def setup_options():
parser = OptionParser()
parser.add_option("-a",
"--assembly",
dest="assembly_filename",
help="Assembly file",
metavar="FILE")
parser.add_option("-r",
"--reads",
dest="reads_filename",
help="input reads",
metavar="FILE")
parser.add_option("-k",
"--kmer",
dest="kmer_size",
help="kmer size",
default=8,
type="int")
(options, args) = parser.parse_args()
should_quit = False
if options.assembly_filename == None or options.reads_filename == None:
parser.error("You failed to provide the mpileup file")
if should_quit:
parser.help()
exit(-1)
return (options, args)
def setup_options():
parser = OptionParser()
parser.add_option("-p",
"--pileup-file",
dest="pileup_filename",
help="pileup file name",
metavar="FILE")
parser.add_option("-o",
"--output",
dest="output_location",
help="output location for depth of coverage tool",
default=None,
metavar="FILE")
parser.add_option("-c",
"--chunks",
dest="total_chunks",
help="total chunks to split the pileup file.",
type="int",
default=1)
(options, args) = parser.parse_args()
should_quit = False
if options.pileup_filename == None:
parser.error("You failed to provide the pileup file")
if should_quit:
parser.help()
exit(-1)
return (options, args)
def setup_options():
parser = OptionParser()
parser.add_option(
"-a", "--abundance-file", dest="abundance_file", help="Assembler provided abundance file", metavar="FILE"
)
parser.add_option("-m", "--mpileup-file", dest="mp_file_loc", help="mpileup output file", metavar="FILE")
parser.add_option("-p", "--pileup-file", dest="pileup_filename", help="pileup file name", metavar="FILE")
parser.add_option(
"-o",
"--output",
dest="output_location",
help="output location for depth of coverage tool",
default=None,
metavar="FILE",
)
parser.add_option(
"-w", "--window-size", dest="window_size", help="window size to sweep over base pairs", type="int", default=1
)
parser.add_option("-g", "--gff", dest="gff_format", default=False, action="store_true")
parser.add_option("-e", "--empirical", dest="use_empirical", default=False, action="store_true")
parser.add_option(
"-i", "--ignore", dest="ignore_ends", help="Ignore the first/last i bps of the read", type="int", default=0
)
parser.add_option("-c", "--chunks", dest="chunks", help="Number of output file chunks.", type="int", default=1)
(options, args) = parser.parse_args()
should_quit = False
if options.mp_file_loc == None:
parser.error("You failed to provide the mpileup file")
if should_quit:
parser.help()
exit(-1)
return (options, args)
def setup_options():
parser = OptionParser()
parser.add_option("-a",
"--assembly",
dest="assembly_filename",
help="Assembly file",
metavar="FILE")
parser.add_option("-r",
"--reads",
dest="reads_filename",
help="input reads",
metavar="FILE")
parser.add_option("-k",
"--kmer",
dest="kmer_size",
help="kmer size",
default=8,
type="int")
parser.add_option("-t",
"--threads",
dest="threads",
help="number of threads",
default=8,
type="int")
parser.add_option("-e",
"--error_rate",
dest="error_rate",
help="error rate (0% by default)",
type="float",
default=1.0)
parser.add_option("-m",
"--max_iterations",
dest="max_iter",
help="max iterations (30 by default)",
type="int",
default=30)
parser.add_option("-p",
"--pileup",
dest="pileup_file",
help="write pileup to this file.",
default=None)
parser.add_option("-s",
"--save-intermediate-files",
dest="save_intermediate_files",
help="save all the intermediate files.",
action='store_true')
(options, args) = parser.parse_args()
should_quit = False
if options.assembly_filename == None or options.reads_filename == None:
parser.error("You failed to provide the mpileup file")
if should_quit:
parser.help()
exit(-1)
return (options, args)
def setup_options():
parser = OptionParser()
parser.add_option("-p", "--pileup-file", dest="pileup_filename", help="pileup file name", metavar="FILE")
parser.add_option("-o", "--output", dest="output_location", help="output location for depth of coverage tool", default=None, metavar="FILE")
parser.add_option("-c", "--chunks", dest="total_chunks", help="total chunks to split the pileup file.", type="int", default = 1)
(options,args) = parser.parse_args()
should_quit = False
if options.pileup_filename == None:
parser.error("You failed to provide the pileup file")
if should_quit:
parser.help()
exit(-1)
return (options,args)
def setup_options():
parser = OptionParser()
parser.add_option("-a",
"--abundance-file",
dest="abundance_file",
help="Assembler provided abundance file",
metavar="FILE")
parser.add_option("-m",
"--mpileup-file",
dest="mp_file_loc",
help="mpileup output file",
metavar="FILE")
parser.add_option("-p",
"--pileup-file",
dest="pileup_filename",
help="pileup file name",
metavar="FILE")
parser.add_option("-o",
"--output",
dest="output_location",
help="output location for depth of coverage tool",
default=None,
metavar="FILE")
parser.add_option("-w",
"--window-size",
dest="window_size",
help="window size to sweep over base pairs",
type="int",
default=1)
parser.add_option("-g",
"--gff",
dest="gff_format",
default=False,
action='store_true')
parser.add_option("-e",
"--empirical",
dest="use_empirical",
default=False,
action='store_true')
parser.add_option("-i",
"--ignore",
dest="ignore_ends",
help="Ignore the first/last i bps of the read",
type="int",
default=0)
parser.add_option("-c",
"--chunks",
dest="chunks",
help="Number of output file chunks.",
type="int",
default=1)
(options, args) = parser.parse_args()
should_quit = False
if options.mp_file_loc == None:
parser.error("You failed to provide the mpileup file")
if should_quit:
parser.help()
exit(-1)
return (options, args)
#parser.formatter._format_option_strings = parser.formatter.format_option_strings
#parser.formatter.format_option_strings = type(parser.formatter.format_option_strings)(_, parser, type(parser))
#option = parser.get_option("-h")
#options = parser.get_option("-h")
#options.help("Show this help message and exit Show help and exit.")
#(options, args) = parser.parse_args()
# Dirty hack for making a short option -hh
option = OptionParser("--hh")
option.add_option = ["-hh"]
option.add_option = []
# Dirty hack for inherent help message of switch -h
option = parser.get_option("-h")
option.help = option.help.capitalize().replace("this help", "basic help")
argv = []
prompt = False
#advancedHelp = True
extraHeaders = []
for arg in sys.argv:
#argv.append(sys.maxunicode(arg, encoding=sys.getfilesystemencoding()))
prompt = "--commi3-shell" in argv
if prompt:
parser.usage = ""
cmdLineOptions.sqlmapShell = True
