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':
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))
filename0 = filename
base, extn = filename.rsplit('.', 1)
extn = extn.lower()
tempfilename = None
if opt.exoncoords:
if extn != 'vcf':
extn = 'tsv'
tempfileno, tempfilename = tempfile.mkstemp(suffix="." + extn)
execprog.execute("exonicFilter", "--exons", opt.exoncoords, "--input",
filename, "--output", tempfilename)
filename = tempfilename
if extn == 'csv':
snps = CSVFileTable(filename=filename)
elif extn == 'vcf':
snps = VCFFile(filename=filename)
elif extn == 'tsv':
snps = TSVFileTable(filename=filename)
elif extn == 'xls':
snps = XLSFileTable(filename=filename)
elif extn == 'xlsx':
snps = XLSXFileTable(filename=filename)
elif extn == 'txt':
snps = TXTFileTable(filename=filename, headers=snpheaders)
else:
raise RuntimeError("Unexpected SNP file extension: %s" % filename)
for h in snpheaders:
if h not in snps.headers():
raise RuntimeError("Required header: %s missing from SNP file %s" %
(h, filename))