def test_nextSNPs(self, b):
bin = ld.VcfBINFile('test/vcf_test/test.bin', self.N, self.snp)
x = bin.nextSNPs(b)
assert x.shape == (5, b)
print np.mean(x, axis=0)
# roundoff error --> can't test equality to zero directly
assert np.all(np.abs(np.mean(x, axis=0)) < 0.01)
assert np.all(np.abs(np.std(x, axis=0) - 1) < 0.01)
def setUp(self):
self.M = 10
self.N = 2
annot = np.array(
(1, 0, 0, 1, 0, 1, 1, 0, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1),
dtype='float64')
self.annot = annot.reshape((10, 2))
self.snp = ps.VcfSNPFile('test/vcf_test/test.ldscore.snp')
self.bin = ld.VcfBINFile('test/vcf_test/test.ldscore.bin', self.N,
self.snp)
def test_nextSNPs_maf_ref(self, b):
bin = ld.VcfBINFile('test/vcf_test/test.bin', self.N, self.snp)
x = bin.nextSNPs(b)
bin._currentSNP -= b
y = bin.nextSNPs(b, minorRef=True)
assert np.all(x == y)
# switch reference alleles
bin.geno = ~bin.geno
bin.freq = np.ones(bin.m) - bin.freq
print bin.geno
bin._currentSNP -= b
z = bin.nextSNPs(b, minorRef=True)
assert np.all(y == z)
def test_bin(self):
bin = ld.VcfBINFile('test/vcf_test/test.bin',
self.N,
self.snp,
mafMin=0.2)
print bin.geno
print len(bin.geno)
print bin.freq
assert bin.m == 4
assert bin.n == self.N
assert len(bin.geno) == bin.n * bin.m
assert bin.geno == self.geno
assert np.all(bin.freq == 0.4 * np.ones(4))
def test_filter_indivs(self):
'''
The genotype matrix should look like this after filtering individuals
011111
011100
010011
The monomorphic SNPs at left should be removed by _filter_monomorphic
'''
k = [1, 2, 3]
bin = ld.VcfBINFile('test/vcf_test/test.bin',
self.N,
self.snp,
keep_indivs=k)
assert bin.n == 3
assert bin.m == 4
assert bin.geno == ba.bitarray('110110101101')
def test_filter_snps_and_indivs(self):
'''
The genotype matrix should look like this after filtering SNPs and individuals
111
110
101
The monomorphic SNP at left should be removed by _filter_monomorphic
'''
ks = [1, 3, 5]
ki = [1, 2, 3]
bin = ld.VcfBINFile('test/vcf_test/test.bin',
self.N,
self.snp,
keep_snps=ks,
keep_indivs=ki)
assert bin.n == 3
assert bin.m == 2
assert bin.geno == ba.bitarray('110101')
def test_filter_snps(self):
'''
The genotype matrix should look like this after filtering SNPs
100
111
110
101
100
The monomorphic SNP at left should be removed by _filter_monomorphic
'''
k = [1, 3, 4]
bin = ld.VcfBINFile('test/vcf_test/test.bin',
self.N,
self.snp,
keep_snps=k)
print bin.geno
assert bin.m == 2
assert bin.n == 5
assert bin.geno == ba.bitarray('0110001010')
def test_nextSNPs_errors2(self):
bin = ld.VcfBINFile('test/vcf_test/test.bin', self.N, self.snp)
bin.nextSNPs(7)
def test_bad_filename(self):
bin = ld.VcfBINFile('test/vcf_test/test.ind', self.N, self.snp)
def test_mafMin(self):
bin = ld.VcfBINFile('test/vcf_test/test.bin',
self.N,
self.snp,
mafMin=0.45)