def showTests(unknown_args):
from spower.calculator.vat import getAllTests
env.logger = getLogger(1)
if len(unknown_args) == 0:
# show all tests
print('\n'.join([
'{}{}{}'.format(
test, ' ' * (22 - len(test)), '\n'.join(
textwrap.wrap('' if obj.__doc__ is None else obj.__doc__,
initial_indent=' ' * 22,
width=78,
subsequent_indent=' ' * 22))[22:])
for test, obj in getAllTests()
]))
else:
names = [x for x in unknown_args if not x.startswith('-')]
if len(names) > 1:
raise ValueError('Please specify only one test')
tests = getAllTests()
if names[0].lower() not in [x[0].lower() for x in tests]:
raise ValueError('Unrecognized test name {}."'.format(names[0]))
# test
test = [y for x, y in tests if x.lower() == names[0].lower()][0]
print('Name: {}'.format(names[0]))
print('Description: {}'.format('\n'.join(
textwrap.wrap(test.__doc__,
initial_indent='',
subsequent_indent=' ' * 15))))
# create an instance of the test and pass -h to it
test(1, ['-h'])
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 __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 showTests(unknown_args):
from spower.calculator.vat import getAllTests
env.logger = getLogger(1)
if len(unknown_args) == 0:
# show all tests
print (
"\n".join(
[
"{}{}{}".format(
test,
" " * (22 - len(test)),
"\n".join(
textwrap.wrap(
"" if obj.__doc__ is None else obj.__doc__,
initial_indent=" " * 22,
width=78,
subsequent_indent=" " * 22,
)
)[22:],
)
for test, obj in getAllTests()
]
)
)
else:
names = [x for x in unknown_args if not x.startswith("-")]
if len(names) > 1:
raise ValueError("Please specify only one test")
tests = getAllTests()
if names[0].lower() not in [x[0].lower() for x in tests]:
raise ValueError('Unrecognized test name {}."'.format(names[0]))
# test
test = [y for x, y in tests if x.lower() == names[0].lower()][0]
print ("Name: {}".format(names[0]))
print (
"Description: {}".format(
"\n".join(textwrap.wrap(test.__doc__, initial_indent="", subsequent_indent=" " * 15))
)
)
# create an instance of the test and pass -h to it
test(1, ["-h"])
from spower.utils import getLogger
from playground import *
if __name__ == "__main__":
d = PlayGround(getLogger(1))
# Generate GF in cases, via PAR model
#- set PAR model
# huge OR resulted
assert True == L.PARModel([.25, .25, 0, 0], True).apply(d.data)
res = d.get(["effect", 'par'])
almost_equal(.5, sum(res["par"]))
almost_equal(
res['effect'],
(3.69538420811764, 2446.0352249655757, 64.6018420615153,
2446.0352249655757, 1.0, 1.0, 1.0, 9.990065341916748e-05,
16.80005324201965, 2446.0352249655757, 1.0, 3.8916187359828944))
almost_equal(
res['par'],
(0.002596439286207404, 0.07529673618148339, 0.01254945603024723,
0.07529673618148339, 0.0, 0.0, 0.0, 0.25, 0.006274726759048802,
0.07529673618148339, 0.0, 0.0026891693800463775))
#- update GF by PAR method
res0 = d.get(["gf0", "gf2"])
assert True == L.PARGFUpdater(2).apply(d.data)
res = d.get(["gf0", "gf2"])
strictly_le(res["gf0"], res0["gf0"])
strictly_ge(res["gf2"], res0["gf2"])
almost_equal(res['gf0'],
(0.9964586302149315, 0.9345310735676225, 0.9875652213478052,
0.9345310735676225, 0.9999000924155059, 0.64071956214016,
0.9341482876914409, 0.9999666969172785, 0.9934107737743848,
0.9345310735676225, 0.9982689749609894, 0.99640017414124))
from spower.utils import getLogger
from playground import *
if __name__ == "__main__":
d = PlayGround(getLogger(1))
# Generate GF in cases, via OR model
#- set OR model
assert True == L.ORModel([0,1.78,0,0.9,1.1]).apply(d.data)
res = d.get(["effect", 'par'])
assert res['effect'] == (1.78, 1.78, 1.78, 1.78, 1.0, 1.1, 1.0, 0.9, 1.78, 1.78, 1.0, 1.78)
almost_equal(res['par'], (0.0007527551788200869, 2.5975946043922594e-05, 0.00015583543875803612, 2.5975946043922594e-05, 0.0, 0.038674581525736176, 0.0, 3.700359640847335e-06, 0.0003116223926300634, 2.5975946043922594e-05, 0.0, 0.000726816919595037))
#- update GF by OR method
res0 = d.get(["gf0", "gf2"])
assert True == L.ORGFUpdater(2.0, 0.01).apply(d.data)
res = d.get(["gf0", "gf2"])
#
for x,y,z in zip(res0['gf0'], res['gf0'], d.get("direction")):
if z == 'd':
assert x > y
else:
assert round(x,5) <= round(y,5)
for x,y,z in zip(res0['gf2'], res['gf2'], d.get("direction")):
if z == 'd':
assert x < y
else:
assert round(x,5) >= round(y,5)
#
almost_equal(res['gf0'], (0.9982956803933704, 0.9999411806025909, 0.9996471369540085, 0.9999411806025909, 0.9999000924155059, 0.616389730164512, 0.9341482876914409, 0.9999699971512321, 0.9992944017432116, 0.9999411806025909, 0.9982689749609894, 0.9983544003888292))
almost_equal(res['gf2'], (5.901075301235597e-07, 7.021750290206489e-10, 2.5275076303345994e-08, 7.021750290206489e-10, 2.4955060214016003e-09, 0.04588573802725315, 0.0011213476914409, 2.223230920032367e-10, 1.0108487126230469e-07, 7.021750290206489e-10, 7.497609894787601e-07, 5.501261115497627e-07))
#
res = d.get(['wt_penetrance','heterozygotes_penetrance','homozygotes_penetrance','all_prevalence'])
from spower.utils import getLogger
from spower.simulator.sampler import Sample
if __name__ == "__main__":
d = Sample(getLogger(1))
d.seed(0, 1)
c = d.clone()
c.seed(0, 1)
from spower.utils import getLogger
from spower.simulator.sampler import Sample
if __name__ == "__main__":
d = Sample(getLogger(1))
d.seed(0, 1)
c = d.clone()
c.seed(0, 1)
