def build(self, root='midpoint', raxml=True, raxml_time_limit=0.5):
from Bio import Phylo, AlignIO
import subprocess, glob, shutil
make_dir(self.run_dir)
os.chdir(self.run_dir)
for seq in self.aln: seq.name=seq.id
AlignIO.write(self.aln, 'temp.fasta', 'fasta')
tree_cmd = ["fasttree"]
if self.nuc: tree_cmd.append("-nt")
tree_cmd.append("temp.fasta")
tree_cmd.append(">")
tree_cmd.append("initial_tree.newick")
os.system(" ".join(tree_cmd))
out_fname = "tree_infer.newick"
if raxml:
if raxml_time_limit>0:
tmp_tree = Phylo.read('initial_tree.newick','newick')
resolve_iter = 0
resolve_polytomies(tmp_tree)
while (not tmp_tree.is_bifurcating()) and (resolve_iter<10):
resolve_iter+=1
resolve_polytomies(tmp_tree)
Phylo.write(tmp_tree,'initial_tree.newick', 'newick')
AlignIO.write(self.aln,"temp.phyx", "phylip-relaxed")
print( "RAxML tree optimization with time limit", raxml_time_limit, "hours")
# using exec to be able to kill process
end_time = time.time() + int(raxml_time_limit*3600)
process = subprocess.Popen("exec raxml -f d -T " + str(self.nthreads) + " -j -s temp.phyx -n topology -c 25 -m GTRCAT -p 344312987 -t initial_tree.newick", shell=True)
while (time.time() < end_time):
if os.path.isfile('RAxML_result.topology'):
break
time.sleep(10)
process.terminate()
checkpoint_files = glob.glob("RAxML_checkpoint*")
if os.path.isfile('RAxML_result.topology'):
checkpoint_files.append('RAxML_result.topology')
if len(checkpoint_files) > 0:
last_tree_file = checkpoint_files[-1]
shutil.copy(last_tree_file, 'raxml_tree.newick')
else:
shutil.copy("initial_tree.newick", 'raxml_tree.newick')
else:
shutil.copy("initial_tree.newick", 'raxml_tree.newick')
try:
print("RAxML branch length optimization")
os.system("raxml -f e -T " + str(self.nthreads) + " -s temp.phyx -n branches -c 25 -m GTRGAMMA -p 344312987 -t raxml_tree.newick")
shutil.copy('RAxML_result.branches', out_fname)
except:
print("RAxML branch length optimization failed")
shutil.copy('raxml_tree.newick', out_fname)
else:
shutil.copy('initial_tree.newick', out_fname)
self.tt_from_file(out_fname, root)
os.chdir('..')
remove_dir(self.run_dir)
self.is_timetree=False
def convert_boottrees(fname_trees):
out_fnames = []
for i, tree in enumerate(Phylo.parse(fname_trees, "newick")):
fname_tree = "%s.codeml-%d" % (fname_trees, i)
Phylo.write(tree, fname_tree, "newick")
out_fnames.append(fname_tree)
return out_fnames
def test_root_with_outgroup(self):
"""Tree.root_with_outgroup: reroot at a given clade."""
# On a large realistic tree, at a deep internal node
tree = Phylo.read(EX_APAF, 'phyloxml')
orig_num_tips = len(tree.get_terminals())
orig_tree_len = tree.total_branch_length()
tree.root_with_outgroup('19_NEMVE', '20_NEMVE')
self.assertEqual(orig_num_tips, len(tree.get_terminals()))
self.assertAlmostEqual(orig_tree_len, tree.total_branch_length())
# Now, at an external node
tree.root_with_outgroup('1_BRAFL')
self.assertEqual(orig_num_tips, len(tree.get_terminals()))
self.assertAlmostEqual(orig_tree_len, tree.total_branch_length())
# Specifying outgroup branch length mustn't change the total tree size
tree.root_with_outgroup('2_BRAFL', outgroup_branch_length=0.5)
self.assertEqual(orig_num_tips, len(tree.get_terminals()))
self.assertAlmostEqual(orig_tree_len, tree.total_branch_length())
tree.root_with_outgroup('36_BRAFL', '37_BRAFL',
outgroup_branch_length=0.5)
self.assertEqual(orig_num_tips, len(tree.get_terminals()))
self.assertAlmostEqual(orig_tree_len, tree.total_branch_length())
# On small contrived trees, testing edge cases
for small_nwk in (
'(A,B,(C,D));',
'((E,F),((G,H)),(I,J));',
'((Q,R),(S,T),(U,V));',
'(X,Y);',
):
tree = Phylo.read(StringIO(small_nwk), 'newick')
orig_tree_len = tree.total_branch_length()
for node in list(tree.find_clades()):
tree.root_with_outgroup(node)
self.assertAlmostEqual(orig_tree_len,
tree.total_branch_length())
def initUI(self):
#field for drawing Ascii tree
self.textEdit = QtGui.QTextEdit()
self.textEdit.setReadOnly(True)
self.textEdit.setFontFamily('Courier')
self.textEdit.setWordWrapMode(True)
#self.textEdit.setStyleSheet('')
# layout
self.layout = QtGui.QVBoxLayout(self)
self.layout.addWidget(self.textEdit)
self.setLayout(self.layout)
#print tree
self.tmpf = open('/tmp/ascii.txt', 'w')
Phylo.draw_ascii(self.tree, self.tmpf)
self.tmpf = open('/tmp/ascii.txt', 'r')
with self.tmpf:
self.data = self.tmpf.read()
self.textEdit.setText(self.data)
self.setGeometry(200, 200, 700, 400)
self.setWindowTitle('Tekstowe wyswietlanie')
self.show()
def test_newick_read_scinot(self):
"""Parse Newick branch lengths in scientific notation."""
