#!/usr/bin/python

import argparse
import logging
import os
import shutil
import signal
import subprocess
import sys
import tempfile


def stop_err(logger, msg):
    logger.critical(msg)
    sys.exit(1)


def restore_sigpipe():
    """
    Needed to handle samtools view
    """
    signal.signal(signal.SIGPIPE, signal.SIG_DFL)


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("--single_or_paired", dest="single_or_paired")
    parser.add_argument("--input", dest="input", metavar="input")
    parser.add_argument(
        "--output_report", dest="output_report", metavar="output_report"
    )
    parser.add_argument("--output_bam", dest="output_bam", metavar="output_report")
    parser.add_argument(
        "--log_report", dest="log_report", metavar="log_filename", 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)

    # ensure the input has a .bam suffix
    tmp_dir = tempfile.mkdtemp(prefix="tmp", suffix="")
    os.chdir(tmp_dir)
    default_reads_name = "submitted_reads.bam"
    os.symlink(args.input, default_reads_name)

    single_or_paired = "-s" if args.single_or_paired == "single" else "-p"
    cmd = ["deduplicate_bismark", single_or_paired, default_reads_name, "--bam"]
    logger.info("Deduplicating with: '%s'", " ".join(cmd))
    process = subprocess.Popen(
        cmd,
        stdout=subprocess.PIPE,
        stderr=subprocess.STDOUT,
        preexec_fn=restore_sigpipe,
    )
    proc_out, proc_err = process.communicate()
    logger.info(proc_out)
    if process.returncode != 0:
        stop_err(
            logger,
            "Bismark deduplication error (also check the log file if any)!\n%s"
            % proc_err,
        )

    deduplicated_out_name = "submitted_reads.deduplicated.bam"
    deduplicated_report_name = "submitted_reads.deduplication_report.txt"
    logger.debug("Moving '%s' to galaxy: '%s'.", deduplicated_out_name, args.output_bam)
    shutil.move(deduplicated_out_name, args.output_bam)
    logger.debug(
        "Moving '%s' to galaxy: '%s'.", deduplicated_report_name, args.output_report
    )
    shutil.move("submitted_reads.deduplication_report.txt", args.output_report)
    logger.debug("Done.")


if __name__ == "__main__":
    __main__()

#!/usr/bin/python

import argparse
import logging
import os
import shutil
import signal
import subprocess
import sys
import tempfile


def stop_err(logger, msg):
    logger.critical(msg)
    sys.exit(1)


def restore_sigpipe():
    """
    Needed to handle samtools view
    """
    signal.signal(signal.SIGPIPE, signal.SIG_DFL)


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("--single_or_paired", dest="single_or_paired")
    parser.add_argument("--input", dest="input", metavar="input")
    parser.add_argument(
        "--output_report", dest="output_report", metavar="output_report"
    )
    parser.add_argument("--output_bam", dest="output_bam", metavar="output_report")
    parser.add_argument(
        "--log_report", dest="log_report", metavar="log_filename", 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)

    # ensure the input has a .bam suffix
    tmp_dir = tempfile.mkdtemp(prefix="tmp", suffix="")
    os.chdir(tmp_dir)
    default_reads_name = "submitted_reads.bam"
    os.symlink(args.input, default_reads_name)

    single_or_paired = "-s" if args.single_or_paired == "single" else "-p"
    cmd = ["deduplicate_bismark", single_or_paired, default_reads_name, "--bam"]
    logger.info("Deduplicating with: '%s'", " ".join(cmd))
    process = subprocess.Popen(
        cmd,
        stdout=subprocess.PIPE,
        stderr=subprocess.STDOUT,
        preexec_fn=restore_sigpipe,
    )
    proc_out, proc_err = process.communicate()
    logger.info(proc_out)
    if process.returncode != 0:
        stop_err(
            logger,
            "Bismark deduplication error (also check the log file if any)!\n%s"
            % proc_err,
        )

    deduplicated_out_name = "submitted_reads.deduplicated.bam"
    deduplicated_report_name = "submitted_reads.deduplication_report.txt"
    logger.debug("Moving '%s' to galaxy: '%s'.", deduplicated_out_name, args.output_bam)
    shutil.move(deduplicated_out_name, args.output_bam)
    logger.debug(
        "Moving '%s' to galaxy: '%s'.", deduplicated_report_name, args.output_report
    )
    shutil.move("submitted_reads.deduplication_report.txt", args.output_report)
    logger.debug("Done.")


if __name__ == "__main__":
    __main__()

#!/usr/bin/python Needed to handle samtools view # ensure the input has a .bam suffix