def ML_tree(infile, outfile, file_type):
# Tree creation with maximum-likelihood algorithm (phyML)
# input : infile = .fasta alignment file that the user can import or paste, outfile = name of output file, file_type = clustal is the clustal too has been used, fasta if muscle tool has been used
# output : .newick file and .png picture to display
# phylogeny page should allow to choose maximum likelihood method
# convert file to phylip
records = SeqIO.parse("static/data/sauvegardes/" + dirName + infile, file_type) # clustal <-> fasta
count = SeqIO.write(records, "static/data/sauvegardes/" + dirName + outfile + ".phylip", "phylip")
print("Converted %i records" % count)
if (user_OS == 'darwin'):
cmd = PhymlCommandline(cmd='static/tools/MacOS/PhyML-3.1/PhyML-3.1_macOS-MountainLion',
input='static/data/sauvegardes/' + dirName + outfile + '.phylip')
if (user_OS == 'linux'):
cmd = PhymlCommandline(cmd='static/tools/Linux/PhyML-3.1/PhyML-3.1_linux64',
input='static/data/sauvegardes/' + dirName + outfile + '.phylip')
if (user_OS == 'win32'):
cmd = PhymlCommandline(cmd= current_path + '/static/tools/Windows/PhyML-3.1/PhyML-3.1_win32.exe',
input='static/data/sauvegardes/' + dirName + outfile + '.phylip')
out_log, err_log = cmd()
tree = Phylo.read('static/data/sauvegardes/' + dirName + outfile + '.phylip_phyml_tree.txt', 'newick')
Phylo.draw(tree, do_show=False)
Phylo.write(tree, 'static/data/sauvegardes/' + dirName + 'tree.txt', "newick")
foo = current_path + '/static/data/sauvegardes/' + dirName + 'tree.png'
plt.savefig(foo)
def ml(self, data_type, input_file):
self.converter(input_file, data_type)
base = os.path.splitext(input_file)[0]
data_file = base + '.phylip'
if data_type == 'DNA':
phyml_cline = PhymlCommandline(input=data_file)
else:
phyml_cline = PhymlCommandline(input=data_file, datatype='aa')
stdout, stderr = phyml_cline()
os.rename(base + '.phylip_phyml_tree', base + '_ml.nw') # tree file is generated
stat_file = base + '.phylip_phyml_stats'
os.remove(data_file)
os.remove(stat_file)
def test_phyml(self):
"""Run PhyML using the wrapper."""
cmd = PhymlCommandline(phyml_exe, input=EX_PHYLIP, datatype="aa")
# Smoke test
try:
out, err = cmd()
self.assertTrue(len(out) > 0)
self.assertEqual(len(err), 0)
# Check the output tree
outfname = EX_PHYLIP + "_phyml_tree.txt"
if not os.path.isfile(outfname):
# NB: Briefly, PhyML dropped the .txt suffix (#919)
outfname = outfname[:-4]
tree = Phylo.read(outfname, "newick")
self.assertEqual(tree.count_terminals(), 4)
except Exception as exc:
self.fail("PhyML wrapper error: %s" % exc)
finally:
# Clean up generated files
for suffix in [
"_phyml_tree.txt", "_phyml_tree", "_phyml_stats.txt",
"_phyml_stats"
]:
fname = EX_PHYLIP + suffix
if os.path.isfile(fname):
os.remove(fname)
def test_phyml(self):
"""Run PhyML using the wrapper."""
