
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11 sys.path.append( os.environ["REPET_PATH"] )
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12
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13 from pyRepet.launcher.programLauncher import programLauncher
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14
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15
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16 def help():
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17 print
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18 print "usage: ",sys.argv[0],"[ options ]"
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19 print "options:"
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20 print " -h: this help"
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21 print " -i: name of the input file (format='fasta')"
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22 print " -P: parameters"
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23 print " -o: name of the output file (format='aligned fasta', default='inFileName'+fa_aln)"
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24 print " -c: clean"
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25 print " -v: verbosity level (default=0/1)"
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26 print
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27
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28
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29 def main():
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30
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31 inFileName = ""
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32 parameters = ""
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33 outFileName = ""
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34 clean = False
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35 verbose = 0
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36
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37 try:
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38 opts, args = getopt.getopt(sys.argv[1:],"hi:P:o:cv:")
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39 except getopt.GetoptError, err:
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40 print str(err); help(); sys.exit(1)
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41 for o,a in opts:
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42 if o == "-h":
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43 help(); sys.exit(0)
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44 elif o == "-i":
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45 inFileName = a
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46 elif o == "-P":
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47 parameters = a
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48 elif o == "-o":
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49 outFileName = a
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50 elif o == "-c":
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51 clean = True
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52 elif o == "-v":
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53 verbose = "yes"
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54
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55 if inFileName == "" and parameters == "":
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56 print "ERROR: missing compulsory options"
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57 help()
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58 sys.exit(1)
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59
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60 if outFileName == "":
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61 outFileName = "%s.fa_aln" % ( inFileName )
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62
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63 if verbose > 0:
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64 print "START %s" % (sys.argv[0].split("/")[-1])
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65 sys.stdout.flush()
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66
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67 pL = programLauncher( inFileName )
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68 pL.launchTcoffee( outFileName, parameters )
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69
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70 if verbose > 0:
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71 print "END %s" % (sys.argv[0].split("/")[-1])
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72 sys.stdout.flush()
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73
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74 return 0
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75
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76
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77 if __name__ == "__main__":
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78 main()
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