def tree_reconstruction(phy_file, method, model, phyformat):
'''Construct tree with given method and model'''
aln = AlignIO.read(phy_file, 'phylip-' + phyformat)
constructor = DistanceTreeConstructor()
calculator = DistanceCalculator(model)
dm = calculator.get_distance(aln)
if method == 'upgma':
tree = constructor.upgma(dm)
elif method == 'nj':
tree = constructor.nj(dm)
tree.ladderize()
for c in tree.find_clades():
if 'Inner' in c.name:
c.name = ''
Phylo.write(tree, args.output + '/tree.nwk', 'newick')
plt.rcParams['font.style'] = 'italic'
plt.rc('font', size=8)
plt.rc('axes', titlesize=14)
plt.rc('xtick', labelsize=10)
plt.rc('ytick', labelsize=10)
plt.rc('figure', titlesize=18)
draw(tree, do_show=False)
plt.savefig(args.output + "/tree.svg", format='svg', dpi=1200)
def draw_tree(self, show_scores: bool = False):
"""
Draws tree.
show_scores: show branch parsimonious scores (optional); default is False
"""
self.show_scores = show_scores
if self.tree is None:
print("Please first build the tree.")
else:
draw(self.tree, label_func=self.get_label)
def draw_tree(self, show_branch_labels=False):
"""
Draws tree.
show_branch_labels: show branch lengths; default is False
"""
if self.tree is None:
print("Please first build the tree.")
else:
if show_branch_labels:
draw(self.tree,
label_func=self.get_label,
branch_labels=(lambda clade: clade.branch_length))
else:
draw(self.tree, label_func=self.get_label)
def plot_tree(tree, title, output_file):
# build the plot
# clear names of nodes that are not leaves
for clade in tree.find_clades():
if clade.name[0:5] == 'Inner':
clade.name = ''
fig, ax = plt.subplots()
axes = fig.add_subplot(1, 1, 1)
fig = draw(tree, axes=axes, do_show=0)
ax.get_xaxis().set_ticks([])
ax.get_yaxis().set_ticks([])
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
ax.spines['bottom'].set_visible(False)
ax.spines['left'].set_visible(False)
plt.gcf().subplots_adjust(right=0.99, left=0.01, top=0.9, bottom=0.1)
plt.suptitle(title)
plt.yticks([])
plt.ylabel('')
plt.savefig(output_file, dpi=200)
plt.close(fig)
def ex01():
alignments = get_alignments()
calculator = DistanceCalculator('blosum62')
constructor = DistanceTreeConstructor()
for a, name in alignments:
dist_matrix = calculator.get_distance(a)
upgma_tree = constructor.upgma(dist_matrix)
nj_tree = constructor.nj(dist_matrix)
print("\n\n>>> {}".format(name))
# print(dist_matrix)
# draw_ascii(upgma_tree)
# draw_ascii(nj_tree)
draw(upgma_tree)
draw(nj_tree)
def draw_tree(tree, duplications):
def branch_labels(node):
if node in duplications:
return '*'
else:
return ''
def label_colors(label):
mapping = {
'Mouse': 'red',
'Human': 'green',
'Beetle': 'blue',
'Fruitfly': 'purple'
}
for species, color in mapping.items():
if label.startswith(species):
return color
return 'black'
from pylab import rcParams
rcParams['figure.figsize'] = 15, 40
draw(tree, branch_labels=branch_labels, label_colors=label_colors)
import matplotlib.pyplot as plt
# Vuelvo a leer el alineamiento, en realidad este paso se puede saltar si se ejecuta el script de una sola vez. En la variable align ya tenemos el alineamiento en clustal
alignment = AlignIO.read(wd + 'sequencesAln.fa',
'fasta') # reading the alignment file
# Creamos la matriz de distancias. No he encontrado la corrección de Jukes-Cantor
calculator = DistanceCalculator('identity')
dm = calculator.get_distance(alignment)
# Available models: identity, blastn, trans, benner6, benner22, benner74, blosum100, blosum30, blosum35, blosum40, blosum45, blosum50, blosum55, blosum60, blosum62, blosum65, blosum70, blosum75, blosum80, blosum85, blosum90, blosum95, feng, fitch, genetic, gonnet, grant, ident, johnson, levin, mclach, miyata, nwsgappep, pam120, pam180, pam250, pam30, pam300, pam60, pam90, rao, risler, structure
# Build with neighbour joining algorithm a tree from dm
constructor = DistanceTreeConstructor()
tree = constructor.nj(dm)
# Build with upgma algorithm a tree from dm
# tree = constructor.upgma(dm)
# Write tree
Phylo.write(tree, wd + 'TreeToCutOff.nwk', 'newick')
#Plot tree
plt.rc(
'font', size=0
) # controls default text sizes #HERE IS THE SETTING FOR THAT ALLOWS ME TO HIDE THE BRANCH TIP LABELS
plt.rc('axes', titlesize=14) # fontsize of the axes title
plt.rc('xtick', labelsize=10) # fontsize of the tick labels
plt.rc('ytick', labelsize=10) # fontsize of the tick labels
plt.rc('figure', titlesize=18) # fontsize of the figure title
draw(tree, do_show=False)
plt.savefig(wd + "TreeToCutOff.svg", format='svg', dpi=1200)
clade_4413.branch_length = (8758 - 4413) clade_2356.branch_length = (8758 - 2356) clade_rat.branch_length = 2356 clade_mouse.branch_length = 2356 clade_8758.branch_length = (17735 - 8758) clade_7481.branch_length = (17735 - 7481) clade_horse.branch_length = 7481 clade_muntjak.branch_length = 7481 clade_17735.branch_length = 18960 - 17735 clade_cat.branch_length = 18960 tree = BaseTree.Tree(root, rooted=True) print(tree) draw(tree) ################################## # Non-coding clade_131584 = BaseTree.Clade(None, "") clade_120079 = BaseTree.Clade(None, "") clade_93169 = BaseTree.Clade(None, "") clade_55571 = BaseTree.Clade(None, "") clade_35195 = BaseTree.Clade(None, "") clade_22904 = BaseTree.Clade(None, "") clade_28998 = BaseTree.Clade(None, "") clade_horse = BaseTree.Clade(None, "horse") clade_cow = BaseTree.Clade(None, "cow") clade_gorilla = BaseTree.Clade(None, "gorilla") clade_orangutan = BaseTree.Clade(None, "orangutan")