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1 #!/usr/bin/env python
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2
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3 """
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4 Launcher for the multifasta parser.
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5 @param b: Name of the batch of sequences
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6 @param g: Name of the gene
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7 @param t: Scientific name of the taxon concerned
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8 @param f: Name of the multifasta input file
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9 """
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10
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11
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12 import os
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13 import sys
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14 import getopt
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15 from commons.core.parsing.Multifasta2SNPFile import Multifasta2SNPFile
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16
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17 CURRENT_DIR = os.getcwd()
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18
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19 def help():
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20
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21 """
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22 Give the list of the command-line options.
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23 """
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24
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25 print "Usage: ",sys.argv[0],"[ options ]"
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26 print " -h: this help"
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27 print "Mandatory option:"
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28 print " -t: Scientific name of the taxon concerned"
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29 print "Exclusive options (use either the first or the second, one should be used)"
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30 print " -f: Name of the multifasta input file in one batch mode"
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31 print " -d: Name of the directory containing multifasta input file(s) in multi-batch mode"
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32 print "Only in one batch mode: mandatory options (when -f is used):"
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33 print " -b: Name of the batch of submitted sequences"
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34 print " -g: Name of the gene"
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35 print ""
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36
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37
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38 def runOneInputFile(batchName, geneName, taxon, inputFileName):
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39 print "Multifasta parseur launched:!\n"
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40 print "-- Input File: " + inputFileName + "\n"
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41 print "-- Batch name: " + batchName + "\n"
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42 print "-- Gene name: " + geneName + "\n"
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43 print "-- Taxon: " + taxon + "\n"
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44 #TODO: gerer le delete des fichiers(mode append)
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45 multifasta2SNPFile = Multifasta2SNPFile(taxon, batchName, geneName)
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46 multifasta2SNPFile.runOneBatch(inputFileName)
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47 print "OK: Files generated!"
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48
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49
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50 def runSeveralInputFile(taxon, rootDirectoryName):
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51 multifasta2SNPFile = Multifasta2SNPFile(taxon)
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52 multifasta2SNPFile.runSeveralBatches(rootDirectoryName)
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53
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54 def main():
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55 batchName = ""
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56 geneName = ""
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57 taxon = ""
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58 inputFileName = ""
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59 rootDirectoryName = ""
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60
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61
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62 try:
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63 opts,args = getopt.getopt(sys.argv[1:],"hb:g:t:f:d:")
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64 except getopt.GetoptError:
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65 print "Invalid options\n"
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66 help()
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67 sys.exit(2)
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68
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69 for o, a in opts:
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70 if o == "-h":
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71 help()
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72 exit(0)
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73 elif o == "-b":
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74 batchName = a
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75 elif o == "-g":
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76 geneName = a
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77 elif o == "-t":
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78 taxon = a
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79 elif o == "-f":
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80 inputFileName = a
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81 elif o == "-d":
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82 rootDirectoryName = os.path.abspath(a)
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83
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84 if taxon == "":
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85 print "*** Error: The mandatory option -t is missing"
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86 help()
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87 sys.exit(1)
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88
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89 if (inputFileName == "" and rootDirectoryName == "") or (inputFileName != "" and rootDirectoryName != ""):
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90 print "*** Error: You have to specify the input mode: choose either -f (for one file) or -d (for one directory of several files)"
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91 help()
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92 sys.exit(1)
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93
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94 if(inputFileName != ""):
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95 if batchName == "" or geneName == "":
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96 print "*** Error: A mandatory option is missing in one batch mode (-b or -g)"
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97 help()
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98 sys.exit(1)
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99
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100 if(inputFileName != ""):
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101 runOneInputFile(batchName, geneName, taxon, inputFileName)
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102 else:
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103 runSeveralInputFile(taxon, rootDirectoryName)
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104
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105
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106 return 0
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107
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108 #------------------------------------------------------------------------------
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109 if __name__ == "__main__":
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110 main() |
