INNER CODE UNIT · Python

run

sanger-pathogens/ariba · ariba/tasks/run.py:8

def run(options):
    reads_not_found = []

    for filename in [options.reads_1, options.reads_2]:
        if not os.path.exists(filename):
            reads_not_found.append(filename)
        elif options.verbose:
            print('Found reads file:', filename)

    if len(reads_not_found):
        print('\nThe following reads file(s) were not found:', file=sys.stderr)
        print(*reads_not_found, sep='\n', file=sys.stderr)
        print('Cannot continue', file=sys.stderr)
        sys.exit(1)

    if (options.reads_1 == options.reads_2):
        print('Same file provided for forwards and reverse reads. Cannot continue', file=sys.stderr)
        sys.exit(1)

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