code: def setup_dirs(data):
      
      ## make output folder for clusters
      pdir = os.path.realpath(data.paramsdict["project_dir"])
      data.dirs.clusts = os.path.join(pdir, "{}_clust_{}"\
                         .format(data.name, data.paramsdict["clust_threshold"]))
      if not os.path.exists(data.dirs.clusts):
          os.mkdir(data.dirs.clusts)
  
      ## make a tmpdir for align files
      data.tmpdir = os.path.abspath(os.path.expanduser(
          os.path.join(pdir, data.name+'-tmpalign')))
      if not os.path.exists(data.tmpdir):
          os.mkdir(data.tmpdir)
  
      ## If ref mapping, init samples and make the refmapping output directory.
      if not data.paramsdict["assembly_method"] == "denovo":
          ## make output directory for read mapping process
          data.dirs.refmapping = os.path.join(pdir, "{}_refmapping".format(data.name))
          if not os.path.exists(data.dirs.refmapping):
              os.mkdir(data.dirs.refmapping)
docs: sets up directories for step3 data