old_contents: import argparse
  
  def parse_cl(in_args):
  	sub_cmds = {"prepare": add_subparser_prepare,
  	            "cluster": add_subparser_cluster}
  	parser = argparse.ArgumentParser(description="small RNA analysis")
  	sub_cmd = None
  	if len(in_args) > 0 and in_args[0] in sub_cmds:
  		subparsers = parser.add_subparsers(help="seqcluster supplemental commands")
  		sub_cmds[in_args[0]](subparsers)
  		sub_cmd = in_args[0]
  	args = parser.parse_args()
  
  	assert sub_cmd is not None
  	kwargs = {"args": args,
  	              sub_cmd: True}
  	return kwargs
  
  def add_subparser_prepare(subparsers):
  	parser = subparsers.add_parser("prepare", help="prepare data")
  	parser.add_argument("-c", "--conf", dest="dir",required=1,
                    help="file with fasta format paths:1st column:path 2nd column:name")
  	parser.add_argument("-o", "--out", dest="out",required=1,
                    help="dir of output files")
  	return parser
  
  def add_subparser_cluster(subparsers):
  	parser = subparsers.add_parser("cluster", help="cluster data")
  	parser.add_argument("-a", "--afile", dest="afile",required=1,
  	                  help="aligned file in bed/sam format")
  	parser.add_argument("-m", "--ma", dest="ffile",required=1,
  	                  help="matrix file with sequences and counts for each sample")
  	parser.add_argument("-g", "--gtf",
  	                   dest="gtf", help="annotate with gtf_file. It will use the 3rd column as the tag to annotate" +
  	                   "\nchr1    source  intergenic      1       11503   .       +       .       ")
  	parser.add_argument("-b", "--bed",
  	                   dest="bed", help="annotate with bed_file. It will use the 4rd column as the tag to annotate" +
  	                   "\nchr1    157783  157886  snRNA   0       -")
  	parser.add_argument("-o", "--out",
  	                   dest="out", help="output dir")
  	parser.add_argument("-i", "--index",required=1,
  	                   dest="index", help="reference fasta")
  	parser.add_argument("-d", "--debug", action="store_true",
  	                   dest="debug", help="max verbosity mode",default=False)
  	parser.add_argument("-s", "--show", action="store_false",
  	                   dest="show", help="no show sequences",default=True)
  	return parser
  
  
new_contents: import argparse
  
  def parse_cl(in_args):
  	sub_cmds = {"prepare": add_subparser_prepare,
  	            "cluster": add_subparser_cluster}
  	parser = argparse.ArgumentParser(description="small RNA analysis")
  	sub_cmd = None
  	if len(in_args) > 0 and in_args[0] in sub_cmds:
  		subparsers = parser.add_subparsers(help="seqcluster supplemental commands")
  		sub_cmds[in_args[0]](subparsers)
  		sub_cmd = in_args[0]
  	args = parser.parse_args()
  
  	assert sub_cmd is not None
  	kwargs = {"args": args,
  	              sub_cmd: True}
  	return kwargs
  
  
  def add_subparser_prepare(subparsers):
      parser = subparsers.add_parser("prepare", help="prepare data")
      parser.add_argument("-c", "--conf", dest="dir", required=1,
              help="file with config file:1st column:path_to_fasta_file ; 2nd column:name")
      parser.add_argument("-o", "--out", dest="out", required=1,
              help="dir of output files")
      return parser
  
  
  def add_subparser_cluster(subparsers):
      parser = subparsers.add_parser("cluster", help="cluster data")
      parser.add_argument("-a", "--afile", dest="afile", required=1,
                        help="aligned file in bed/sam format")
      parser.add_argument("-m", "--ma", dest="ffile", required=1,
                        help="matrix file with sequences and counts for each sample")
      parser.add_argument("-g", "--gtf",
                         dest="gtf", help="annotate with gtf_file. It will use the 3rd column as the tag to annotate" +
                         "\nchr1    source  intergenic      1       11503   .       +       .       ")
      parser.add_argument("-b", "--bed",
                         dest="bed", help="annotate with bed_file. It will use the 4rd column as the tag to annotate" +
                         "\nchr1    157783  157886  snRNA   0       -")
      parser.add_argument("-o", "--out",
                         dest="out", help="output dir", required=1)
      parser.add_argument("-i", "--index",
                         dest="index", help="reference fasta")
      parser.add_argument("-d", "--debug", action="store_true",
                         dest="debug", help="max verbosity mode", default=False)
      parser.add_argument("-s", "--show", action="store_false",
                         dest="show", help="no show sequences", default=False)
      return parser
  
subject: correct arguments