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

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']:
      splitseq = re.split('N+', record.sequence)
      for i in range(len(splitseq)):
         print >>outfp, '>%s.%d\n%s' % (record.name, i+1, splitseq[i])
    
   else: print >>outfp, '>%s\n%s' % (record['name'], record['sequence'])