def determine_score_type(args):
with FileOrGzip(args.fastq) as infile:
count = 0
letter_freq = collections.defaultdict(int)
for rid, seq, qual in fastq.read(infile):
count += 1
for l in qual:
letter_freq[l] += 1
if count == 5000:
break
print guess_score_type(letter_freq)
def to_phred33(args):
if args.score_type == "phred64":
table = phred64_to_phred33
elif args.score_type == "solexa":
table = solexa_to_phred33
elif args.score_type == "phred33+":
table = phred33plus_to_phred33
out = "@{0}\n{1}\n+\n{2}"
with FileOrGzip(args.fastq) as infile:
for rid, rseq, rqual in fastq.read(infile):
print out.format(rid, rseq, rqual.translate(table))
