comparison tools/mira4_0/mira4.py @ 31:fd95aaef8818 draft

planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit bc3d484c5cd68ddcf456db2fff489d584aa2034c

30:b506e3b779fa

#Do we need any PYTHONPATH magic?
from mira4_make_bam import make_bam

WRAPPER_VER = "0.0.4" #Keep in sync with the XML file

def sys_exit(msg, err=1):
    sys.stderr.write(msg+"\n")
    sys.exit(err)


def get_version(mira_binary):
    """Run MIRA to find its version number"""
    # At the commend line I would use: mira -v | head -n 1

out_log = options.log

try:
    mira_path = os.environ["MIRA4"]
except KeyError:
    sys_exit("Environment variable $MIRA4 not set")
mira_binary = os.path.join(mira_path, "mira")
if not os.path.isfile(mira_binary):
    sys_exit("Missing mira under $MIRA4, %r\nFolder contained: %s"
             % (mira_binary, ", ".join(os.listdir(mira_path))))
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))))

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

if not manifest:
    sys_exit("Manifest is required")
elif not os.path.isfile(manifest):
    sys_exit("Missing input MIRA manifest file: %r" % manifest)


try:
    threads = int(os.environ.get("GALAXY_SLOTS", "1"))
except ValueError:

    sys.stderr.write("\n%s\nEnd of manifest\n%s\n" % ("="*60, "="*60))


def collect_output(temp, name, handle):
    """Moves files to the output filenames (global variables)."""
    n3 = (temp, name, name, name)
    f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
    if not os.path.isdir(f):
        log_manifest(manifest)
        sys_exit("Missing output folder")
    if not os.listdir(f):
        log_manifest(manifest)
        sys_exit("Empty output folder")
    missing = []

    old_maf = "%s/%s_out.maf" % (f, name)
    if not os.path.isfile(old_maf):
        #Triggered extractLargeContigs.sh?

            msg = make_bam(mira_convert, out_maf, ref_fasta, out_bam, handle)
        else:
            #Not collecting the MAF file, use original location        
            msg = make_bam(mira_convert, old_maf, ref_fasta, out_bam, handle)
        if msg:
            sys_exit(msg)

def clean_up(temp, name):
    folder = "%s/%s_assembly" % (temp, name)
    if os.path.isdir(folder):
        shutil.rmtree(folder)

    handle.write("Return error code %i from command:\n" % return_code)
    handle.write(cmd + "\n")
    handle.close()
    clean_up(temp, name)
    log_manifest(manifest)
    sys_exit("Return error code %i from command:\n%s" % (return_code, cmd),
             return_code)
handle.flush()

if os.path.isfile("MIRA_assembly/MIRA_d_results/ec.log"):
    handle.write("\n")
    handle.write("====================== Extract Large Contigs failed ==========================\n")

31:fd95aaef8818

#Do we need any PYTHONPATH magic?
from mira4_make_bam import make_bam

WRAPPER_VER = "0.0.4" #Keep in sync with the XML file


def get_version(mira_binary):
    """Run MIRA to find its version number"""
    # At the commend line I would use: mira -v | head -n 1

out_log = options.log

try:
    mira_path = os.environ["MIRA4"]
except KeyError:
    sys.exit("Environment variable $MIRA4 not set")
mira_binary = os.path.join(mira_path, "mira")
if not os.path.isfile(mira_binary):
    sys.exit("Missing mira under $MIRA4, %r\nFolder contained: %s"
             % (mira_binary, ", ".join(os.listdir(mira_path))))
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))))

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

if not manifest:
    sys.exit("Manifest is required")
elif not os.path.isfile(manifest):
    sys.exit("Missing input MIRA manifest file: %r" % manifest)


try:
    threads = int(os.environ.get("GALAXY_SLOTS", "1"))
except ValueError:

    sys.stderr.write("\n%s\nEnd of manifest\n%s\n" % ("="*60, "="*60))


def collect_output(temp, name, handle):
    """Moves files to the output filenames (global variables)."""
    f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
    if not os.path.isdir(f):
        log_manifest(manifest)
        sys.exit("Missing output folder")
    if not os.listdir(f):
        log_manifest(manifest)
        sys.exit("Empty output folder")
    missing = []

    old_maf = "%s/%s_out.maf" % (f, name)
    if not os.path.isfile(old_maf):
        #Triggered extractLargeContigs.sh?

            msg = make_bam(mira_convert, out_maf, ref_fasta, out_bam, handle)
        else:
            #Not collecting the MAF file, use original location        
            msg = make_bam(mira_convert, old_maf, ref_fasta, out_bam, handle)
        if msg:
            sys.exit(msg)

def clean_up(temp, name):
    folder = "%s/%s_assembly" % (temp, name)
    if os.path.isdir(folder):
        shutil.rmtree(folder)

    handle.write("Return error code %i from command:\n" % return_code)
    handle.write(cmd + "\n")
    handle.close()
    clean_up(temp, name)
    log_manifest(manifest)
    sys.stderr.write("Return error code %i from command:\n" % return_code)
    sys.stderr.write(cmd + "\n")
    sys.exit(eturn_code)
handle.flush()

if os.path.isfile("MIRA_assembly/MIRA_d_results/ec.log"):
    handle.write("\n")
    handle.write("====================== Extract Large Contigs failed ==========================\n")