def test_subset_Snp2Dist(self): #!!!move these to another test class
logging.info("in test_subset")
snpreader = Bed(self.currentFolder + "/../examples/toydata.5chrom.bed",count_A1=False)
snp2dist = snpreader.as_dist(max_weight=2)
sub = snp2dist[::2,::2]
distdata1 = sub.read()
expected = snpreader.as_dist(max_weight=2)[::2,::2].read()
np.testing.assert_array_almost_equal(distdata1.val, expected.val, decimal=10)
logging.info("done with test")
def test_snp_dist2(self):
logging.info("in test_snp_dist2")
snpreader = Bed(self.currentFolder + "/../examples/toydata.5chrom.bed",
count_A1=False)
snp2dist = snpreader.as_dist(max_weight=2)
s = str(snp2dist)
_fortesting_JustCheckExists().input(snp2dist)
def test_roundtrip(self):
max_weight = 2
snpreader1 = Bed(self.currentFolder + "/../examples/toydata.5chrom.bed",count_A1=True)
snpdata1 = snpreader1.read()
distreader1 = snpreader1.as_dist(max_weight)
snpreader2 = distreader1.as_snp(max_weight)
assert snpdata1.allclose(snpreader2.read(),equal_nan=True)
snpdata1.val[0,0] = np.nan
assert snpdata1.allclose(snpdata1.as_dist(max_weight).as_snp(max_weight).read(),equal_nan=True)
def test_intersection_Snp2Dist(self):
from pysnptools.distreader._snp2dist import _Snp2Dist
from pysnptools.snpreader import Pheno, Bed
from pysnptools.distreader._subset import _DistSubset
from pysnptools.snpreader._subset import _SnpSubset
from pysnptools.util import intersect_apply
snp_all = Bed(self.currentFolder + "/../examples/toydata.5chrom.bed",count_A1=True)
k = snp_all.as_dist(max_weight=2)
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.snpreader,_SnpSubset) and not isinstance(k1,_DistSubset)
#What happens with fancy selection?
k2 = k[::2,:]
assert isinstance(k2,_Snp2Dist)
logging.info("Done with test_intersection")
