#NEWLINE# def Parser( ) : #NEWLINE# #INDENT# the_parser = argparse . ArgumentParser ( ) #NEWLINE# the_parser . add_argument ( '--input' , action = 'store' , nargs = '+' , help = 'input fastq files' ) #NEWLINE# the_parser . add_argument ( '--output' , action = 'store' , type = str , help = 'output, clipped fasta file' ) #NEWLINE# the_parser . add_argument ( '--output_format' , action = 'store' , type = str , help = 'output format, fasta or fastq' ) #NEWLINE# the_parser . add_argument ( '--adapter_to_clip' , action = 'store' , type = str , help = 'adapter sequence to clip' ) #NEWLINE# the_parser . add_argument ( '--min' , action = 'store' , type = int , help = 'minimal size of clipped sequence to keep' ) #NEWLINE# the_parser . add_argument ( '--max' , action = 'store' , type = int , help = 'maximal size of clipped sequence to keep' ) #NEWLINE# the_parser . add_argument ( '--Nmode' , action = 'store' , type = str , choices = [ 'accept' , 'reject' ] , help = 'accept or reject sequences with N for clipping' ) #NEWLINE# args = the_parser . parse_args ( ) #NEWLINE# args . adapter_to_clip = args . adapter_to_clip . upper ( ) #NEWLINE# return the_parser