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")