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 = list(map(str, list(range(1, 100)))) + ["X", "Y", "MT"]
chrreg.add_labels(opt.counts, labels)
chrreg.default_chrom_order()
chrorder = lambda l: chrreg.chrom_order(chrreg.label2chrom(opt.counts, l))
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:
opt.quiet = True
if opt.maxreads == None:
opt.maxreads = 1e+20
progress = ProgressText(quiet=opt.quiet)
from dataset import XLSFileTable, CSVFileTable, TSVFileTable, XLSXFileTable, TXTFileTable, BEDFile, VCFFile
progress.stage("Read SNV data", len(opt.snvs))
snvheaders = filter(None, """
CHROM POS REF ALT
""".split())
snvdata = {}
# extrasnvheaders = []
# usedsnvheaders = set()
snvchroms = defaultdict(set)
for filename in opt.snvs:
base, extn = filename.rsplit('.', 1)
