quality score distribution from fastq

qualDist.py

#!/usr/bin/env python

usage="""
## quality score distribution from fastq
gunzip -c fastq.gz | python qualDist.py
"""

import sys
 
num = 0
cnt = {}
all_q = []
 
for line in sys.stdin:
    num += 1
    if num%4 == 0:
        for q in line.strip():
            # translate to ascii numeric value
            q1 = ord(q)
            #print "q1: %s" % q1
             
            all_q.append(q1)
             
            # tally num occurences of each obs value
            if q1 not in cnt: cnt[q1] = 0
            cnt[q1] += 1
            #print "cnt: %s" % cnt
print(len(all_q))
avg_q = sum(all_q)/float(len(all_q))
print "avg qual score: %s" % avg_q
 
## output distribution of values
#for k in cnt: 
    # print "score: %s count:  %d" % (k, cnt[k])
    # print k, cnt[k]