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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
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7 from pyRepet.launcher.programLauncher import programLauncher
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8
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9
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10 def help():
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11 print
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12 print "usage: launchPrank.py [ options ]"
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13 print "options:"
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14 print " -h: this help"
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15 print " -i: name of the input file (format=fasta)"
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16 print " -o: name of the output file (format=aligned fasta, default='inFileName'+fa_aln)"
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17 print " -P: Prank's parameters"
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18 print " -c: clean"
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19 print " -v: verbose (default=0/1)"
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20 print
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21
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22
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23 def main():
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24 """
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25 Launch PRANK.
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26 """
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27 inFileName = ""
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28 outFileName = ""
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29 parameters = ""
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30 clean = False
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31 verbose = 0
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32
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33 try:
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34 opts, args = getopt.getopt( sys.argv[1:], "hi:o:P:cv:" )
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35 except getopt.GetoptError, err:
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36 print str(err)
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37 help()
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38 sys.exit(1)
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39 for o,a in opts:
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40 if o == "-h":
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41 help()
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42 sys.exit(0)
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43 elif o == "-i":
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44 inFileName = a
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45 elif o == "-o":
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46 outFileName = a
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47 elif o == "-P":
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48 parameters = a
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49 elif o == "-c":
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50 clean = True
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51 elif o == "-v":
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52 verbose = int(a)
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53
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54 if inFileName == "":
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55 print "ERROR: missing input file (-i)"
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56 help()
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57 sys.exit(1)
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58
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59 if not os.path.exists( inFileName ):
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60 print "ERROR: can't find file '%s'" % ( inFileName )
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61 help()
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62 sys.exit(1)
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63
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64 if verbose > 0:
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65 print "START %s" % ( sys.argv[0].split("/")[-1] )
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66 sys.stdout.flush()
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67
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68 if outFileName == "":
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69 outFileName = "%s.fa_aln" % ( inFileName )
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70
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71 pL = programLauncher( inFileName )
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72 returnStatus = pL.launchPrank( outFileName, parameters, "yes", verbose )
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73 if returnStatus != 0:
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74 print "ERROR: launchPrank() returned '%i'" % ( returnStatus )
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75 sys.exit(1)
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76
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77 if verbose > 0:
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78 print "END %s" % ( sys.argv[0].split("/")[-1] )
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79 sys.stdout.flush()
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80
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81 return 0
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82
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83
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84 if __name__ == "__main__":
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85 main()
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