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
from os.path import join, dirname, realpath, split try: scriptdir = dirname(realpath(__file__)) except NameError: scriptdir = dirname(realpath(sys.argv[0])) sys.path.append(join(scriptdir, '..', '..', 'common', 'src')) from optparse_gui import OptionParser, OptionGroup, ProgressText parser = OptionParser(version=VERSION) regexs = OptionGroup(parser, "Filename Matching") parser.add_option("--counts", type="file", dest="counts", default=None, help="Output file from readCounts. Required.", notNone=True, filetypes=[("readCount Output", "*.tsv")]) parser.add_option("--cosmic", type="file", dest="cosmic", default=None, help="COSMIC Mutants.", filetypes=[("COSMIC Annotations", "*.tsv;*.tsv.gz")]) parser.add_option("--darned", type="file", dest="darned", default=None, help="DARNED annotations.", filetypes=[("DARNED Annotations", "*.txt")])
except NameError: scriptdir = dirname(realpath(sys.argv[0])) sys.path.append(join(scriptdir, '..', '..', 'common', 'src')) from version import VERSION VERSION = '1.0.4 (%s)' % (VERSION, ) from optparse_gui import OptionParser parser = OptionParser(version=VERSION) parser.add_option("--exons", type="file", dest="exons", default=None, help="Exonic coordinates (sored). Required.", notNone=True, filetypes=[("Exonic Coordinates", "*.txt")]) parser.add_option("--input", type="file", dest="input", default=None, help="Input SNVs. Required", filetypes=[("Input SNV File", "*.vcf;*.csv;*.tsv;*.xls;*.xlsx;*.txt")]) parser.add_option("--output", type="savefile", dest="output", default=None, help="Output file. Required",
from version import VERSION VERSION = '1.0.6 (%s)' % (VERSION,) from os.path import join, dirname, realpath, split try: scriptdir = dirname(realpath(__file__)) except NameError: scriptdir = dirname(realpath(sys.argv[0])) sys.path.append(join(scriptdir, '..', '..', 'common', 'src')) from optparse_gui import OptionParser, OptionGroup, ProgressText parser = OptionParser(version=VERSION) regexs = OptionGroup(parser, "Filename Matching") parser.add_option("--counts", type="file", dest="counts", default=None, help="Output file from readCounts. Required.", notNone=True, filetypes=[("readCount Output", "*.tsv")]) parser.add_option("--cosmic", type="file", dest="cosmic", default=None, help="COSMIC Mutants.", filetypes=[("COSMIC Annotations", "*.tsv;*.tsv.gz")]) parser.add_option("--darned", type="file", dest="darned", default=None, help="DARNED annotations.", 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.",