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1 #!/usr/bin/env python
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2
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3 # DEPRECATED
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4
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5 import user, os, sys, getopt, exceptions
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6
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7 if not os.environ.has_key( "REPET_PATH" ):
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8 print "*** Error: no environment variable REPET_PATH"
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9 sys.exit(1)
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10 sys.path.append( os.environ["REPET_PATH"] )
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11
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12 import pyRepet.launcher.programLauncher
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13 import pyRepet.seq.fastaDB
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14 from pyRepet.seq.BioseqDB import *
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15
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16 #------------------------------------------------------------------------------
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17
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18 def help():
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19
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20 print
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21 print "DEPRECATED"
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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 " -i: name of the input file (format='fasta')"
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27 print " -o: name of the output file (default=inFileName+'.fa_aln')"
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28 print " -v: verbose (default=0/1)"
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29 print
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30
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31 #------------------------------------------------------------------------------
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32
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33 def main():
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34
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35 """
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36 This program launches MAFFT to build a multiple sequence alignment.
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37 """
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38
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39 inFileName = ""
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40 outFileName = ""
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41 verbose = 0
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42
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43 try:
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44 opts,args=getopt.getopt(sys.argv[1:],"hi:o:v:")
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45 except getopt.GetoptError:
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46 help()
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47 sys.exit(1)
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48 for o,a in opts:
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49 if o == "-h":
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50 help()
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51 sys.exit(0)
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52 elif o == "-i":
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53 inFileName = a
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54 elif o == "-o":
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55 outFileName = a
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56 elif o == "-v":
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57 verbose = int(a)
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58
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59 if inFileName == "":
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60 print "*** Error: missing compulsory options"
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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 "beginning of %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 verbose > 0:
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69 print "build a multiple alignment from '%s'..." % ( inFileName )
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70 sys.stdout.flush()
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71
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72 pyRepet.seq.fastaDB.shortenSeqHeaders( inFileName )
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73
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74 bsDB = BioseqDB( inFileName+".shortH" )
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75 bsDB.upCase()
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76 bsDB.save( inFileName+".shortHtmp" )
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77 del bsDB
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78 os.rename( inFileName+".shortHtmp", inFileName+".shortH" )
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79
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80 pL = pyRepet.launcher.programLauncher.programLauncher( inFileName+".shortH" )
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81 pL.launchMafft( outFileName=inFileName+".shortH.fa_aln", verbose=verbose )
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82
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83 pyRepet.seq.fastaDB.retrieveInitSeqHeaders( inFileName+".shortH.fa_aln",
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84 inFileName+".shortHlink",
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85 inFileName+".shortH.fa_aln.initH",
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86 verbose-1 )
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87
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88 if outFileName == "":
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89 outFileName = "%s.fa_aln" % ( inFileName )
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90 os.system( "mv %s.shortH.fa_aln.initH %s" % ( inFileName, outFileName ) )
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91
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92 for f in [inFileName+".shortH",inFileName+".shortH.fa_aln",inFileName+".shortHlink"]:
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93 os.remove( f )
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94
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95 if verbose > 0:
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96 print "%s finished successfully" % (sys.argv[0].split("/")[-1])
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97 sys.stdout.flush()
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98
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99 return 0
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100
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101 #------------------------------------------------------------------------------
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102
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103 if __name__ == '__main__':
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104 main()
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