Mercurial > repos > nedias > blast_tool
view blast_entry.py @ 4:0145fdbdcf90 draft default tip
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author | nedias |
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date | Wed, 12 Oct 2016 18:16:53 -0400 |
parents | 0c471588f014 |
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#!/usr/bin/env python """ Python script, served as the entry of BLAST API 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 blast_tool # Usage message usage = """Use as follows: $ python blast_entry.py -i input_seq_file -o output_xml -f format -p blast_program -d blast_database """ # 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("-o", "--output", dest="output", default=None, help="Output of Blast result in xml form", metavar="FILE") parser.add_option("-v", "--version", dest="version", default=False, action="store_true", help="Show version and quit") parser.add_option("-f", "--format", dest="format", default="fasta", help="Set the format of input file") parser.add_option("-p", "--program", dest="program", default="blastp", help="Define which BLAST API is used") parser.add_option("-d", "--database", dest="database", default="nr", help="Define which database to search from") options, args = parser.parse_args() # Show version data (TODO:consider move to blast_tool.py) if options.version: print("v0.1.0") sys.exit(0) # Call actual function else: blast_tool.exec_tool(options)