tree = Phylo.read(StringIO("(foo:1e-1,bar:0.1)"), 'newick')
clade_a = tree.clade[0]
self.assertEqual(clade_a.name, 'foo')
self.assertAlmostEqual(clade_a.branch_length, 0.1)
"""Additional tests to check correct parsing"""
tree = Phylo.read(StringIO("(A:1, B:-2, (C:3, D:4):-2)"),'newick')
self.assertEqual(tree.distance('A'),1)
self.assertEqual(tree.distance('B'),-2)
self.assertEqual(tree.distance('C'),1)
self.assertEqual(tree.distance('D'),2)
tree = Phylo.read(StringIO("((A:1, B:-2):-5, (C:3, D:4):-2)"),'newick')
self.assertEqual(tree.distance('A'),-4)
self.assertEqual(tree.distance('B'),-7)
self.assertEqual(tree.distance('C'),1)
self.assertEqual(tree.distance('D'),2)
tree = Phylo.read(StringIO("((:1, B:-2):-5, (C:3, D:4):-2)"),'newick')
distances = {-4.0:1,-7.0:1,1:1,2:1}
for x in tree.get_terminals():
entry = int(tree.distance(x))
distances[entry] -= distances[entry]
self.assertEqual(distances[entry],0)
tree = Phylo.read(StringIO("((:\n1\n,\n B:-2):-5, (C:3, D:4):-2);"),'newick')
distances = {-4.0:1,-7.0:1,1:1,2:1}
for x in tree.get_terminals():
entry = int(tree.distance(x))
distances[entry] -= distances[entry]
self.assertEqual(distances[entry],0)
def test_draw_ascii(self):
"""Tree to Graph conversion, if networkx is available."""
handle = StringIO()
tree = Phylo.read(EX_APAF, 'phyloxml')
Phylo.draw_ascii(tree, file=handle)
Phylo.draw_ascii(tree, file=handle, column_width=120)
handle.close()
def test_convert_phyloxml_filename(self):
"""Write phyloxml to a given filename."""
trees = Phylo.parse("PhyloXML/phyloxml_examples.xml", "phyloxml")
tmp_filename = tempfile.mktemp()
count = Phylo.write(trees, tmp_filename, "phyloxml")
os.remove(tmp_filename)
self.assertEqual(13, count)
def reroot_tree_with_outgroup(tree_name, outgroups):
clade_outgroups = GubbinsCommon.get_monophyletic_outgroup(tree_name, outgroups)
outgroups = [{"name": taxon_name} for taxon_name in clade_outgroups]
tree = Phylo.read(tree_name, "newick")
tree.root_with_outgroup(*outgroups)
Phylo.write(tree, tree_name, "newick")
tree = dendropy.Tree.get_from_path(tree_name, "newick", preserve_underscores=True)
tree.deroot()
tree.update_bipartitions()
output_tree_string = tree.as_string(
schema="newick",
suppress_leaf_taxon_labels=False,
suppress_leaf_node_labels=True,
suppress_internal_taxon_labels=False,
suppress_internal_node_labels=False,
suppress_rooting=True,
suppress_edge_lengths=False,
unquoted_underscores=True,
preserve_spaces=False,
store_tree_weights=False,
suppress_annotations=True,
annotations_as_nhx=False,
suppress_item_comments=True,
node_label_element_separator=" ",
)
with open(tree_name, "w+") as output_file:
output_file.write(output_tree_string.replace("'", ""))
output_file.closed
def phylo2newick(self, t):
"""
Convert Phylo into Newick tree string.
"""
output = StringIO()
Phylo.write(t, output, "newick")
return output.getvalue()
def make_tree_figure(wanted_seqs, trop_dict, tree_file):
mat_data = get_pairwise_distances(wanted_seqs, tree_file = tree_file)
tree = Phylo.read(open(tree_file), 'newick')
net = Phylo.to_networkx(tree)
node_mapping = {}
clade = 1
for node in net.nodes():
if node.name is None:
node_mapping[node] = 'Clade-%i' % clade
clade += 1
else:
node_mapping[node] = node.name
new_net = networkx.relabel_nodes(net, node_mapping)
colors = []
for node in new_net.nodes():
if node.startswith('Clade'):
colors.append('w')
elif trop_dict[node]:
colors.append('g')
elif not trop_dict[node]:
colors.append('r')
else:
print node
#print colors, len(colors), len(new_net.nodes())
pos = networkx.graphviz_layout(new_net, 'twopi')
networkx.draw_networkx(new_net, pos, with_labels = False, node_color = colors)
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 genTaxTree(resolver, namesdict, logger, taxonomy=None, draw=False):
"""Return Phylo from TaxonNamesResolver class."""
