def next(self):
'''Return the next record in the file.'''
line = self.reader.next()
row = re.split(self._separator, line)
chrom = row[0]
if self._prepend_chr:
chrom = 'chr' + chrom
pos = int(row[1])
if row[2] != '.':
ID = row[2]
else:
ID = None
ref = row[3]
alt = self._map(self._parse_alt, row[4].split(','))
try:
qual = int(row[5])
except ValueError:
try:
qual = float(row[5])
except ValueError:
qual = None
filt = row[6]
# Record whether FILTER field was explicitly set in input VCF.
if filt == '.':
# VCF convention for "filters not applied" (i.e. field was not explicitly set).
filterSet = False
else:
filterSet = True
if filt == 'PASS' or filt == '.':
filt = []
else:
filt = filt.split(';')
info = self._parse_info(row[7])
try:
fmt = row[8]
except IndexError:
fmt = None
record = _Record(chrom, pos, ID, ref, alt, qual, filt,
info, fmt, self._sample_indexes)
record.filterSet = filterSet
if fmt is not None:
samples = self._parse_samples(row[9:], fmt, record)
record.samples = samples
return record
def next(self, line=None):
"""Return the next record in the file."""
if not line:
line = self.reader.next()
while line.startswith('#'):
line = self.reader.next()
row = re.split(self._separator, line.rstrip())
chrom = row[0]
if self._prepend_chr:
chrom = 'chr' + chrom
pos = int(row[1])
if row[2] != '.':
ID = row[2]
else:
ID = None
ref = row[3]
alt = map_bad(parse_alt, row[4].split(','))
try:
qual = int(row[5])
except ValueError:
try:
qual = float(row[5])
except ValueError:
qual = None
filt = row[6]
if filt == '.':
filt = None
elif filt == 'PASS':
filt = []
else:
filt = filt.split(';')
info = self._parse_info(row[7])
try:
fmt = row[8]
except IndexError:
fmt = None
else:
if fmt == '.':
fmt = None
record = _Record(chrom, pos, ID, ref, alt, qual, filt,
info, fmt, self._sample_indexes)
if fmt is not None:
samples = self._parse_samples(row[9:], fmt, record)
record.samples = samples
return record
def next(self):
'''Return the next record in the file.'''
try:
line = self.reader.next()
except:
return True
row = re.split('\t| +', line.strip())
chrom = row[0]
if self._prepend_chr:
chrom = 'chr' + chrom
pos = int(row[1])
queryId = row[2]
if row[2] != '.':
ID = row[2]
else:
ID = None
ref = row[3]
queryAlt = row[4]
alt = self._map(self._parse_alt, row[4].split(','))
try:
qual = int(row[5])
except ValueError:
try:
qual = float(row[5])
except ValueError:
qual = None
filt = row[6].split(';') if ';' in row[6] else row[6]
if filt == 'PASS':
filt = None
try:
fmt = row[8]
except IndexError:
fmt = None
entryDbId = self.db.createEntry( self.vcfId, chrom, pos, queryId, ref, queryAlt, qual, filt, fmt)
info = self._parse_info(row[7], entryDbId)
record = _Record(chrom, pos, ID, ref, alt, qual, filt,
info, fmt, self._sample_indexes)
if fmt is not None:
samples = self._parse_samples(row[9:], fmt, record, entryDbId)
record.samples = samples
return False
def next(self):
'''Return the next record in the file.'''
line = self.reader.next()
row = re.split(self._separator, line.rstrip())
chrom = row[0]
if self._prepend_chr:
chrom = 'chr' + chrom
pos = int(row[1])
if row[2] != '.':
ID = row[2]
else:
ID = None
ref = row[3]
alt = self._map(self._parse_alt, row[4].split(','))
try:
qual = int(row[5])
except ValueError:
try:
qual = float(row[5])
except ValueError:
qual = None
filt = row[6]
if filt == '.':
filt = None
elif filt == 'PASS':
filt = []
else:
filt = filt.split(';')
info = self._parse_info(row[7])
try:
fmt = row[8]
except IndexError:
fmt = None
else:
if fmt == '.':
fmt = None
record = _Record(chrom, pos, ID, ref, alt, qual, filt, info, fmt,
self._sample_indexes)
if fmt is not None:
samples = self._parse_samples(row[9:], fmt, record)
record.samples = samples
return record
def next(self):
'''Return the next record in the file.'''
line = self.reader.next()
row = self._row_pattern.split(line.rstrip())
chrom = row[0]
if self._prepend_chr:
chrom = 'chr' + chrom
pos = int(row[1])
if row[2] != '.':
ID = row[2]
else:
ID = None
ref = row[3]
alt = self._map(self._parse_alt, row[4].split(','))
try:
qual = int(row[5])
except ValueError:
try:
qual = float(row[5])
except ValueError:
qual = None
filt = row[6]
if filt == '.':
filt = None
elif filt == 'PASS':
filt = []
else:
filt = filt.split(';')
info = self._parse_info(row[7])
try:
fmt = row[8]
except IndexError:
fmt = None
else:
if fmt == '.':
fmt = None
record = _Record(chrom, pos, ID, ref, alt, qual, filt,
info, fmt, self._sample_indexes)
if fmt is not None:
samples = self._parse_samples(row[9:], fmt, record)
record.samples = samples
return record
def next(self):
"""Return the next record in the file."""
line = self.reader.next()
row = re.split(self._separator, line.rstrip())
chrom = row[0]
if self._prepend_chr:
chrom = "chr" + chrom
pos = int(row[1])
if row[2] != ".":
ID = row[2]
else:
ID = None
ref = row[3]
alt = self._map(self._parse_alt, row[4].split(","))
try:
qual = int(row[5])
except ValueError:
try:
qual = float(row[5])
except ValueError:
qual = None
filt = row[6]
if filt == ".":
filt = None
elif filt == "PASS":
filt = []
else:
filt = filt.split(";")
info = self._parse_info(row[7])
try:
fmt = row[8]
except IndexError:
fmt = None
else:
if fmt == ".":
fmt = None
record = _Record(chrom, pos, ID, ref, alt, qual, filt, info, fmt, self._sample_indexes)
if fmt is not None:
samples = self._parse_samples(row[9:], fmt, record)
record.samples = samples
return record
