def __init__(self, hub, short_label=None, long_label=None,
genomes_file=None, genomes_filename=None, email="",
url=None, filename=None):
"""
Represents a top-level track hub container.
hub : str
Top-level name of the hub.
short_label : str
Short label for the hub, alias for UCSC parameter shortLabel.
long_label : str
Long label for the hub, alias for UCSC parameter longLabel. If
None, will copy `short_label`.
genomes_file : GenomesFile
If you already have a GenomesFile created, you can add it here;
otherwise when one is created you'll have to add one later with the
`add_genomes_file` method.
email : str
Email that will be provided in the hub for contact info
url : str
Deprecated.
filename : str
If None, defaults to the value of `hub` plus ".hub.txt". When
uploaded, the filename is relative to the uploaded location.
"""
HubComponent.__init__(self)
if url is not None:
self.url = url
warnings.DeprecationWarning(
'url is no longer used for Hub objects')
self.hub = hub
if not short_label:
short_label = hub
self.short_label = short_label
if not long_label:
long_label = short_label
self.long_label = long_label
self.email = email
self.genomes_file = None
if genomes_file is not None:
self.add_genomes_file(genomes_file)
if filename is None:
filename = hub + '.hub.txt'
self.filename = filename
def stop(self, stoplogging=False):
log.info('Stopping %s' % SERVER_SOFTWARE)
self.startstop_lock.acquire()
try:
# Stop listeners
for l in self.listeners:
l.ready = False
# Encourage a context switch
time.sleep(0.01)
for l in self.listeners:
if l.isAlive():
l.join()
# Stop Monitor
self._monitor.stop()
if self._monitor.isAlive():
self._monitor.join()
# Stop Worker threads
self._threadpool.stop()
if stoplogging:
logging.shutdown()
msg = "Calling logging.shutdown() is now the responsibility of \
the application developer. Please update your \
applications to no longer call rocket.stop(True)"
try:
import warnings
raise warnings.DeprecationWarning(msg)
except ImportError:
raise RuntimeError(msg)
finally:
self.startstop_lock.release()
def save_results(y_true, y_score, outputpath):
'''Save ground truth and scores
:param y_true: the ground truth labels, shape: (n_samples, n_classes) for multi-label, and (n_samples,) for other tasks
:param y_score: the predicted score of each class, shape: (n_samples, n_classes)
:param outputpath: path to save the result csv
'''
warnings.DeprecationWarning("Only kept for backward compatiblility." +
"Please use `Evaluator` API instead. ")
idx = []
idx.append('id')
for i in range(y_true.shape[1]):
idx.append('true_%s' % (i))
for i in range(y_score.shape[1]):
idx.append('score_%s' % (i))
df = pd.DataFrame(columns=idx)
for id in range(y_score.shape[0]):
dic = {}
dic['id'] = id
for i in range(y_true.shape[1]):
dic['true_%s' % (i)] = y_true[id][i]
for i in range(y_score.shape[1]):
dic['score_%s' % (i)] = y_score[id][i]
df_insert = pd.DataFrame(dic, index=[0])
df = df.append(df_insert, ignore_index=True)
df.to_csv(outputpath,
sep=',',
index=False,
header=True,
encoding="utf_8_sig")
# Global array type setting. See use_arraytype().
__arraytype = None
# Try to import the necessary modules.
try:
import pygame._numpysurfarray as numpysf
__hasnumpy = True
__arraytype = "numpy"
except ImportError:
__hasnumpy = False
try:
if not __hasnumpy:
import pygame._numericsurfarray as numericsf
__arraytype = "numeric"
warnings.warn(warnings.DeprecationWarning(
"Numeric support to be removed in Pygame 1.9.3"))
else:
f, p, d = imp.find_module('Numeric')
f.close()
__hasnumeric = True
except ImportError:
__hasnumeric = False
if not __hasnumpy and not __hasnumeric:
raise ImportError("no module named numpy or Numeric found")
from pygame.pixelcopy import array_to_surface
def blit_array (surface, array):
"""pygame.surfarray.blit_array(Surface, array): return None