def build_phylogeny_trees():
path = "out/homologous_gene_sequences/"
output_path = "out/aligned_homologous_gene_sequences/"
for homologous_gene_sequence in os.listdir(path):
input = path + homologous_gene_sequence
output = output_path + homologous_gene_sequence
clustal_omega = ClustalOmegaCommandline(infile=input, outfile=output, verbose=True, auto=True)
os.system(str(clustal_omega))
multi_seq_align = AlignIO.read(output, 'fasta')
# Distance Matrix
calculator = DistanceCalculator('identity')
dist_mat = calculator.get_distance(multi_seq_align)
tree_constructor = DistanceTreeConstructor()
phylo_tree = tree_constructor.upgma(dist_mat)
Phylo.draw(phylo_tree)
print('\nPhylogenetic Tree\n', homologous_gene_sequence)
Phylo.draw_ascii(phylo_tree)
Phylo.write([phylo_tree], 'out/phylogenetic_trees/{}_tree.nex'.format(homologous_gene_sequence), 'nexus')
def printGeneTree(self):
"""
Print gene trees with matplotlib and in the terminal for the four largest target ORFs of coronaviruses.
Takes a .phy file containing multiple alligned sequences, generates a matrix based on sequence composition
and compares each sequence (genome) to one another. sequences with grater scores (similarity) are ranked closer
together on the phylogenetic trees.
input: A .phy file that contains coronavirus gene sequences to draw phylogenetic tree
output: A visual representation of a gene tree on terminal and matplotlib
"""
align = AlignIO.read(
self.newPhylip,
'phylip') # Reads created .phy file containing the SeqRecord
#print (align) # prints concatenated allignments
calculator = DistanceCalculator('identity')
dm = calculator.get_distance(align) # Calculate the distance matrix
print(
'\n======================================== DISTANCE MATRIX =======================================\n'
)
print(dm, "\n\n") # Print the distance Matrix
constructor = DistanceTreeConstructor(
) # Construct the phylogenetic tree using UPGMA algorithm
tree = constructor.upgma(dm)
print(
'\n========================================= GENE TREE ===========================================\n'
)
Phylo.draw(
tree
) # Draw the phylogenetic tree (must install matplotlib to use this formatting)
Phylo.draw_ascii(tree) # Print the phylogenetic tree in terminal
def main_new(fastafile, bkp):
distance_name = ["ab", "ac", "bc"]
temp = SeqIO.to_dict(SeqIO.parse(fastafile, "fasta"))
seq_name = [*temp]
aln = AlignIO.read(open(fastafile), 'fasta')
calculator = DistanceCalculator('blosum62')
segment_1 = calculator.get_distance(aln[:, :bkp])
segment_2 = calculator.get_distance(aln[:, bkp:])
distance = [
segment_1[seq_name[1]][0], segment_1[seq_name[2]][0],
segment_1[seq_name[2]][1], segment_2[seq_name[1]][0],
segment_2[seq_name[2]][0], segment_2[seq_name[2]][1]
]
#distance=[segment_1[seq_name[1]][0],segment_1[seq_name[2]][0],segment_1[seq_name[2]][1],segment_2[seq_name[1]][0],segment_2[seq_name[2]][0],segment_2[seq_name[2]][1]];
compare_distance = [
abs(distance[0] - distance[3]),
abs(distance[1] - distance[4]),
abs(distance[2] - distance[5])
] ##in order of ab,ac,bc
temp2 = distance_name[compare_distance.index(min(compare_distance))]
string = "abc"
string = string.replace(temp2[0], "")
string = string.replace(temp2[1], "")
rec = seq_name["abc".index(string)]
return rec
def plot_alignment_heatmap(alignments, trans_dict=None, title="Percent difference"):
# calculate distance - https://biopython.org/wiki/Phylo
calculator = DistanceCalculator('identity')
dm = calculator.get_distance(alignments)
if trans_dict is None:
# create a translation dictionary for human understandable labels
trans_dict = dict(
(alignment.id, " ".join(alignment.description.split()[1:3])) for alignment in alignments
)
# create dataframe from distance matrix for easier plotting
df = pd.DataFrame(
dm.matrix,
index=[trans_dict[name] for name in dm.names],
columns=[trans_dict[name] for name in dm.names]
)
plt.figure()
sns.heatmap(
df * 100,
fmt='3.2f',
annot=True,
linewidths=0.5,
cmap=sns.light_palette("navy"),
cbar=False,
square=True
)
plt.title(title)
plt.tight_layout()
return plt.gcf()
def plot_phylo_tree(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
"""
# calculate distance - https://biopython.org/wiki/Phylo
calculator = DistanceCalculator('identity')
dm = calculator.get_distance(align)
# construct a tree
constructor = DistanceTreeConstructor()
tree = constructor.upgma(dm)
# remove the names for the non-terminals for better visual appeal
for non_terminal in tree.get_nonterminals():
non_terminal.name = ''
# change accession numbers into human more understandable names
for terminal in tree.get_terminals():
terminal.name = accession_numbers[re.match("(^\S*)(?=\.)",
terminal.name)[0]]
print(Phylo.draw_ascii(tree))
# plot the tree
fig, ax = plt.subplots(1, 1)
