class RandomRead(object):
def __init__(self, read_len, default_qa, max_muts=3):
self.count = 0
self.read_len = read_len
self.default_qa = default_qa
self.max_muts = max_muts
self.ln_dist = LnDist(max_muts)
def __call__(self, desc, seq):
try:
start = random.randint(0, len(seq) - self.read_len)
read = seq[start:start + self.read_len]
l = self.read_len
except ValueError: # if len(seq) > opts.read_len
read = seq
start = 0
l = len(read)
# do mutations:
if self.max_muts > 0:
n_muts = self.ln_dist.next()
while n_muts > 0:
i = random.randint(0, l - 1)
base = random.choice('ACTG')
seq = seq[:i] + base + seq[i + 1:] # strings are immutable
n_muts -= 1
self.count += 1
short_desc = '|'.join(desc.split('|')[:4]) + ('<%d-%d>' %
(start, start + l))
return '@%s %d-%d\n%s\n+\n%s' % (short_desc, start, start + l, read,
self.default_qa * l)
class RandomRead(object):
def __init__(self, read_len, default_qa, max_muts=3):
self.count=0
self.read_len=read_len
self.default_qa=default_qa
self.max_muts=max_muts
self.ln_dist=LnDist(max_muts)
def __call__(self, desc, seq):
try:
start=random.randint(0, len(seq)-self.read_len)
read=seq[start:start+self.read_len]
l=self.read_len
except ValueError: # if len(seq) > opts.read_len
read=seq
start=0
l=len(read)
# do mutations:
if self.max_muts > 0:
n_muts=self.ln_dist.next()
while n_muts>0:
i=random.randint(0, l-1)
base=random.choice('ACTG')
seq=seq[:i]+base+seq[i+1:] # strings are immutable
n_muts-=1
self.count+=1
short_desc='|'.join(desc.split('|')[:4]) + ('<%d-%d>' % (start, start+l))
return '@%s %d-%d\n%s\n+\n%s' % (short_desc, start, start+l, read, self.default_qa*l)
def __init__(self, read_len, default_qa, max_muts=3):
self.count = 0
self.read_len = read_len
self.default_qa = default_qa
self.max_muts = max_muts
self.ln_dist = LnDist(max_muts)
def __init__(self, read_len, default_qa, max_muts=3):
self.count=0
self.read_len=read_len
self.default_qa=default_qa
self.max_muts=max_muts
self.ln_dist=LnDist(max_muts)