def setUp(self):
self.data_fname = 'test/data/test.fcd'
self.project_fname = 'test/data/test.fcp'
self.probability_fname = 'test/data/test_probability.fcp'
self.express_fname = 'test/data/test_express.fcp'
self.binning_fname = 'test/data/test_binning.fcp'
self.raw = h5py.File(self.project_fname, 'r')
self.probability = fivec.FiveC(self.probability_fname, 'r')
self.express = fivec.FiveC(self.express_fname, 'r')
self.binning = fivec.FiveC(self.binning_fname, 'r')
def setUp(self):
self.project_fname = 'test/data/test_probability.fcp'
self.binned_fname = 'test/data/test_binned.hdf5'
self.heatmap_fname = 'test/data/test.fch'
self.data = h5py.File(self.binned_fname, 'r')
self.heatmap = h5py.File(self.heatmap_fname, 'r')
self.project = fivec.FiveC(self.project_fname, 'r', silent=True)
def test_fivec_project_express(self):
subprocess.call("./bin/hifive 5c-normalize express -q -o test/data/test_temp.fcp -e 100 -d -w cis %s" %
self.project_fname, shell=True)
project = fivec.FiveC("test/data/test_temp.fcp", 'r', silent=True)
self.assertTrue(numpy.allclose(self.express.corrections, project.corrections),
"learned express correction values don't match target values")
self.assertTrue(numpy.allclose(self.express.region_means, project.region_means),
"region means don't match target values")
def test_fivec_project_probability(self):
subprocess.call("./bin/hifive 5c-normalize probability -q -o test/data/test_temp.fcp -b 100 -l 0.5 -p %s" %
self.project_fname, shell=True)
project = fivec.FiveC("test/data/test_temp.fcp", 'r', silent=True)
self.assertTrue(numpy.allclose(self.probability.corrections, project.corrections),
"learned correction values don't match target values")
self.assertTrue(numpy.allclose(self.probability.region_means, project.region_means),
"region means don't match target values")
def test_fivec_project_binning(self):
subprocess.call("./bin/hifive 5c-normalize binning -q -o test/data/test_temp.fcp -i 10 -t 1.0 -y cis -v len -n 5 -u even %s" %
self.project_fname, shell=True)
project = fivec.FiveC("test/data/test_temp.fcp", 'r', silent=True)
self.assertTrue(numpy.allclose(self.binning.binning_corrections, project.binning_corrections),
"learned binning correction values don't match target values")