def ReadTSV(filename):
snvheaders = [_f for _f in """CHROM POS REF ALT""".split() if _f]
base, extn = filename.rsplit('.', 1)
extn = extn.lower()
if extn == 'csv':
snvs = CSVFileTable(filename=filename)
elif extn == 'tsv':
snvs = TSVFileTable(filename=filename)
elif extn == 'xls':
snvs = XLSFileTable(filename=filename)
elif extn == 'xlsx':
snvs = XLSXFileTable(filename=filename)
elif extn == 'txt':
snvs = TXTFileTable(filename=filename, headers=snvheaders)
else:
raise RuntimeError("Unexpected SNV file extension: %s" % filename)
for h in snvheaders:
if h not in snvs.headers():
raise RuntimeError("Required header: %s missing from SNV file %s" %
(h, filename))
assert (snvs.headers()[:4] == snvheaders)
chrom = set()
snvdata = []
for r in snvs:
ri = list(map(r.get, snvs.headers()))
chrom.add(ri[0])
snvdata.append(ri)
return ["\t".join(snvs.headers())], chrom, snvdata
snvs = CSVFileTable(filename=filename)
elif extn == 'vcf':
snvs = VCFFile(filename=filename)
elif extn == 'tsv':
snvs = TSVFileTable(filename=filename)
elif extn == 'xls':
snvs = XLSFileTable(filename=filename)
elif extn == 'xlsx':
snvs = XLSXFileTable(filename=filename)
elif extn == 'txt':
snvs = TXTFileTable(filename=filename, headers=snvheaders)
else:
raise RuntimeError("Unexpected SNV file extension: %s" % filename)
for h in snvheaders:
if h not in snvs.headers():
raise RuntimeError("Required header: %s missing from SNV file %s" %
(h, filename))
for h in snvs.headers():
if h in snvheaders:
continue
# if h not in extrasnvheaders:
# extrasnvheaders.append(h)
for r in snvs:
chr = r[snvheaders[0]].strip()
snvchroms[filename].add(chr)
locus = int(r[snvheaders[1]].strip())
ref = r[snvheaders[2]].strip()
alt = r[snvheaders[3]].strip()
if r.get('INFO:INDEL'):
snvs = CSVFileTable(filename=filename)
elif extn == 'vcf':
snvs = VCFFile(filename=filename)
elif extn == 'tsv':
snvs = TSVFileTable(filename=filename)
elif extn == 'xls':
snvs = XLSFileTable(filename=filename)
elif extn == 'xlsx':
snvs = XLSXFileTable(filename=filename)
elif extn == 'txt':
snvs = TXTFileTable(filename=filename, headers=snvheaders)
else:
raise RuntimeError("Unexpected SNV file extension: %s" % filename)
for h in snvheaders:
if h not in snvs.headers():
raise RuntimeError(
"Required header: %s missing from SNV file %s" % (h, filename))
for h in snvs.headers():
if h in snvheaders:
continue
# if h not in extrasnvheaders:
# extrasnvheaders.append(h)
for r in snvs:
chr = r[snvheaders[0]].strip()
snvchroms[filename].add(chr)
locus = int(r[snvheaders[1]].strip())
ref = r[snvheaders[2]].strip()
alt = r[snvheaders[3]].strip()
elif extn == 'vcf':
counts = VCFFile(filename=filename)
elif extn == 'tsv':
counts = TSVFileTable(filename=filename)
elif extn == 'xls':
counts = XLSFileTable(filename=filename)
elif extn == 'xlsx':
counts = XLSXFileTable(filename=filename)
elif extn == 'txt':
counts = TXTFileTable(filename=filename, headers=txtheaders)
else:
raise RuntimeError("Unexpected ReadCounts file extension: %s" %
filename)
for h in headers:
if h not in counts.headers():
raise RuntimeError(
"Required header: %s missing from ReadCounts file %s" %
(h, filename))
for r in counts:
try:
chr = str(int(float(r[headers[0]])))
except ValueError:
chr = r[headers[0]].strip()
locus = int(float(r[headers[1]]))
ref = r[headers[2]].strip()
alt = r[headers[3]].strip()
snvkey = (filename, chr, locus, ref, alt)
rg = r[headers[4]].strip()
nref = int(float(r[headers[5]]))
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:
raise RuntimeError("Unexpected count file extension: %s" % filename)
if countheaders == None:
countheaders = counts.headers()
else:
assert countheaders == counts.headers()
assert 'CHROM' in countheaders
assert 'POS' in countheaders
assert 'REF' in countheaders
assert 'ALT' in countheaders
assert 'Junctions' in countheaders
for r in counts:
for k in list(r.keys()):
if r.get(k) in ("", None):
del r[k]
chr = r['CHROM']
pos = r['POS']
ref = r['REF']
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:
raise RuntimeError("Unexpected count file extension: %s" % filename)
if countheaders == None:
countheaders = counts.headers()
else:
assert countheaders == counts.headers()
assert 'CHROM' in countheaders
assert 'POS' in countheaders
assert 'REF' in countheaders
assert 'ALT' in countheaders
assert 'Junctions' in countheaders
for r in counts:
for k in r.keys():
if r.get(k) in ("", None):
del r[k]
chr = r['CHROM']
pos = r['POS']
ref = r['REF']
