import sys
sys.path.insert(0, '/u/t/dev/screed')
import screed
from screed.fastq import fastq_iter

import khmer

hasher = khmer.HashtableIntersect(15, *khmer.PRIMES_1m)

filename = '/scratch/gpgc/iowa/850.2.fq'

for n, record in enumerate(fastq_iter(open(filename))):
    if n % 10000 == 0:
        print>>sys.stderr, '...', n
    if n > 10**6:
        break

    sequence = record['sequence']
    if 'N' in sequence:
        continue

    print '>%s\n%s' % (record['name'], record['sequence'])