def plot_phylo_tree_pars(align: MultipleSeqAlignment, accession_numbers: dict):
"""
Plots a phylogenetic tree
:param align: MultipleSeqAlignment with the alignment result to be plotted
:param accession_numbers: dict of accession numbers and their translation to human-understandable names
:return: figure-handle of the plotted phylogenetic tree
"""
scorer = ParsimonyScorer()
searcher = NNITreeSearcher(scorer)
constructor = ParsimonyTreeConstructor(searcher)
tree = constructor.build_tree(align)
print(Phylo.draw_ascii(tree))
# plot the tree
fig, ax = plt.subplots(1, 1)
# remove the names for the non-terminals for better visual appeal
for non_terminal in tree.get_nonterminals():
non_terminal.name = ''
# draw the resulting tree
Phylo.draw(tree, show_confidence=False, axes=ax, do_show=False)
ax.set_xlim(right=0.8)
return fig
def create_tree_parsimony_impl(msa):
calculator = DistanceCalculator('identity')
constructor = DistanceTreeConstructor(distance_calculator=calculator, method='nj')
starting_tree = constructor.build_tree(msa)
scorer = ParsimonyScorer()
searcher = NNITreeSearcher(scorer)
constructor = ParsimonyTreeConstructor(searcher=searcher,starting_tree=starting_tree)
tree = constructor.build_tree(msa)
Phylo.write(tree, "../../data/created/tree" + str(random.randint(0,10000000)) + ".nex", "nexus")
Phylo.draw(tree,do_show=False)
plt.savefig("../../data/created/createdTree_parsimony.png")
return "../../data/created/createdTree_parsimony.png"
def test_build_tree(self):
aln = AlignIO.read('TreeConstruction/msa.phy', 'phylip')
tree1 = Phylo.read('./TreeConstruction/upgma.tre', 'newick')
tree2 = Phylo.read('./TreeConstruction/nj.tre', 'newick')
alphabet = ['A', 'T', 'C', 'G']
step_matrix = [[0], [2.5, 0], [2.5, 1, 0], [1, 2.5, 2.5, 0]]
matrix = _Matrix(alphabet, step_matrix)
scorer = ParsimonyScorer(matrix)
searcher = NNITreeSearcher(scorer)
constructor = ParsimonyTreeConstructor(searcher, tree1)
best_tree = constructor.build_tree(aln)
Phylo.write(best_tree, './TreeConstruction/pars1.tre', 'newick')
constructor.starting_tree = tree2
best_tree = constructor.build_tree(aln)
Phylo.write(best_tree, './TreeConstruction/pars2.tre', 'newick')
constructor.starting_tree = None
best_tree = constructor.build_tree(aln)
Phylo.write(best_tree, './TreeConstruction/pars3.tre', 'newick')
def test_build_tree(self):
aln = AlignIO.read("TreeConstruction/msa.phy", "phylip")
tree1 = Phylo.read("./TreeConstruction/upgma.tre", "newick")
tree2 = Phylo.read("./TreeConstruction/nj.tre", "newick")
alphabet = ["A", "T", "C", "G"]
step_matrix = [[0], [2.5, 0], [2.5, 1, 0], [1, 2.5, 2.5, 0]]
matrix = _Matrix(alphabet, step_matrix)
scorer = ParsimonyScorer(matrix)
searcher = NNITreeSearcher(scorer)
constructor = ParsimonyTreeConstructor(searcher, tree1)
best_tree = constructor.build_tree(aln)
Phylo.write(best_tree, os.path.join(temp_dir, "pars1.tre"), "newick")
constructor.starting_tree = tree2
best_tree = constructor.build_tree(aln)
Phylo.write(best_tree, os.path.join(temp_dir, "pars2.tre"), "newick")
constructor.starting_tree = None
best_tree = constructor.build_tree(aln)
Phylo.write(best_tree, os.path.join(temp_dir, "pars3.tre"), "newick")
def test_build_tree(self):
aln = AlignIO.read(open('TreeConstruction/msa.phy'), 'phylip')
tree1 = Phylo.read('./TreeConstruction/upgma.tre', 'newick')
tree2 = Phylo.read('./TreeConstruction/nj.tre', 'newick')
alphabet = ['A', 'T', 'C', 'G']
step_matrix = [[0],
[2.5, 0],
[2.5, 1, 0],
[ 1, 2.5, 2.5, 0]]
matrix = _Matrix(alphabet, step_matrix)
scorer = ParsimonyScorer(matrix)
searcher = NNITreeSearcher(scorer)
constructor = ParsimonyTreeConstructor(searcher, tree1)
best_tree = constructor.build_tree(aln)
Phylo.write(best_tree, './TreeConstruction/pars1.tre', 'newick')
constructor.starting_tree = tree2
best_tree = constructor.build_tree(aln)
Phylo.write(best_tree, './TreeConstruction/pars2.tre', 'newick')
constructor.starting_tree = None
best_tree = constructor.build_tree(aln)
Phylo.write(best_tree, './TreeConstruction/pars3.tre', 'newick')
filePath = input("Enter the text file path:")
alignment = fastaToPhy(textToFasta(filePath))
distanceCalculator = DistanceCalculator('identity')
distanceMatrix = distanceCalculator.get_distance(alignment)
print('Distance Matrix:')
print(distanceMatrix)
print()
distanceConstructor = DistanceTreeConstructor()
##############################UPGMA##############################
UPGMATree = distanceConstructor.upgma(distanceMatrix)
Phylo.draw(UPGMATree)
print('UPGMA Phylogenetic Tree:')
Phylo.draw_ascii(UPGMATree)
##############################NJ##############################
NJTree = distanceConstructor.nj(distanceMatrix)
Phylo.draw(NJTree)
print('Neighbor joining Phylogenetic Tree:')
Phylo.draw_ascii(NJTree)
##############################PARSIMONY##############################
parsimonyScorer = Phylo.TreeConstruction.ParsimonyScorer()
searcher = Phylo.TreeConstruction.NNITreeSearcher(parsimonyScorer)
parsimonyConstructor = ParsimonyTreeConstructor(searcher, NJTree)
parsimonyTree = parsimonyConstructor.build_tree(alignment)
print('Parsimony Phylogenetic Tree:')
Phylo.draw_ascii(parsimonyTree)
Phylo.draw(parsimonyTree)
def build_parsimony_tree(alignment):
scorer = ParsimonyScorer()
searcher = NNITreeSearcher(scorer)
constructor = ParsimonyTreeConstructor(searcher)
return constructor.build_tree(alignment)
# print(stdout, stderr)
# print(cline)
aln = AlignIO.read('outAlign.aln', 'clustal')
# print(aln)
calculator = DistanceCalculator('identity')
dm = calculator.get_distance(aln)
print(dm)
constructor = DistanceTreeConstructor(calculator, 'nj')
tree = constructor.build_tree(aln)
print(tree)
scorer = ParsimonyScorer()
searcher = NNITreeSearcher(scorer)
constructor = ParsimonyTreeConstructor(searcher, tree)
pars_tree = constructor.build_tree(aln)
egfr_phy = pars_tree.as_phyloxml()
print(pars_tree)
print(egfr_phy)
print(list(pars_tree.find_elements('Inner3')))
for clade in egfr_phy.get_terminals():
key = clade.name
accession = PhyloXML.Accession(key, 'NCBI')
mol_seq = PhyloXML.MolSeq(lookup[key], is_aligned=True)
sequence = PhyloXML.Sequence(type='aa',
accession=accession,
mol_seq=mol_seq)