# Stabilize phyml tests by running in single threaded mode by default.
# Note: PHYMLCPUS environment is specific to Debian and derivatives.
if not os.getenv("PHYMLCPUS"):
os.putenv("PHYMLCPUS", "1")
cmd = PhymlCommandline(phyml_exe, input=EX_PHYLIP, datatype="aa")
# Smoke test
try:
out, err = cmd()
self.assertGreater(len(out), 0)
self.assertEqual(len(err), 0)
# Check the output tree
outfname = EX_PHYLIP + "_phyml_tree.txt"
if not os.path.isfile(outfname):
# NB: Briefly, PhyML dropped the .txt suffix (#919)
outfname = outfname[:-4]
tree = Phylo.read(outfname, "newick")
self.assertEqual(tree.count_terminals(), 4)
except Exception as exc:
self.fail(f"PhyML wrapper error: {exc}")
finally:
# Clean up generated files
for suffix in [
"_phyml_tree.txt",
"_phyml_tree",
"_phyml_stats.txt",
"_phyml_stats",
]:
fname = EX_PHYLIP + suffix
if os.path.isfile(fname):
os.remove(fname)
def compute_tree(self, sequencing_data, app='FastTree'):
tmp = mkdtemp()
phylip_path = sequencing_data.to_phylip(f'{tmp}/sequences.phylip')
if app == 'phyml' and len(sequencing_data) < 2000:
phyml_cmd = PhymlCommandline(input=phylip_path)
phyml_cmd()
self.tree_path = f'{self.outdir}/sequences_phyml_tree.txt'
elif app == 'FastTree':
if app == 'phyml':
print('Fallback to FastTree (too many OTUs)')
self.tree_path = f'{self.outdir}/tree.nwk'
with open(self.tree_path, 'w') as file_handle:
proc = subprocess.Popen(['FastTree', '-nt', phylip_path],
stdout=file_handle)
proc.wait()
else:
sys.exit('Unknown application {}'.format(app))
self.root_tree()
def construc_tree(file_name_with_path, file_name, dict):
phyml = PhymlCommandline(input=file_name_with_path + '.phy')
phyml()
tree = Phylo.read(file_name_with_path + ".phy_phyml_tree.txt", "newick")
for leaf in tree.get_terminals():
leaf.name = dict[leaf.name]
Phylo.write(tree, file_name_with_path + ".phy_phyml_tree.txt", "newick")
return 0
def create_gene_tree(msa_phy, bootstrap):
'Runs PhyML to make gene trees'
print("Creating ML gene tree...")
cmdline = PhymlCommandline("phyml",
input=msa_phy,
datatype='aa',
bootstrap=bootstrap)
out_log, err_log = cmdline()
def ml_tree(aln, name):
from Bio.Phylo.Applications import PhymlCommandline
AlignIO.write(aln, '%s.phy' %name, 'phylip-relaxed')
cmdline = PhymlCommandline(input='%s.phy' %name, datatype='nt', alpha='e', bootstrap=100)
print (cmdline)
cmdline()
mtree = Phylo.read('%s.phy_phyml_tree.txt' %name,'newick')
return mtree
def _runphyml(self):
""""Run phyml.
Input a phylip formatted alignment file and describe the datatype
('nt' or 'aa').
"""
run_phyml = PhymlCommandline(self.phyml_exe,
input=self.phyml_input,
datatype=self.datatype)
out_log, err_log = run_phyml()
self.phyml_log(out_log)
self.phyml_log(err_log)
def make_core_tree(path_to_seq, jmodel_gamma, jmodel_model, jmodel_pinv):
handle2 = AlignIO.read(open(path_to_seq), "fasta") #name!
h = open(path_to_seq + "_align_phylip", "w") #name!
h.write(handle2.format("phylip"))
h.close()
phyml_exe = "/afs/andrew.cmu.edu/usr23/lleung/phyml/phyml"
cmdline = PhymlCommandline(phyml_exe,
input=path_to_seq + "_align_phylip",
alpha=jmodel_gamma,
prop_invar=jmodel_pinv,
model=jmodel_model)
if jmodel_pinv == 0.0:
if jmodel_gamma == 0.0:
cmdline = PhymlCommandline(phyml_exe,
input=path_to_seq + "_align_phylip",
model=jmodel_model)
else:
cmdline = PhymlCommandline(phyml_exe,
input=path_to_seq + "_align_phylip",
alpha=jmodel_gamma,
model=jmodel_model)
#change name of alignment file and the model
stdo, stder = cmdline()
def runphyml(gene):
""" Run phyml to generate tree results. """
# Use the phyml executable file
phyml_exe = None
# This is mainly intended for windows use or use with an executable file
exe_name = "PhyML-3.1_win32.exe" if sys.platform == "win32" else "phyml"
phyml_exe = exe_name
# Create the command & run phyml
# Input a phylip formatted alignment file and describe the datatype ('nt' or 'aa')
run_phyml = PhymlCommandline(phyml_exe,
input=gene + '_aligned.phy',
datatype='nt')
print(run_phyml)
out_log, err_log = run_phyml()
def test_phyml(self):
"""Run PhyML using the wrapper."""
