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1 # -*- coding: utf-8 -*-
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2 import sys, getopt, os
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3
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4
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5 class Args:
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6
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7 def __init__(self):
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8 """
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9 Instanciate Files object
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10 """
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11 self.input = None
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12 self.output_dir = None
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13 self.pattern = None
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14 self.site_res_5 = None
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15 self.site_res_3 = None
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16 self.getargs()
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17
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18 def usage(self, info):
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19 text = None
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20 text = "Fibronectin script.\n\n"
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21 if (info): text += info
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22 temp = "Option\t\t\t\tfile\t\t\tDescription\n"
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23 text += temp
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24 text += '-' * (len(temp) + 60)
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25 text += '\n'
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26 text += "-i, --input\t\t\tfile.fasta\t\tFasta file that contains the DNA sequences\n"
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27 text += "-o, --output_dir\t\t/path/for/output\tDirectory where output files will be written\n"
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28 text += "-p, --pattern\t\t\tstring\t\t\tPattern of the sequence bank\n"
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29 text += "-5, --restriction-site-5\tstring\t\t\tSequence of the restriction site in 5'\n"
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30 text += "-3, --restriction-site-3\tstring\t\t\tSequence of the restriction site in 3'\n"
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31 return text
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32
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33 def case(self):
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34 # Test des fichiers et repertoires
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35 if not self.input:
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36 sys.exit(self.usage("input (-i,--input) : \"%s\" must be indicated\n" % (self.input)))
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37 if not self.output_dir:
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38 sys.exit(self.usage("output directory (-o,--output_dir) : \"%s\" must be indicated\n" % (self.output_dir)))
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39 if not self.pattern:
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40 sys.exit(
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41 self.usage("Pattern of the sequence bank (-p,--pattern) : \"%s\" must be indicated\n" % (self.pattern)))
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42 if not self.site_res_5:
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43 sys.exit(self.usage(
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44 "Sequence of the restriction site in 5' (-5,--restriction-site-5) : \"%s\" must be indicated\n" % (
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45 self.site_res_5)))
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46 if not self.site_res_3:
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47 sys.exit(self.usage(
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48 "Sequence of the restriction site in 3' (-3,--restriction-site-3) : \"%s\" must be indicated\n" % (
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49 self.site_res_3)))
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50
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51 def data_format(self):
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52 """
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53 Check if information are correct
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54 """
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55 # Run without arguments
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56 if len(sys.argv) == 1:
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57 sys.exit(self.usage(None))
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58 # Test input file argument
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59 if self.input:
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60 if not os.path.isfile(self.input):
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61 print(self.input)
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62 print(os.path.isfile(self.input))
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63 #sys.exit(self.usage("Error with \"%s\" : -i required an input file\n" % self.multilist))
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64
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65 # Determine les fichiers fournis en arguments
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66
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67 def getargs(self):
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68 """
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69 Determine the files provided as arguments
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70 @return: Choosen options
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71 """
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72 # Sans argument
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73 if len(sys.argv) <= 1: sys.exit("Do './fibronectin.py -h' for a usage summary")
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74 # test des option
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75 try:
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76 (opts, args) = getopt.getopt(sys.argv[1:], "i:o:p:5:3:h",
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77 ["input=", "output_dir=", "pattern=", "site_res_5=", "site_res_3="])
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78 except getopt.GetoptError as err:
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79 # print help information and exit:
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80 print(str(err)) # will print something like "option -a not recognized"
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81 sys.exit(self.usage(None))
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82 # Identification of options
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83 for (o, a) in opts:
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84 if o in ("-i", "--input"):
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85 self.input = a
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86 elif o in ("-o", "--output_dir"):
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87 self.output_dir = a
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88 elif o in ("-p", "--pattern"):
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89 self.pattern = a
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90 elif o in ("-5", "--restriction-site-5"):
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91 self.site_res_5 = a
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92 elif o in ("-3", "--restriction-site-3"):
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93 self.site_res_3 = a
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94 elif o in ("-h", "--help"):
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95 sys.exit(self.usage(None))
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96 else:
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97 assert False, "unhandled option"
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98 # Verification of cases
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99 self.case()
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100 self.data_format()
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