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#parser.add_option("", "--fixDot", dest="fixDot", action="store_true", help="replace dots in cell meta IDs with dashes (for R)")
#parser.add_option("-t", "--geneType", dest="geneType", help="type of gene IDs in expression matrix. values like 'symbols', or 'gencode22', 'gencode28' or 'gencode-m13'.")
#parser.add_option("", "--bamDir", dest="bamDir", help="directory with BAM files, one per cell. Merges small BAM files into one per cell cluster.")
parser.add_option("", "--clusterOrder", dest="clusterOrder", help="file with cluster names in the order that they should appear in the track. default is alphabetical order.")
parser.add_option("-s", "--skipBarchart", dest="skipBarchart", help="do not create the bar chart graph", action="store_true")
#parser.add_option("", "--name", dest="name", help="name of track hub.")
#parser.add_option("", "--email", dest="email", help="contact email for track hub. Default is %default, taken from the env. variable CBEMAIL", default=CBEMAIL)
#parser.add_option("-f", "--file", dest="file", action="store", help="run on file")
#parser.add_option("", "--test", dest="test", action="store_true", help="do something")
(options, args) = parser.parse_args()
if not options.exprMatrix and not isfile(options.inConf) and not options.init:
parser.print_help()
exit(1)
cellbrowser.setDebug(options.debug)
return args, options