def parseParams(self): ''' Use OptionParser to get parameters ''' global check_interval if len(sys.argv) == 1 and self.is_win32: try: from optparse_gui import OptionParser use_gui = True except: raw_input('Need opparse_gui to enter options on Windows') sys.exit() else: from optparse import OptionParser use_gui = False parser = OptionParser() # options parser.add_option("--method", dest="method", help="method to transfer, e.g. --method=mv", type="choice", choices=['mv','rsync'], default='rsync' if sys.platform != 'win32' else "mv") parser.add_option("--source_path", dest="source_path", help="Mounted parent path to transfer, e.g. --source_path=/mnt/ddframes", metavar="PATH") parser.add_option("--camera_host", dest="camera_host", help="Camera computer hostname in leginondb, e.g. --camera_host=gatank2") parser.add_option("--destination_head", dest="dest_path_head", help="Specific head destination frame path to transfer if multiple frame transfer is run for one source to frame paths not all mounted on the same computer, e.g. --destination_head=/data1", metavar="PATH", default='') parser.add_option("--check_interval", dest="check_interval", help="Seconds between checking for new frames", type="int", default=check_interval) # parsing options (options, optargs) = parser.parse_args(sys.argv[1:]) if len(optargs) > 0: print "Unknown commandline options: "+str(optargs) if not use_gui and len(sys.argv) < 2: parser.print_help() sys.exit() params = {} for i in parser.option_list: if isinstance(i.dest, str): params[i.dest] = getattr(options, i.dest) self.checkOptionConflicts(params) # set global variable check_interval check_interval = options.check_interval return params
dest="tumordnare", default=r'SDNA', help="Somatic/Tumor DNA filename regular expression. Default: SDNA.", remember=True, name="Somatic DNA RE") regexs.add_option( "--tumortransre", type="str", dest="tumortransre", default=r'TRNA', help="Tumor transcriptome filename regular expression. Default: TRNA.", remember=True, name="Tumor Transcr. RE") parser.add_option_group(regexs) opt, args = parser.parse_args() regex = {} regex["GDNA"] = opt.normaldnare regex["NRNA"] = opt.normaltransre regex["SDNA"] = opt.tumordnare regex["TRNA"] = opt.tumortransre progress = ProgressText() base = os.path.split(os.path.abspath(opt.counts))[0] TRNA = {} NRNA = {} GDNA = {} SDNA = {}
filetypes=[("DARNED Annotations", "*.txt")]) regexs.add_option("--normaldnare", type="str", dest="normaldnare", default=r'GDNA', help="Germline/Normal DNA filename regular expression. Default: GDNA.", remember=True, name="Germline DNA RE") regexs.add_option("--normaltransre", type="str", dest="normaltransre", default=r'NRNA', help="Normal transcriptome filename regular expression. Default: NRNA.", remember=True, name="Normal Transcr. RE") regexs.add_option("--tumordnare", type="str", dest="tumordnare", default=r'SDNA', help="Somatic/Tumor DNA filename regular expression. Default: SDNA.", remember=True, name="Somatic DNA RE") regexs.add_option("--tumortransre", type="str", dest="tumortransre", default=r'TRNA', help="Tumor transcriptome filename regular expression. Default: TRNA.", remember=True, name="Tumor Transcr. RE") parser.add_option_group(regexs) opt, args = parser.parse_args() regex = {} regex["GDNA"] = opt.normaldnare regex["NRNA"] = opt.normaltransre regex["SDNA"] = opt.tumordnare regex["TRNA"] = opt.tumortransre progress = ProgressText() base = os.path.split(os.path.abspath(opt.counts))[0] TRNA = {}; NRNA = {}; GDNA = {}; SDNA = {} from chromreg import ChromLabelRegistry chrreg = ChromLabelRegistry() labels = map(str,range(1,100)) + ["X","Y","MT"]