def run(self):
'''run multiple replicates'''
if self.data['verbosity'] <= 1:
iterations = range(self.data['replicates'])
else:
widgets = ['{0} : '.format(self.data['name']), Percentage(),
' ', Bar('='), ' ', ETA()]
pbar = ProgressBar(widgets=widgets, maxval=self.data['replicates'],
term_width=get_terminal_size()[0] - 5)
iterations = pbar((i for i in range(self.data['replicates'])))
nJobs = max(min(self.data['jobs'], self.data['replicates']), 1)
workQueue = Queue()
resQueue = Queue()
# put all replicates + stop signals in queue
for replicate in range(self.data['replicates']):
workQueue.put(replicate)
for i in range(nJobs):
workQueue.put(None)
# spawn workers
procs = [Process(target = self.calculate,
args = (workQueue, resQueue)) for j in range(nJobs)]
for p in procs:
p.start()
# collect the results off the queue
for i in iterations:
try:
self.__save(resQueue.get())
except KeyboardInterrupt as e:
raise ValueError("calculator terminated!")
for p in procs:
p.join()
if self.failure_count.value():
env.logger.info("{} invalid replicate(s)".format(self.failure_count.value()))
self.data['replicates'] = self.data['replicates'] - self.failure_count.value()
return {} if len(self.result) == 0 else dict(list(self.data.items()) + list(self.result.items()))
def __init__(self, args, unknown_args):
self.args = args
self.unknown_args = unknown_args
self.option = checkInput(args)
#
env.logger = getLogger(max(min(args.verbosity - 1, 2), 0),
fn=os.path.splitext(args.output[0])[0],
fv=2 if args.verbosity is not 0 else 0)
env.logger.debug('\n{0}\n{1}\n{0}'.format(
"=" * min(len(args.cmd), 100), args.cmd))
self.logger = env.logger.info if args.verbosity != 1 else printinfo
#
self.logger('Loading data from [{}] ...'.format(args.data))
if self.option == 1:
self.file = SFSFile(args.data)
else:
self.file = GFile(args.data)
self.groups = self.file.getnames()
self.logger('{:,d} units found'.format(len(self.groups)))
# load non-missing data
# to annotate to each variant position wether or not it is missing from assocation analysis
# name it chip_file because it mimics the behavior of exome chip design
if args.missing_unlisted:
self.chip_file = SFSFile(args.missing_unlisted)
else:
self.chip_file = None
# set limit
if self.args.limit:
self.limit = min(max(1, args.limit), len(self.groups))
self.logger('{:,d} units will be analyzed'.format(self.limit))
else:
self.limit = len(self.groups)
self.result = ResultManager(args.output,
action='w' if not args.append else 'a')
if self.args.verbosity == 1:
# widgets = [FormatLabel('scanning: unit %(value)d - '), BouncingBar(marker=RotatingMarker())]
widgets = [
FormatLabel('scanning: unit %(value)d - '),
Percentage(), ' ',
Bar('>'), ' ',
ETA()
]
self.pbar = ProgressBar(widgets=widgets,
maxval=self.limit,
term_width=get_terminal_size()[0] -
5).start()
else:
# use each group's progress bar or not progress bar at all
self.pbar = ProgressBarNull()
# this is buffer object to hold all input dict to a list
self.data_buffer = [] if self.args.replicates < 0 else None
def run(self):
'''run multiple replicates'''
if self.data['verbosity'] <= 1:
iterations = range(self.data['replicates'])
else:
widgets = [
'{0} : '.format(self.data['name']),
Percentage(), ' ',
Bar('='), ' ',
ETA()
]
pbar = ProgressBar(widgets=widgets,
maxval=self.data['replicates'],
term_width=get_terminal_size()[0] - 5)
iterations = pbar((i for i in range(self.data['replicates'])))
nJobs = max(min(self.data['jobs'], self.data['replicates']), 1)
workQueue = Queue()
resQueue = Queue()
# put all replicates + stop signals in queue
for replicate in range(self.data['replicates']):
workQueue.put(replicate)
for i in range(nJobs):
workQueue.put(None)
# spawn workers
procs = [
Process(target=self.calculate, args=(workQueue, resQueue))
for j in range(nJobs)
]
for p in procs:
p.start()
# collect the results off the queue
for i in iterations:
try:
self.__save(resQueue.get())
except KeyboardInterrupt as e:
raise ValueError("calculator terminated!")
for p in procs:
p.join()
if self.failure_count.value():
env.logger.info("{} invalid replicate(s)".format(
self.failure_count.value()))
self.data['replicates'] = self.data[
'replicates'] - self.failure_count.value()
return {} if len(self.result) == 0 else dict(
list(self.data.items()) + list(self.result.items()))
def __init__(self, args, unknown_args):
self.args = args
self.unknown_args = unknown_args
self.option = checkInput(args)
#
env.logger = getLogger(
max(min(args.verbosity - 1, 2), 0),
fn=os.path.splitext(args.output[0])[0],
fv=2 if args.verbosity is not 0 else 0,
)
env.logger.debug("\n{0}\n{1}\n{0}".format("=" * min(len(args.cmd), 100), args.cmd))
self.logger = env.logger.info if args.verbosity != 1 else printinfo
#
self.logger("Loading data from [{}] ...".format(args.data))
if self.option == 1:
self.file = SFSFile(args.data)
else:
self.file = GFile(args.data)
self.groups = self.file.getnames()
self.logger("{:,d} units found".format(len(self.groups)))
# load non-missing data
# to annotate to each variant position wether or not it is missing from assocation analysis
# name it chip_file because it mimics the behavior of exome chip design
if args.missing_unlisted:
self.chip_file = SFSFile(args.missing_unlisted)
else:
self.chip_file = None
# set limit
if self.args.limit:
self.limit = min(max(1, args.limit), len(self.groups))
self.logger("{:,d} units will be analyzed".format(self.limit))
else:
self.limit = len(self.groups)
self.result = ResultManager(args.output, action="w" if not args.append else "a")
if self.args.verbosity == 1:
# widgets = [FormatLabel('scanning: unit %(value)d - '), BouncingBar(marker=RotatingMarker())]
widgets = [FormatLabel("scanning: unit %(value)d - "), Percentage(), " ", Bar(">"), " ", ETA()]
self.pbar = ProgressBar(widgets=widgets, maxval=self.limit, term_width=get_terminal_size()[0] - 5).start()
else:
# use each group's progress bar or not progress bar at all
self.pbar = ProgressBarNull()
# this is buffer object to hold all input dict to a list
self.data_buffer = [] if self.args.replicates < 0 else None
