Mercurial > repos > iuc > sqlite_to_tabular
diff sqlite_to_tabular.py @ 0:859064f07be4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
author | iuc |
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date | Tue, 18 Jul 2017 09:07:26 -0400 |
parents | |
children | c1b700bc0150 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sqlite_to_tabular.py Tue Jul 18 09:07:26 2017 -0400 @@ -0,0 +1,60 @@ +#!/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('-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) + except Exception as e: + exit('Error: %s' % (e)) + + +if __name__ == "__main__": + __main__()