def test_get_dist_matrix(self):
"""Test dnadiff pairwise on multiple bins and get the resulting
distance matrix"""
names = [
"sample0_gt1000_bin0",
"sample0_gt1000_bin10",
"sample0_gt1000_bin11",
"sample0_gt1000_bin1",
"sample0_gt1000_bin2",
"sample1_gt1000_bin51",
"sample1_gt1000_bin67",
"sample1_gt1000_bin6",
]
files = [ospj(DATA_PATH, "{}.fa".format(n)) for n in names]
dnadiff_dist_matrix.run_dnadiff_pairwise(files, names,
TMP_BASENAME_DIR)
for f in [
ospj(TMP_BASENAME_DIR,
"{}_vs_{}".format(names[i], names[j]), "out.report")
for i in range(len(names))
for j in range(i + 1, len(names))]:
ok_(os.path.exists(f))
matrix = dnadiff_dist_matrix.get_dist_matrix(TMP_BASENAME_DIR, names,
50)
matrix_exp = np.genfromtxt(ospj(DATA_PATH, "expected_dist_matrix.tsv"),
delimiter="\t")
np.testing.assert_almost_equal(matrix, matrix_exp, decimal=2)
def test_get_dist_matrix(self):
"""Test dnadiff pairwise on multiple bins and get the resulting
distance matrix"""
names = [
"sample0_gt1000_bin0",
"sample0_gt1000_bin10",
"sample0_gt1000_bin11",
"sample0_gt1000_bin1",
"sample0_gt1000_bin2",
"sample1_gt1000_bin51",
"sample1_gt1000_bin67",
"sample1_gt1000_bin6",
]
files = [ospj(DATA_PATH, "{}.fa".format(n)) for n in names]
dnadiff_dist_matrix.run_dnadiff_pairwise(files, names,
TMP_BASENAME_DIR)
for f in [
ospj(TMP_BASENAME_DIR, "{}_vs_{}".format(names[i], names[j]),
"out.report") for i in range(len(names))
for j in range(i + 1, len(names))
]:
ok_(os.path.exists(f))
matrix = dnadiff_dist_matrix.get_dist_matrix(TMP_BASENAME_DIR, names,
50)
matrix_exp = np.genfromtxt(ospj(DATA_PATH, "expected_dist_matrix.tsv"),
delimiter="\t")
np.testing.assert_almost_equal(matrix, matrix_exp, decimal=2)
def test_run_dnadiff_pairwise(self):
"""Test dnadiff pairwise on multiple bins"""
names = ["bin{0}".format(i) for i in range(3)]
dnadiff_dist_matrix.run_dnadiff_pairwise(
[ospj(DATA_PATH, b) for b in
["sample0_gt1000_bin0.fa", "sample0_gt1000_bin1.fa",
"sample0_gt1000_bin2.fa"]],
names, TMP_BASENAME_DIR)
for f in [
ospj(TMP_BASENAME_DIR,
"{}_vs_{}".format(names[i], names[j]), "out.report")
for i in range(len(names))
for j in range(i + 1, len(names))]:
ok_(os.path.exists(f))
def test_run_dnadiff_pairwise(self):
"""Test dnadiff pairwise on multiple bins"""
names = ["bin{0}".format(i) for i in range(3)]
dnadiff_dist_matrix.run_dnadiff_pairwise([
ospj(DATA_PATH, b) for b in [
"sample0_gt1000_bin0.fa", "sample0_gt1000_bin1.fa",
"sample0_gt1000_bin2.fa"
]
], names, TMP_BASENAME_DIR)
for f in [
ospj(TMP_BASENAME_DIR, "{}_vs_{}".format(names[i], names[j]),
"out.report") for i in range(len(names))
for j in range(i + 1, len(names))
]:
ok_(os.path.exists(f))