def do_facmd(args, dbh=None):
if dbh is None:
dbh = get_dbhandler(args)
if args.verbose != 0:
set_verbosity(args.verbose)
executed = 0
if args.clear is not False:
do_clear( args, dbh )
executed += 1
if args.findpeaks is not False:
do_findpeaks( args, dbh )
executed += 1
if args.scan is not False:
do_scan(args, dbh)
executed += 1
if args.preannotate is not False:
do_preannotate(args, dbh)
executed += 1
if args.alignladder is not False:
do_alignladder(args, dbh)
executed += 1
if args.call is not False:
do_call(args, dbh)
executed += 1
if args.bin is not False:
do_bin(args, dbh)
executed += 1
if args.postannotate is not False:
do_postannotate(args, dbh)
executed += 1
if args.setallele is not False:
do_setallele(args, dbh)
executed += 1
if args.showladderpca is not False:
do_showladderpca( args, dbh )
executed += 1
if args.listassay is not False:
do_listassay( args, dbh )
executed += 1
if args.listpeaks is not False:
do_listpeaks( args, dbh )
executed += 1
if args.showtrace is not False:
do_showtrace( args, dbh )
executed += 1
if args.showz is not False:
do_showz( args, dbh )
executed += 1
if executed == 0:
cerr('WARN - unknown command, nothing to do!')
else:
cerr('INFO - executed %d command(s)' % executed)
def do_facmd(args, dbh=None):
if dbh is None:
dbh = get_dbhandler(args)
if args.verbose != 0:
set_verbosity(args.verbose)
executed = 0
if args.clear is not False:
do_clear( args, dbh )
executed += 1
if args.findpeaks is not False:
do_findpeaks( args, dbh )
executed += 1
if args.scan is not False:
do_scan(args, dbh)
executed += 1
if args.preannotate is not False:
do_preannotate(args, dbh)
executed += 1
if args.alignladder is not False:
do_alignladder(args, dbh)
executed += 1
if args.call is not False:
do_call(args, dbh)
executed += 1
if args.bin is not False:
do_bin(args, dbh)
executed += 1
if args.postannotate is not False:
do_postannotate(args, dbh)
executed += 1
if args.setallele is not False:
do_setallele(args, dbh)
executed += 1
if args.showladderpca is not False:
do_showladderpca( args, dbh )
executed += 1
if args.listassay is not False:
do_listassay( args, dbh )
executed += 1
if args.listpeaks is not False:
do_listpeaks( args, dbh )
executed += 1
if args.showtrace is not False:
do_showtrace( args, dbh )
executed += 1
if args.showz is not False:
do_showz( args, dbh )
executed += 1
if executed == 0:
cerr('WARN - unknown command, nothing to do!')
else:
cerr('INFO - executed %d command(s)' % executed)
def do_dbmgr(args, dbh=None, warning=True):
if not dbh:
dbh = get_dbhandler(args, initial=args.initdb)
if args.uploadfsa is not False:
do_uploadfsa(args, dbh)
elif args.initbatch is not False:
do_initbatch(args, dbh)
elif args.showbatches is not False:
do_showbatches(args, dbh)
elif args.showsample is not False:
do_showsample(args, dbh)
elif args.initsample is not False:
do_initsample(args, dbh)
elif args.importpanel is not False:
do_importpanel(args, dbh)
elif args.exportpanel is not False:
do_exportpanel(args, dbh)
elif args.importmarker is not False:
do_importmarker(args, dbh)
elif args.initdb is not False:
do_initdb(args, dbh)
elif args.clearfsa is not False:
do_clearfsa(args, dbh)
elif args.reassignmarker is not False:
do_reassignmarker(args, dbh)
elif args.initbin is not False:
do_initbin(args, dbh)
elif args.viewbin is not False:
do_viewbin(args, dbh)
elif args.updatebins is not False:
do_updatebins(args, dbh)
elif args.removebatch is not False:
do_removebatch(args, dbh)
elif args.removefsa is not False:
do_removefsa(args, dbh)
elif args.setbinbatch is not False:
do_setbinbatch(args, dbh)
elif args.exportfsa is not False:
do_exportfsa(args, dbh)
elif args.renamefsa is not False:
do_renamefsa(args, dbh)
#elif args.viewpeakcachedb is not False:
# do_viewpeakcachedb(args, dbh)
elif args.dumppeaks is not False:
do_dumppeaks(args, dbh)
else:
if warning:
cerr('Unknown command, nothing to do!')
return False
return True
def do_dbmgr(args, dbh = None, warning=True):
if not dbh:
dbh = get_dbhandler(args, initial = args.initdb)
if args.uploadfsa is not False:
do_uploadfsa(args, dbh)
elif args.initbatch is not False:
do_initbatch(args, dbh)
elif args.showbatches is not False:
do_showbatches(args, dbh)
elif args.showsample is not False:
do_showsample(args, dbh)
elif args.initsample is not False:
do_initsample(args, dbh)
elif args.importpanel is not False:
do_importpanel(args, dbh)
elif args.exportpanel is not False:
do_exportpanel(args, dbh)
elif args.importmarker is not False:
do_importmarker(args, dbh)
elif args.initdb is not False:
do_initdb(args, dbh)
elif args.clearfsa is not False:
do_clearfsa(args, dbh)
elif args.reassignmarker is not False:
do_reassignmarker(args, dbh)
elif args.initbin is not False:
do_initbin(args, dbh)
elif args.viewbin is not False:
do_viewbin(args, dbh)
elif args.updatebins is not False:
do_updatebins(args, dbh)
elif args.removebatch is not False:
do_removebatch(args, dbh)
elif args.removefsa is not False:
do_removefsa(args, dbh)
elif args.setbinbatch is not False:
do_setbinbatch(args, dbh)
elif args.exportfsa is not False:
do_exportfsa(args, dbh)
elif args.renamefsa is not False:
do_renamefsa(args, dbh)
elif args.viewpeakcachedb is not False:
do_viewpeakcachedb(args, dbh)
elif args.dumppeaks is not False:
do_dumppeaks(args, dbh)
else:
if warning:
cerr('Unknown command, nothing to do!')
return False
return True
def do_convert(args, dbh=None):
if not dbh and (args.sqldb or args.fsdb):
dbh = get_dbhandler(args)
if args.fsa2tab:
do_fsa2tab(args)
elif args.genemapper2tab:
do_genemapper2tab(args, dbh)
elif args.checkfsa:
do_checkfsa(args)
else:
cerr('Unknown command, nothing to do!')
return False
return True
def do_convert(args, dbh=None):
if not dbh and (args.sqldb or args.fsdb):
dbh = get_dbhandler(args)
if args.fsa2tab:
do_fsa2tab(args)
elif args.genemapper2tab:
do_genemapper2tab(args, dbh)
elif args.checkfsa:
do_checkfsa(args)
else:
cerr('Unknown command, nothing to do!')
return False
return True