コード例 #1
0
ファイル: ete_upgrade_tools.py プロジェクト: sjbn/ete
def _main():
    parser = ArgumentParser()
    parser.add_argument("-v", dest="verbose", action="store_true")
    parser.add_argument("--debug", dest="debug", action="store_true")
    parser.add_argument("--dir", dest='directory', type=str, default='')
    parser.add_argument("--cpu", dest='cores', type=int, default=1)
    parser.add_argument(dest="targets", nargs="*")
    args = parser.parse_args()
    APPSPATH = os.path.expanduser("~/.etetoolkit/ext_apps-latest/")
    ETEHOMEDIR = os.path.expanduser("~/.etetoolkit/")

    if pexist(pjoin('/etc/etetoolkit/', 'ext_apps-latest')):
        # if a copy of apps is part of the ete distro, use if by default
        APPSPATH = pjoin('/etc/etetoolkit/', 'ext_apps-latest')
        ETEHOMEDIR = '/etc/etetoolkit/'
    else:
        # if not, try a user local copy
        APPSPATH = pjoin(ETEHOMEDIR, 'ext_apps-latest')

    TARGET_DIR = args.directory

    while not pexist(TARGET_DIR):
        TARGET_DIR = input('target directory? [%s]:' % ETEHOMEDIR).strip()
        if TARGET_DIR == '':
            TARGET_DIR = ETEHOMEDIR
            break

    if TARGET_DIR == ETEHOMEDIR:
        try:
            os.mkdir(ETEHOMEDIR)
        except OSError:
            pass

    version_file = "latest.tar.gz"
    print(colorify('Downloading latest version of tools...', "green"),
          file=sys.stderr)
    sys.stderr.flush()

    urlretrieve(
        "https://github.com/jhcepas/ext_apps/archive/%s" % version_file,
        pjoin(TARGET_DIR, version_file))
    print(colorify('Decompressing...', "green"), file=sys.stderr)
    tfile = tarfile.open(pjoin(TARGET_DIR, version_file), 'r:gz')
    tfile.extractall(TARGET_DIR)
    print(colorify('Compiling tools...', "green"), file=sys.stderr)
    sys.path.insert(0, pjoin(TARGET_DIR, 'ext_apps-latest'))
    import compile_all
    s = compile_all.compile_all(targets=args.targets,
                                verbose=args.verbose,
                                cores=args.cores)
    return s
コード例 #2
0
def get_latest_nprdp(basedir):
    avail_dbs = []
    for fname in glob(os.path.join(basedir, "*.db")):
        m = re.search("npr\.([\d\.]+)\.db", fname)
        if m:
            avail_dbs.append([float(m.groups()[0]), fname])

    if avail_dbs:
        avail_dbs.sort()
        print(avail_dbs)
        if avail_dbs:
            last_db = avail_dbs[-1][1]
            print("Using latest db file available:", os.path.basename(last_db))
            return last_db
    else:
        #tries compressed data
        compressed_path = pjoin(basedir, "nprdata.tar.gz")
        if pexist(compressed_path):
            import tarfile
            tar = tarfile.open(compressed_path)
            for member in tar:
                print(member.name)
                m = re.search("npr\.([\d\.]+)\.db", member.name)
                if m:
                    print(member)
                    avail_dbs.append([float(m.groups()[0]), member])

    return None
コード例 #3
0
ファイル: ete_upgrade_tools.py プロジェクト: abdo3a/ete
def _main():
    parser = ArgumentParser()
    parser.add_argument("-v", dest="verbose", action="store_true")
    parser.add_argument("--debug", dest="debug", action="store_true")
    parser.add_argument("--dir", dest='directory', type=str, default='')
    parser.add_argument("--cpu", dest='cores', type=int, default=1)
    parser.add_argument(dest="targets", nargs="*")    
    args = parser.parse_args()
    APPSPATH = os.path.expanduser("~/.etetoolkit/ext_apps-latest/")
    ETEHOMEDIR = os.path.expanduser("~/.etetoolkit/")

    if pexist(pjoin('/etc/etetoolkit/', 'ext_apps-latest')):
        # if a copy of apps is part of the ete distro, use if by default
        APPSPATH = pjoin('/etc/etetoolkit/', 'ext_apps-latest')
        ETEHOMEDIR = '/etc/etetoolkit/'
    else:
        # if not, try a user local copy
        APPSPATH = pjoin(ETEHOMEDIR, 'ext_apps-latest')

    
    TARGET_DIR = args.directory
    
    while not pexist(TARGET_DIR):
        TARGET_DIR = input('target directory? [%s]:' %ETEHOMEDIR).strip()
        if TARGET_DIR == '':
            TARGET_DIR = ETEHOMEDIR
            break

    if TARGET_DIR == ETEHOMEDIR:
        try:
            os.mkdir(ETEHOMEDIR)
        except OSError:
            pass

    version_file = "latest.tar.gz"
    print (colorify('Downloading latest version of tools...', "green"), file=sys.stderr)
    sys.stderr.flush()

    urlretrieve("https://github.com/jhcepas/ext_apps/archive/%s" %version_file, pjoin(TARGET_DIR, version_file))
    print(colorify('Decompressing...', "green"), file=sys.stderr)
    tfile = tarfile.open(pjoin(TARGET_DIR, version_file), 'r:gz')
    tfile.extractall(TARGET_DIR)
    print(colorify('Compiling tools...', "green"), file=sys.stderr)
    sys.path.insert(0, pjoin(TARGET_DIR, 'ext_apps-latest'))
    import compile_all
    s = compile_all.compile_all(targets=args.targets, verbose=args.verbose, cores=args.cores)
    return s
コード例 #4
0
def clear_tempdir():
    base_dir = GLOBALS.get("basedir", None)
    out_dir = GLOBALS["output_dir"]
    scratch_dir = GLOBALS.get("scratch_dir", GLOBALS.get("dbdir", base_dir))
    if base_dir and base_dir != out_dir:
        try:
            log.log(20, "Copying new db files to output directory %s..." %out_dir)
            if not pexist(out_dir):
                os.makedirs(out_dir)
            if os.system("cp -a %s/* %s/" %(scratch_dir, out_dir)):
                log.error("Could not copy data from scratch directory!")
            log.log(20, "Deleting temp directory %s..." %scratch_dir)
        except Exception as e:
            print(e)
            log.error("Could not copy data from scratch directory!")
            pass
        # By all means, try to remove temp data
        try: shutil.rmtree(scratch_dir)
        except OSError: pass
コード例 #5
0
        else:
            median = nums[midPos]
        return median
    _max = max
    _min = min
else:
    _std = numpy.std
    _max = numpy.max
    _min = numpy.min
    _mean = numpy.mean
    _median = numpy.median


log = logging.getLogger("main")
DEBUG = lambda: log.level <= 10
hascontent = lambda f: pexist(f) and os.path.getsize(f) > 0
GLOBALS = {
    "running_jobs": set(), # Keeps a list of jobs consuming cpu
    "cached_status": {}, # Saves job and task statuses by id to be
                         # used them within the same get_status cycle
}

class _DataTypes(object):
    def __init__(self):
        self.msf = 100
        self.alg_fasta = 200
        self.alg_phylip = 201
        self.alg_nt_fasta = 202
        self.alg_nt_phylip = 203

        self.clean_alg_fasta = 225