Mercurial > repos > nedias > orf_tools
view entry.py @ 3:0095bf758b19 draft
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author | nedias |
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date | Wed, 12 Oct 2016 00:03:53 -0400 |
parents | 3814470e221a |
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#!/usr/bin/env python """ Python script, served as the entry of open reading frame searching tool Separated the API with actual functionality (for Galaxy and future Web API) Use -v or --version to get the version, -h or --help for help. Author Nedias Sept 2016 """ import sys from optparse import OptionParser import orf_tool # Usage message usage = """Use as follows: $ python entry.py -i input_seq_file -l length_of_designated_match """ # User OptionParser to separate all optional arguments of the commandline parser = OptionParser(usage=usage) parser.add_option('-i', '--input', dest='input', default=None, help='Input sequences filename', metavar="FILE") parser.add_option("-l", "--length", dest="length", default=100, help="Set the length of designated match, length is the percentage of the longest match") parser.add_option("-f", "--format", dest="format", default="fasta", help="Set the format of input file") parser.add_option("-v", "--version", dest="version", default=False, action="store_true", help="Show version and quit") parser.add_option("-a", "--outputall", dest="outputa", default=None, help="Output of all matches", metavar="FILE") parser.add_option("-d", "--outputdest", dest="outputd", default=None, help="Output of designated matches", metavar="FILE") options, args = parser.parse_args() # Show version data (TODO:consider move to orf_tool.py) if options.version: print("v0.1.0") sys.exit(0) # Call actual function else: orf_tool.exec_tool(options)