scripts/release/rfamseq_generator.py
def parse_arguments():
	"""
	Uses python's argparse to parse the command line arguments
	
	return: Argparse parser object
	"""

	# create a new argument parser object
    	parser = argparse.ArgumentParser(description='Merges genomes into a unified fasta file (Rfamseq)')

    	# group required arguments together
    	req_args = parser.add_argument_group("required arguments")
    	req_args.add_argument('--project_dir', help='a project directory where the genome directories reside',
                        type=str, required=True)
	
    	parser.add_argument('-f', help='a file containing a list of valid UPIDs', type=str)
    	parser.add_argument('--all', help='merges all genomes to build the new Rfamseq', action="store_true")
	parser.add_argument('--out', help='a name for the output and or full destination path', type=str)
	parser.add_argument('--type', help='the type of the file to merge (fasta, tblout, rfamseq, genseq)', 
				choices=['fasta', 'tblout', 'rfamseq', 'genseq'], type=str, default='fasta')
	
	return parser

	Uses python's argparse to parse the command line arguments
	
	return: Argparse parser object
	
Uses python's argparse to parse the command line arguments
return: Argparse parser object
Uses python ' s argparse to parse the command line arguments return : Argparse parser object
def parse_arguments():
    	parser = argparse.ArgumentParser(description='Merges genomes into a unified fasta file (Rfamseq)')
    	req_args = parser.add_argument_group("required arguments")
    	req_args.add_argument('--project_dir', help='a project directory where the genome directories reside',
                        type=str, required=True)
    	parser.add_argument('-f', help='a file containing a list of valid UPIDs', type=str)
    	parser.add_argument('--all', help='merges all genomes to build the new Rfamseq', action="store_true")
	parser.add_argument('--out', help='a name for the output and or full destination path', type=str)
	parser.add_argument('--type', help='the type of the file to merge (fasta, tblout, rfamseq, genseq)', 
				choices=['fasta', 'tblout', 'rfamseq', 'genseq'], type=str, default='fasta')
	return parser
def parse_arguments ( ) : parser = argparse . ArgumentParser ( description = 'Merges genomes into a unified fasta file (Rfamseq)' ) req_args = parser . add_argument_group ( "required arguments" ) req_args . add_argument ( '--project_dir' , help = 'a project directory where the genome directories reside' , type = str , required = True ) parser . add_argument ( '-f' , help = 'a file containing a list of valid UPIDs' , type = str ) parser . add_argument ( '--all' , help = 'merges all genomes to build the new Rfamseq' , action = "store_true" ) parser . add_argument ( '--out' , help = 'a name for the output and or full destination path' , type = str ) parser . add_argument ( '--type' , help = 'the type of the file to merge (fasta, tblout, rfamseq, genseq)' , choices = [ 'fasta' , 'tblout' , 'rfamseq' , 'genseq' ] , type = str , default = 'fasta' ) return parser
Uses python's argparse to parse the command line arguments
return: Argparse parser object
Uses python ' s argparse to parse the command line arguments return : Argparse parser object
"""
	Uses python's argparse to parse the command line arguments
	
	return: Argparse parser object
	""" # create a new argument parser object # group required arguments together