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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 from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders
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9
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10
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11 def help():
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12 print
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13 print "usage: ",sys.argv[0],"[ options ]"
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14 print "options:"
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15 print " -h: this help"
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16 print " -i: name of the input file (aligned fasta)"
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17 print " -c: clean"
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18 print " -v: verbose (default=0)"
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19 print
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20
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21
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22 def main():
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23
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24 inFileName = ""
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25 clean = False
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26 verbose = 0
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27 try:
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28 opts,args=getopt.getopt(sys.argv[1:],"hi:cv:")
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29 except getopt.GetoptError, err:
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30 print str(err)
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31 help(); sys.exit(1)
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32 for o,a in opts:
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33 if o == "-h":
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34 help(); sys.exit(0)
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35 elif o == "-i":
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36 inFileName = a
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37 elif o == "-c":
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38 clean = True
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39 elif o == "-v":
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40 verbose = int(a)
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41 if inFileName == "":
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42 print "ERROR: missing compulsory options"
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43 help(); sys.exit(1)
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44
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45 if verbose > 0:
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46 print "START %s" % (sys.argv[0].split("/")[-1])
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47 sys.stdout.flush()
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48
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49 csh = ChangeSequenceHeaders()
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50 csh.setInputFile( inFileName )
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51 csh.setFormat( "fasta" )
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52 csh.setStep( 1 )
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53 csh.setPrefix( "seq" )
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54 csh.setLinkFile( inFileName+".shortHlink" )
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55 csh.setOutputFile( inFileName+".shortH" )
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56 csh.run()
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57
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58 pL = programLauncher( inFileName+".shortH" )
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59
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60 pL.launchSreformat( outFormat="phylip", outFileName=inFileName+".shortH.phylip", verbose=verbose )
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61
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62 pL.reset( inFileName+".shortH.phylip" )
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63
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64 pL.launchPhyML( verbose=verbose )
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65
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66 csh.setInputFile( inFileName+".shortH.phylip_phyml_tree.txt" )
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67 csh.setFormat( "newick" )
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68 csh.setStep( 2 )
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69 csh.setLinkFile( inFileName+".shortHlink" )
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70 csh.setOutputFile( inFileName+"_phyml.newick" )
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71 csh.run()
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72
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73 if clean:
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74 for f in [ inFileName+".shortH", inFileName+".shortHlink", inFileName+".shortH.phylip",
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75 inFileName+".shortH.phylip_phyml_lk.txt", inFileName+".shortH.phylip_phyml_tree.txt" ]:
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76 os.remove( f )
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77 os.system( "mv %s.shortH.phylip_phyml_stat.txt %s_phyml.txt" % ( inFileName, inFileName ) )
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78
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79 if verbose > 0:
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80 print "END %s" % (sys.argv[0].split("/")[-1])
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81 sys.stdout.flush()
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82
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83 return 0
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84
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85
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86 if __name__ == "__main__":
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87 main()
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