run_experiment.py

from os import getenv
from dotenv import load_dotenv
from subprocess import run
from argparse import ArgumentParser, RawTextHelpFormatter


def run_experiment(args):
    load_dotenv()

    graphaligner = getenv('GRAPHALIGNER')
    run(
        f'{graphaligner} -t {args.threads} -x vg -f {args.fastq} -g {args.graph} '
        f'-a {args.alignment}_graphaligner.gam'.split()
    )

    graphchainer = getenv('GRAPHCHAINER')
    run(
        f'{graphchainer} -t {args.threads} -f {args.fastq} -g {args.graph} '
        f'-a {args.alignment}_graphchainer.gam '.split()
    )

    minigraph = getenv('MINIGRAPH')
    run(
        f'{minigraph} -t {args.threads} -c {args.graph} {args.fastq}'.split(),
        stdout=open(f'{args.alignment}_minigraph.gaf', 'wb')
    )

    minichain = getenv('MINICHAIN')
    run(
        f'{minichain} -t {args.threads} -c {args.graph} {args.fastq}'.split(),
        stdout=open(f'{args.alignment}_minichain.gaf', 'wb')
    )


if __name__ == '__main__':

    parser = ArgumentParser(
        description='''
               Run aligners GraphAligner, GraphChainer, minigraph and minichain on the vg/gfa and fastq files specified.            
            ''',
        formatter_class=RawTextHelpFormatter
    )

    requiredNamed = parser.add_argument_group('required arguments')
    requiredNamed.add_argument('-g', '--graph', type=str, help='Input vg/gfa file', required=True)
    requiredNamed.add_argument('-fq', '--fastq', type=str, help='Input fastq file', required=True)
    requiredNamed.add_argument(
        '-a', '--alignment', type=str, help='Output gam/gaf files (without extension)', required=True
    )

    parser.add_argument('-t', '--threads', type=int, help='Number of threads', default=30)

    run_experiment(parser.parse_args())