annotate bismark2report_wrapper.py @ 22:8c191acde702 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 3005cec91ca52f9d28aa2fe0bd4190555abafc35

#!/usr/bin/python

import argparse
import logging
import subprocess
import sys


def stop_err(logger, msg):
    logger.critical(msg)
    sys.exit()


def log_subprocess_output(logger, pipe):
    for line in iter(pipe.readline, b""):
        logger.debug(line.decode().rstrip())


def get_arg():
    parser = argparse.ArgumentParser()
    parser.add_argument(
        "--alignment_report",
        dest="alignment_report",
        action="store",
        metavar="alignment_report",
        type=str,
    )
    parser.add_argument(
        "--dedup_report",
        dest="dedup_report",
        action="store",
        metavar="dedup_report",
        type=str,
    )
    parser.add_argument(
        "--splitting_report",
        dest="splitting_report",
        action="store",
        metavar="splitting_report",
        type=str,
    )
    parser.add_argument(
        "--mbias_report",
        dest="mbias_report",
        action="store",
        metavar="mbias_report",
        type=str,
    )
    parser.add_argument(
        "--nucleotide_report",
        dest="nucleotide_report",
        action="store",
        metavar="nucleotide_report",
        type=str,
    )
    parser.add_argument(
        "--output_html_report",
        dest="output_html_report",
        action="store",
        metavar="output_html_report",
        type=str,
    )
    parser.add_argument(
        "--log_report",
        dest="log_report",
        action="store",
        metavar="log_report",
        type=str,
    )
    args = parser.parse_args()
    return args


def __main__():
    args = get_arg()
    logger = logging.getLogger("bismark_deduplicate_wrapper")
    logger.setLevel(logging.DEBUG)
    ch = logging.StreamHandler(sys.stdout)
    if args.log_report:
        ch.setLevel(logging.WARNING)
        handler = logging.FileHandler(args.log_report)
        handler.setLevel(logging.DEBUG)
        logger.addHandler(handler)
    else:
        ch.setLevel(logging.DEBUG)
    logger.addHandler(ch)

    cmd = [
        "bismark2report",
        "--verbose",
        "--alignment_report",
        args.alignment_report,
        "--output",
        args.output_html_report,
    ]

    if args.dedup_report:
        cmd.extend(["--dedup_report", args.dedup_report])
    if args.splitting_report:
        cmd.extend(["--splitting_report", args.splitting_report])
    if args.mbias_report:
        cmd.extend(["--mbias_report", args.mbias_report])
    if args.nucleotide_report:
        cmd.extend(["--nucleotide_report", args.nucleotide_report])

    logger.info("Generating report with: '%s'", " ".join(cmd))
    process = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
    with process.stdout:
        log_subprocess_output(logger, process.stdout)
    exitcode = process.wait()
    if exitcode != 0:
        stop_err(
            logger,
            "Bismark pretty report error (also check the log file if any)!\n%s"
            % process.stderr,
        )


if __name__ == "__main__":
    __main__()