def test_format_phylip(self):
dm = DistanceMatrix(self.names, self.matrix)
handle = StringIO()
dm.format_phylip(handle)
lines = handle.getvalue().splitlines()
self.assertEqual(len(lines), len(dm) + 1)
self.assertTrue(lines[0].endswith(str(len(dm))))
for name, line in zip(self.names, lines[1:]):
self.assertTrue(line.startswith(name))
def test_format_phylip(self):
dm = DistanceMatrix(self.names, self.matrix)
handle = StringIO()
dm.format_phylip(handle)
lines = handle.getvalue().splitlines()
self.assertEqual(len(lines), len(dm) + 1)
self.assertTrue(lines[0].endswith(str(len(dm))))
for name, line in zip(self.names, lines[1:]):
self.assertTrue(line.startswith(name))
def dendrogram_biopython(condensed_distance_matrix_jaccard, organisms):
"""
Create a lower triangle matrix. Then create a biopython dendrogram.
Parameters
----------
condensed_distance_matrix_jaccard: ndarray
Condensed Jaccard distance matrix
organisms: list
organisms names
"""
from Bio.Phylo.TreeConstruction import DistanceTreeConstructor, DistanceMatrix
from Bio.Phylo import draw_ascii
lower_triangle_matrix = [
list(v[:i + 1])
for i, v in enumerate(squareform(condensed_distance_matrix_jaccard))
]
constructor = DistanceTreeConstructor()
dm = DistanceMatrix(organisms, lower_triangle_matrix)
tree = constructor.nj(dm)
draw_ascii(tree)
dm.format_phylip(open('test.phy', 'w'))
s1_prob += t_mat[j][base_num[s1[k-1]]][base_num[s1[k]]]
s2_prob=0
for k in range(1, len(s2)):
s2_prob += t_mat[i][base_num[s2[k-1]]][base_num[s2[k]]]
distance1 = s1_prob+s2_prob
'''
distance2 = np.linalg.norm(t_mat[i] - t_mat[j], ord=2)
#temp1.append(distance1)
temp2.append(distance2)
#d_mat1.append(temp1)
d_mat2.append(temp2)
#distance_matrix1 = DistanceMatrix(names, d_mat1)
#distance_matrix1.format_phylip(open(path+str(replicate)+"/d_matMM.phy", 'wt'))
distance_matrix2 = DistanceMatrix(names, d_mat2)
distance_matrix2.format_phylip(
open(path + str(replicate) + "/d_matl2.phy", 'wt'))
'''
calculator = DistanceCalculator('ident')
constructor_nj = DistanceTreeConstructor(calculator, 'nj')
tree_nj = constructor_nj.build_tree(aln)
print(tree_nj)
Phylo.write(tree_nj, 'out_tre', 'newick')
'''