def test_nextSNPs(self):
for b in [1, 2, 3]:
bed = ld.PlinkBEDFile('test/plink_test/plink.bed', self.N, self.bim)
x = bed.nextSNPs(b)
assert x.shape == (5, b)
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 test_nextSNPs_maf_ref(self):
b = 4
bed = ld.PlinkBEDFile('test/plink_test/plink.bed', self.N, self.bim)
x = bed.nextSNPs(b)
bed._currentSNP -= b
y = bed.nextSNPs(b, minorRef=True)
assert np.all(x == -y)
def test_nextSNPs_maf_ref(self):
b = 4
bed = ld.PlinkBEDFile(os.path.join(PLINK_TEST_FILES_DIR, 'plink.bed'),
self.N, self.bim)
x = bed.nextSNPs(b)
bed._currentSNP -= b
y = bed.nextSNPs(b, minorRef=True)
assert np.all(x == -y)
def test_filter_snps(self):
keep_snps = [1, 4]
bed = ld.PlinkBEDFile('test/plink_test/plink.bed', self.N, self.bim,
keep_snps=keep_snps)
assert bed.m == 1
assert bed.n == 5
# pad bits are initialized with random memory --> can't test them
assert bed.geno[0:10] == ba.bitarray('0001011111')
def test_filter_indivs_and_snps(self):
keep_indivs = [0, 1]
keep_snps = [1, 5]
bed = ld.PlinkBEDFile('test/plink_test/plink.bed', self.N, self.bim,
keep_snps=keep_snps, keep_indivs=keep_indivs)
assert bed.m == 1
assert bed.n == 2
print bed.geno
assert bed.geno[0:4] == ba.bitarray('0001')
def test_filter_indivs(self):
keep_indivs = [0, 1]
bed = ld.PlinkBEDFile('test/plink_test/plink.bed', self.N, self.bim,
keep_indivs=keep_indivs)
assert bed.m == 2
assert bed.n == 2
# pad bits are initialized with random memory --> can't test them
assert bed.geno[0:4] == ba.bitarray('0001')
assert bed.geno[8:12] == ba.bitarray('0001')
def test_filter_snps(self):
keep_snps = [1, 4]
bed = ld.PlinkBEDFile(os.path.join(PLINK_TEST_FILES_DIR, 'plink.bed'),
self.N,
self.bim,
keep_snps=keep_snps)
assert bed.m == 1
assert bed.n == 5
# pad bits are initialized with random memory --> can't test them
assert bed.geno[0:10] == ba.bitarray('0001011111')
def test_filter_indivs(self):
keep_indivs = [0, 1]
bed = ld.PlinkBEDFile(os.path.join(PLINK_TEST_FILES_DIR, 'plink.bed'),
self.N,
self.bim,
keep_indivs=keep_indivs)
assert bed.m == 2
assert bed.n == 2
# pad bits are initialized with random memory --> can't test them
assert bed.geno[0:4] == ba.bitarray('0001')
assert bed.geno[8:12] == ba.bitarray('0001')
def test_filter_indivs_and_snps(self):
keep_indivs = [0, 1]
keep_snps = [1, 5]
bed = ld.PlinkBEDFile(os.path.join(PLINK_TEST_FILES_DIR, 'plink.bed'),
self.N,
self.bim,
keep_snps=keep_snps,
keep_indivs=keep_indivs)
self.assertEqual(bed.m, 1)
self.assertEqual(bed.n, 2)
print(bed.geno)
self.assertTrue(bed.geno[0:4] == ba.bitarray('0001'))
def test_nextSNPs(self):
b_num = [3, 2, 1]
for b in b_num:
bed = ld.PlinkBEDFile(
os.path.join(PLINK_TEST_FILES_DIR, 'plink.bed'), self.N,
self.bim)
x = bed.nextSNPs(b)
print("x", x)
print(np.std(x, axis=0))
self.assertEqual(x.shape, (5, b))
self.assertTrue(np.all(np.abs(np.mean(x, axis=0)) < 0.01))
self.assertTrue(np.all(np.abs(np.std(x, axis=0) - 1) < 0.01))
def test_bed(self):
bed = ld.PlinkBEDFile('test/plink_test/plink.bed', self.N, self.bim)
# remove three monomorphic SNPs
print bed.geno
print bed.m
assert bed.m == 4
# no individuals removed
print bed.n
assert self.N == bed.n
# 5 indivs * 4 polymorphic SNPs
print len(bed.geno)
assert len(bed.geno) == 64
print bed.freq
correct = np.array(
[0.59999999999999998, 0.59999999999999998, 0.625, 0.625])
assert np.all(bed.freq == correct)
def test_bed(self):
bed = ld.PlinkBEDFile(os.path.join(PLINK_TEST_FILES_DIR, 'plink.bed'),
self.N, self.bim)
# remove three monomorphic SNPs
print(bed.geno)
print(bed.m)
assert bed.m == 4
# no individuals removed
print(bed.n)
assert self.N == bed.n
# 5 indivs * 4 polymorphic SNPs
print(len(bed.geno))
assert len(bed.geno) == 64
print(bed.freq)
correct = np.array(
[0.59999999999999998, 0.59999999999999998, 0.625, 0.625])
assert np.all(bed.freq == correct)
def test_nextSNPs_errors1(self):
bed = ld.PlinkBEDFile('test/plink_test/plink.bed', self.N, self.bim)
bed.nextSNPs(0)
def test_bad_filename(self):
bed = ld.PlinkBEDFile('test/plink_test/plink.bim', 9, self.bim)
def test_nextSNPs_errors2(self):
bed = ld.PlinkBEDFile(os.path.join(PLINK_TEST_FILES_DIR, 'plink.bed'),
self.N, self.bim)
bed.nextSNPs(5)
def test_bad_filename(self):
bed = ld.PlinkBEDFile(os.path.join(PLINK_TEST_FILES_DIR, 'plink.bim'),
9, self.bim)
