--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/tools/srptCreateTable.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,134 @@
+#!/usr/bin/env python
+
+import os
+import sys
+import getopt
+import ConfigParser
+
+from commons.core.sql.DbMySql import DbMySql
+
+
+def help():
+    print
+    print "usage: %s [ options ]" % ( sys.argv[0].split("/")[-1] )
+    print "options:"
+    print "     -h: this help"
+    print "     -f: name of the input file"
+    print "     -n: name of the MySQL table"
+    print "     -t: table type (fasta|align|path|set|match|map|TEclassif|cluster)"
+    print "     -o: overwrite (default=False)"
+    print "     -c: configuration file from TEdenovo or TEannot pipeline"
+    print "     -H: MySQL host (if no configuration file)"
+    print "     -U: MySQL user (if no configuration file)"
+    print "     -P: MySQL password (if no configuration file)"
+    print "     -D: MySQL database (if no configuration file)"
+    print "     -T: MySQL port (if no configuration file, default=3306)"
+    print "     -v: verbose (default=0/1)"
+    print
+
+
+def main():
+    """
+    This program loads data from a file into a MySQL table.
+    """
+    filename = ""
+    tablename = ""
+    filetype = ""
+    overwrite = False
+    configFileName = ""
+    host = ""
+    user = ""
+    passwd = ""
+    dbname = ""
+    port = 0
+    verbose = 0
+
+    try:
+        opts, args = getopt.getopt( sys.argv[1:], "hf:t:n:oc:H:U:P:D:T:v:" )
+    except getopt.GetoptError, err:
+        sys.stderr.write( "%s\n" % str(err) )
+        help()
+        sys.exit(1)
+    for o,a in opts:
+        if o == "-h":
+            help()
+            sys.exit(0)
+        elif o == "-f":
+            filename = a
+        elif o == "-n":
+            tablename = a
+        elif o == "-t":
+            filetype = a
+        elif o == "-o":
+            overwrite = True
+        elif o == "-c":
+            configFileName = a
+        elif o == "-H":
+            host = a
+        elif o == "-U":
+            user = a 
+        elif o == "-P":
+            passwd = a
+        elif o == "-D":
+            dbname = a
+        elif o == "-T":
+            port = int(a)
+        elif o == "-v":
+            verbose = int(a)
+
+    if  filename == "" or tablename == "" or filetype == "":
+        print "ERROR: missing compulsory options"
+        help()
+        sys.exit(1)
+
+    if configFileName != "":
+        config = ConfigParser.ConfigParser()
+        config.readfp( open(configFileName) )
+        host = config.get("repet_env","repet_host")
+        user = config.get("repet_env","repet_user")
+        passwd = config.get("repet_env","repet_pw")
+        dbname = config.get("repet_env","repet_db")
+        port = config.get("repet_env","repet_port")
+
+    if host == "" and os.environ.get( "REPET_HOST" ) != "":
+        host = os.environ.get( "REPET_HOST" )
+    if user == "" and os.environ.get( "REPET_USER" ) != "":
+        user = os.environ.get( "REPET_USER" )
+    if passwd == "" and os.environ.get( "REPET_PW" ) != "":
+        passwd = os.environ.get( "REPET_PW" )
+    if dbname == "" and os.environ.get( "REPET_DB" ) != "":
+        dbname = os.environ.get( "REPET_DB" )
+    if port == 0 and os.environ.get( "REPET_PORT" ) != "":
+        port = int( os.environ.get( "REPET_PORT" ) )
+        
+    if host == "":
+        print "ERROR: missing host"
+        sys.exit(1)
+    if user == "":
+        print "ERROR: missing user"
+        sys.exit(1)
+    if passwd == "":
+        print "ERROR: missing password"
+        sys.exit(1)
+    if dbname == "":
+        print "ERROR: missing db name"
+        sys.exit(1)
+    if port == 0:
+        print "ERROR: missing port"
+        sys.exit(1)
+
+    db = DbMySql(user, host, passwd, dbname, port )
+
+    if not os.path.exists( filename ):
+        print "ERROR: input file '%s' doesn't exist" % ( filename )
+        sys.exit(1)
+
+    db.createTable( tablename, filetype, filename, overwrite)
+
+    db.close()
+
+    return 0
+
+
+if __name__ == "__main__":
+    main()