def main(): # Define an argument parser to pull arguments from the command line parser = argparse.ArgumentParser( description='Run a local blast query on a variety of sequences.') # f1 argument parser.add_argument('-f', metavar='-f', nargs='+', required=True, help='A list of filenames or Refseq ids ') # f2 argument parser.add_argument('-g', metavar='-g', nargs='+', required=True, type=int, help='Genomes passed by taxid: 9606, 562, 2697049') # Output file parser.add_argument('-o', metavar='-o', nargs='+', required=True, help='The name of the output file') # e value argument parser.add_argument('-e', nargs='?', default=10, type=int, help='e-value threshold. Defaults to 10.') # Parse arguments args = parser.parse_args() # Generate the blast object with the arguments blast = Blast(args) # Get the filenames of the query sequences needed filenames = blast.pull_sequences() # Run the blast query blast.format_file() blast.run_blast(filenames)