def load_pams(pam_dir):
"""Loads PAMs from CSV files in the specified directory
Args:
pam_dir (str): A directory containing PAM CSV files
"""
pams = []
for fn in glob.glob(os.path.join(pam_dir, '*.csv')):
with open(fn) as in_f:
pams.append(
Matrix.load_csv(in_f, num_header_rows=1, num_header_cols=3))
return pams
def test_valid(self, valid_phylo_beta_diversity_package):
"""Test the method with valid data.
Args:
valid_phylo_beta_diversity_package (tuple): A tuple of information that
together forms a valid phylogenetic beta diversity package.
Note:
* Test values were determined from example at
https://rdrr.io/rforge/betapart/man/phylo.beta.pair.html
"""
(pam_fn, tree_fn, _, _, _, test_beta_sim_fn, test_beta_sne_fn,
test_beta_sor_fn, _, _, _, test_phylo_beta_sim_fn,
test_phylo_beta_sne_fn,
test_phylo_beta_sor_fn) = valid_phylo_beta_diversity_package
with open(pam_fn) as in_f:
pam = Matrix.load_csv(in_f, num_header_rows=1, num_header_cols=1)
tree = TreeWrapper.from_filename(tree_fn)
with open(test_beta_sim_fn) as in_f:
test_beta_sim = Matrix.load_csv(in_f,
num_header_rows=1,
num_header_cols=1)
with open(test_beta_sne_fn) as in_f:
test_beta_sne = Matrix.load_csv(in_f,
num_header_rows=1,
num_header_cols=1)
with open(test_beta_sor_fn) as in_f:
test_beta_sor = Matrix.load_csv(in_f,
num_header_rows=1,
num_header_cols=1)
with open(test_phylo_beta_sim_fn) as in_f:
test_phylo_beta_sim = Matrix.load_csv(in_f,
num_header_rows=1,
num_header_cols=1)
with open(test_phylo_beta_sne_fn) as in_f:
test_phylo_beta_sne = Matrix.load_csv(in_f,
num_header_rows=1,
num_header_cols=1)
with open(test_phylo_beta_sor_fn) as in_f:
test_phylo_beta_sor = Matrix.load_csv(in_f,
num_header_rows=1,
num_header_cols=1)
(beta_sim, phylo_beta_sim, beta_sne, phylo_beta_sne, beta_sor,
phylo_beta_sor) = pbd.calculate_phylo_beta_diversity_sorensen(
pam, tree)
# Check matrix outputs to see if they are within tolerance
assert np.allclose(beta_sim, test_beta_sim)
assert np.allclose(phylo_beta_sim, test_phylo_beta_sim)
assert np.allclose(beta_sne, test_beta_sne)
assert np.allclose(phylo_beta_sne, test_phylo_beta_sne)
assert np.allclose(beta_sor, test_beta_sor)
assert np.allclose(phylo_beta_sor, test_phylo_beta_sor)
def test_valid(self, valid_phylo_beta_diversity_package):
"""Test the method with valid data
Note:
* Test values were determined from example at
https://rdrr.io/rforge/betapart/man/phylo.beta.pair.html
"""
(pam_fn, tree_fn, test_beta_jac_fn, test_beta_jne_fn, test_beta_jtu_fn,
_, _, _, test_phylo_beta_jac_fn, test_phylo_beta_jne_fn,
test_phylo_beta_jtu_fn, _, _, _) = valid_phylo_beta_diversity_package
with open(pam_fn) as in_f:
pam = Matrix.load_csv(in_f, num_header_rows=1, num_header_cols=1)
tree = TreeWrapper.from_filename(tree_fn)
with open(test_beta_jac_fn) as in_f:
test_beta_jac = Matrix.load_csv(in_f,
num_header_rows=1,
num_header_cols=1)
with open(test_beta_jne_fn) as in_f:
test_beta_jne = Matrix.load_csv(in_f,
num_header_rows=1,
num_header_cols=1)
with open(test_beta_jtu_fn) as in_f:
test_beta_jtu = Matrix.load_csv(in_f,
num_header_rows=1,
num_header_cols=1)
with open(test_phylo_beta_jac_fn) as in_f:
test_phylo_beta_jac = Matrix.load_csv(in_f,
num_header_rows=1,
num_header_cols=1)
with open(test_phylo_beta_jne_fn) as in_f:
test_phylo_beta_jne = Matrix.load_csv(in_f,
num_header_rows=1,
num_header_cols=1)
with open(test_phylo_beta_jtu_fn) as in_f:
test_phylo_beta_jtu = Matrix.load_csv(in_f,
num_header_rows=1,
num_header_cols=1)
(beta_jtu, phylo_beta_jtu, beta_jne, phylo_beta_jne, beta_jac,
phylo_beta_jac) = pbd.calculate_phylo_beta_diversity_jaccard(
pam, tree)
# Check matrix outputs to see if they are within tolerance
assert np.allclose(beta_jtu, test_beta_jtu)
assert np.allclose(phylo_beta_jtu, test_phylo_beta_jtu)
assert np.allclose(beta_jne, test_beta_jne)
assert np.allclose(phylo_beta_jne, test_phylo_beta_jne)
assert np.allclose(beta_jac, test_beta_jac)
assert np.allclose(phylo_beta_jac, test_phylo_beta_jac)