cmd = PhymlCommandline(phyml_exe, input=EX_PHYLIP, datatype='aa')
# Smoke test
try:
out, err = cmd()
self.assertTrue(len(out) > 0)
self.assertEqual(len(err), 0)
# Check the output tree
tree = Phylo.read(EX_PHYLIP + '_phyml_tree.txt', 'newick')
self.assertEqual(tree.count_terminals(), 4)
finally:
# Clean up generated files
for suffix in ['_phyml_tree.txt', '_phyml_stats.txt']:
fname = EX_PHYLIP + suffix
if os.path.isfile(fname):
os.remove(fname)
def build_ml_phyml(alignment, outfile, work_dir=".", **kwargs):
"""
build maximum likelihood tree of DNA seqs with PhyML
"""
phy_file = op.join(work_dir, "work", "aln.phy")
AlignIO.write(alignment, file(phy_file, "w"), "phylip-relaxed")
phyml_cl = PhymlCommandline(cmd=PHYML_BIN("phyml"), input=phy_file, **kwargs)
logging.debug("Building ML tree using PhyML: %s" % phyml_cl)
stdout, stderr = phyml_cl()
tree_file = phy_file + "_phyml_tree.txt"
if not op.exists(tree_file):
print("***PhyML failed.", file=sys.stderr)
return None
sh("cp {0} {1}".format(tree_file, outfile), log=False)
logging.debug("ML tree printed to %s" % outfile)
return outfile, phy_file
def phylo(run):
# Draw phylogenic tree from BLAST
result_handle = open("blast%s.xml" % run)
blast_record = NCBIXML.read(result_handle)
print("\tCollecting Sequences") # Extract sequences from BLAST result
def get_seqs(source):
for aln in source:
for hsp in aln.hsps:
yield SeqRecord(Seq(hsp.sbjct), id=aln.accession)
break
seqs = get_seqs(blast_record.alignments,)
SeqIO.write(seqs, 'Phylo/family.fasta', 'fasta')
print("\tAligning Sequences")
cmdline = MuscleCommandline(input="Phylo/family.fasta", out="Phylo/family.aln", clw=True)
cmdline()
AlignIO.convert("Phylo/family.aln", "clustal", "Phylo/family.phy", "phylip-relaxed")
print("\tGenerating Tree...")
cmdline = PhymlCommandline(input="Phylo/family.phy")
out_log, err_log = cmdline()
print("\tDrawing Tree")
tree = Phylo.read("Phylo/family.phy_phyml_tree.txt", "newick")
Phylo.draw_ascii(tree)
return
print ("clustalw output:\n %s"%(clustaltextout))
# read in the alignment file and create a MultipleSeqAlignment object
clustalalignment = AlignIO.read("p53_homologous.aln", "clustal")
#write the alignment to a format that can be read by PhyML
alignout_filename = "p53_homologous.out"
AlignIO.write(clustalalignment,alignout_filename,"phylip-relaxed")
print("Making tree (takes around 75 seconds): ")
# specify the location of the phyml executable (this depends on your machine)
phyml_exe_path = r"D:\SCHOOL\fall 2020\Biological Models in Python\Week 7\PhyML-3.1_win32.exe"
#optional check to see if that path exists
assert os.path.isfile(phyml_exe_path), "PhyML executable missing"
# create an instance of a Bio.AlignApplication that can be called like a function and runs phyml
phymlcmd = PhymlCommandline(cmd=phyml_exe_path,input=alignout_filename)
phymltextout,phymltexterr = phymlcmd()
print ("PhyML output:\n%s"%(phymltextout))
tree_filename = alignout_filename + "_phyml_tree.txt"
tree = Phylo.read(tree_filename, "newick")
print("Ascii tree:\n")
Phylo.draw_ascii(tree)
print("The nucleotide file has been converted to relaxed-phylip format.")
