Mercurial > repos > iuc > syndiva

annotate args.py @ 0:0254731f047b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
author iuc
date Thu, 23 Jun 2022 22:32:13 +0000
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0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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1 # -*- coding: utf-8 -*-
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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2 import getopt
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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3 import os
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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4 import sys
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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5
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6
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7 def usage(info) -> str:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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8 text = "SynDivA script.\n\n"
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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9 if info:
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10 text += info
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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11 temp = "Option\t\t\t\tfile\t\t\tDescription\n"
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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12 text += temp
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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13 text += '-' * (len(temp) + 60)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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14 text += '\n'
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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15 text += "-i, --input\t\t\tfile.fasta\t\tFasta file that contains the DNA sequences\n"
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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16 text += "-o, --output_dir\t\t/path/for/output\tDirectory where output files will be written\n"
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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17 text += "-p, --pattern\t\t\tstring\t\t\tPattern of the sequence bank\n"
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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18 text += "-5, --restriction-site-5\tstring\t\t\tSequence of the restriction site in 5'\n"
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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19 text += "-3, --restriction-site-3\tstring\t\t\tSequence of the restriction site in 3'\n"
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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20 return text
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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23 def get_os_path_join(directory, filename):
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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24 return os.path.join(directory, filename)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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27 def get_os_path_name(input):
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28 return os.path.basename(input)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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31 def check_pattern(pattern):
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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32 authorized_pattern_letter = ['A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M',
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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33 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y', ':', '0',
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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34 '1', '2', '3', '4', '5', '6', '7', '8', '9', '-', '*']
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35 return len([letter in authorized_pattern_letter for letter in pattern]) == len(pattern)
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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36
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37
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38 class Args:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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39
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40 def __init__(self):
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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41 """
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42 Instanciate Files object
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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43 """
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44 self.input = None
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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45 self.output_dir = None
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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46 self.pattern = None
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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47 self.site_res_5 = None
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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48 self.site_res_3 = None
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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49 self.getargs()
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50
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51 def case(self):
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52 # Test des fichiers et repertoires
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53 if not self.input:
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54 sys.exit(usage("input (-i,--input) : \"%s\" must be indicated\n" % (self.input)))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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55 if not self.output_dir:
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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56 sys.exit(usage("output directory (-o,--output_dir) : \"%s\" must be indicated\n" % (self.output_dir)))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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57 if not self.pattern:
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58 sys.exit(
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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59 usage("Pattern of the sequence bank (-p,--pattern) : \"%s\" must be indicated\n" % (self.pattern)))
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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60 if not self.site_res_5:
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61 sys.exit(usage(
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62 "Sequence of the restriction site in 5' (-5,--restriction-site-5) : \"%s\" must be indicated\n" % (
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63 self.site_res_5)))
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64 if not self.site_res_3:
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65 sys.exit(usage(
0254731f047b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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66 "Sequence of the restriction site in 3' (-3,--restriction-site-3) : \"%s\" must be indicated\n" % (
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67 self.site_res_3)))
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68
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69 def data_format(self):
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70 """
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71 Check if information are correct
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72 """
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73 # Run without arguments
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74 if len(sys.argv) == 1:
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75 sys.exit(usage(None))
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76 # Test input file argument
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77 if self.input and not os.path.isfile(self.input):
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78 print(self.input)
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79 print(os.path.isfile(self.input))
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80
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81 def getargs(self):
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82 """
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83 Determine the files provided as arguments
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84 @return: Choosen options
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85 """
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86 # Sans argument
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87 if len(sys.argv) <= 1:
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88 sys.exit("Do './fibronectin.py -h' for a usage summary")
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89 # options test
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90 try:
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91 (opts, args) = getopt.getopt(sys.argv[1:], "i:o:p:5:3:h",
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92 ["input=", "output_dir=", "pattern=", "site_res_5=", "site_res_3="])
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93 except getopt.GetoptError as err:
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94 # print help information and exit:
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95 print(str(err)) # will print something like "option -a not recognized"
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96 sys.exit(usage(None))
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97 # Identification of options
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98 for (o, a) in opts:
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99 if o in ("-i", "--input"):
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100 self.input = a
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101 elif o in ("-o", "--output_dir"):
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102 self.output_dir = a
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103 elif o in ("-p", "--pattern"):
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104 self.pattern = a
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105 elif o in ("-5", "--restriction-site-5"):
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106 self.site_res_5 = a
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107 elif o in ("-3", "--restriction-site-3"):
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108 self.site_res_3 = a
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109 elif o in ("-h", "--help"):
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110 sys.exit(usage(None))
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111 else:
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112 assert False, "unhandled option"
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113 # Verification of cases
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114 self.case()
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115 self.data_format()