def test_subset_Dist2Snp(self):
logging.info("in test_subset")
distreader = DistNpz(self.currentFolder + "/../examples/toydata.dist.npz")
dist2snp = distreader.as_snp(max_weight=10)
dssub = dist2snp[::2,::2]
snpdata1 = dssub.read()
expected = distreader.as_snp(max_weight=10)[::2,::2].read()
np.testing.assert_array_almost_equal(snpdata1.val, expected.val, decimal=10)
logging.info("done with test")
def test_dist_snp2(self):
logging.info("in test_dist_snp2")
distreader = DistNpz(self.currentFolder +
"/../examples/toydata.dist.npz")
dist2snp = distreader.as_snp(max_weight=33)
s = str(dist2snp)
_fortesting_JustCheckExists().input(dist2snp)
def test_npz(self):
logging.info("in test_npz")
distreader = DistNpz(self.currentFolder + "/../examples/toydata.dist.npz")
snpdata1 = distreader.as_snp(max_weight=1.0).read()
s = str(snpdata1)
output = "tempdir/distreader/toydata.snp.npz"
create_directory_if_necessary(output)
SnpNpz.write(output,snpdata1)
snpreader2 = SnpNpz(output)
snpdata2 = snpreader2.read()
np.testing.assert_array_almost_equal(snpdata1.val, snpdata2.val, decimal=10)
logging.info("done with test")
def test_intersection_Dist2Snp(self):
from pysnptools.snpreader._dist2snp import _Dist2Snp
from pysnptools.snpreader import Pheno
from pysnptools.distreader._subset import _DistSubset
from pysnptools.snpreader._subset import _SnpSubset
from pysnptools.util import intersect_apply
dist_all = DistNpz(self.currentFolder + "/../examples/toydata.dist.npz")
k = dist_all.as_snp(max_weight=25)
pheno = Pheno(self.currentFolder + "/../examples/toydata.phe")
pheno = pheno[1:,:] # To test intersection we remove a iid from pheno
k1,pheno = intersect_apply([k,pheno])
assert isinstance(k1.distreader,_DistSubset) and not isinstance(k1,_SnpSubset)
#What happens with fancy selection?
k2 = k[::2,:]
assert isinstance(k2,_Dist2Snp)
logging.info("Done with test_intersection")
