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)
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)
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:
opt.quiet = True
progress = ProgressText(quiet=opt.quiet)
import pysam
from dataset import XLSFileTable, CSVFileTable, TSVFileTable, XLSXFileTable, TXTFileTable, BEDFile, VCFFile
progress.stage("Read SNP data", len(opt.snps))
snpheaders = filter(None, """
CHROM POS REF ALT
""".split())
snpdata = {}
extrasnpheaders = []
usedsnpheaders = set()
for filename in opt.snps:
base, extn = filename.rsplit('.', 1)
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:
opt.quiet = True
progress = ProgressText(quiet=opt.quiet)
from pysamimport import pysam
from dataset import XLSFileTable, CSVFileTable, TSVFileTable, XLSXFileTable, TXTFileTable, BEDFile, VCFFile
progress.stage("Read SNV data", len(opt.snvs))
snvheaders = [_f for _f in """
CHROM POS REF ALT
""".split() if _f]
snvdata = {}
extrasnvheaders = []
usedsnvheaders = set()
for filename in opt.snvs:
base, extn = filename.rsplit('.', 1)
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"]
chrreg.add_labels(opt.counts,labels)
chrreg.default_chrom_order()
chrorder = lambda l: chrreg.chrom_order(chrreg.label2chrom(opt.counts,l))
progress.stage("Parsing read-counts")
f = open(opt.counts, 'r')
reader = csv.DictReader(f, delimiter='\t')
break
matrix = None
if opt.matrix:
if opt.matrix == "Ref:Var":
matrix = (lambda d: "%(Ref)s:%(Var)s" % d)
elif opt.matrix == "Ref;Var":
matrix = (lambda d: "%(Ref)s;%(Var)s" % d)
elif opt.matrix == "VAF":
matrix = (lambda d: "%(VAF)s" % d)
progress = None
if not opt.output:
opt.quiet = True
progress = ProgressText(quiet=opt.quiet)
doublequote = lambda s: '"%s"' % (s, )
indent = lambda s, n: "\n".join([(" " * n) + l for l in s.splitlines()])
args = []
args.extend(["-c", doublequote(" ".join(opt.counts))])
if matrix:
args.extend(["-M", opt.matrix])
if opt.minreads != minreads_default:
args.extend(["-m", str(opt.minreads)])
args.extend(["-o", doublequote(opt.output)])
if opt.quiet:
args.extend(["-q"])
cmdargs = " ".join(args)
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
opts.mates = False
progress = None
if not opt.output:
opt.quiet = True
progress = ProgressText(quiet=opt.quiet)
import pysam
from dataset import XLSFileTable, CSVFileTable, TSVFileTable, XLSXFileTable, TXTFileTable, BEDFile, VCFFile
progress.stage("Read SNP data", len(opt.snps))
snpheaders = [_f for _f in """
CHROM POS REF ALT
""".split() if _f]
snvdata = {}
snvchroms = defaultdict(set)
extrasnpheaders = []
usedsnpheaders = set()
for filename in opt.snps:
filename0 = filename
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:
opt.quiet = True
progress = ProgressText(quiet=opt.quiet)
from pysamimport import pysam
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()
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:
opt.quiet = True
progress = ProgressText(quiet=opt.quiet)
sumkeys = [
_f for _f in map(
str.strip, """
SNPJuncIntronCount SNPJuncNoIntronCount NoSNPJuncIntronCount NoSNPJuncNoIntronCount SNPMateCount NoSNPMateCount SNPCount NoSNPCount MatesCount NotMatesCount IntronCount NoIntronCount SpanningReads RemovedDuplicateReads SNPLociReads"""
.split()) if _f
]
countdata = defaultdict(dict)
progress.stage("Read SNP/Junction counts")
from dataset import XLSFileTable, CSVFileTable, TSVFileTable, XLSXFileTable, TXTFileTable
countheaders = None
for filename in opt.counts:
base, extn = filename.rsplit('.', 1)
path, base = os.path.split(base)
extn = extn.lower()
except ValueError:
parser.error("Bad Max. Read option", **error_kwargs)
continue
break
readfilter = filterFactory.get(opt.filter)
if opt.readgroup:
readgroup = groupFactory.get(opt.readgroup)
else:
readgroup = None
progress = None
if not opt.output:
opt.quiet = True
progress = ProgressText(quiet=opt.quiet)
doublequote = lambda s: '"%s"' % (s, )
indent = lambda s, n: "\n".join([(" " * n) + l for l in s.splitlines()])
args = []
args.extend(["-s", doublequote(" ".join(opt.snvs))])
args.extend(["-r", doublequote(" ".join(opt.alignments))])
if opt.filter != filter_default:
args.extend(["-f", doublequote(opt.filter)])
if opt.minreads != minreads_default:
args.extend(["-m", str(opt.minreads)])
if opt.maxreads != maxreads_default:
args.extend(["-M", str(opt.maxreads)])
if opt.readgroup != readgroup_default:
args.extend(
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:
opt.quiet = True
progress = ProgressText(quiet=opt.quiet)
sumkeys = filter(None, map(str.strip, """
SNPJuncIntronCount SNPJuncNoIntronCount NoSNPJuncIntronCount NoSNPJuncNoIntronCount SNPMateCount NoSNPMateCount SNPCount NoSNPCount MatesCount NotMatesCount IntronCount NoIntronCount SpanningReads RemovedDuplicateReads SNPLociReads""".split()))
countdata = defaultdict(dict)
progress.stage("Read SNP/Junction counts")
from dataset import XLSFileTable, CSVFileTable, TSVFileTable, XLSXFileTable, TXTFileTable
countheaders = None
for filename in opt.counts:
base, extn = filename.rsplit('.', 1)
path, base = os.path.split(base)
extn = extn.lower()
if extn == 'csv':
counts = CSVFileTable(filename=filename)
elif extn == 'tsv':
counts = TSVFileTable(filename=filename)
