code: def somatic(args):
      
      p = OptionParser(somatic.__doc__)
      opts, args = p.parse_args(args)
  
      if len(args) < 3:
          sys.exit(not p.print_help())
  
      ref, bams = args[0], args[1:]
      tcmd = "~/export/speedseq/bin/speedseq somatic"
      tcmd += " -t 32 -F .2 -C 3 -q 30"
      cmds = []
      for b in bams:
          pf = b.split(".")[0]
          cmd = tcmd
          cmd += " -o {0}".format(pf)
          others = ",".join(sorted(set(bams) - set([b])))
          cmd += " {0} {1} {2}".format(ref, others, b)
          cmds.append(cmd)
  
      write_file("somatic.sh", "\n".join(cmds))
docs: %prog somatic ref.fasta *.bam > somatic.sh
  
      Useful to identify somatic mutations in each sample compared to all other
      samples. Script using SPEEDSEQ-somatic will be written to stdout.