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
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
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
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
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