original_docstring: 
      Parse the arguments from the user
      
docstring: Parse the arguments from the user
docstring_tokens: Parse the arguments from the user
code: def parse_arguments(args):
      """
      Parse the arguments from the user
      """
      parser = argparse.ArgumentParser(
          description= "Rename files from barcodes to sample names\n",
          formatter_class=argparse.RawTextHelpFormatter)
      parser.add_argument(
          "-i", "--input",
          help="the input folder containing the fastq files\n[REQUIRED]",
          metavar="<input_folder>",
          required=True)
      parser.add_argument(
          "-b", "--input-barcodes",
          help="the tab-delimited file of sample names and barcodes\n[REQUIRED]",
          metavar="<barcodes.tsv>",
          required=True)
      parser.add_argument(
          "-o", "--output",
          help="the output folder to write the new fastq files\n[REQUIRED]",
          metavar="<output_folder>",
          required=True)
      parser.add_argument(
          "--input-basename1",
          help="the basename of the input file with SEQ replacing the barcode for R1",
          default="1_ABCD.1.SEQ.unmapped.1.fastq.gz")
      parser.add_argument(
          "--input-basename2",
          help="the basename of the input file with SEQ replacing the barcode for R2",
          default="1_ABCD.1.SEQ.unmapped.2.fastq.gz")
      parser.add_argument(
          "--output-basename1",
          help="the basename of the output file with SAMPLE to be replaced with the sample name for R1",
          default="SAMPLE.R1.fastq.gz")
      parser.add_argument(
          "--output-basename2",
          help="the basename of the output file with SAMPLE to be replaced with the sample name for R2",
          default="SAMPLE.R2.fastq.gz")
  
      return parser.parse_args()
code_tokens: def parse_arguments ( args ) : parser = argparse . ArgumentParser ( description = "Rename files from barcodes to sample names\n" , formatter_class = argparse . RawTextHelpFormatter ) parser . add_argument ( "-i" , "--input" , help = "the input folder containing the fastq files\n[REQUIRED]" , metavar = "<input_folder>" , required = True ) parser . add_argument ( "-b" , "--input-barcodes" , help = "the tab-delimited file of sample names and barcodes\n[REQUIRED]" , metavar = "<barcodes.tsv>" , required = True ) parser . add_argument ( "-o" , "--output" , help = "the output folder to write the new fastq files\n[REQUIRED]" , metavar = "<output_folder>" , required = True ) parser . add_argument ( "--input-basename1" , help = "the basename of the input file with SEQ replacing the barcode for R1" , default = "1_ABCD.1.SEQ.unmapped.1.fastq.gz" ) parser . add_argument ( "--input-basename2" , help = "the basename of the input file with SEQ replacing the barcode for R2" , default = "1_ABCD.1.SEQ.unmapped.2.fastq.gz" ) parser . add_argument ( "--output-basename1" , help = "the basename of the output file with SAMPLE to be replaced with the sample name for R1" , default = "SAMPLE.R1.fastq.gz" ) parser . add_argument ( "--output-basename2" , help = "the basename of the output file with SAMPLE to be replaced with the sample name for R2" , default = "SAMPLE.R2.fastq.gz" ) return parser . parse_args ( )
short_docstring: Parse the arguments from the user
short_docstring_tokens: Parse the arguments from the user
comment: """
      Parse the arguments from the user
      """