Mercurial > repos > iuc > sqlite_to_tabular
view sqlite_to_tabular.py @ 8:5a4ae7678bc5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 1647065a8e6e8d8c98cd0d2194b695fb9425f541"
author | iuc |
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date | Thu, 23 Jan 2020 07:36:57 -0500 |
parents | c1b700bc0150 |
children |
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#!/usr/bin/env python from __future__ import print_function import optparse import os.path import sys from query_db import describe_tables, get_connection, run_query def __main__(): # Parse Command Line parser = optparse.OptionParser() parser.add_option('-s', '--sqlitedb', dest='sqlitedb', default=None, help='The SQLite Database') parser.add_option('-q', '--query', dest='query', default=None, help='SQL query') parser.add_option('-Q', '--query_file', dest='query_file', default=None, help='SQL query file') parser.add_option('-n', '--no_header', dest='no_header', default=False, action='store_true', help='Include a column headers line') parser.add_option('-c', '--comment_char', dest='comment_char', default='', help='comment character to prefix column header line') parser.add_option('-o', '--output', dest='output', default=None, help='Output file for query results') (options, args) = parser.parse_args() # determine output destination if options.output is not None: try: outputPath = os.path.abspath(options.output) outputFile = open(outputPath, 'w') except Exception as e: exit('Error: %s' % (e)) else: outputFile = sys.stdout query = None if options.query_file is not None: with open(options.query_file, 'r') as fh: query = fh.read() elif options.query is not None: query = options.query if query is None: try: describe_tables(get_connection(options.sqlitedb), outputFile) except Exception as e: exit('Error: %s' % (e)) exit(0) else: try: run_query(get_connection(options.sqlitedb), query, outputFile, no_header=options.no_header, comment_char=options.comment_char) except Exception as e: exit('Error: %s' % (e)) if __name__ == "__main__": __main__()