ranks = resolver.retrieve('classification_path_ranks')
qnames = resolver.retrieve('query_name')
lineages = resolver.retrieve('classification_path')
# replace ' ' with '_' for taxon tree
qnames = [re.sub("\s", "_", e) for e in qnames]
resolved_names_bool = [e in namesdict.keys() for e in qnames]
ranks = [ranks[ei] for ei, e in enumerate(resolved_names_bool) if e]
lineages = [lineages[ei] for ei, e in enumerate(resolved_names_bool) if e]
# identify unresolved names
unresolved_names = [qnames[ei] for ei, e in enumerate(resolved_names_bool)
if not e]
idents = [qnames[ei] for ei, e in enumerate(resolved_names_bool) if e]
statement = "Unresolved names: "
for each in unresolved_names:
statement += " " + each
logger.debug(statement)
# make taxdict
taxdict = TaxDict(idents=idents, ranks=ranks, lineages=lineages,
taxonomy=taxonomy)
# make treestring
treestring = taxTree(taxdict)
if not taxonomy:
d = 22 # default_taxonomy + 1 in tnr
else:
d = len(taxonomy) + 1
# add outgroup
treestring = '({0},outgroup:{1});'.format(treestring[:-1], float(d))
tree = Phylo.read(StringIO(treestring), "newick")
if draw:
Phylo.draw_ascii(tree)
return tree
def draw_tree(tree, node_label = node_label_func, branch_label = lambda x:None,
cmap = cm.jet, axes = None, cb = True):
'''
plots a tree on an empty canvas including a scalebar of length 0.005
'''
import matplotlib.pyplot as plt
from Bio import Phylo
if axes is None:
fig = plt.figure(figsize = (8,6))
axes = plt.subplot(111)
Phylo.draw(tree, label_func = node_label,
show_confidence = False,branch_labels = branch_label, axes=axes)
axes.axis('off')
xlimits = axes.get_xlim()
ylimits = axes.get_ylim()
x0 = xlimits[0]+(xlimits[1]-xlimits[0])*0.05
x1 = x0+0.005
y0 = ylimits[0]+(ylimits[1]-ylimits[0])*0.05
plt.plot([x0,x1], [y0,y0], lw=2, c='k')
plt.text(x0+0.0025, y0+(ylimits[1]-y0)*0.01, '0.005', ha='center')
# fake a colorbar
if cb:
sm = plt.cm.ScalarMappable(cmap=cmap, norm=plt.Normalize(vmin=0, vmax=100))
sm._A = []
cbar = plt.colorbar(sm, ticks=[0,100], shrink=0.5, aspect=10,pad=-0.05)
cbar.set_ticklabels(['worst','best'])
plt.draw()
return axes
def get_tree(tree_file, name_tree):
tree = Phylo.read( open(tree_file, 'r'), "newick")
tree_name = Phylo.read( open(name_tree, 'r'), "newick")
#set node number for nonterminal nodes and specify root node
numInternalNode = 0
for clade in tree.get_nonterminals():
clade.name = 'N' + str(numInternalNode)
clade.branch_length = clade.confidence
numInternalNode += 1
for clade_iter in range(len(tree.get_terminals())):
clade = tree.get_terminals()[clade_iter]
clade.branch_length = clade.confidence
clade.name = tree_name.get_terminals()[clade_iter].name
tree_phy = tree.as_phyloxml(rooted = 'True')
tree_nx = Phylo.to_networkx(tree_phy)
triples = ((u.name, v.name, d['weight']) for (u, v, d) in tree_nx.edges(data = True)) # data = True to have the blen as 'weight'
T = nx.DiGraph()
edge_to_blen = {}
for va, vb, blen in triples:
edge = (va, vb)
T.add_edge(*edge)
edge_to_blen[edge] = blen
edge_list = edge_to_blen.keys()
edge_list.sort(key = lambda node: int(node[0][1:]))
return edge_to_blen, edge_list
def measure_D_net(G,qmod,qcon):
D_net_dic = {}
D_net_ret = {}
D_net = []
for u in G: D_net_dic[u] = {}
for u in sorted(G):
key1 = "Taxon" + str(u)
tmp_row = []
for v in sorted(G):
key2 = "Taxon" + str(v)
if u < v: continue
D_net_dic[u][v] = 1.0 - G.dmc_likelihood(u,v,qmod,qcon)
tmp_row.append(D_net_dic[u][v])
print D_net_dic[u][v],
D_net.append(tmp_row)
print '\n'
names = []
for u in G: names.append('Taxon'+str(u))
print names
print D_net
D_net_final = _DistanceMatrix(names,D_net)
#print D_net_final.names
constructor = DistanceTreeConstructor()
tree_dmc = constructor.upgma(D_net_final)
#print tree_dmc
Phylo.write(tree_dmc,'ph_dmc.nre','newick')
return D_net_final
def distance_matrix(cls, cluster_list):
print cluster_list
dists = Distance.objects.filter(rep_accnum1__in=cluster_list, rep_accnum2__in=cluster_list)
distance_pairs = {g.rep_accnum1 + '_' + g.rep_accnum2: g.distance for g in dists.all()}
matrix = []
for i in range(0,len(cluster_list)):
matrix_iteration = []
for j in range(0,i+1):
if i == j:
matrix_iteration.append(0)
elif cluster_list[i] + '_' + cluster_list[j] in distance_pairs:
matrix_iteration.append(distance_pairs[cluster_list[i] + '_' + cluster_list[j]])
elif cluster_list[j] + '_' + cluster_list[i] in distance_pairs:
matrix_iteration.append(distance_pairs[cluster_list[j] + '_' + cluster_list[i]])
else:
raise("Error, can't find pair!")
