flowcraft/templates/process_assembly_mapping.py
def filter_bam(coverage_info, bam_file, min_coverage, output_bam):
    """Uses Samtools to filter a BAM file according to minimum coverage

    Provided with a minimum coverage value, this function will use Samtools
    to filter a BAM file. This is performed to apply the same filter to
    the BAM file as the one applied to the assembly file in
    :py:func:`filter_assembly`.

    Parameters
    ----------
    coverage_info : OrderedDict or dict
        Dictionary containing the coverage information for each contig.
    bam_file : str
        Path to the BAM file.
    min_coverage : int
        Minimum coverage required for a contig to pass the filter.
    output_bam : str
        Path to the generated filtered BAM file.
    """

    # Get list of contigs that will be kept
    contig_list = [x for x, vals in coverage_info.items()
                   if vals["cov"] >= min_coverage]

    cli = [
        "samtools",
        "view",
        "-bh",
        "-F",
        "4",
        "-o",
        output_bam,
        "-@",
        "1",
        bam_file,
    ]

    cli += contig_list

    logger.debug("Runnig samtools view subprocess with command: {}".format(
        cli))

    p = subprocess.Popen(cli, stdout=PIPE, stderr=PIPE)
    stdout, stderr = p.communicate()

    # Attempt to decode STDERR output from bytes. If unsuccessful, coerce to
    # string
    try:
        stderr = stderr.decode("utf8")
        stdout = stdout.decode("utf8")
    except (UnicodeDecodeError, AttributeError):
        stderr = str(stderr)
        stdout = str(stdout)

    logger.info("Finished samtools view subprocess with STDOUT:\\n"
                "======================================\\n{}".format(stdout))
    logger.info("Fished samtools view subprocesswith STDERR:\\n"
                "======================================\\n{}".format(stderr))
    logger.info("Finished samtools view with return code: {}".format(
        p.returncode))

    if not p.returncode:
        # Create index
        cli = [
            "samtools",
            "index",
            output_bam
        ]

        logger.debug("Runnig samtools index subprocess with command: "
                     "{}".format(cli))

        p = subprocess.Popen(cli, stdout=PIPE, stderr=PIPE)
        stdout, stderr = p.communicate()

        try:
            stderr = stderr.decode("utf8")
            stdout = stdout.decode("utf8")
        except (UnicodeDecodeError, AttributeError):
            stderr = str(stderr)
            stdout = str(stdout)

        logger.info("Finished samtools index subprocess with STDOUT:\\n"
                    "======================================\\n{}".format(
            stdout))
        logger.info("Fished samtools index subprocesswith STDERR:\\n"
                    "======================================\\n{}".format(
            stderr))
        logger.info("Finished samtools index with return code: {}".format(
            p.returncode))
def filter_bam(coverage_info, bam_file, min_coverage, output_bam):
    """Uses Samtools to filter a BAM file according to minimum coverage

    Provided with a minimum coverage value, this function will use Samtools
    to filter a BAM file. This is performed to apply the same filter to
    the BAM file as the one applied to the assembly file in
    :py:func:`filter_assembly`.

    Parameters
    ----------
    coverage_info : OrderedDict or dict
        Dictionary containing the coverage information for each contig.
    bam_file : str
        Path to the BAM file.
    min_coverage : int
        Minimum coverage required for a contig to pass the filter.
    output_bam : str
        Path to the generated filtered BAM file.
    """

    # Get list of contigs that will be kept
    contig_list = [x for x, vals in coverage_info.items()
                   if vals["cov"] >= min_coverage]

    cli = [
        "samtools",
        "view",
        "-bh",
        "-F",
        "4",
        "-o",
        output_bam,
        "-@",
        "1",
        bam_file,
    ]

    cli += contig_list

    logger.debug("Runnig samtools view subprocess with command: {}".format(
        cli))

    p = subprocess.Popen(cli, stdout=PIPE, stderr=PIPE)
    stdout, stderr = p.communicate()

    # Attempt to decode STDERR output from bytes. If unsuccessful, coerce to
    # string
    try:
        stderr = stderr.decode("utf8")
        stdout = stdout.decode("utf8")
    except (UnicodeDecodeError, AttributeError):
        stderr = str(stderr)
        stdout = str(stdout)

    logger.info("Finished samtools view subprocess with STDOUT:\\n"
                "======================================\\n{}".format(stdout))
    logger.info("Fished samtools view subprocesswith STDERR:\\n"
                "======================================\\n{}".format(stderr))
    logger.info("Finished samtools view with return code: {}".format(
        p.returncode))

    if not p.returncode:
        # Create index
        cli = [
            "samtools",
            "index",
            output_bam
        ]

        logger.debug("Runnig samtools index subprocess with command: "
                     "{}".format(cli))

        p = subprocess.Popen(cli, stdout=PIPE, stderr=PIPE)
        stdout, stderr = p.communicate()

        try:
            stderr = stderr.decode("utf8")
            stdout = stdout.decode("utf8")
        except (UnicodeDecodeError, AttributeError):
            stderr = str(stderr)
            stdout = str(stdout)

        logger.info("Finished samtools index subprocess with STDOUT:\\n"
                    "======================================\\n{}".format(
            stdout))
        logger.info("Fished samtools index subprocesswith STDERR:\\n"
                    "======================================\\n{}".format(
            stderr))
        logger.info("Finished samtools index with return code: {}".format(
            p.returncode))
Uses Samtools to filter a BAM file according to minimum coverage

    Provided with a minimum coverage value, this function will use Samtools
    to filter a BAM file. This is performed to apply the same filter to
    the BAM file as the one applied to the assembly file in
    :py:func:`filter_assembly`.

    Parameters
    ----------
    coverage_info : OrderedDict or dict
        Dictionary containing the coverage information for each contig.
    bam_file : str
        Path to the BAM file.
    min_coverage : int
        Minimum coverage required for a contig to pass the filter.
    output_bam : str
        Path to the generated filtered BAM file.