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)
