def write_record(self, CHROM, POS, ID, REF, ALT, gtype, INFO='.'):
"""Write a fully specified VCF record.
WARNING: 'REF' isn't checked against the reference genome.
Do nothing if 'REF' contains characters outside ACGT (notably N).
Return whether anything was written.
"""
write = util.is_proper_strand(REF)
if write:
QUAL = 20 # Default 1/100 error probability.
FILTER = 'PASS'
FORMAT = 'GT'
print(CHROM,
POS,
ID,
REF,
ALT,
QUAL,
FILTER,
INFO,
FORMAT,
gtype,
sep='\t',
file=self._output)
return write
def random_sequence(self, chrom, length):
"""Return a random segment of given 'length' from given 'chrom'.
Not quite random: the sequence won't have any "N".
"""
while True:
start = random.randint(0, len(self._fasta[chrom]) - length)
seq = self.ref(chrom, start, start + length)
if util.is_proper_strand(seq):
return seq
def random_sequence(self, chrom, length):
"""Return a random segment of given 'length' from given 'chrom'.
Not quite random: the sequence won't have any "N".
"""
while True:
start = random.randint(0, len(self._fasta[chrom]) - length)
seq = self.ref(chrom, start, start + length)
if util.is_proper_strand(seq):
return seq
def write_record(self, CHROM, POS, ID, REF, ALT, gtype):
"""Write a fully specified VCF record.
WARNING: 'REF' isn't checked against the reference genome.
Do nothing if 'REF' contains characters outside ACGT (notably N).
Return whether anything was written.
"""
write = util.is_proper_strand(REF)
if write:
QUAL = 20 # Default 1/100 error probability.
FILTER = 'PASS'
FORMAT = 'GT'
print(CHROM, POS + 1, ID, REF, ALT, QUAL, FILTER, '.', FORMAT, gtype,
sep='\t', file=self._output)
return write