matrix.append(matrix_iteration)
#print matrix_iteration
cluster_list = [s.encode('ascii', 'ignore') for s in cluster_list]
matrix_obj = _DistanceMatrix(names=cluster_list, matrix=matrix)
constructor = DistanceTreeConstructor()
tree = constructor.nj(matrix_obj)
tree.ladderize()
#Phylo.draw_ascii(tree)
output = StringIO.StringIO()
Phylo.write(tree, output, 'newick')
tree_str = output.getvalue()
#print tree_str
return tree_str
def rootTree(f, root,output):
tree = Phylo.read(f,'newick')
if ',' in root:
taxa = root.split(',')
root = tree.common_ancestor(taxa)
tree.root_with_outgroup(root)
Phylo.write(tree,output,'newick')
def make_trees(self, force=False):
for i, (root, _, files) in enumerate(os.walk(self.seed_directory)):
if i==0: #skip base path
continue
hist_type = os.path.basename(root)
print "Creating tree for", hist_type
final_tree_name = os.path.join(self.trees_path, "{}_no_features.xml".format(hist_type))
if not force and os.path.isfile(final_tree_name):
continue
if not os.path.exists(self.trees_path):
os.makedirs(self.trees_path)
#Combine all variants for a core histone type into one unaligned fasta file
combined_seed_file = os.path.join(self.trees_path, "{}.fasta".format(hist_type))
combined_seed_aligned = os.path.join(self.trees_path, "{}_aligned.fasta".format(hist_type))
with open(combined_seed_file, "w") as combined_seed:
for seed in files:
if not seed.endswith(".fasta"): continue
for s in SeqIO.parse(os.path.join(self.seed_directory, hist_type, seed), "fasta"):
s.seq = s.seq.ungap("-")
SeqIO.write(s, combined_seed, "fasta")
#Create trees and convert them to phyloxml
tree = os.path.join(self.trees_path, "{}_aligned.ph".format(hist_type))
subprocess.call(["muscle", "-in", combined_seed_file, '-out', combined_seed_aligned])
print " ".join(["clustalw2", "-infile={}".format(combined_seed_aligned), "-outfile={}".format(final_tree_name), '-tree'])
subprocess.call(["clustalw2", "-infile={}".format(combined_seed_aligned), "-outfile={}".format(final_tree_name), '-tree'])
Phylo.convert(tree, 'newick', final_tree_name, 'phyloxml')
def get_tree(newicktree):
tree = Phylo.read( newicktree, "newick")
#set node number for nonterminal nodes and specify root node
numInternalNode = 0
for clade in tree.get_nonterminals():
clade.name = 'N' + str(numInternalNode)
numInternalNode += 1
tree_phy = tree.as_phyloxml(rooted = 'True')
tree_nx = Phylo.to_networkx(tree_phy)
triples = ((u.name, v.name, d['weight']) for (u, v, d) in tree_nx.edges(data = True)) # data = True to have the blen as 'weight'
T = nx.DiGraph()
edge_to_blen = {}
for va, vb, blen in triples:
edge = (va, vb)
T.add_edge(*edge)
edge_to_blen[edge] = blen
# Now assign node_to_num
leaves = set(v for v, degree in T.degree().items() if degree == 1)
internal_nodes = set(list(T)).difference(leaves)
node_names = list(internal_nodes) + list(leaves)
# Prepare for generating self.tree so that it has same order as the self.x_process
nEdge = len(edge_to_blen) # number of edges
l = nEdge / 2 + 1 # number of leaves
k = l - 1 # number of internal nodes. The notation here is inconsistent with Alex's for trying to match my notes.
leaf_branch = [edge for edge in edge_to_blen.keys() if edge[0][0] == 'N' and str.isdigit(edge[0][1:]) and not str.isdigit(edge[1][1:])]
out_group_branch = [edge for edge in leaf_branch if edge[0] == 'N0' and not str.isdigit(edge[1][1:])] [0]
internal_branch = [x for x in edge_to_blen.keys() if not x in leaf_branch]
assert(len(internal_branch) == k-1) # check if number of internal branch is one less than number of internal nodes
return list(leaves), out_group_branch
def write_clusters(seqfname, tree, clusters, unclustered):
"""Write output files: clusters & unique as FASTA, tree as phyloXML."""
is_aln = seqfname.endswith('.aln')
seq_idx = SeqIO.to_dict(SeqIO.parse(seqfname,
'clustal' if is_aln else 'fasta'))
def write_cluster(cluster, fname):
"""Write the sequences of cluster tips to a FASTA file."""
