old_contents: import os
  import sys
  import argparse
  import shutil
  import subprocess
  
  # ---------------------------- Variable initialization ---------------------------
  
  MEMORY = 2000
  CPU = 8
  LSF_GROUP = "/family_srch"
  
  # --------------------------------------------------------------------------------
  
  def check_seed_format(seed_alignment, format="stockholm"):
  	"""
  	Checks if a SEED alignment is in a specific format
  
  	return: void
  	"""
  	
  	pass
  
  # --------------------------------------------------------------------------------
  
  def create_family_directory(dirname, seed_alignment, dest_dir):
  	"""
  	Creates a new Rfam family directory and sets all the files required
  	to launch rfsearch.
  
  	dirname: A name for the new Rfam family in the format str_str
  	seed_alignment: A valid seed alignment in stockholm format
  	dest_dir: The base directory where the new family directory will be 
  	created
  
  	return: void
  	"""
  	
  	# check if destination directory existis
  	if not os.path.exists(dest_dir):
  		sys.exit("\nDestination directory does not exist!\n")
  
  	# go on with creating a new family directory
  	family_dir = os.path.join(dest_dir, dirname)
  	os.mkdir(family_dir)
  	
  	shutil.copy(seed_alignment, os.path.join(family_dir, SEED))
  	
  # --------------------------------------------------------------------------------
  
  def launch_new_rfsearch(family_dir):
  	"""
  	family_dir: The location of a valid family directory
  	
  	return: void 
  	"""
  
  	lsf_err_file = os.path.join(family_dir, "auto_rfsearch.err")
  	lsf_out_file = os.path.join(family_dir, "auto_rfsearch.out")
  
  	# LSF command to be executed
  	cmd = ("bsub -M %s -R \"rusage[mem=%s]\" -o %s -e %s -n %s -g %s -q production-rh74 "
            "-J %s \"cd %s && rfsearch.pl -t 30 -cnompi -q production-rh74 -relax\"")
  
  	# call command
  	subprocess.call(cmd % (MEMORY, MEMORY, lsf_out_file, lsf_err_file,
                           CPU, LSF_GROUP, rfam_acc, family_dir), shell=True)
  	
  
  # --------------------------------------------------------------------------------
  
  def parse_arguments():
  	"""
  	Does basic command line argument parsing 
  	
  	return: Argparse object
  	"""
  	
  	parser = argparse.ArgumentParser(description='Rfam family Auro-Builder')
  	# group required arguments together
  
  	req_args = parser.add_argument_group("required arguments")
  	req_args.add_argument('--input', help='a directory with multiple SEEDs or a single SEED')
  	req_args.add_argument('--dest-dir', help='destination directory where create new \
  				family directories', type=str, required=True)
  
  	return parser
  # --------------------------------------------------------------------------------	
  
  
  if __name__ == '__main__':
  
  	parser = parse_arguments()
  	args = parser.parse_args()
  
  	if (args.input is dir):
  		seeds = os.listdir(args.input)
  	else:
  		seeds = [args.input]
  	
  	for seed in seeds:
  		dirname = seed.partition('.')[0]
  		create_family_directory(dirname, seed, args.dest_dir) 
  
  
new_contents: import os
  import sys
  import argparse
  import shutil
  import subprocess
  
  # ---------------------------- Variable initialization ---------------------------
  
  MEMORY = 2000
  CPU = 8
  LSF_GROUP = "/family_srch"
  
  # --------------------------------------------------------------------------------
  
  def check_seed_format(seed_alignment, format="stockholm"):
  	"""
  	Checks if a SEED alignment is in a specific format
  
  	return: void
  	"""
  	
  	pass
  
  # --------------------------------------------------------------------------------
  
  def create_family_directory(dirname, seed_alignment, dest_dir):
  	"""
  	Creates a new Rfam family directory and sets all the files required
  	to launch rfsearch.
  
  	dirname: A name for the new Rfam family in the format str_str
  	seed_alignment: A valid seed alignment in stockholm format
  	dest_dir: The base directory where the new family directory will be 
  	created
  
  	return: void
  	"""
  	
  	# check if destination directory existis
  	if not os.path.exists(dest_dir):
  		sys.exit("\nDestination directory does not exist!\n")
  
  	# go on with creating a new family directory
  	family_dir = os.path.join(dest_dir, dirname)
  	os.mkdir(family_dir)
  	
  	shutil.copy(seed_alignment, os.path.join(family_dir, "SEED"))
  	
  # --------------------------------------------------------------------------------
  
  def launch_new_rfsearch(family_dir):
  	"""
  	family_dir: The location of a valid family directory
  	
  	return: void 
  	"""
  
  	lsf_err_file = os.path.join(family_dir, "auto_rfsearch.err")
  	lsf_out_file = os.path.join(family_dir, "auto_rfsearch.out")
  
  	# LSF command to be executed
  	cmd = ("bsub -M %s -R \"rusage[mem=%s]\" -o %s -e %s -n %s -g %s -q production-rh74 "
            "-J %s \"cd %s && rfsearch.pl -t 30 -cnompi -q production-rh74 -relax\"")
  
  	# call command
  	subprocess.call(cmd % (MEMORY, MEMORY, lsf_out_file, lsf_err_file,
                           CPU, LSF_GROUP, rfam_acc, family_dir), shell=True)
  	
  
  # --------------------------------------------------------------------------------
  
  def parse_arguments():
  	"""
  	Does basic command line argument parsing 
  	
  	return: Argparse object
  	"""
  	
  	parser = argparse.ArgumentParser(description='Rfam family Auro-Builder')
  	# group required arguments together
  
  	req_args = parser.add_argument_group("required arguments")
  	req_args.add_argument('--input', help='a directory with multiple SEEDs or a single SEED')
  	req_args.add_argument('--dest-dir', help='destination directory where create new \
  				family directories', type=str, required=True)
  
  	return parser
  # --------------------------------------------------------------------------------	
  
  
  if __name__ == '__main__':
  
  	parser = parse_arguments()
  	args = parser.parse_args()
  
  	if (args.input is dir):
  		seeds = os.listdir(args.input)
  	else:
  		seeds = [args.input]
  	
  	for seed in seeds:
  		dirname = seed.partition('.')[0]
  		create_family_directory(dirname, seed, args.dest_dir) 
  
  
subject: Fix variable type