def tally_qual_scores_gz_bowtie(gz_filename, output, strand, reverse_pos):
quals_at = defaultdict(lambda: defaultdict(lambda: 0))
f = BowTieReader(gz_filename, False)
max_phred_seen = 42
count = 0
for r in f:
if strand is not None and r['strand']!=strand:
continue
count += 1
r_qual = r['qual']
if reverse_pos:
r_qual = r_qual[::-1]
for pos,q in enumerate(r_qual):
assert ord(q) - 33 >= 0 # for combined reads it is possible to go above 41
quals_at[pos][ord(q) - 33] += 1
max_phred_seen = max(max_phred_seen, ord(q) - 33)
# sanity check
for pos in quals_at:
sum(quals_at[pos]) == count
poses = quals_at.keys()
poses.sort()
print >> sys.stderr, "{0} reads used".format(count)
with open(output, 'w') as f:
f.write("POS," + ",".join([str(x) for x in xrange(max_phred_seen)]) + '\n')
for pos in poses:
f.write(str(pos) + ',' + ",".join([str(quals_at[pos][x]) for x in xrange(max_phred_seen)]) + '\n')