records = [seq_idx[seqid] for seqid in sorted(cluster)]
with open(fname, 'w+') as handle:
for rec in records:
write_fasta(rec, handle, do_ungap=is_aln)
logging.info("Wrote %s (%d sequences)", fname, len(records))
colors = [BranchColor(*map(lambda x: int(x*255), rgb))
for rgb in ColorSpiral().get_colors(len(clusters))]
for i, item in enumerate(sorted(clusters.iteritems(), reverse=True,
key=lambda kv: len(kv[1]))):
clade, cluster = item
write_cluster(cluster, os.path.basename(seqfname) + '.' + str(i))
clade.color = colors[i]
clade.width = 2
if unclustered:
write_cluster(unclustered, os.path.basename(seqfname) + '.Unique')
treefname = os.path.basename(seqfname) + '.xml'
Phylo.write(tree, treefname, 'phyloxml')
logging.info("Wrote %s", treefname)
def plot_tree(tree): from Bio import Phylo from tree_util import to_Biopython, color_BioTree_by_attribute btree = to_Biopython(tree) color_BioTree_by_attribute(btree,"cHI", transform = lambda x:x) Phylo.draw(btree, label_func = lambda x: 'X' if x.serum else '' if x.HI_info else '', show_confidence= False) #, branch_labels = lambda x:x.mutations)
def serialize_trees(self, tree_uri='', format='newick', trees=None, handle=None):
'''Retrieve trees serialized to any format supported by Biopython.
Current options include 'newick', 'nexus', 'phyloxml', 'nexml', and 'cdao'
Example:
>>> treestore.serialize_trees('http://www.example.org/test/')
'''
if handle: s = handle
else: s = StringIO()
if tree_uri: tree_uri = self.uri_from_id(tree_uri)
if trees is None:
trees = [(x for x in self.get_trees(tree_uri)).next()]
if not trees:
raise Exception('Tree to be serialized not found.')
if format == 'cdao':
bp.write(trees, s, format, tree_uri=tree_uri)
elif format == 'ascii':
bp._utils.draw_ascii((i for i in trees).next(), file=s)
else:
bp.write(trees, s, format)
if handle: return
return s.getvalue()
def generate_new_files(fname) :
# to get gene names that slr can handle (short enough)
newfname = fname.replace(".", "_.")
# generate a fasta file with new ids
d = {}
sequences = []
runningids = 1
for record in SeqIO.parse(fname, 'fasta') :
d[record.id] = "flyg%s" % runningids
record.id = d[record.id]
record.name = ""
record.description = ""
sequences.append(record)
runningids += 1
SeqIO.write(sequences, newfname, "fasta")
if not RUN_RAXML :
# generate a treefile with new ids
treefile = fname.replace("fasta", "tree")
newtreefile = newfname.replace("fasta", "tree")
tree = Phylo.read(treefile, 'newick')
for node in tree.get_terminals():
node.name = d[node.name]
Phylo.write(tree, newtreefile, 'newick')
return newfname
def GetExec():
Recs = os.listdir(os.getcwd())
newList=[]
j = 0
listdata=dict()
k = 0
while k < len(Recs):
(name, ext) = os.path.splitext(Recs[k])
if len(ext)>3 and ext[0:4]=='.dnd':
tree = Phylo.read(Recs[k], "newick")
tree.rooted = True
newList.append([tree,'ok'])
listdata[j] = j,str(Recs[k])
j+=1
elif len(ext)>3 and ext[0:4]=='.xml':
tree = Phylo.read(Recs[k], "phyloxml")
tree.rooted = True
newList.append([tree,'ok'])
listdata[j] = j,str(Recs[k])
j+=1
k += 1
return [newList,listdata]
def reroot_tree_with_outgroup(tree_name, outgroups):
clade_outgroups = GubbinsCommon.get_monophyletic_outgroup(tree_name, outgroups)
outgroups = [{'name': taxon_name} for taxon_name in clade_outgroups]
tree = Phylo.read(tree_name, 'newick')
tree.root_with_outgroup(*outgroups)
Phylo.write(tree, tree_name, 'newick')
tree = dendropy.Tree.get_from_path(tree_name, 'newick',
preserve_underscores=True)
tree.deroot()
tree.update_splits()
output_tree_string = tree.as_string(
'newick',
taxon_set=None,
suppress_leaf_taxon_labels=False,
suppress_leaf_node_labels=True,
suppress_internal_taxon_labels=False,
suppress_internal_node_labels=False,
suppress_rooting=True,
suppress_edge_lengths=False,
unquoted_underscores=True,
preserve_spaces=False,
store_tree_weights=False,
suppress_annotations=True,
annotations_as_nhx=False,
suppress_item_comments=True,
node_label_element_separator=' ',
node_label_compose_func=None
)
output_file = open(tree_name, 'w+')
output_file.write(output_tree_string.replace('\'', ''))
output_file.closed
def showMatplotlibTreeWindow(self):
if self.chosenFileName == '':
self.showOpenFileDialog()
if self.tree != 0:
self.tree.root.color = '#808080'
Phylo.draw(self.tree, branch_labels = lambda c: c.branch_length)
def drawConsensusTreeBioNexus(self):
if self.path1 != '' and self.path2 != '':
#get files extensions
self.fileExtension1 = (os.path.splitext(self.path1)[1])[1:]
self.fileExtension2 = (os.path.splitext(self.path2)[1])[1:]
#open tree files
self.trees = []
#first tree
self.f = open(self.path1, 'r')
self.tree1 = Trees.Tree(self.f.read())
self.trees.append(self.tree1)
self.f.close()
#second tree
self.f = open(self.path2, 'r')
self.tree2 = Trees.Tree(self.f.read())
self.trees.append(self.tree2)
self.f.close()
#generate consensus tree
self.consensus_tree = Trees.consensus(self.trees)
#draw tree
self.handle = StringIO(self.consensus_tree.to_string(plain_newick=True))
self.tree = Phylo.read(self.handle, 'newick')
self.tree.root.color = '#808080'
Phylo.draw(self.tree)
def main():
args = parse_args()
tree = Phylo.read(args.input_file, args.input_type)
tree = tree.as_phyloxml()
if args.zchemat_kolorowania == 'eba':
get_colors_and_groups = get_eukariota_group
elif args.zchemat_kolorowania == 'fungi':
get_colors_and_groups = get_fungus_groups
elif args.zchemat_kolorowania == 'opisto':
get_colors_and_groups = get_opisto_groups
for branch in tree.get_nonterminals():
try:
branch.confidence.type = "bootstrap"
branch.name = branch.confidence.value
except AttributeError:
pass
colors, list_of_groups = get_colors_and_groups()
for leaf in tree.get_terminals():
name = leaf.name.strip()
try:
index = name.index(".")
name = name[index + 3:]
except:
name = "_".join(name.split("_")[-2:])
for color, members in zip(colors, list_of_groups):
if name in members:
leaf.color = color
Phylo.write(tree, args.output_file, "phyloxml")
def drawConsensusTreeDendropy(self):
if self.path1 != '' and self.path2 != '':
#get files extensions
self.fileExtension1 = (os.path.splitext(self.path1)[1])[1:]
self.fileExtension2 = (os.path.splitext(self.path2)[1])[1:]
#open tree files
self.tree1 = dendropy.Tree.get_from_path(self.path1, self.fileExtension1)
self.tree2 = dendropy.Tree.get_from_path(self.path2, self.fileExtension2)
#prepare tree list
self.trees = dendropy.TreeList()
self.trees.append(self.tree1)
self.trees.append(self.tree2)
#generate consensus tree
self.consensus_tree = self.trees.consensus(min_freq=0.2)
#draw tree
self.handle = StringIO(self.consensus_tree._as_newick_string())
# POPRAWIONY BLAD Z KONWERSJA DO BUFORA
#self.handle = StringIO(self.consensus_tree.to_string(plain_newick=True))
self.tree = Phylo.read(self.handle, 'newick')
self.tree.root.color = '#808080'
Phylo.draw(self.tree)
def write ( self, phytrees_file ) :
"""
Save all trees stored at the PhyTrees object in the 'phytrees_file' (in
newick format). A file with a detailed report of the trees will be
created replacing the extension of 'phytrees_file' by ".rep". If
'phytrees_file' contains a relative path, the current working directory
will be used to get the absolute path. If any file already exists, it
will be overwritten without warning.
Arguments :
phytrees_file ( string )
New PhyTrees tree file.
Raises :
IOError
If the path provided doesn't exist.
"""
data_filepath = get_abspath(phytrees_file)
report_filepath = os.path.splitext(data_filepath)[0] + '.rep'
# Generate a single string with all the report content
str_report = '\n'.join([' '.join(x) for x in self._report])
# Write all the information in the PhyTrees files
try :
Phylo.write(self.data, data_filepath, 'newick')
with open(report_filepath, 'w') as report_file :
report_file.write('Num. trees: {:d}\nHistory:\n' \
'{:s}'.format(len(self), str_report))
except IOError :
raise
except :
if ( os.path.isfile(data_filepath) ) :
os.remove(data_filepath)
if ( os.path.isfile(report_filepath) ) :
os.remove(report_filepath)
raise
confidences = []
for c in clade.clades:
#if not c.confidence is None:
confidences.append(c.confidence)
confidences += parse(c)
return confidences
texDir = '/Users/ahenschel/Github/FreqRT/ManuscriptBootstrapping/Tables'
nwkFiles = [n for n in sys.argv[1:] if n.endswith('.nwk')]
if not nwkFiles:
print("Provide newick files through command line, e.g.: Data/*.nwk")
else:
data = []
for nwkFile in nwkFiles:
tree = Phylo.read(nwkFile, format='newick')
rec = infoFromName(nwkFile)
confidences = np.array(parse(tree.root), dtype=np.float)
nrNans = np.sum(np.isnan(confidences))
nrNansPct = nrNans / len(confidences)
rec += (np.nanmean(confidences), np.nanmedian(confidences), nrNans,
nrNansPct)
data.append(rec)
if True:
plt.clf()
Phylo.draw(tree)
plt.savefig(f'{nwkFile[:-4]}.svg', figsize=(18, 12), dpi=300)
plt.close()
#input("Press enter")
#break
columns = 'Loci NrLoci Thresh Build Pops AvgConf MedConf Miss MissPct'.split(
def __init__(self, newick_tree):
self.tree = Phylo.read(
newick_tree, "newick", values_are_confidence=True, rooted=True
)
def test_get_score(self):
aln = AlignIO.read("TreeConstruction/msa.phy", "phylip")
tree = Phylo.read("./TreeConstruction/upgma.tre", "newick")
scorer = ParsimonyScorer()
score = scorer.get_score(tree, aln)
self.assertEqual(score, 2 + 1 + 2 + 2 + 1 + 1 + 1 + 3)
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)
score = scorer.get_score(tree, aln)
self.assertEqual(score, 3.5 + 2.5 + 3.5 + 3.5 + 2.5 + 1 + 2.5 + 4.5)
