Mercurial > repos > jpetteng > ectyper

comparison ecoli_serotyping/commandLineOptions.py @ 6:fe3ceb5c4214 draft

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author jpetteng
date Fri, 05 Jan 2018 15:43:14 -0500
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5:a202cc394af8 6:fe3ceb5c4214
1 #!/usr/bin/env python
2
3 import argparse
4
5
6 def parse_command_line(args=None):
7 """
8 The options for both the serotyper, and virulence finder.
9 The returned object is used by both, but the options do not
10 necessarily apply to both.
11
12 Args:
13 args: Optional args to be passed to argparse.parse_args()
14
15 Returns:
16 The populated argparse Namespace
17 """
18
19 def check_percentage(value):
20 """
21 type checker for percentage input
22 """
23 ivalue = int(value)
24 if ivalue <= 0 or ivalue > 100:
25 raise argparse.ArgumentTypeError(
26 "{0} is an invalid positive int percentage value".format(value)
27 )
28 return ivalue
29
30 parser = argparse.ArgumentParser()
31 parser.add_argument(
32 "-i",
33 "--input",
34 help="Location of new file(s). Can be a single file or \
35 a directory",
36 required=True
37 )
38
39 parser.add_argument(
40 "-d",
41 "--percentIdentity",
42 type=check_percentage,
43 help="Percentage of identity wanted to use against the\
44 database. From 0 to 100, default is 90%%.",
45 default=90
46 )
47
48 parser.add_argument(
49 "-l",
50 "--percentLength",
51 type=check_percentage,
52 help="Percentage of length wanted to use against the \
53 database. From 0 to 100, default is 50%%.",
54 default=50
55 )
56
57 parser.add_argument(
58 "--verify",
59 action="store_true",
60 help="Enable E. Coli. verification"
61 )
62
63 parser.add_argument(
64 "-s",
65 "--species",
66 action="store_true",
67 help="Enable species identification when non-ecoli genome is found\n\
68 Note: refseq downloading is required when running this option for the first time."
69 )
70
71 parser.add_argument(
72 '--detailed',
73 action='store_true',
74 help='Enable detailed output'
75 )
76
77 parser.add_argument(
78 "-o",
79 "--output",
80 help="Directory location of output files."
81 )
82
83 if args is None:
84 return parser.parse_args()
85 return parser.parse_args(args)