gistfile1.rb

#!/usr/bin/env ruby
#

i = 0 
fq_entries = 0
STDIN.each_line do |l|
  id     = l.match(/^([_\w]+)\s/)
  cs_seq = l.match(/\sCS:Z:([ACGT0123.]+)\s/)
  qual   = l.match(/\sCQ:Z:(.+)\s+CM/)
  if id && cs_seq && qual
    printf("@%s\n%s\n+\n%s\n", id[1], cs_seq[1], qual[1])
    fq_entries = fq_entries + 1
  end
  i = i + 1
  STDERR.printf("\r%d:%d", i, fq_entries) if i % 10000 == 0
end