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"]
