diff sqlite_to_tabular.py @ 0:3708ff0198b7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
author iuc
date Tue, 18 Jul 2017 09:07:07 -0400
parents
children 8a33b442ecd9
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sqlite_to_tabular.py	Tue Jul 18 09:07:07 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__()