def main() :
if (len(argv) < 2) or (argv[1] in ('-h', '--help', 'help')) :
usage()
return 1
command = argv[1]
if command not in get_commands() :
print >> stderr, "Error: unknown command '%s'" % command
usage()
return 1
if command == 'test' :
test_system(output=True)
return 0
options = parse_args(command, argv[2:])
log = setup_logging(options['verbose'])
check_options(command, options, log)
test_system(command, options, exit_on_failure=True)
System.tempdir(options['outdir']) # some objects need this set
wf = WorkFlow(options)
if command == 'preprocess' :
return wf.preprocess()
elif command == 'summary' :
return wf.summary()
elif command == 'cluster' :
return wf.cluster()
elif command == 'label' :
return wf.label()
elif command == 'showcounts' :
return wf.showcounts()
elif command == 'showlabels' :
return wf.showlabels()
elif command == 'phylogeny' :
return wf.phylogeny()
elif command == 'heatmap' :
return wf.heatmap()
elif command == 'wasabi' :
return wf.wasabi()
else :
print >> stderr, "'%s' appears to be partially implemented!" % command
return 1
