def do_quality_any(fastq, rnum):
sequence = fastq.seq
quality = fastq.qual
#five possible errors 3 base changes a deletion or insertion
seq = ''
qual = ''
for i in range(0, len(sequence)):
rate = phred33_to_rate(quality[i])
if rnum.random() > rate:
seq += sequence[i]
qual += quality[i]
continue
type = rnum.choice(['ins', 'del', 'mis', 'mis', 'mis'])
if type == 'mis':
seq += rnum.different_random_nt(sequence[i])
qual += quality[i]
elif type == 'ins':
if rnum.random() < 0.5:
seq += sequence[i] + rnum.random_nt()
qual += quality[i] + quality[i]
else:
seq += rnum.random_nt() + sequence[i]
qual += quality[i] + quality[i]
#for del type we do nothing ... cause its not getting added
return Fastq([fastq.name, seq, '+', qual])
def do_quality_any(fastq,rnum):
sequence = fastq.seq
quality = fastq.qual
#five possible errors 3 base changes a deletion or insertion
seq = ''
qual = ''
for i in range(0,len(sequence)):
rate = phred33_to_rate(quality[i])
if rnum.random() > rate:
seq += sequence[i]
qual += quality[i]
continue
type = rnum.choice(['ins','del','mis','mis','mis'])
if type == 'mis':
seq += rnum.different_random_nt(sequence[i])
qual += quality[i]
elif type == 'ins':
if rnum.random() < 0.5:
seq += sequence[i]+rnum.random_nt()
qual += quality[i]+quality[i]
else:
seq += rnum.random_nt()+sequence[i]
qual += quality[i]+quality[i]
#for del type we do nothing ... cause its not getting added
return Fastq([fastq.name,seq,'+',qual])
def do_quality_mismatch(fastq, rnum):
sequence = fastq.seq
quality = fastq.qual
#five possible errors 3 base changes a deletion or insertion
seq = ''
qual = ''
for i in range(0, len(sequence)):
rate = phred33_to_rate(quality[i])
if rnum.random() > rate:
seq += sequence[i]
qual += quality[i]
continue
seq += rnum.different_random_nt(sequence[i])
qual += quality[i]
#for del type we do nothing ... cause its not getting added
return Fastq([fastq.name, seq, '+', qual])
def do_quality_mismatch(fastq,rnum):
sequence = fastq.seq
quality = fastq.qual
#five possible errors 3 base changes a deletion or insertion
seq = ''
qual = ''
for i in range(0,len(sequence)):
rate = phred33_to_rate(quality[i])
if rnum.random() > rate:
seq += sequence[i]
qual += quality[i]
continue
seq += rnum.different_random_nt(sequence[i])
qual += quality[i]
#for del type we do nothing ... cause its not getting added
return Fastq([fastq.name,seq,'+',qual])