comparison tools/mira4_0/mira4_convert.py @ 39:bbf14bb9607b draft default tip

planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6

38:cee8f9005e43

def run(cmd):
    # Avoid using shell=True when we call subprocess to ensure if the Python
    # script is killed, so too is the child process.
    try:
        child = subprocess.Popen(cmd, universal_newlines=True,
                                 stdout=subprocess.PIPE, stderr=subprocess.PIPE)
    except Exception as err:
        sys.exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
    # Use .communicate as can get deadlocks with .wait(),
    stdout, stderr = child.communicate()
    return_code = child.returncode
    if return_code:
        cmd_str = " ".join(cmd)  # doesn't quote spaces etc
        if stderr and stdout:
            sys.exit("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr))
        else:
            sys.exit("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr))


def get_version(mira_binary):
    """Run MIRA to find its version number."""
    # At the commend line I would use: mira -v | head -n 1
    # however there is some pipe error when doing that here.
    cmd = [mira_binary, "-v"]
    try:
        child = subprocess.Popen(cmd,
                                 stdout=subprocess.PIPE,
                                 stderr=subprocess.STDOUT)
    except Exception as err:
        sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
        sys.exit(1)
    ver, tmp = child.communicate()
    del child
    return ver.split("\n", 1)[0].strip()


# Parse Command Line
usage = """Galaxy MIRA4 wrapper script v%s - use as follows:

$ python mira4_convert.py ...

This will run the MIRA miraconvert binary and collect its output files as directed.
""" % WRAPPER_VER
parser = OptionParser(usage=usage)
parser.add_option("--input", dest="input",
                  default=None, metavar="FILE",
                  help="MIRA input filename")
parser.add_option("-x", "--min_length", dest="min_length",
                  default="0",
                  help="Minimum contig length")
parser.add_option("-y", "--min_cover", dest="min_cover",
                  default="0",
                  help="Minimum average contig coverage")
parser.add_option("-z", "--min_reads", dest="min_reads",
                  default="0",
                  help="Minimum reads per contig")
parser.add_option("--maf", dest="maf",
                  default="", metavar="FILE",
                  help="MIRA MAF output filename")
parser.add_option("--ace", dest="ace",
                  default="", metavar="FILE",
                  help="ACE output filename")
parser.add_option("--bam", dest="bam",
                  default="", metavar="FILE",
                  help="Unpadded BAM output filename")
parser.add_option("--fasta", dest="fasta",
                  default="", metavar="FILE",
                  help="Unpadded FASTA output filename")
parser.add_option("--cstats", dest="cstats",
                  default="", metavar="FILE",
                  help="Contig statistics filename")
parser.add_option("-v", "--version", dest="version",
                  default=False, action="store_true",
                  help="Show version and quit")
options, args = parser.parse_args()
if args:
    sys.exit("Expected options (e.g. --input example.maf), not arguments")

input_maf = options.input

if "MIRA4" in os.environ:
    mira_path = os.environ["MIRA4"]
    mira_convert = os.path.join(mira_path, "miraconvert")
    if not os.path.isfile(mira_convert):
        sys.exit("Missing miraconvert under $MIRA4, %r\nFolder contained: %s"
                 % (mira_convert, ", ".join(os.listdir(mira_path))))
else:
    sys.stderr.write("DEBUG: Since $MIRA4 is not set, assuming mira binaries are on $PATH.\n")
    mira_path = None
    mira_convert = "miraconvert"

mira_convert_ver = get_version(mira_convert)
if not mira_convert_ver.strip().startswith("4.0"):
    sys.exit("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_convert_ver, mira_convert))
if options.version:
    print("%s, MIRA wrapper version %s" % (mira_convert_ver, WRAPPER_VER))
    sys.exit(0)

if not input_maf:

39:bbf14bb9607b

def run(cmd):
    # Avoid using shell=True when we call subprocess to ensure if the Python
    # script is killed, so too is the child process.
    try:
        child = subprocess.Popen(
            cmd, universal_newlines=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE
        )
    except Exception as err:
        sys.exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
    # Use .communicate as can get deadlocks with .wait(),
    stdout, stderr = child.communicate()
    return_code = child.returncode
    if return_code:
        cmd_str = " ".join(cmd)  # doesn't quote spaces etc
        if stderr and stdout:
            sys.exit(
                "Return code %i from command:\n%s\n\n%s\n\n%s"
                % (return_code, cmd_str, stdout, stderr)
            )
        else:
            sys.exit(
                "Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr)
            )


def get_version(mira_binary):
    """Run MIRA to find its version number."""
    # At the commend line I would use: mira -v | head -n 1
    # however there is some pipe error when doing that here.
    cmd = [mira_binary, "-v"]
    try:
        child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
    except Exception as err:
        sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
        sys.exit(1)
    ver, tmp = child.communicate()
    del child
    return ver.split("\n", 1)[0].strip()


# Parse Command Line
usage = (
    """Galaxy MIRA4 wrapper script v%s - use as follows:

$ python mira4_convert.py ...

This will run the MIRA miraconvert binary and collect its output files as directed.
"""
    % WRAPPER_VER
)
parser = OptionParser(usage=usage)
parser.add_option(
    "--input", dest="input", default=None, metavar="FILE", help="MIRA input filename"
)
parser.add_option(
    "-x", "--min_length", dest="min_length", default="0", help="Minimum contig length"
)
parser.add_option(
    "-y",
    "--min_cover",
    dest="min_cover",
    default="0",
    help="Minimum average contig coverage",
)
parser.add_option(
    "-z", "--min_reads", dest="min_reads", default="0", help="Minimum reads per contig"
)
parser.add_option(
    "--maf", dest="maf", default="", metavar="FILE", help="MIRA MAF output filename"
)
parser.add_option(
    "--ace", dest="ace", default="", metavar="FILE", help="ACE output filename"
)
parser.add_option(
    "--bam", dest="bam", default="", metavar="FILE", help="Unpadded BAM output filename"
)
parser.add_option(
    "--fasta",
    dest="fasta",
    default="",
    metavar="FILE",
    help="Unpadded FASTA output filename",
)
parser.add_option(
    "--cstats",
    dest="cstats",
    default="",
    metavar="FILE",
    help="Contig statistics filename",
)
parser.add_option(
    "-v",
    "--version",
    dest="version",
    default=False,
    action="store_true",
    help="Show version and quit",
)
options, args = parser.parse_args()
if args:
    sys.exit("Expected options (e.g. --input example.maf), not arguments")

input_maf = options.input

if "MIRA4" in os.environ:
    mira_path = os.environ["MIRA4"]
    mira_convert = os.path.join(mira_path, "miraconvert")
    if not os.path.isfile(mira_convert):
        sys.exit(
            "Missing miraconvert under $MIRA4, %r\nFolder contained: %s"
            % (mira_convert, ", ".join(os.listdir(mira_path)))
        )
else:
    sys.stderr.write(
        "DEBUG: Since $MIRA4 is not set, assuming mira binaries are on $PATH.\n"
    )
    mira_path = None
    mira_convert = "miraconvert"

mira_convert_ver = get_version(mira_convert)
if not mira_convert_ver.strip().startswith("4.0"):
    sys.exit(
        "This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_convert_ver, mira_convert)
    )
if options.version:
    print("%s, MIRA wrapper version %s" % (mira_convert_ver, WRAPPER_VER))
    sys.exit(0)

if not input_maf: