streamer.py

in bwa/bwamem.c reduce chunk_size to a smaller value otherwise it will not return for ages:
  
      o->chunk_size = 10000;



import subprocess
import select

p = subprocess.Popen(['bin/bwa/bwa', 'mem', 'ref/NC_018143.fna', '/dev/stdin'], stdin=subprocess.PIPE, stdout=subprocess.PIPE)

for n in xrange(1, 1000):
    p.stdin.write("""@D00200:279:C9JU8ANXX:1:1104:18072:2078 1:N:0:1
ATGCGATGCGCCCCTATCGACTCGAAATGGGCACGCGCTGGGCACCGCGCCGCAAGAGCCTGTACGAATATTGGG
+
BBBBAFFBGCFCEGGGGGGEGGGGGFFFGDFGGGGGGGBDBBGGGGGG>GGGG>B9FFGGGB9BDGBD=GEECGG
@D00200:279:C9JU8ANXX:1:1104:18161:2080 1:N:0:1
CCGCAAGGCGATGAGCCAGATCACCGGCGCACTCGTCGGCGTGGCGCTCGTGCTGTCGGCGGTGTTCGTGCCGGT
+
CCCCCEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGG>
""")
    output = ''
    while (select.select([p.stdout],[],[],0)[0]!=[]):
       output += p.stdout.read(1)
    if output:
       print output