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comparison entry.py @ 1:3814470e221a draft

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author nedias
date Wed, 12 Oct 2016 00:03:34 -0400
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0:ec8fe63afdb8 1:3814470e221a
1 #!/usr/bin/env python
2 """
3 Python script, served as the entry of open reading frame searching tool
4 Separated the API with actual functionality (for Galaxy and future Web API)
5
6 Use -v or --version to get the version, -h or --help for help.
7
8 Author Nedias Sept 2016
9
10 """
11 import sys
12 from optparse import OptionParser
13 import orf_tool
14
15 # Usage message
16 usage = """Use as follows:
17 $ python entry.py -i input_seq_file -l length_of_designated_match
18 """
19
20 # User OptionParser to separate all optional arguments of the commandline
21 parser = OptionParser(usage=usage)
22 parser.add_option('-i', '--input', dest='input',
23 default=None, help='Input sequences filename',
24 metavar="FILE")
25 parser.add_option("-l", "--length", dest="length",
26 default=100,
27 help="Set the length of designated match, length is the percentage of the longest match")
28 parser.add_option("-f", "--format", dest="format",
29 default="fasta",
30 help="Set the format of input file")
31 parser.add_option("-v", "--version", dest="version",
32 default=False, action="store_true",
33 help="Show version and quit")
34 parser.add_option("-a", "--outputall", dest="outputa",
35 default=None,
36 help="Output of all matches",
37 metavar="FILE")
38 parser.add_option("-d", "--outputdest", dest="outputd",
39 default=None,
40 help="Output of designated matches",
41 metavar="FILE")
42
43 options, args = parser.parse_args()
44
45 # Show version data (TODO:consider move to orf_tool.py)
46 if options.version:
47 print("v0.1.0")
48 sys.exit(0)
49
50 # Call actual function
51 else:
52 orf_tool.exec_tool(options)
53
54