alphabet = [
"A",
"C",
"D",
"E",
"F",
"G",
"H",
"I",
"K",
"L",
"M",
"N",
"P",
"Q",
"R",
"1",
"2",
"T",
"V",
"W",
"Y",
"*",
"-",
]
step_matrix = [
[0],
[2, 0],
[1, 2, 0],
[1, 2, 1, 0],
[2, 1, 2, 2, 0],
[1, 1, 1, 1, 2, 0],
[2, 2, 1, 2, 2, 2, 0],
[2, 2, 2, 2, 1, 2, 2, 0],
[2, 2, 2, 1, 2, 2, 2, 1, 0],
[2, 2, 2, 2, 1, 2, 1, 1, 2, 0],
[2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 0],
[2, 2, 1, 2, 2, 2, 1, 1, 1, 2, 2, 0],
[1, 2, 2, 2, 2, 2, 1, 2, 2, 1, 2, 2, 0],
[2, 2, 2, 1, 2, 2, 1, 2, 1, 1, 2, 2, 1, 0],
[2, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 1, 1, 0],
[1, 1, 2, 2, 1, 2, 2, 2, 2, 1, 2, 2, 1, 2, 2, 0],
[2, 1, 2, 2, 2, 1, 2, 1, 2, 2, 2, 1, 2, 2, 1, 2, 0],
[1, 2, 2, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1, 0],
[1, 2, 1, 1, 1, 1, 2, 1, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 0],
[2, 1, 2, 2, 2, 1, 2, 2, 2, 1, 2, 3, 2, 2, 1, 1, 2, 2, 2, 0],
[2, 1, 1, 2, 1, 2, 1, 2, 2, 2, 3, 1, 2, 2, 2, 1, 2, 2, 2, 2, 0],
[2, 1, 2, 1, 2, 1, 2, 2, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 1, 1, 0],
[
3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
3, 0
],
]
matrix = _Matrix(alphabet, step_matrix)
scorer = ParsimonyScorer(matrix)
score = scorer.get_score(tree, aln)
self.assertEqual(score, 3 + 1 + 3 + 3 + 2 + 1 + 2 + 5)
def readtrees(self):
return Phylo.parse(self.infile, 'newick')
def test_newick_read_scinot(self):
"""Parse Newick branch lengths in scientific notation."""
tree = Phylo.read(StringIO("(foo:1e-1,bar:0.1)"), 'newick')
clade_a = tree.clade[0]
self.assertEqual(clade_a.name, 'foo')
self.assertAlmostEqual(clade_a.branch_length, 0.1)
def test_newick_read_multiple(self):
"""Parse a Nexus file with multiple trees."""
trees = list(Phylo.parse(EX_NEXUS, 'nexus'))
self.assertEqual(len(trees), 3)
for tree in trees:
self.assertEqual(len(tree.get_terminals()), 9)
def setUp(self):
self.phylogenies = list(Phylo.parse(EX_PHYLO, 'phyloxml'))
def test_newick(self):
"""Read a Newick file with one tree."""
tree = Phylo.read(EX_NEWICK, 'newick')
self.assertEqual(len(tree.get_terminals()), 28)
print(err.decode("utf-8"))
print(p2_status)
f = open(sequence_ids_outfile, 'r')
sequence_ids_output_file = csv.reader(f)
sequence_header_list = {}
for entry in sequence_ids_output_file:
sequence_id = entry[0]
description = entry[1]
seq_type = entry[2]
sequence_header_list[sequence_id] = [description, seq_type]
f.close()
if (p2_status == 0):
best_tree = Phylo.read(mega_best_tree_infile, 'newick')
print(best_tree)
best_tree.root_with_outgroup(
{'name': 'b30065_LXYB01000004_Acholeplasma_laidlawii_PG8R10'})
best_tree.rooted = True
#Phylo.draw(best_tree)
#pylab.savefig(mega_tree_filename + '.png')
Phylo.write(best_tree, mega_tree_filename + '.nwk', 'newick')
Phylo.write(best_tree, mega_tree_filename + '.xml', 'phyloxml')
f_out = open(subgroups_tree_outfile, 'w')
for fasta_record in SeqIO.parse(subgroups_tree_file, "fasta"):
seq_id = fasta_record.id
if __name__ == "__main__":
options = get_options()
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import seaborn as sns
sns.set_style('white')
import os
import pandas as pd
import numpy as np
from Bio import Phylo
t = Phylo.read(options.tree, 'newick')
print ' Max distance to create better plots'
mdist = max([t.distance(t.root, x) for x in t.get_terminals()])
print ' Load roary'
roary = pd.read_table(options.spreadsheet, sep=',', low_memory=False)
print ' Set index (group name)'
roary.set_index('Gene', inplace=True)
print ' Find tagged genes'
if options.tag is not None:
if "Inference" in roary.columns:
roary_info = roary[["Inference"]].copy()
roary.drop(["Inference"], axis=1, inplace=True)
VF = roary_info[roary_info.applymap(
lambda x: options.tag.upper() in x.upper()).values].index
