def qual_trim(args):
if args.solexa:
args.b = 64
func = solexa_to_phred
elif args.illumina5:
func = illumina_64B
else:
func = illumina_33
if args.b not in (33, 64):
raise Exception("wrong quality score base")
if args.l < 1:
raise Exception("specify longer read length")
if args.p < 0 or args.p > 1:
raise Exception("bad error probability cutoff")
if not args.solexa and args.q < 0:
raise Exception("bad quality score cutoff")
if args.q:
cutoff = args.q
else:
cutoff = calc_qual_score(args.p, args.solexa)
base = args.b
minlen = args.l
ns = re.compile('N', re.IGNORECASE)
fastqs = fastq_record(get_file_obj(args.FASTQ))
for read in fastqs:
read = read.rstrip().split("\n")
qual = read[3]
s, max_s = 0, 0
max_i = len(read[3])
if minlen > max_i:
continue
for i in reversed(range(max_i)):
q = func(ord(qual[i]) - base)
s += cutoff - q
if s < 0:
break
if s > max_s:
max_s, max_i = s, i
read[1] = read[1][:max_i]
read[3] = read[3][:max_i]
n_num = len(ns.findall(read[1]))
if n_num < len(read[1]) and len(read[1]) >= minlen:
print("\n".join(read))
def fastq_input_prep(fastq, ratio, temp_dir):
"""Write FASTQ in the temporary directory, and retrun
(subsampled) FASTQ name, the total read count,
standard deviation of read lengths.
"""
num = int(1 / ratio)
read_count = 0.0
stats = {}
fq_out = "{}/input.fq".format(temp_dir)
fq_obj = get_file_obj(fastq)
fout = open(fq_out, "w")
for i, rec in enumerate(fastq_record(fq_obj)):
if i % num == 0:
fout.write(rec)
read_count += 1
L = len(rec.split("\n")[1])
stats[L] = stats.get(L, 0) + 1
fout.close()
fq_obj.close()
mean = sum([L * c for L, c in stats.items()]) / read_count
sum_square = sum([(L - mean)**2 * c for L, c in stats.items()])
sd = (sum_square / read_count)**0.5
return fq_out, read_count, sd
def fastq_input_prep(fastq, ratio, temp_dir):
"""Write FASTQ in the temporary directory, and retrun
(subsampled) FASTQ name, the total read count,
standard deviation of read lengths.
"""
num = int(1/ratio)
read_count = 0.0
stats = {}
fq_out = "{}/input.fq".format(temp_dir)
fq_obj = get_file_obj(fastq)
fout = open(fq_out, "w")
for i, rec in enumerate(fastq_record(fq_obj)):
if i % num == 0:
fout.write(rec)
read_count += 1
L = len(rec.split("\n")[1])
stats[L] = stats.get(L,0) + 1
fout.close()
fq_obj.close()
mean = sum([L*c for L,c in stats.items()]) / read_count
sum_square = sum([(L-mean)**2 * c for L,c in stats.items()])
sd = (sum_square / read_count)**0.5
return fq_out, read_count, sd
