--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/tools/srptGameXmlMaker.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,283 @@
+#!/usr/bin/env python
+
+import user, os, sys, getopt, ConfigParser
+from os import listdir
+
+def setup_env():
+    if "REPET_PATH" in os.environ.keys():
+        sys.path.append( os.environ["REPET_PATH"] )
+    else:
+        print "*** Error: no environment variable REPET_PATH ***"
+        sys.exit(1)
+setup_env()
+
+from pyRepet.sql.RepetDBMySQL import *
+from pyRepet.gamexml.Xml_writer import *
+from pyRepet.gamexml.computational import *
+
+#------------------------------------------------------------------------------
+
+def help():
+
+    print ""
+    print "usage:",sys.argv[0],"[options]"
+    print "options:"
+    print "     -h: this help"
+    print "     -f: fasta file (required to generate new '.gamexml' files)"
+    print "     -n: annotation tier_name"
+    print "     -g: gamexml file (for Apollo). If it's not mentionned, all '.gamexml' files will be updated with the result file"
+    print "     -l: light gameXML file (without sequence)"
+    print "     -r: result files (require -n)"
+    print "     -R: reverse the query and subject of Blaster results"
+    print "     -s: tier_name of an annotation to remove from a gameXML file"
+    print "     -t: file of table name to use to create the gamexml files (tier name 'tab' format 'tab' table name)"
+    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 "     -v: verbose (default=0/1/2)"
+    print ""
+
+#------------------------------------------------------------------------------
+
+def automatisation( result_file, tier_name, reverse, comput ):
+
+    if verbose > 1:
+        print "Auto update"; sys.stdout.flush()
+    writer = Xml_writer()
+    file_liste = []
+    liste_comp = []
+    liste_comp = listdir('./')
+
+    if result_file != "":
+        for j in liste_comp:
+            if writer.file_in_keys( j, comput ):
+                file_liste = file_liste + [j]
+
+        for i in file_liste:
+            writer.update_gamexml( i, result_file, tier_name, comput )
+
+    else:
+        for j in liste_comp:
+            if j.find( "gamexml" ) != -1:
+                writer.parse_gamexml( j )
+                writer.verif_name_prog( tier_name )
+                writer.write( j )
+                if verbose > 1:
+                    print tier_name + " program from " +j +" removed"
+
+#------------------------------------------------------------------------------
+
+def main():
+
+    f_result = ""
+    f_gamexml = ""
+    f_fasta = ""
+    f_table = ""
+    tier_name = ""
+    substract_name = ""
+    no_seq = 0
+    configFileName = ""
+    host = ""
+    user = ""
+    passwd = ""
+    dbname = ""
+    verbose = 0
+
+    try:
+        options,arguments=getopt.getopt(sys.argv[1:],"hn:f:g:r:s:lRt:c:H:U:P:D:v:",["help","tier_name=","fasta","gamexml","result","substract_program","light","reverse_result","table"])
+    except getopt.GetoptError:
+        help()
+        sys.exit(1)
+    if options == []:
+        help()
+        sys.exit(1)
+    for o,a in options:
+        if o == "-h" or o == "--help":
+            help()
+            sys.exit(0)
+        elif o == "-f" or o == "--fasta":
+            f_fasta = a
+        elif o == "-g" or o == "--gamexml":
+            f_gamexml = a 
+        elif o == "-n" or o == "--tier_name":
+            tier_name = a
+        elif o == "-r" or o == "--result":
+            f_result = a
+        elif o == "-s" or o == "--subtract_program":
+            substract_name = a
+        elif o == "-l" or o == "--light":
+            no_seq = 1
+        elif o == "-R" or o == "--reverse_result":
+            writer.set_reverse()
+        elif o == "-t" or o == "--table":
+            f_table = a
+        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 == "-v":
+            verbose = int(a)
+
+    if tier_name == "" and substract_name == "" and f_result != "":
+        print "*** Error: option -n required"
+        help()
+        sys.exit(1)
+
+    if f_fasta == "" and f_gamexml == "":
+        print "*** Error: options -g or -f required"
+        help()
+        sys.exit(1)
+    
+    if substract_name!="" and f_result!="" :
+        print "Error: option -s and -r together"
+        help()
+        sys.exit(1)
+
+
+    if verbose > 0:
+        print "\nbeginning of %s" % (sys.argv[0].split("/")[-1])
+        sys.stdout.flush()
+
+    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")
+
+    if host == "" and os.environ.get( "REPET_HOST" ) != None:
+        host = os.environ.get( "REPET_HOST" )
+    if user == "" and os.environ.get( "REPET_USER" ) != None:
+        user = os.environ.get( "REPET_USER" )
+    if passwd == "" and os.environ.get( "REPET_PW" ) != None:
+        passwd = os.environ.get( "REPET_PW" )
+    if dbname == "" and os.environ.get( "REPET_DB" ) != None:
+        dbname = os.environ.get( "REPET_DB" )
+
+    writer = Xml_writer()
+
+    # create the dico
+    comput = computational()
+
+    # create all the ".gamexml" files (option '-f')
+    if f_fasta != "":
+        writer.create_gamexml( f_fasta, f_result, tier_name, comput, no_seq )
+
+    # 
+    if f_result != "":
+       if f_gamexml != "":
+           key = ".".join( f_gamexml.split(".")[:-1] )
+       else:
+           key = ""
+       format = writer.find_type_file( f_result )
+       resFile = open( f_result )
+       if format == "path":
+	       comput.load_dico_path_from_file( key, f_result )
+
+    if f_table != "":
+            if verbose > 1:
+                print "parsing file %s... " % ( f_gamexml ); sys.stdout.flush()
+	    writer.parse_gamexml( f_gamexml )
+
+	    if f_gamexml != "":
+##                key=".".join(f_gamexml.split(".")[:-1])
+                key = f_gamexml.split(".")[0]
+	    else:
+                key = ""
+
+	    tfile = open( f_table )
+	    lines = tfile.readlines()
+	    for l in lines:
+                if l[0] == "#":
+                    continue
+                tok = l.split()
+                #print tok
+                if len(tok) == 0:
+                    break
+                tier_name = tok[0]
+                format = tok[1]
+                table = tok[2]
+                alias = ""
+                if verbose > 1:
+                    print "table: " + table + " (format=" + format + ")"
+                if len(tok) > 3:
+                    alias = tok[3]
+                    if verbose > 1:
+                        print " alias=" + alias
+
+                if host == "" or user == "" or passwd == "" or dbname == "":
+                    print "*** Error: missing information about MySQL connection"
+                    sys.exit(1)
+                db = RepetDB( user, host, passwd, dbname )
+
+                if format == "path":
+                    comput.load_dico_path_from_table( db, key, table, alias )
+                    writer.update_gamexml_comput( tier_name, comput )
+                elif format == "rpath":
+                    comput.load_dico_rpath_from_table( db, key, table, alias )
+                elif format == "ipath":
+                    comput.load_dico_ipath_from_table( db, key, table, alias )
+                    writer.update_gamexml_comput( tier_name, comput )
+                elif format == "align":
+                    comput.load_dico_align_from_table( db, key, table, alias )
+                    writer.update_gamexml_comput( tier_name, comput )
+                elif format == "map":
+                    comput.load_dico_map_from_table( db, key, table, alias )
+                    writer.update_gamexml_comput( tier_name, comput )
+                elif format == "rmap":
+                    comput.load_dico_rmap_from_table( db, key, table, alias )
+                    writer.update_gamexml_comput( tier_name, comput )
+                elif format == "set":
+                    comput.load_dico_set_from_table( db, key, table, alias )
+                    writer.update_gamexml_comput( tier_name, comput )
+                elif format == "annot":
+                    comput.load_dico_annot_from_table( db, key, table, alias )
+                    writer.update_gamexml_annot( table, comput )
+                elif format == "annot_set":
+                    comput.load_dico_annotset_from_table( db, key, table, alias )
+                    writer.update_gamexml_annot( table, comput )
+                else:
+                    print "*** Error: unknown format '%s'" % ( format )
+                    sys.exit(1)
+            writer.write(f_gamexml)
+
+            db.close()
+
+    # 
+    if f_gamexml == "" and f_result != "" and f_fasta == "":
+        automatisation( f_result, tier_name, writer.get_reverse(), comput )
+
+    # update a ".gamexml" file (options '-g' and '-t')
+    if f_gamexml != "" and f_result != "":
+        writer.update_gamexml( f_gamexml, f_result, tier_name, comput )
+
+    # remove a comput
+    if substract_name != "" and tier_name == "":
+        if f_gamexml != "":
+            writer.parse_gamexml( f_gamexml )
+            writer.verif_name_prog( substract_name )
+            writer.write( f_gamexml )
+            if verbose > 1:
+                print substract_name + " program from " + f_gamexml +" removed"
+        else:
+            automatisation( "", substract_name, 0, None )
+
+    if verbose > 0:
+        print "%s finished successfully\n" % (sys.argv[0].split("/")[-1])
+        sys.stdout.flush()
+
+    return 0
+
+#------------------------------------------------------------------------------
+
+if __name__ == '__main__':
+    main()