def __init__(self, *args, **kwargs):
if wx.GetApp() is None:
self.app = wx.App(False)
self.args = False
if kwargs.has_key('args'):
self.args = kwargs['args']
del kwargs['args']
dotfile = None
if 'dotfile' in kwargs:
dotfile = kwargs['dotfile']
del kwargs['dotfile']
OptionParser.__init__(self, *args, **kwargs)
self.dotfile = self.find_dotfile(dotfile)
def __init__( self, *args, **kwargs ):
if wx.GetApp() is None:
self.app = wx.App( False )
self.args = False
if kwargs.has_key('args'):
self.args = kwargs['args']
del kwargs['args']
dotfile = None
if 'dotfile' in kwargs:
dotfile = kwargs['dotfile']
del kwargs['dotfile']
OptionParser.__init__( self, *args, **kwargs )
self.dotfile = self.find_dotfile(dotfile)
from collections import defaultdict
from version import VERSION
VERSION = '%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")])
shutil.rmtree(d, ignore_errors=True)
atexit.register(cleanup)
if not GUI() and len(sys.argv) == 2 and sys.argv[1] == '--GUI':
from optparse_gui.needswx import *
sys.exit(1)
if GUI() and len(sys.argv) == 1:
from optparse_gui import OptionParserGUI
parser = OptionParserGUI(version=VERSION)
error_kwargs = {'exit': False}
sys.excepthook = excepthook
else:
parser = OptionParser(version=VERSION)
error_kwargs = {}
advanced = OptionGroup(parser, "Advanced")
parser.add_option("-s",
"--snvs",
type="files",
dest="snvs",
default=None,
help="Single-Nucleotide-Variant files. Required.",
name="SNV Files",
notNone=True,
remember=True,
filetypes=[("SNV Files",
"*.vcf;*.csv;*.tsv;*.xls;*.xlsx;*.txt")])
parser.add_option("-r",
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
import operator
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 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")])
import gzip
import re
from collections import defaultdict
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',