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1 #!/usr/bin/env python
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2
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3 import argparse
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4
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5
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6 def parse_command_line(args=None):
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7 """
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8 The options for both the serotyper, and virulence finder.
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9 The returned object is used by both, but the options do not
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10 necessarily apply to both.
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11
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12 Args:
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13 args: Optional args to be passed to argparse.parse_args()
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14
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15 Returns:
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16 The populated argparse Namespace
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17 """
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18
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19 def check_percentage(value):
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20 """
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21 type checker for percentage input
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22 """
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23 ivalue = int(value)
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24 if ivalue <= 0 or ivalue > 100:
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25 raise argparse.ArgumentTypeError(
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26 "{0} is an invalid positive int percentage value".format(value)
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27 )
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28 return ivalue
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29
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30 parser = argparse.ArgumentParser()
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31 parser.add_argument(
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32 "-i",
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33 "--input",
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34 help="Location of new file(s). Can be a single file or \
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35 a directory",
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36 required=True
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37 )
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38
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39 parser.add_argument(
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40 "-d",
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41 "--percentIdentity",
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42 type=check_percentage,
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43 help="Percentage of identity wanted to use against the\
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44 database. From 0 to 100, default is 90%%.",
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45 default=90
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46 )
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47
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48 parser.add_argument(
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49 "-l",
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50 "--percentLength",
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51 type=check_percentage,
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52 help="Percentage of length wanted to use against the \
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53 database. From 0 to 100, default is 50%%.",
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54 default=50
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55 )
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56
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57 parser.add_argument(
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58 "--verify",
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59 action="store_true",
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60 help="Enable E. Coli. verification"
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61 )
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62
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63 parser.add_argument(
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64 "-s",
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65 "--species",
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66 action="store_true",
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67 help="Enable species identification when non-ecoli genome is found\n\
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68 Note: refseq downloading is required when running this option for the first time."
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69 )
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70
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71 parser.add_argument(
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72 '--detailed',
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73 action='store_true',
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74 help='Enable detailed output'
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75 )
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76
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77 parser.add_argument(
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78 "-o",
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79 "--output",
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80 help="Directory location of output files."
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81 )
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82
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83 if args is None:
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84 return parser.parse_args()
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85 return parser.parse_args(args)
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