#! /usr/bin/env python
import sys
from screed.fasta import fasta_iter

outfp = open(sys.argv[2], 'w')

for n, record in enumerate(fasta_iter(open(sys.argv[1]))):
   if n % 100000 == 0:
      print >>sys.stderr, '...', n

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

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