def random_flip(sequence, rnum=None):
randin = rnum
if not randin:
randin = RandomSource()
if randin.random() < 0.5:
return rc(sequence)
return sequence
class MakeErrors:
def __init__(self, rand=None, seed=None):
if rand:
self.random = rand
else:
self.random = RandomSource()
if seed:
self.random = RandomSource(seed)
#### context information ####
self._before_base = None
self._after_base = None
#### set the reference base to change for del,mismatch ###
self._observed_base = None
#### set waht to change base to for ins or mismatch
self._modified_base = None
def set_before_context(self, base):
self._before_base = base
def set_after_context(self, base):
self._after_base = base
def set_observed_base(self, base):
self._observed_base = base
def set_modified_base(self, base):
self._modified_base = base
def random_substitution(self, fastq, rate):
sequence = fastq.seq
seq = ""
for i in range(len(sequence)):
# check context
prev = None
if i >= 1:
prev = sequence[i - 1]
next = None
if i < len(sequence) - 1:
next = sequence[i + 1]
if self._before_base and (not prev or prev != self._before_base):
seq += sequence[i]
continue
if self._after_base and (not next or next != self._after_base):
seq += sequence[i]
continue
if self._observed_base and (sequence[i] != self._observed_base):
seq += sequence[i]
continue
rnum = self.random.random()
if rnum < rate:
if not self._modified_base:
seq += self.random.different_random_nt(sequence[i])
else:
seq += self._modified_base
else:
seq += sequence[i]
return Fastq([fastq.name, seq, "+", fastq.qual])
def random_deletion(self, fastq, rate):
sequence = fastq.seq
quality = fastq.qual
seq = ""
qual = None
if quality:
qual = ""
for i in range(len(sequence)):
# check context
prev = None
if i >= 1:
prev = sequence[i - 1]
next = None
if i < len(sequence) - 1:
next = sequence[i + 1]
if self._before_base and (not prev or prev != self._before_base):
seq += sequence[i]
if quality:
qual += quality[i]
continue
if self._after_base and (not next or next != self._after_base):
seq += sequence[i]
if quality:
qual += quality[i]
continue
if self._observed_base and (sequence[i] != self._observed_base):
seq += sequence[i]
if quality:
qual += quality[i]
continue
rnum = self.random.random()
if rnum >= rate:
seq += sequence[i]
if quality:
qual += quality[i]
return Fastq([fastq.name, seq, "+", qual])
def random_insertion(self, rate, max_inserts=1):
sequence = fastq.seq
quality = fastq.qual
seq = ""
qual = None
ibase = rate_to_phred33(rate)
if quality:
qual = ""
z = 0
while self.random.random() < rate and z < max_inserts:
if self._before_base:
break # can't do this one
if self._after_base:
if self._after_base != sequence[1]:
break
z += 1
if self._modified_base:
seq += self._modified_base
if quality:
qual += ibase
else:
seq += self.random.random_nt()
if quality:
qual += ibase
z = 0
for i in range(len(sequence)):
# check context
prev = sequence[i]
next = None
if i < len(sequence) - 1:
next = sequence[i + 1]
if self._before_base and (not prev or prev != self._before_base):
seq += sequence[i]
if quality:
qual += quality[i]
continue
if self._after_base and (not next or next != self._after_base):
seq += sequence[i]
if quality:
qual += quality[i]
continue
seq += sequence[i]
if quality:
qual += quality[i]
while self.random.random() < rate and z < max_inserts:
z += 1
if self._modified_base:
seq += self._modified_base
if quality:
qual += ibase
else:
seq += self.random.random_nt()
if quality:
qual += ibase
z = 0
return Fastq([fastq.name, seq, "+", qual])
def random_flip(self, sequence):
if self.random.random() < 0.5:
return rc(sequence)
return sequence
