How to use the nanocomp.utils.init_logs function in NanoComp

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github wdecoster / nanocomp / nanocomp / NanoComp.py View on Github external
def main():
    '''
    Organization function
    -setups logging
    -gets inputdata
    -calls plotting function
    '''
    settings, args = utils.get_args()
    try:
        utils.make_output_dir(args.outdir)
        utils.init_logs(args)
        args.format = utils.check_valid_format(args.format)
        sources = {
            "fastq": args.fastq,
            "bam": args.bam,
            "cram": args.cram,
            "summary": args.summary,
            "fasta": args.fasta,
            "ubam": args.ubam,
        }
        if args.split_runs:
            split_dict = utils.validate_split_runs_file(args.split_runs)
        if args.pickle:
            from nanoget import combine_dfs
            datadf = combine_dfs(dfs=[pickle.load(open(p, 'rb')) for p in args.pickle],
                                 names=args.names,
                                 method="track")