# draw the resulting tree
Phylo.draw(tree, show_confidence=False, axes=ax, do_show=False)
ax.set_xlim(right=0.8)
return fig
def fastaToNJTree(fastaFile, outputFile):
aln = AlignIO.read(fastaFile, 'fasta')
calculator = DistanceCalculator('identity')
dm = calculator.get_distance(aln)
constructor = DistanceTreeConstructor(calculator, 'nj')
tree = constructor.build_tree(aln)
Phylo.write(tree, outputFile, 'newick')
def calculate_weight_vector(aln_obj,
algorithm='pairwise',
calc_mx='identity',
repeat=1000,
nucl=False):
alg_types = ['voronoi', 'pairwise']
if algorithm not in alg_types:
raise ValueError("Invalid algorithm type. Expected one of: %s" %
alg_types)
i = 0
if algorithm == 'voronoi':
calculator = DistanceCalculator(calc_mx)
convergence_vr = [0] * len(aln_obj)
while i < repeat:
test_seq = generate_sequence_sampled_from_alignment(aln_obj)
wei_vr = list()
for seq_obj in aln_obj:
wei_vr.append(calculator._pairwise(seq_obj.seq, test_seq))
closest_seq = min(wei_vr)
closest_sequences = [
i for i, j in enumerate(wei_vr) if j == closest_seq
]
for pos in closest_sequences:
convergence_vr[pos] += 1 / len(closest_sequences)
i += 1
return [i / sum(convergence_vr) for i in convergence_vr]
if algorithm == 'pairwise':
tree = tree_construct(aln_obj, nucl=nucl, calc_mx=calc_mx)
distance_sums = list()
for seq_obj in aln_obj:
curr_seq_dist = 0
for seq_obj2 in aln_obj:
curr_seq_dist += tree.distance(seq_obj.id, seq_obj2.id)
distance_sums.append(curr_seq_dist)
return [i / sum(distance_sums) for i in distance_sums]
def dna(file_path, file_format, algorithm):
# Read the sequences and align
aln = AlignIO.read(file_path, file_format)
# Print the alignment
print(aln)
# Calculate the distance matrix
calculator = DistanceCalculator('identity')
dm = calculator.get_distance(aln)
# Print the distance Matrix
print('\nDistance Matrix\n===================')
print(calculator)
# Construct the phylogenetic tree using choosen algorithm
constructor = DistanceTreeConstructor()
if algorithm.lower() == 'upgma':
tree = constructor.upgma(dm)
elif algorithm.lower() == 'nj':
tree = constructor.nj(dm)
else:
click.echo('Invalid algorithm!')
# Draw the phylogenetic tree
Phylo.draw(tree)
# Print the phylogenetic tree in the terminal
print('\nPhylogenetic Tree\n===================')
Phylo.draw_ascii(tree)
def consensus(msa):
alignment = MultipleSeqAlignment(msa)
calculator = DistanceCalculator('identity')
dm = calculator.get_distance(alignment)
constructor = DistanceTreeConstructor(calculator, 'nj')
tree = constructor.build_tree(alignment)
print tree
def tree(from_cluster,to_cluster, grupa):
consensus_trees = []
for i in [x for x in range(from_cluster,to_cluster)]:
msa = AlignIO.read('msa\msa_rodzina_' + str(i)+ '_s.fasta', 'fasta')
print i
calculator = DistanceCalculator('identity')
try:
dm = calculator.get_distance(msa)
constructor = DistanceTreeConstructor(calculator, 'nj')
trees = bootstrap_trees(msa, 50, constructor)
trees_list = list(trees)
not_included = set([])
for j in range(len(trees_list)):
target_tree = trees_list[j]
support_tree = get_support(target_tree, trees_list)
for node in support_tree.get_nonterminals():
if node.confidence < 50:
not_included.add(j)
trees = [trees_list[k] for k in range(len(trees_list)) if k not in not_included]
if len(trees) > 0:
consensus_trees.append(majority_consensus(trees))
except:
ValueError
Phylo.write(consensus_trees,"drzewa_wynikowe_" + str(grupa),"newick")
def nj_tree_constructor(x):
constructor = DistanceTreeConstructor()
calculator = DistanceCalculator("identity")
dm = calculator.get_distance(x)
njtree = constructor.nj(dm)
print(njtree)
Phylo.draw_ascii(njtree)
def construct_id_dm(seq_df,
seq_fpath,
align_outpath="tmp/iddm_align.fasta",
ordered=False,
aligned=False,
kalign_silent=True):
"""Constructs an np.ndarray corresponding to the identity distance matrix of records in seq_df
:param seq_df: DataFrame of OrthoDB/ NCBI sequence records; should only contain records for which identity
distance matrix will be computed
:param seq_fpath: Path of fasta file containing at least all of the records in seq_df. Can contain more records
than are in seq_df - a temporary file containing only the records in seq_df.index will be generated (filtered_fpath)
:param align_outpath: Optional filepath. If provided, the resulting alignment will be stored there. Otherwise,
written to a temporary file (tmp/iddm_align.fasta)
:param ordered: boolean. True: distance matrix rows will be ordered by the order of records in seq_df.index;
False: distance matrix rows will be ordered by the order of records in seq_fpath
:return: id_dm: np.ndarray of identity distance matrix calculated by AlignIO
:return: align_srs: pandas Series object containing aligned sequences
"""
from Bio.Phylo.TreeConstruction import DistanceCalculator
from Bio import AlignIO
# Filter records in seq_fpath to new fasta only containing records in seq_df.index
# filtered_outpath = "tmp/iddm.fasta"
filtered_fpath = "tmp/alias_matches.fasta"
filter_fasta_infile(seq_df.index,
seq_fpath,
outfile_path=filtered_fpath,
ordered=ordered)
if not aligned:
# KAlign sequences in filtered_outpath, write to align_outpath
with open(filtered_fpath,
'r') as filtered_f, open(align_outpath,
'wt',
encoding='utf-8') as align_f:
args = ['kalign']
if kalign_silent:
subprocess.run(args=args,
stdin=filtered_f,
stdout=align_f,
stderr=subprocess.PIPE,
text=True)
else:
subprocess.run(args=args,
stdin=filtered_f,
stdout=align_f,
text=True)
else:
align_outpath = filtered_fpath
align_srs = fasta_to_srs(align_outpath)
with open(align_outpath) as aligned_f:
aln = AlignIO.read(aligned_f, 'fasta')
calculator = DistanceCalculator('identity')
id_dm_obj = calculator.get_distance(aln)
# Convert AlignIO object to np.ndarray
for i, r in enumerate(id_dm_obj):
if i == 0:
id_dm = np.array(r)
else:
id_dm = np.vstack((id_dm, r))
return id_dm, align_srs
def buildTree(FASTAFile):
myAlignment = AlignIO.read(FASTAFile, "fasta")
# Create a tip mapping from the fasta file
tipMapping = {}
for record in myAlignment:
tipMapping[record.id] = str(record.seq)
# Compute a distance matrix and construct tree
calculator = DistanceCalculator("identity")
myMatrix = calculator.get_distance(myAlignment)
constructor = DistanceTreeConstructor()
upgmaTree = constructor.nj(myMatrix)
upgmaTree.root_at_midpoint()
Phylo.draw(upgmaTree)
# Convert phyloxml tree to newick
# biopython does not provide a function to do this so it was necessary
# to write to a buffer in newick to convert then get rid of unneeded info
for clade in upgmaTree.get_terminals():
clade.name = "\"" + clade.name + "\""
buf = cStringIO.StringIO()
Phylo.write(upgmaTree, buf, 'newick', plain = True)
tree = buf.getvalue()
tree = re.sub(r'Inner\d*', '', tree)
tree = tree.replace(";", "")
tree = literal_eval(tree) #newick format
# RLR tree required for maxParsimony function
tree = NewicktoRLR(tree)
return tree
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 get_tree(aln, kind='nj'):
from Bio.Phylo.TreeConstruction import DistanceCalculator,DistanceTreeConstructor
calculator = DistanceCalculator('identity')
dm = calculator.get_distance(aln)
constructor = DistanceTreeConstructor()
tree = constructor.nj(dm)
return dm, tree
def consensus(msa):
alignment = MultipleSeqAlignment(msa)
calculator = DistanceCalculator('identity')
dm = calculator.get_distance(alignment)
constructor = DistanceTreeConstructor(calculator, 'nj')
tree = constructor.build_tree(alignment)
print tree
def build_trees(filename, tree_name):
# Compute alignment with ClustalW algorithm
clustalw_cline = ClustalwCommandline("clustalw",
infile="{}.fa".format(filename))
clustalw_cline()
alignment = AlignIO.read("{}.aln".format(filename), format="clustal")
# Create distance matrix
calculator = DistanceCalculator('blosum62')
dist_matrix = calculator.get_distance(alignment)
# Build phylogenetic trees using upgma and nj methods
constructor = DistanceTreeConstructor()
upgma_tree = constructor.upgma(dist_matrix)
nj_tree = constructor.nj(dist_matrix)
# Draw the trees
label_func = lambda clade: "" if clade.name.startswith("Inner") else clade
Phylo.draw(upgma_tree, label_func=label_func, do_show=False)
plt.title("{} × upgma".format(tree_name))
plt.show()
Phylo.draw(nj_tree, label_func=label_func, do_show=False)
plt.title("{} × nj".format(tree_name))
plt.show()
def upgma_tree_constructor(x):
constructor = DistanceTreeConstructor()
calculator = DistanceCalculator("identity")
dm = calculator.get_distance(x)
upgmatree = constructor.upgma(dm)
print(upgmatree)
Phylo.draw_ascii(upgmatree)
def main():
file_name = "data/coding.fa"
# file_name = "data/cons_noncode.fa"
alignment = MultipleSeqAlignment([], Gapped(IUPAC.unambiguous_dna, "-"))
for seq_record in SeqIO.parse(file_name, "fasta"):
alignment.extend([seq_record])
print("Number of characters in alignment:", len(alignment[0]))
####################
# Neighbor joining #
####################
calculator = DistanceCalculator('identity')
dm = calculator.get_distance(alignment)
constructor = DistanceTreeConstructor()
start = time.time()
tree = constructor.nj(dm)
end = time.time()
print("Neighbor joining ran in {} seconds.".format(end - start))
Phylo.draw(tree, label_func=get_label)
#########
# UPGMA #
#########
start = time.time()
tree = constructor.upgma(dm)
end = time.time()
print("UPGMA ran in {} seconds.".format(end - start))
Phylo.draw(tree, label_func=get_label)
def main():
calculator = DistanceCalculator()
# Exercise 1
print("Exercise 1:")
genomeAfrican = getGenome("genomes/africanAligned.fasta")
genomeIndian = getGenome("genomes/indianAligned.fasta")
genomeMammoth = getGenome("genomes/mammothAligned.fasta")
distAM = calculator._pairwise(genomeAfrican, genomeMammoth)
distIM = calculator._pairwise(genomeIndian, genomeMammoth)
print("Distance between African and Mammoth is {}.".format(distAM))
print("Distance between Indian and Mammoth is {}.".format(distIM))
# Exercise 3
print("\nExercise 3:")
genomeWhale = getGenome("genomes/whaleAligned.fasta")
genomeCow = getGenome("genomes/cowAligned.fasta")
genomeHippo = getGenome("genomes/hippoAligned.fasta")
distWC = calculator._pairwise(genomeWhale, genomeCow)
distWH = calculator._pairwise(genomeWhale, genomeHippo)
print("Distance between Whale and Cow is {}.".format(distWC))
print("Distance between Whale and Hippo is {}.".format(distWH))
def main():
alignment = AlignIO.read(open("protein.fasta"), "fasta")
calculator = DistanceCalculator('identity')
dm = calculator.get_distance(alignment)
constructor = DistanceTreeConstructor(calculator, 'upgma')
tree = constructor.build_tree(alignment)
tree.ladderize()
Phylo.draw(tree)
def get_tree():
#biopython-extract the unrooted tree
aln = AlignIO.read('agc.aln', 'clustal')
calculator = DistanceCalculator('identity')
dm = calculator.get_distance(aln)
constructor = DistanceTreeConstructor()
tree = constructor.nj(dm)
return tree
def build_tree(aln, kind='nj'):
"""Build a tree with bio.phylo module"""
from Bio.Phylo.TreeConstruction import DistanceCalculator,DistanceTreeConstructor
calculator = DistanceCalculator('identity')
dm = calculator.get_distance(aln)
constructor = DistanceTreeConstructor()
tree = constructor.nj(dm)
return dm, tree
def test_nonmatching_seqs(self):
aln = AlignIO.read(StringIO(">Alpha\nA-A--\n>Gamma\n-Y-Y-"), "fasta")
# With a proper scoring matrix -- no matches
dmat = DistanceCalculator('blosum62').get_distance(aln)
self.assertEqual(dmat['Alpha', 'Alpha'], 0.)
self.assertEqual(dmat['Alpha', 'Gamma'], 1.)
# Comparing characters only -- 4 misses, 1 match
dmat = DistanceCalculator().get_distance(aln)
self.assertEqual(dmat['Alpha', 'Alpha'], 0.)
self.assertAlmostEqual(dmat['Alpha', 'Gamma'], 4. / 5.)
def createTree(file):
aln = AlignIO.read(file, 'phylip')
# Calculate the distance matrix
calculator = DistanceCalculator('identity')
dm = calculator.get_distance(aln)
# Construct the phylogenetic tree using UPGMA algorithm
constructor = DistanceTreeConstructor()
tree = constructor.upgma(dm)
Phylo.write(tree, 'new.xml', 'phyloxml')
def D_seq_matrix(fasta_file):
aln = AlignIO.read(fasta_file, 'fasta')
calculator = DistanceCalculator('identity')
dm = calculator.get_distance(aln)
constructor = DistanceTreeConstructor()
tree_seq = constructor.upgma(dm)
#print tree_dmc
Phylo.write(tree_seq,'ph_seq.nre','newick')
print dm.names
return dm
def __init__(self, input_filename, searcher):
# Read the aligned sequences and align
self.aligned_file = AlignIO.read(input_filename, format='clustal')
self.searcher = searcher
# Calculate the distance matrix
calculator = DistanceCalculator('identity')
self.distance_matrix = calculator.get_distance(self.aligned_file)
matplotlib.rc('font', size=6)
def cluster_by_cdr3(results_table, output_dir):
df1 = pd.read_csv(results_table)
res_df = pd.DataFrame()
fasta_file = output_dir + "/cdr3.fasta"
with open(fasta_file, 'w+') as fas:
for i, row in df1.iterrows():
if type(row["CDR3 first"]) is not str:
continue
fas.write(">" + "_".join(row["Patient"].split(" ")) + ":" +
row["well_id"] + ":" + row["V first"] + "\n")
fas.write(row["CDR3 first"] + "\n")
alignment_file = align_func.clustalw_align(fasta_file, sys.stdout)
aln = AlignIO.read(alignment_file, 'clustal')
calculator = DistanceCalculator('identity')
dm = calculator.get_distance(aln)
with open(output_dir + '/dm.pkl', 'wb') as f:
pickle.dump(dm, f, protocol=0)
l = list(combinations(range(len(dm.names)), 2))
distmat = np.repeat(np.inf, len(l))
for index in range(len(l)):
distmat[index] = dm.matrix[l[index][1]][l[index][0]]
with open(output_dir + '/distmat.pkl', 'wb') as f:
pickle.dump(distmat, f, protocol=0)
Z = linkage(distmat, method='average')
max_d = 0.05
clusters = fcluster(Z, max_d, criterion='distance')
patient_col = [x.split("_W")[0] for x in dm.names]
well_col = ['W' + x.split("_W")[1].split("_")[0] for x in dm.names]
df2 = pd.DataFrame(data={
"cluster": clusters,
"Patient": patient_col,
"well_id": well_col
})
table = pd.merge(df2, df1, on=["Patient", "well_id"], how="inner")
table = table[[
'cluster', 'Patient', 'Amp Batch', 'well_id', 'cell_name', '#reads',
'#umi distribution', "V first", "V first counts", "V second",
"V second counts", "D first", "D first counts", "D second",
"D second counts", "J first", "J first counts", "J second",
"J second counts", "CDR3 first", "CDR3 first counts", "CDR3 second",
"CDR3 second counts"
]]
table.to_csv(output_dir + '/full_results.csv')
def MSAOBJ(Align):
calculator = DistanceCalculator('identity')
MSAlst = []
for indx in Align.index:
ind = [a == indx for a in Align.index]
seq = Seq(list(Align[ind].iloc[0])[0])
MSAlst.append(SeqRecord(seq,id=indx))
align = MultipleSeqAlignment(MSAlst)
dm = calculator.get_distance(align)
return(align,dm)
def build_tree_NJ(msa, distanceMatrix=None):
if not distanceMatrix:
distCalculator = DistanceCalculator("identity")
distanceMatrix = distCalculator.get_distance(msa)
# Construct the tree with the distance Matrix
constructor = DistanceTreeConstructor()
tree = constructor.nj(distanceMatrix)
# Make the tree rooted
#tree.root_at_midpoint()
#return newick format
return "[&R] " + tree.format("newick").strip()
def phyloxml_from_msa(msa, phyloxml):
from Bio import AlignIO
from Bio.Phylo.TreeConstruction import DistanceCalculator
from Bio.Phylo.TreeConstruction import DistanceTreeConstructor
from Bio import Phylo
ms_alignment = AlignIO.read(msa, "fasta")
calculator = DistanceCalculator("ident")
dist_matrix = calculator.get_distance(ms_alignment)
constructor = DistanceTreeConstructor()
tree = constructor.upgma(dist_matrix)
Phylo.write(tree, phyloxml, "phyloxml")
def generar_arbol(file, indice):
with open(file, "r") as aln:
alineamiento = AlignIO.read(aln, "clustal")
calculator = DistanceCalculator('identity')
dm = calculator.get_distance(alineamiento)
constructor = DistanceTreeConstructor(calculator)
nj = constructor.nj(dm) # Neighbor Joining
Phylo.draw(nj)
path = './static/assets/arbol_filogenetico' + indice + '.png'
pylab.savefig(path, format='png')
def calculate_distance_matrix(self, type, file):
in_file = file
# print(type(in_file))
if type == 'DNA':
matrix_type = 'blastn'
else:
matrix_type = 'blosum62'
calculator = DistanceCalculator(matrix_type)
alignment = AlignIO.read(in_file, "fasta")
dm = calculator.get_distance(alignment)
return dm
def blosumnj(filename):
aln = AlignIO.read(open(filename), 'fasta')
print(aln)
calculator = DistanceCalculator('blosum62')
dm = calculator.get_distance(aln)
print(dm)
from Bio.Phylo.TreeConstruction import DistanceTreeConstructor
constructor = DistanceTreeConstructor(calculator, 'nj')
tree = constructor.build_tree(aln)
print(tree)
def distance(inFile, model='identity'):
"""
Given an alingment file (in fasta format), this function return a distance matrix.
Module required:
- AlignIO (from Bio)
- DistanceCalculator (from Bio.Phylo.TreeConstruction)
Usage: <inFile> <model (default = 'identity')>
"""
aln = AlignIO.read(inFile, 'fasta') # read the alignment
calculator = DistanceCalculator(model) # prepare the mode to calculate the distance
dm = calculator.get_distance(aln) # calculate the distance of the alignment
return dm
def __get_dm(self):
from Bio.Phylo.TreeConstruction import DistanceCalculator
import numpy as np
calculator = DistanceCalculator('identity')
dm = calculator.get_distance(self.aln)
dm_array = np.zeros(shape=(self.ns, self.ns))
for row in range(0, self.ns):
for cln in range(0, self.ns):
if cln > row:
dm_array[row, cln] = dm[cln][row]
else:
dm_array[row, cln] = dm[row][cln]
return dm_array
def get_dist_matrix (file):
aln = AlignIO.read(open('tmp/'+file), 'clustal')
calculator = DistanceCalculator('blosum62')
dist_matrix = calculator.get_distance(aln)
i=0
j=0
da_list = list()
for row in dist_matrix:
print ('New Row!')
j=0
for column in row:
if i<j: # with this, you take out the 0's so n = (N²-N)/2
print (dist_matrix[i,j])
da_list.append(dist_matrix[i,j])
j+=1
i+=1
return (da_list)
def test_nj(self):
tree = self.constructor.nj(self.dm)
self.assertTrue(isinstance(tree, BaseTree.Tree))
# tree_file = StringIO()
# Phylo.write(tree, tree_file, 'newick')
ref_tree = Phylo.read('./TreeConstruction/nj.tre', 'newick')
self.assertTrue(Consensus._equal_topology(tree, ref_tree))
# ref_tree.close()
# create a matrix of length 2
calculator = DistanceCalculator('blosum62')
self.min_dm = calculator.get_distance(self.aln)
for i in range(len(self.min_dm) - 2):
del self.min_dm[len(self.min_dm) - 1]
min_tree = self.constructor.nj(self.min_dm)
self.assertTrue(isinstance(min_tree, BaseTree.Tree))
ref_min_tree = Phylo.read('./TreeConstruction/nj_min.tre', 'newick')
self.assertTrue(Consensus._equal_topology(min_tree, ref_min_tree))
def distances_to_seq(alignment, sequence, distance_model="identity"):
"""A tool for computing not the complete sequence-sequence distance matrix,
but only the distances to certain sequences.
Beware: relies on a protected member of DistanceCalculator.
:param alignment: A MultipleSeqAlignment object.
:param sequence: A SeqRecord object. Must be of the same length as the
records in the alignment.
:param distance_model: One of either 'identity', 'blastn', or 'trans'.
Defines the distance of a nucleotide pair. See
Bio.Phylo.TreeConstruction.DistanceCalculator documentation.
:returns: A list of distances between the given sequence and all sequences
in the MSA, in the order in which the sequences are in the MSA.
"""
dcalc = DistanceCalculator(distance_model)
output = [dcalc._pairwise(sequence, msa_seq) for msa_seq in alignment]
return output
def test_distance_calculator(self):
aln = AlignIO.read(open('TreeConstruction/msa.phy'), 'phylip')
calculator = DistanceCalculator('identity')
dm = calculator.get_distance(aln)
self.assertEqual(dm['Alpha', 'Beta'], 1 - (10 * 1.0 / 13))
calculator = DistanceCalculator('blastn')
dm = calculator.get_distance(aln)
self.assertEqual(dm['Alpha', 'Beta'], 1 - (38 * 1.0 / 65))
calculator = DistanceCalculator('trans')
dm = calculator.get_distance(aln)
self.assertEqual(dm['Alpha', 'Beta'], 1 - (49 * 1.0 / 78))
calculator = DistanceCalculator('blosum62')
dm = calculator.get_distance(aln)
self.assertEqual(dm['Alpha', 'Beta'], 1 - (53 * 1.0 / 84))
from Bio.Phylo.TreeConstruction import DistanceCalculator, DistanceTreeConstructor
from Bio import AlignIO
from Bio.Phylo.Consensus import *
from Bio import Phylo
clusters = 508
consensus_trees = []
#drzewa konsensusowe dla wszystkich klastrow
for i in [x for x in range(100,clusters) if x != 354]:
msa = AlignIO.read('msa_klaster' + str(i) + '_s.fasta', 'fasta')
calculator = DistanceCalculator('identity')
dm = calculator.get_distance(msa)
constructor = DistanceTreeConstructor(calculator, 'nj')
trees = bootstrap_trees(msa, 50, constructor)
trees_list = list(trees)
not_included = set([])
for j in range(len(trees_list)):
target_tree = trees_list[j]
support_tree = get_support(target_tree, trees_list)
for node in support_tree.get_nonterminals():
if node.confidence < 50:
not_included.add(j)
trees = [trees_list[k] for k in range(len(trees_list)) if k not in not_included]
if len(trees) > 0:
consensus_trees.append(majority_consensus(trees))
def makeDistanceTree():
aln = AlignIO.read('Tests/TreeConstruction/msa.phy', 'phylip')
calculator = DistanceCalculator('identity')
dm = calculator.get_distance(aln)
constructor = DistanceTreeConstructor(calculator, 'nj')
tree = constructor.build_tree(aln)
from Bio.Phylo.TreeConstruction import DistanceCalculator
from Bio import AlignIO
# the alignmnet is pretty much the elementary structure
aln = AlignIO.read('./msa.phy', 'phylip')
# print aln
# SingleLetterAlphabet() alignment with 5 rows and 13 columns
# AACGTGGCCACAT Alpha
# AAGGTCGCCACAC Beta
# GAGATTTCCGCCT Delta
# GAGATCTCCGCCC Epsilon
# CAGTTCGCCACAA Gamma
# Several thigns can be done witht he alignment: get a distance matrix from it:
dstcalc = DistanceCalculator('identity')
dm = dstcalc.get_distance(aln)
# DistanceMatrix(names=['Alpha', 'Beta', 'Gamma', 'Delta', 'Epsilon'], matrix=[[0], [0.23076923076923073, 0], [0.3846153846153846, 0.23076923076923073, 0], [0.5384615384615384, 0.5384615384615384, 0.5384615384615384, 0], [0.6153846153846154, 0.3846153846153846, 0.46153846153846156, 0.15384615384615385, 0]])
print "What's the get_distance(aln) from DistanceCalculator('identity') object?"
print type(dm)
print dm
# Alpha 0
# Beta 0.230769230769 0
# Gamma 0.384615384615 0.230769230769 0
# Delta 0.538461538462 0.538461538462 0.538461538462 0
# Epsilon 0.615384615385 0.384615384615 0.461538461538 0.153846153846 0
# build a tree from it.
from Bio.Phylo.TreeConstruction import DistanceTreeConstructor
construc0 = DistanceTreeConstructor(dstcalc, 'nj')
# i = 0
# while i < len(sequences):
# if sequences[i] in temp_dict:
# i += 14
# else:
# temp_dict[sequences[i]] = sequences[i + 1 : i + 13]
# new_file.write(str(i) + "\n")
# for item in temp_dict[sequences[i]]:
# new_file.write(item)
# i += 14
fasta_files = file_handlers.find_files(file_paths, "fasta")
for path in fasta_files:
file_name = file_handlers.get_file_name(path)
print file_name
name_list = file_name.split(".")
# derep_out_file = ''.join(name_list[0] + '_uniques.fasta')
dm_out_file = "".join(name_list[0] + "_dm.txt")
# cmd = ['usearch -derep_fulllength ' + path + ' -fastaout ' + derep_out_file]
# subprocess.call(cmd, shell=True)
new_file = open("/Users/andrea/repositories/AMPHORA2/muscle_alignments/" + dm_out_file, "w")
aln = AlignIO.read(path, "fasta")
calculator = DistanceCalculator(
"identity"
) # identity is the name of the model(scoring matrix) to calculate the distance. The identity model is the default one and can be used both for DNA and protein sequence.
dm = calculator.get_distance(aln)
new_file.write(dm)
new_file.close()
def NNIheuristic(FASTAFile, sampleSize, threshold, outputDir):
""""Find the maximum parsimony score for that tree"""
random.seed(0)
outputFile = FASTAFile.replace(".align", ".out")
if "/" in outputFile:
outputFile = outputFile[outputFile.rfind("/"):]
output = open(outputDir + "/" + outputFile, 'w')
output.write("*****************RUN STARTS HERE!*****************")
#start time
startTime = time.clock()
output.write("\n" + "Filename: " + FASTAFile + "\n")
output.write("Program Start: {:%Y-%m-%d %H:%M:%S}".format(datetime.datetime.now()) + "\n")
output.write("Sample Size: " + str(sampleSize) + "\nThreshold: " + str(threshold) + "\n\n")
# Import fasta alignment file
myAlignment = AlignIO.read(FASTAFile, "fasta")
# Create a tip mapping from the fasta file
tipMapping = {}
for record in myAlignment:
tipMapping[record.id] = str(record.seq)
# Compute a distance matrix and construct tree
calculator = DistanceCalculator("identity")
myMatrix = calculator.get_distance(myAlignment)
output.write("matrix constructed here")
constructor = DistanceTreeConstructor()
upgmaTree = constructor.upgma(myMatrix)
output.write("constructed upgma tree")
# Convert phyloxml tree to newick
# biopython does not provide a function to do this so it was necessary
# to write to a buffer in newick to convert then get rid of unneeded info
for clade in upgmaTree.get_terminals():
clade.name = "\"" + clade.name + "\""
buf = cStringIO.StringIO()
Phylo.write(upgmaTree, buf, 'newick', plain = True)
tree = buf.getvalue()
tree = re.sub(r'Inner\d*', '', tree)
tree = tree.replace(";", "")
tree = literal_eval(tree) #newick format
output.write("created the original tree into newick format")
# RLR tree required for maxParsimony function
tree = NewicktoRLR(tree)
score = maxParsimony(tree, tipMapping)
graph = nx.Graph()
makeGraph(graph, tree)
output.write("made a graph")
leaves = getLeaves(tree)
currentFeasible = isFeasible(graph,leaves)
output.write("tested isFeasible")
# Perform NNI heuristic
counter = 0
loopCounter = 0
while True:
output.write("in the while loop")
loopCounter += 1
output.write("Loop Iteration: " + str(loopCounter) + "\n")
output.write("Loop Start Time: {:%H:%M:%S}".format(datetime.datetime.now()) + "\n")
output.write("Current Tree\nFeasibility: " + str(currentFeasible) + "\nScore: " + str(score) + "\nTree:\n" + str(tree) + "\n\n")
NNIs = allNNIs(tree)
if len(NNIs)-1 < sampleSize:
sampleSize = len(NNIs)-1
toScore = random.sample(NNIs, sampleSize)
# add feasibility test
output.write("starting feasibility test")
feasible = []
infeasible = []
for tree in toScore:
graph = nx.Graph()
makeGraph(graph, tree)
leaves = getLeaves(tree)
if isFeasible(graph, leaves): #if this tree is possible
feasible.append(tree)
else:
infeasible.append(tree) #if this tree is not possible
output.write("Number of Feasible Neighbor Trees: " + str(len(feasible)) + "\n")
output.write("Number of Infeasible Neighbor Trees: " + str(len(infeasible)) + "\n")
if len(feasible) != 0: #if feasible trees were found
if isFeasible(graph, leaves): #if this NNI is possible
feasible.append(tree)
else:
infeasible.append(tree) #if this NNI is not possible
if len(feasible) != 0: #if feasible NNIs were found
scoredList = map(lambda x: (maxParsimony(x, tipMapping), x), feasible)
sortedList = sorted(scoredList)
counter = 0
if not currentFeasible or sortedList[0][0] < score:
score = sortedList[0][0]
tree = sortedList[0][1]
currentFeasible = True
output.write("Found a New Feasible Tree!\n\n")
else:
output.write("Best Possible Feasible Tree Found\n" + str(tree) + "\n" + "Score: " + str(score) + "\n\n")
break
else: #if no possible trees we're found
if currentFeasible: #checks if the original tree was feasible
output.write("No Feasible Neighbors, Best Possible Feasible Tree\n" + str(tree) + "\n\n")
break
counter += 1
output.write("Threshold counter: " + str(counter) + "\n\n")
if counter >= threshold:
output.write("Threshold Met: No Feasible Tree Found\n")
stopTime = (time.clock() - startTime)
output.write("Program Stop: " + str(stopTime) + " seconds\n\n")
return
output.write("Searching Infeasible Space\n")
scoredList = map(lambda x: (maxParsimony(x, tipMapping), x), infeasible)
sortedList = sorted(scoredList)
choseNeighbor = False
for neighbor in sortedList: #if the original tree was infeasible and no feasible neighbors were found, take the next best infeasible tree and run again
if neighbor[0] > score:
score = neighbor[0]
tree = neighbor[1]
choseNeighbor = True
break
if not choseNeighbor:
score = sortedList[-1][0]
tree = sortedList[-1][1]
currentFeasible = False
output.write("Next Best Infeasible Tree\n\n")
endTime = (time.clock() - startTime)
output.write("Program End: " + str(endTime) + " seconds\n\n")
#outputTree = RLRtoNewick(tree)
#print "Final score", score
return
## pad sequences so that they all have the same length
#for record in records:
# if len(record.seq) != maxlen:
# sequence = str(record.seq).ljust(maxlen, '.')
# record.seq = Seq.Seq(sequence)
#assert all(len(record.seq) == maxlen for record in records)
## write to temporary file and do alignment
#output_file = '{}_padded.fasta'.format(os.path.splitext(input_file)[0])
#with open(output_file, 'w') as f:
# SeqIO.write(records, f, 'fasta')
#alignment = AlignIO.read(output_file, "fasta")
#cline = ClustalwCommandline("clustalw2", infile=input_file)
#print(cline)
#print type(cline)
muscle_cline = MuscleCommandline(input=input_file)
stdout, stderr = muscle_cline()
alignment = AlignIO.read(StringIO(stdout), "fasta")
print(alignment)
#alignment = AlignIO.read('../data/ls_orchid.fasta', 'fasta')
#print alignment
calculator = DistanceCalculator('ident')
dm = calculator.get_distance(alignment)
constructor = DistanceTreeConstructor()
tree = constructor.upgma(dm)
Phylo.write(tree, 'phyloxml.xml', 'phyloxml')
def setUp(self):
self.aln = AlignIO.read(open('TreeConstruction/msa.phy'), 'phylip')
calculator = DistanceCalculator('blosum62')
self.dm = calculator.get_distance(self.aln)
self.constructor = DistanceTreeConstructor(calculator)
# Bruno Azenha Goncalves
# ICMC - USP
# Python program to build phylogenetic tree
from Bio import AlignIO
from Bio import Phylo
import numpy as np
from Bio.Phylo.TreeConstruction import DistanceCalculator
from Bio.Phylo.TreeConstruction import DistanceTreeConstructor
# Reads the alignment files
alignApe = AlignIO.read('genomes/human_primates_aligned.fasta', 'fasta')
alignHIV = AlignIO.read('genomes/alignedHIV.fasta', 'fasta')
# Creates the distance matrix
calculator = DistanceCalculator('ident')
dm_ape = calculator.get_distance(alignApe)
dm_hiv = calculator.get_distance(alignHIV)
# Jukes Cantor corrections
dm_ape_corrected = dm_ape
for d in dm_ape_corrected.matrix:
d[:] = [-3/4*np.log(1-4/3*x) for x in d]
dm_hiv_corrected = dm_hiv
for d in dm_hiv_corrected.matrix:
d[:] = [-3/4*np.log(1-4/3*x) for x in d]
# Constructs the tree using the upgma algorithm
def noFeasibleTest(FASTAFile, sampleSize, outputDir):
""""takes a FASTAFile, constructs a UPGMA Tree from the file data, converts this tree to RLR format,
tries to find the tree with the lowest parsimony score (ignores feasibility check)"""
random.seed(0)
outputFile = FASTAFile.replace(".align", ".out")
if "/" in outputFile:
outputFile = outputFile[outputFile.rfind("/"):]
output = open(outputDir + "/" + outputFile, 'w')
output.write("*****************RUN STARTS HERE!*****************")
#start time
startTime = time.clock()
output.write("\n" + "Filename: " + FASTAFile + "\n")
output.write("Program Start: {:%Y-%m-%d %H:%M:%S}".format(datetime.datetime.now()) + "\n")
output.write("Sample Size: " + str(sampleSize) + "\n\n")
# Import fasta alignment file
myAlignment = AlignIO.read(FASTAFile, "fasta")
# Create a tip mapping from the fasta file
tipMapping = {}
for record in myAlignment:
tipMapping[record.id] = str(record.seq)
# Compute a distance matrix and construct tree
calculator = DistanceCalculator("identity")
myMatrix = calculator.get_distance(myAlignment)
constructor = DistanceTreeConstructor()
upgmaTree = constructor.upgma(myMatrix)
# Convert phyloxml tree to newick
# biopython does not provide a function to do this so it was necessary
# to write to a buffer in newick to convert then get rid of unneeded info
for clade in upgmaTree.get_terminals():
clade.name = "\"" + clade.name + "\""
buf = cStringIO.StringIO()
Phylo.write(upgmaTree, buf, 'newick', plain = True)
tree = buf.getvalue()
tree = re.sub(r'Inner\d*', '', tree)
tree = tree.replace(";", "")
tree = literal_eval(tree) #newick format
# RLR tree required for maxParsimony function
tree = NNI.NewicktoRLR(tree)
score = NNI.maxParsimony(tree, tipMapping)
# Perform NNI heuristic
loopCounter = 0
while True:
loopCounter += 1
output.write("Loop Iteration: " + str(loopCounter) + "\n")
output.write("Loop Start Time: {:%H:%M:%S}".format(datetime.datetime.now()) + "\n")
output.write("Current Tree\nScore: " + str(score) + "\nTree:\n" + str(tree) + "\n\n")
NNIs = NNI.allNNIs(tree)
if len(NNIs)-1 < sampleSize:
sampleSize = len(NNIs)-1
toScore = random.sample(NNIs, sampleSize)
scoredList = map(lambda x: (NNI.maxParsimony(x, tipMapping), x), toScore)
sortedlist = sorted(scoredList)
if sortedlist[0][0] < score:
score = sortedlist[0][0]
tree = sortedlist[0][1]
output.write("Found A More Parsimonious Tree!\n\n")
else:
break
output.write("No Neighbors With Better Scores Found\n\n")
output.write("Final Tree:\n" + str(tree) + "\nScore: " + str(score) + "\n\n")
endTime = (time.clock() - startTime)
output.write("Program End: " + str(endTime) + " seconds\n\n")
return