Example temporary script calling only argparse for usage information

usage_script.py

import argparse
import logging as logger
import multiprocessing as mp
logger.basicConfig(
    format='%(asctime)s : %(name)s : %(levelname)s : %(message)s',
    datefmt='%m/%d/%Y %I:%M:%S %p',
    level=logger.DEBUG)

# This is pulled directly from autometa/common/coverage.py
parser = argparse.ArgumentParser(description='Construct contig coverage table given an input assembly and reads.')
# Notice! the usage information resembles the name of the script...
# So you will need to update the usage within the ArgumentParser..
# I.e.
# parser = argparse.ArgumentParser(
#     usage='coverage.py',
#     description='Construct contig coverage table given an input assembly and reads.')
parser.add_argument('-f','--assembly', help='</path/to/metagenome.fasta>', required=True)
parser.add_argument('-1', '--fwd-reads', help='</path/to/forwards-reads.fastq>', nargs='*')
parser.add_argument('-2', '--rev-reads', help='</path/to/reverse-reads.fastq>', nargs='*')
parser.add_argument('-U', '--se-reads', help='</path/to/single-end-reads.fastq>', nargs='*')
parser.add_argument('--sam', help='</path/to/alignments.sam>')
parser.add_argument('--bam', help='</path/to/alignments.bam>')
parser.add_argument('--lengths', help='</path/to/lengths.tsv>')
parser.add_argument('--bed', help='</path/to/alignments.bed>')
parser.add_argument('--nproc',
    help=f'Num processors to use. (default: {mp.cpu_count()})',
    default=mp.cpu_count(),
    type=int)
parser.add_argument('--from-spades',
    help='Extract k-mer coverages from contig IDs. (Input assembly is output from SPAdes)',
    action='store_true',
    default=False)
parser.add_argument('--out', help='</path/to/coverages.tsv>', required=True)
args = parser.parse_args()