# Convert the amino acid file
print("Convert the amino acid fasta aligned file to relaxed-phylip format.")
AlignIO.convert(Gene[0] + "_cds_aa_aligned.fasta", "fasta", Gene[0] + "_cds_aa_aligned.phy", "phylip-relaxed")
os.system("cp " + Gene[0] + "_cds_aa_aligned.phy " + )
print("The amino acid file has been converted to relaxed-phylip format.")
# Directory change to output directory
os.chdir(h)
# -----------------------------------------------------------------------------
# Create the command & run phyml
# Input a phylip formatted alignment file and describe the datatype ('nt' or 'aa')
# Use the nucleotide aligned file with PhyML
run_phyml_nucl = PhymlCommandline(input=f + '/' + Gene[0] + '_cds_nucl_aligned.phy', datatype='nt')
print("\n" + "The following PhyML command is being run: "), print(run_phyml_nucl)
out_log_nucl, err_log_nucl = run_phyml_nucl()
print(out_log_nucl, err_log_nucl)
# -----------------------------------------------------------------------------
# Use the amino acid aligned file with PhyML
run_phyml_aa = PhymlCommandline(input=f + '/' + Gene[0] + '_cds_aa_aligned.phy', datatype='aa')
print("\n" + "The following PhyML command is being run: "), print(run_phyml_aa)
out_log_aa, err_log_aa = run_phyml_aa()
print(out_log_aa, err_log_aa)
print("PhyML tree files and stats have been created." + "\n")
# -----------------------------------------------------------------------------
# -----------------------------------------------------------------------------
os.chdir(test_out)
# Convert the file to relaxed-phylip format
print("Convert the file to relaxed-phylip format.")
AlignIO.convert(Gene[0] + "_cds_aligned.fasta", "fasta",
Gene[0] + "_aligned.phy", "phylip-relaxed")
y = r'C:\Users\shutchins2\Desktop\"In Progress"\Code\GBK2TREE\"Alignments & Trees"\"Alignment Scripts and Files"' + "\\"
os.system("move " + Gene[0] + "_aligned.phy " + y)
print("The file has been converted to relaxed-phylip format.")
os.chdir(home)
# Create the command & run phyml
# Input a phylip formatted alignment file and describe the datatype ('nt' or 'aa')
run_phyml = PhymlCommandline(phyml_exe,
input=Gene[0] + '_aligned.phy',
datatype='nt')
print("\n" +
"The following PhyML command is being run: "), print(run_phyml)
out_log, err_log = run_phyml()
#tree = Phylo.read('HTR1D_aligned.phy', 'newick')
#Phylo.draw_ascii(tree)
# Move phyml output files to appropriate directory
os.system("move " + Gene[0] + "_aligned._phyml_tree.txt " + x)
os.system("move " + Gene[0] + "_aligned._phyml_stats.txt " + x)
os.system("move " + Gene[0] + "_aligned.phy " + x)
print("PhyML tree files and stats have been created." + "\n")
#------------------------------------------------------------------------------
aln = AlignIO.read('Hemoglobina_speciesnames.aln', 'clustal')
tree = Phylo.read('Hemoglobina_speciesnames.dnd', 'newick')
# ### Build tree using Maximum Likelihoog (ML)
# In[6]:
from Bio.Phylo.TreeConstruction import *
from Bio import AlignIO
from Bio.Phylo.Applications import PhymlCommandline
AlignIO.convert("Hemoglobina_speciesnames.aln", "clustal",
"Hemoglobina_speciesnames.phy", "phylip-relaxed")
phyml_cl = PhymlCommandline(input='Hemoglobina_speciesnames.phy',
datatype='aa',
alpha='e',
bootstrap='120')
out_log, err_log = phyml_cl()
