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)
extn = extn.lower()
if extn == 'csv':
snvs = CSVFileTable(filename=filename)
elif extn == 'vcf':
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))
progress.stage("Parsing read-counts")
f = open(opt.counts, mode='rt', encoding='utf8')
reader = csv.DictReader(f, delimiter='\t')
types2files = defaultdict(set)
files2types = defaultdict(set)
for row in reader:
key = (row['CHROM'], row['POS'])
filename = row['AlignedReads']
for k in row:
if k.endswith('Count') and row[k] != "":
row[k] = int(row[k])
if k.endswith('Sc') and row[k] != "":
row[k] = float(row[k])
if re.search(regex["GDNA"], filename) and key not in GDNA:
GDNA[key] = row
types2files["GDNA"].add(filename)
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)
extn = extn.lower()
if extn == 'csv':
snvs = CSVFileTable(filename=filename)
elif extn == 'vcf':
snvs = VCFFile(filename=filename)
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)
extn = extn.lower()
if extn == 'csv':
snvs = CSVFileTable(filename=filename)
elif extn == 'vcf':
ReadCounts Files (-c): %s
Matrix Output (-M): %s
Min. Reads (-m): %s%s
Quiet (-q): %s
Outfile File (-o): %s
Command-Line: readCountsMatrix %s
""" % (", ".join(opt.counts), None if not matrix else opt.matrix, opt.minreads,
"" if opt.matrix not in ("Ref:Var", "Ref;Var") or opt.minreads == 0 else
" (ignored)", opt.quiet, opt.output, cmdargs)
progress.message(execution_log)
from dataset import XLSFileTable, CSVFileTable, TSVFileTable, XLSXFileTable, TXTFileTable
progress.stage("Read ReadCounts input files", len(opt.counts))
headers = "CHROM POS REF ALT ReadGroup RefCount SNVCount GoodReads".split()
# NOTE: This *MUST* correspond to the columns in the readCounts .txt file output
txtheaders = "CHROM POS REF ALT ReadGroup SNVCountForward SNVCountReverse RefCountForward RefCountReverse SNVCount RefCount GoodReads".split(
)
allrg = set()
vafmatrix = defaultdict(dict)
for filename in opt.counts:
base, extn = filename.rsplit('.', 1)
extn = extn.lower()
if extn == 'csv':
counts = CSVFileTable(filename=filename)
elif extn == 'vcf':
counts = VCFFile(filename=filename)
elif extn == 'tsv':
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)
extn = extn.lower()
if extn == 'csv':
snps = CSVFileTable(filename=filename)
elif extn == 'vcf':
snps = VCFFile(filename=filename)
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')
types2files = defaultdict(set)
files2types = defaultdict(set)
for row in reader:
key = (row['CHROM'],row['POS'])
filename = row['AlignedReads']
for k in row:
if k.endswith('Count') and row[k] != "":
row[k] = int(row[k])
if k.endswith('Sc') and row[k] != "":
row[k] = float(row[k])
if re.search(regex["GDNA"],filename) and key not in GDNA:
GDNA[key] = row; types2files["GDNA"].add(filename); files2types[filename].add("GDNA")
if re.search(regex["NRNA"],filename) and key not in NRNA:
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
base, extn = filename.rsplit('.', 1)
extn = extn.lower()
tempfilename = None
if opt.exoncoords:
if extn != 'vcf':
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()
for filename in opt.snvs:
base, extn = filename.rsplit(".", 1)
extn = extn.lower()
if extn == "csv":
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()
if extn == 'csv':
counts = CSVFileTable(filename=filename)
elif extn == 'tsv':
counts = TSVFileTable(filename=filename)
elif extn == 'xls':
counts = XLSFileTable(filename=filename)
elif extn == 'xlsx':
counts = XLSXFileTable(filename=filename)
else:
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)
elif extn == 'xls':
counts = XLSFileTable(filename=filename)
elif extn == 'xlsx':
counts = XLSXFileTable(filename=filename)
else:
