def setUp(self):
self.data_fname = 'test/data/test.hcd'
self.project_fname = 'test/data/test.hcp'
self.probbin_fname = 'test/data/test_probbin.hcp'
self.probpois_fname = 'test/data/test_probpois.hcp'
self.express_fname = 'test/data/test_express.hcp'
self.binning_fname = 'test/data/test_binning.hcp'
self.data = h5py.File(self.project_fname, 'r')
self.probbin = hic.HiC(self.probbin_fname, 'r')
self.probpois = hic.HiC(self.probpois_fname, 'r')
self.express = hic.HiC(self.express_fname, 'r')
self.binning = hic.HiC(self.binning_fname, 'r')
def setUp(self):
self.project_fname = 'test/data/test_probbin.hcp'
self.binned_fname = 'test/data/test_binned.hdf5'
self.heatmap_fname = 'test/data/test.hch'
self.data = h5py.File(self.binned_fname, 'r')
self.heatmap = h5py.File(self.heatmap_fname, 'r')
self.project = hic.HiC(self.project_fname, 'r', silent=True)
def test_hic_project_binning(self):
subprocess.call(
"./bin/hifive hic-normalize binning -q -m 20000 -o test/data/test_temp.hcp -r 5 -y cis -t 1.0 -v len,distance -s 3,3 -u even,fixed-const %s"
% (self.project_fname),
shell=True)
project = hic.HiC("test/data/test_temp.hcp", 'r', silent=True)
self.assertTrue(
numpy.allclose(self.binning.binning_corrections,
project.binning_corrections),
"learned binning correction values don't match target values")
def test_hic_project_express(self):
subprocess.call(
"./bin/hifive hic-normalize express -q -m 20000 -o test/data/test_temp.hcp -e 100 -w cis -f 10 %s"
% (self.project_fname),
shell=True)
project = hic.HiC("test/data/test_temp.hcp", '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.chromosome_means,
project.chromosome_means),
"chromosome means don't match target values")
def test_hic_project_probability_poisson(self):
subprocess.call(
"./bin/hifive hic-normalize probability -q -m 20000 -o test/data/test_temp.hcp -b 15 -l 0.4 -g 0.0015 -p -a poisson %s"
% (self.project_fname),
shell=True)
project = hic.HiC("test/data/test_temp.hcp", 'r', silent=True)
self.assertTrue(
numpy.allclose(self.probpois.corrections,
project.corrections,
atol=1e-1),
"learned correction values don't match target values")
self.assertTrue(
numpy.allclose(self.probpois.chromosome_means,
project.chromosome_means,
atol=1e-4),
"chromosome means don't match target values")