# In[7]:
mltree = Phylo.read('Hemoglobina_speciesnames.phy_phyml_tree.txt', 'newick')
Phylo.draw_ascii(mltree)
# ### Build tree using Neighbour Joining (NJ)
# In[8]:
aln = AlignIO.read('Hemoglobina_speciesnames.aln', 'clustal')
constructor = DistanceTreeConstructor()
tot = 0
for ide, count in motifs:
tot += count
print('Found ' + str(tot) + ' occurences of "' + motif + '" in ' + upper)
print(len(motifs))
break
#print (motifs)
quit()
call(
'clustalo -i ../scripts/output/unaligned.fa -o phyAlign.clu --force --outfmt=clu',
shell=True)
AlignIO.convert('phyAlign.clu', 'clustal', 'phyAlign.phy', 'phylip-relaxed')
cmdline = PhymlCommandline(input='phyAlign.phy',
alpha='e',
bootstrap=1,
sequential=False)
call(str(cmdline), shell=True)
my_tree = Phylo.read("phyAlign.phy_phyml_tree.txt", "newick")
Phylo.draw(my_tree, show_confidence=False)
quit()
seqs = [
'MANNNSDRQGLEPRVIRTLGSQALSGPSISNRTSSSE',
'ANPHFSKNVKEAMIKTASPTPLSTPIYRIAQACDRCRSKKTRCDGKRPQCSQCAAVGFECRISDKLLRKAYPKGYTESLEERVRELEAENKRLLALCDIKEQQISLVSQSRPQTSTDNTINGNFKHDLKDAPLNLSSTNIYLLNQTVNKQLQNGKMDGDNSGSAMSPLGAPPPPPHKDHLCDGVSCTNHLHVKPTSTSLNDPTAISFEQDEAPGLPAVKALKSMTTHQRSTQLATLVSLSIPRSTEEILFIPQLLTRIRQIFGFNSKQCLYTVSLLSSLKNRLPAPRLLAPSTSTKLKEKDEDK',
'KLDDDSAFVKRFQSTNLSEFVDLKKFLISLKFNINSFSKQSEKPANDQDDELLSLTEIKELLHLFFKFWSNQVPILNNDHFLIYFNNFVEVVKHLSTENLETNNTTKSTVTTNHEIFALKLLMMLQMGLLVKIKMEKIKYTVPKNPKAKYARLMAYYHQLSLIIPKNPYFLNMSTTSLPSLQLLSLASFYYLNVGDISAIYGVRGRIVSMAQQLRLHRCPSAVLSVHSNPVLQKFEQSERRLLFWAIYYVDVFASLQLGVPRLLKDFDIECALPISDVEYKDQLSMENEKADKKAKKIQLQGQVSSFSLQIIRFAKILGNILDSIFKRGMMDERITSEVALVHENALDNWRNQLPEMYYFQITVNGTVNLDEIRATNQRNTETKFDKKDIILFEKKILLLFYFLAKSMIHLPVIATKPLPKNVDNATKKKQSMFNNDSKGATNQDHMILDVDMTSPAIRTSSSYIILQQATNATLTIFQAINSMYLPLPLNVSRTLIRFSLLCARGSLEYTKGGALFLDNKNLLLDTIKDIENDRLLDLPGIASWHTLKLFDMSINLLLKAPNVKVERLDKFLEKKLNYYNRLMGLPPATTTSLKPLFGSQSKNSLENRQRTPNVKRENPEHEYLYGNDSNNNNNSEAGHSPMTNTTNGNK'
]
#r = requests.post('https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi?', data=(('db','cdd'), ('queries',seq), ('tdata','hits')))
assert os.path.isfile(clustalw_exe), "Clustal W executable missing"
stdout, stderr = cline()
# %% convert alignment file from fasta from muscle in Poseidon to phyli-relaxed
msaFile = "/muscleAlignmentCoralSeq.msa"
outFile = "/muscleAlignmentCoralSeq.phy"
import os
path = os.getcwd()
#path = "/Users/kgrabb/Documents/2018.05CoralLarvae/Genomes/Poseidon/blastResults/v2"
print(path)
print(path + msaFile)
inputFile = path + msaFile
outputFile = path + outFile
viewFile = pd.read_csv(inputFile)
print(viewFile.head(5))
AlignIO.convert(inputFile, "fasta", outputFile, "phylip-relaxed")
# %% use PhyML. feed in phy alignment with the command line wrapper
from Bio.Phylo.Applications import PhymlCommandline
cmdline = PhymlCommandline(input=outputFile,
datatype="aa",
model="WAG",
alpha="e",
bootstrap=100)
out_log, err_log = cmdline()
# %%
# this command writes a file in a fromat suitable for Phyml (software for molecular phylogeny)
AlignIO.write(alignment[:, 60:300], "phyml.phy", "phylip-relaxed")
# Some general alignment analysis tools are available in module Bio.Align as AlignInfo
summary_align = AlignInfo.SummaryInfo(alignment)
consensus = summary_align.gap_consensus()
print(consensus)
