annotate sqlite_to_tabular.py @ 2:123b9ca5e26a draft default tip

planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit ae4f3ee9048be3ebc9fa3bc0783e73ac31082899-dirty

#!/usr/bin/env python

import sys
import re
import os.path
import optparse
import sqlite3 as sqlite


def regex_match(expr, item):
    return re.match(expr, item) is not None


def regex_search(expr, item):
    return re.search(expr, item) is not None


def regex_sub(expr, replace, item):
    return re.sub(expr, replace, item)


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', action='store_true', default=False, 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, e:
            print >> sys.stderr, "failed: %s" % e
            exit(3)
    else:
        outputFile = sys.stdout

    query = None
    if (options.query_file is not None):
        with open(options.query_file, 'r') as fh:
            query = ''
            for line in fh:
                query += line
    elif (options.query is not None):
        query = options.query

    if (query is None):
        try:
            conn = sqlite.connect(options.sqlitedb)
            c = conn.cursor()
            tables_query = "SELECT name,sql FROM sqlite_master WHERE type='table' ORDER BY name"
            rslt = c.execute(tables_query).fetchall()
            for table, sql in rslt:
                print >> sys.stderr, "Table %s:" % table
                try:
                    col_query = 'SELECT * FROM %s LIMIT 0' % table
                    cur = conn.cursor().execute(col_query)
                    cols = [col[0] for col in cur.description]
                    print >> sys.stderr, " Columns: %s" % cols
                except Exception, exc:
                    print >> sys.stderr, "Error: %s" % exc
        except Exception, exc:
            print >> sys.stderr, "Error: %s" % exc
        exit(0)
    try:
        conn = sqlite.connect(options.sqlitedb)
        conn.create_function("re_match", 2, regex_match)
        conn.create_function("re_search", 2, regex_search)
        conn.create_function("re_sub", 3, regex_sub)
        cur = conn.cursor()
        results = cur.execute(query)
        if not options.no_header:
            outputFile.write("#%s\n" % '\t'.join([str(col[0]) for col in cur.description]))
        for i, row in enumerate(results):
            outputFile.write("%s\n" % '\t'.join([str(val) if val is not None else '' for val in row]))
    except Exception, exc:
        print >> sys.stderr, "Error: %s" % exc
        exit(1)

if __name__ == "__main__":
    __main__()