# advanced.add_option("-d", "--debug", action="store_true", dest="debug", default=False, remember=True,
# help="Debug.", name="Debug")
parser.add_option("-o",
"--output",
type="savefile",
dest="output",
remember=True,
help="Output file. Leave empty for console ouptut.",
default="",
name="Output File",
filetypes=[("All output formats",
"*.xlsx;*.xls;*.csv;*.tsv;*.txt"),
("Excel", "*.xlsx"), ("Excel2003", "*.xls"),
("CSV", "*.csv"), ("TSV", "*.tsv"),
("Text", "*.txt")])
parser.add_option_group(advanced)
opt = None
while True:
if 'exit' in error_kwargs:
try:
opt, args = parser.parse_args(opts=opt)
except UserCancelledError:
sys.exit(0)
else:
opt, args = parser.parse_args()
break
progress = None
if not opt.output:
help="Scale read counts at high-coverage loci to ensure at most this many good reads at SNV locus per alignment file. Values greater than 1 indicate absolute read counts, otherwise the value indicates the coverage distribution percentile. Default=No maximum.", name="Max. Reads")
readcounts.add_option("-f", "--alignmentfilter", action="store_false", dest="filter", default=True, remember=True,
help="(Turn off) alignment filtering by length, edits, etc.", name="Filter Alignments")
readcounts.add_option("-U", "--uniquereads", action="store_true", dest="unique", default=False, remember=True,
help="Consider only distinct reads.", name="Unique Reads")
readcounts.add_option("-t", "--threadsperbam", type="int", dest="tpb", default=1, remember=True,
help="Worker threads per alignment file. Indicate no threading with 0. Default=1.",
name="Threads/BAM")
readcounts.add_option("-q", "--quiet", action="store_true", dest="quiet", default=False, remember=True,
help="Quiet.", name="Quiet")
parser.add_option("-o", "--output", type="savedir", dest="output", remember=True,
help="Output folder. Required.", default=None, notNone=True,
name="Output Folder")
parser.add_option_group(exfilt)
parser.add_option_group(readcounts)
parser.add_option_group(regexs)
parser.add_option_group(snvannot)
opt = None
while True:
if 'exit' in error_kwargs:
try:
opt, args = parser.parse_args(opts=opt)
except UserCancelledError:
sys.exit(0)
else:
opt, args = parser.parse_args()
break
advanced.add_option("-f", "--alignmentfilter", action="store_false", dest="filter", default=True, remember=True,
help="(Turn off) alignment filtering by length, edits, etc.", name="Filter Alignments")
advanced.add_option("-U", "--uniquereads", action="store_true", dest="unique", default=False, remember=True,
help="Consider only distinct reads.", name="Unique Reads")
advanced.add_option("-t", "--threadsperbam", type="int", dest="tpb", default=0, remember=True,
help="Worker threads per alignment file. Indicate no threading with 0. Default=0.", name="Threads/BAM")
advanced.add_option("-q", "--quiet", action="store_true", dest="quiet", default=False, remember=True,
help="Quiet.", name="Quiet")
advanced.add_option("-d", "--debug", action="store_true", dest="debug", default=False, remember=True,
help="Debug.", name="Debug")
parser.add_option("-o", "--output", type="savefile", dest="output", remember=True,
help="Output file. Leave empty for console ouptut.", default="",
name="Output File", filetypes=[("All output formats", "*.xlsx;*.xls;*.csv;*.tsv;*.txt"),
("Excel", "*.xlsx"), ("Excel2003", "*.xls"),
("CSV", "*.csv"), ("TSV", "*.tsv"), ("Text", "*.txt")])
parser.add_option_group(advanced)
opt = None
while True:
if 'exit' in error_kwargs:
try:
opt, args = parser.parse_args(opts=opt)
except UserCancelledError:
sys.exit(0)
else:
opt, args = parser.parse_args()
break
progress = None
if not opt.output:
help="Scale read counts at high-coverage loci to ensure at most this many good reads at SNV locus per alignment file. Values greater than 1 indicate absolute read counts, otherwise the value indicates the coverage distribution percentile. Default=No maximum.", name="Max. Reads")
readcounts.add_option("-f", "--alignmentfilter", action="store_false", dest="filter", default=True, remember=True,
help="(Turn off) alignment filtering by length, edits, etc.", name="Filter Alignments")
readcounts.add_option("-U", "--uniquereads", action="store_true", dest="unique", default=False, remember=True,
help="Consider only distinct reads.", name="Unique Reads")
readcounts.add_option("-t", "--threadsperbam", type="int", dest="tpb", default=1, remember=True,
help="Worker threads per alignment file. Indicate no threading with 0. Default=1.",
name="Threads/BAM")
readcounts.add_option("-q", "--quiet", action="store_true", dest="quiet", default=False, remember=True,
help="Quiet.", name="Quiet")
parser.add_option("-o", "--output", type="savedir", dest="output", remember=True,
help="Output folder. Required.", default=None, notNone=True,
name="Output Folder")
parser.add_option_group(exfilt)
parser.add_option_group(readcounts)
parser.add_option_group(regexs)
parser.add_option_group(snvannot)
opt = None
while True:
if 'exit' in error_kwargs:
try:
opt, args = parser.parse_args(opts=opt)
except UserCancelledError:
sys.exit(0)
else:
opt, args = parser.parse_args()
break