#
# if we have phyml locally, we can run it with this code
# otherwise, we can run it online http://atgc.lirmm.fr/phyml
from Bio.Phylo.Applications import PhymlCommandline
cmdline = PhymlCommandline(input='phyml.phy',
datatype='aa',
model='LG',
alpha='e',
bootstrap=100)
# module for delaing phylogenetic trees
from Bio import Phylo
# loading file into an object “tree”
tree = Phylo.read("./data/phyml_phy_phyml_tree.txt", "newick")
# text visualization
Phylo.draw_ascii(tree)
#
# matplotlib visualization
# get_ipython().magic('matplotlib notebook')
Phylo.draw(tree)
plt.show(block=True)
def build_tree(msa_file, original, file_name="tree", bootstrap=10):
"""
Build a phylogenetic tree based on a multiple sequence alignment.
http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc217
PhyML site: http://www.atgc-montpellier.fr/
"New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies:
Assessing the Performance of PhyML 3.0." Guindon S., Dufayard J.F.,
Lefort V., Anisimova M., Hordijk W., Gascuel O. Systematic Biology,
59(3):307-21, 2010.
Color based on novelty
"""
# See https://biopython.org/wiki/Phylo for general code and settings
# Convert to phyllip format
tree_file = file_name # for convenience
AlignIO.convert(msa_file, "clustal", tree_file, "phylip-relaxed",
alphabet=IUPAC.protein)
# NOTE: make sure file name is "phyml"
PhyML = PhymlCommandline("./PhyML")
PhyML.input = tree_file
PhyML.datatype = 'aa' # Specify that amino acids are being input
PhyML.model = 'LG' # Amino acid substitution matrix
PhyML.alpha = 'e'
# non-parametric bootstrap relplicates; 100 is point of dimiishing returns
PhyML.bootstrap = bootstrap
# Run tree generation, print success/failure
print("Building distance tree from multiple sequence alignment...\n")
stdout, stderr = PhyML()
print(stdout + stderr)
print(f"Newick tree saved as {tree_file + '_phyml_tree.txt'}")
# Read in tree file, convert to XML (to be able to add color, etc.)
tree = Phylo.read(tree_file + "_phyml_tree.txt", "newick")
tree = tree.as_phyloxml()
# Stylize the tree
# Colorblind-safe colors can be checked with ColorOracle: http://colororacle.org/
for clade in tree.find_clades():
# Bold lines
clade.width = 3
# Red if known gene or false positive
if str(clade.name).startswith("gi|"):
clade.color = "#e4002b"
# Blue for originally searched gene
elif clade.name == original.id:
clade.color = "#006db6"
# Black for comparitor nodes
elif clade.name is not None and not clade.color:
clade.color = "#000000"
# Gray for non-terminal nodes
elif not clade.name:
clade.color = "#63666a"
# Green for novel genes
if str(clade.name).endswith("***"):
clade.color = "#00bf71"
# Configure plot. Image size determined based on number of nodes
tree_len = len(tree.get_terminals())
plt.rc("font", size=18) # Bigger font for easier reading
fig = plt.figure(figsize=(1.6 * tree_len, tree_len), dpi=300)
axes = fig.add_subplot(1, 1, 1)
Phylo.draw(tree, axes=axes, do_show=False)
# Save white background image
fig.savefig(f"{tree_file}.png", format='png',
bbox_inches='tight', dpi=300)
# Save transparent image
fig.savefig(f"{tree_file}_transparent.png", format='png',
bbox_inches='tight', dpi=300, transparent=True)
print(f"Tree images saved as {tree_file + '.png'} "
f"and {tree_file + '_transparent.png'} to {os.getcwd()}\n")