def test_package_names(self):
os.chdir(self.tmpdir)
os.symlink('.', 'bazel-testlogs')
self.make_result(name='coal/sub_test')
self.make_result(name='coal/other_test')
self.make_result(name='some/deep/package/go_test')
coalesce.main()
with open('_artifacts/junit_bazel.xml') as f:
data = f.read()
root = ET.fromstring(data)
names = [x.attrib['name'] for x in root.findall('testcase')]
self.assertEqual(names, ['//coal:other_test', '//coal:sub_test', '//some/deep/package:go_test'])
def test_package_names(self):
os.chdir(self.tmpdir)
os.putenv('WORKSPACE', self.tmpdir)
os.symlink('.', 'bazel-testlogs')
self.make_result(name='coal/sub_test')
self.make_result(name='coal/other_test')
self.make_result(name='some/deep/package/go_test')
coalesce.main()
# Pass the encoding parameter to avoid ascii decode error for some
# platform.
with open('_artifacts/junit_bazel.xml', encoding='utf-8') as fp:
data = fp.read()
root = ET.fromstring(data)
names = [x.attrib['name'] for x in root.findall('testcase')]
self.assertEqual(names, [
'//coal:other_test', '//coal:sub_test',
'//some/deep/package:go_test'
])
def main():
split.main('webwxgetms01.gif')
coalesce.main(' PHP ')
def main(args):
## Run contribution allele dropping simulations
if not os.path.isfile(os.path.expanduser(args.contrib_outfile)):
assert args.contrib_iterations is not None, "Missing iterations " +\
"for allele dropping simulations"
contrib_args = argparse.Namespace(regionfile=args.proband_regions,
verbose=args.verbose,
pedfile=args.pedfile,
outfile=args.contrib_outfile,
iterations=args.contrib_iterations)
ind_contrib.main(contrib_args)
## Run coalescence simulations if file does not already exist
if not os.path.isfile(os.path.expanduser(args.climb_outfile)):
assert args.climb_iterations is not None, "Missing iterations " +\
"for allele climbing simulations"
coalesce_args = argparse.Namespace(sim_homs=args.sim_homs,
pedfile=args.pedfile,
outfile=args.climb_outfile,
iterations=args.climb_iterations,
kinship=args.kinship,
verbose=args.verbose)
if 'hetfile' in vars(args):
vars(coalesce_args)['hetfile'] = args.hetfile
if 'homfile' in vars(args):
vars(coalesce_args)['homfile'] = args.homfile
coalesce.main(coalesce_args)
## Calculate control likelihoods of each simulated tree
if (not os.path.isfile(os.path.expanduser(args.control_outfile))
and os.path.isfile(os.path.expanduser(args.contrib_outfile))):
control_args = argparse.Namespace(pedfile=args.pedfile,
climb_likfile=args.climb_outfile,
outfile=args.control_outfile,
contrib_file=args.contrib_outfile,
freq_params=args.freq_params,
verbose=args.verbose)
control_lik.main(control_args)
## Calculate estimated regional allele frequencies
if (args.regional_freq_outfile is not None and
(not os.path.isfile(os.path.expanduser(args.regional_freq_outfile))
and os.path.isfile(os.path.expanduser(args.contrib_outfile)))):
N, n, k = [float(x) for x in args.freq_params.split(',')]
observed_freq = 1. * k / n
regional_freq_args = argparse.Namespace(
regionsfile=args.regions_to_calculate,
pedfile=args.pedfile,
contrib_h5=args.contrib_outfile,
climb_likfile=args.climb_outfile,
observed_freq=observed_freq,
control_freq_likfile=args.control_outfile,
freq_params=args.freq_params,
outfile=args.regional_freq_outfile)
regional_freq.main(regional_freq_args)