from Bio import Phylo
selgenes = ["rrs", "atpB"]
sgstat = {
"rrs": [1499, 18],
"psaB": [1790, 21],
"tufA": [1225, 13],
"atpB": [3510, 66],
"rpoB": [3765, 56]
}
#rnconv = { "p9" : "tufA", "p34" : "rpl19", "p4" : "psaB", "p6" : "atpB", "p2" : "rpoB" }
fig, ax = plt.subplots(1, len(selgenes), figsize=(40, 20), dpi=80)
for k in range(len(selgenes)):
gene = selgenes[k]
tree = Phylo.read("fragments_" + gene + ".nwk", 'newick')
matplotlib.rcParams["font.size"] = 28
matplotlib.rcParams["lines.linewidth"] = 3
leafs = tree.get_terminals(order="postorder")
bspnum = 0
spid = "bsponge"
labelconv = {
"p_salinaru": "Picocystis salinarum",
"myrmecia": "Myrmecia israeliensis",
"botyococcu": "Botryococcus braunii",
"coccomyxa": "Coccomyxa subellipsoidea",
"c_parasiti": "Choricystis parasitica",
"bsponge": "Sponge symbiont",
"h_reticala": "Hydrodictyon reticulatum",
"m_jurisii": "Mychonastes jurisii",
return colors['darkblue']
elif c.split(" ")[0] == "GR":
return colors['blue']
elif c.split(" ")[0] == "G":
return colors['seagreen']
elif c.split(" ")[0] == "GH":
return colors['green']
elif c.split(" ")[0] == "S":
return colors['lime']
elif c.split(" ")[0] == "O":
return colors['gold']
elif c.split(" ")[0] == "GV":
return colors['darkorange']
elif c.split(" ")[0] == "V":
return colors['tomato']
elif c.split(" ")[0] == "L":
return colors['red']
matplotlib.rc('font', size=30)
fig = plt.figure(figsize=(35, 25), dpi=100)
axes = fig.add_subplot(1, 1, 1)
Phylo.draw(tree,
axes=axes,
do_show=False,
label_func=labels,
label_colors=labels_col)
plt.axis('off')
plt.savefig("plots/tree3.svg", format="svg", transparent=True)
Phylo.draw_ascii(tree)
#Alinhamento multiplo e arvore filogenética
help(ClustalwCommandline)
cline = ClustalwCommandline(
"clustalw2",
infile=
"C:/Users/Zé Freitas/Desktop/Mestrado/Labs_Bioinf/Trabalho prático/scripts/Labs_Bioinf/Proibitina/Probitina_MA.fasta"
)
print(cline)
cline = MuscleCommandline(
input=
"C:/Users/Zé Freitas/Desktop/Mestrado/Labs_Bioinf/Trabalho prático/scripts/Labs_Bioinf/Proibitina/Proibitina_MA.fasta",
out="Proibitina_MA.aln",
clw=True)
print(cline)
#Leitura de ficheiro do alinhamento multiplo
alignment = AlignIO.read(
"C:/Users/Zé Freitas/Desktop/Mestrado/Labs_Bioinf/Trabalho prático/scripts/Labs_Bioinf/Proibitina/Proibitinalinhados.fasta",
"fasta")
print(alignment)
#Leitura do ficheiro da arvore filogenética
arvore = Phylo.read(
"C:/Users/Zé Freitas/Desktop/Mestrado/Labs_Bioinf/Trabalho prático/scripts/Labs_Bioinf/Proibitina/Proibitinarvore.dnd",
"newick")
print(arvore)
Phylo.draw_ascii(arvore)
ax.tick_params(labelsize=fs * 0.8)
ax.set_ylim([0, 1.1 * np.max(yi)])
plt.tight_layout()
plt.legend(fontsize=fs * 0.8)
if __name__ == '__main__':
import matplotlib.pyplot as plt
import time
plt.ion()
# tree_file = '../data/H3N2_NA_allyears_NA.20.nwk'
# date_file = '../data/H3N2_NA_allyears_NA.20.metadata.csv'
tree_file = '../data/ebola.nwk'
date_file = '../data/ebola.metadata.csv'
T = Phylo.read(tree_file, 'newick')
#T.root_with_outgroup('A/Canterbury/58/2000|CY009150|09/05/2000|New_Zealand||H3N2/8-1416')
dates = {}
with open(date_file) as ifile:
ifile.readline()
for line in ifile:
if line[0] != '#':
fields = line.strip().split(',')
dates[fields[0]] = float(fields[1])
for l in T.get_terminals():
l.numdate = dates[l.name]
branch_variance = lambda x: (x.branch_length +
(0.0005
if x.is_terminal() else 0.0)) / 19000.0
def test_newick_read_single3(self):
"""Read Nexus file with one tree."""
tree = Phylo.read(EX_NEXUS2, "nexus")
self.assertEqual(len(tree.get_terminals()), 658)
def GRAViTyDendrogramAndHeatmapConstruction(
ShelveDir,
IncludeIncompleteGenomes=False,
SimilarityMeasurementScheme="PG",
p=1,
Dendrogram=True,
Dendrogram_LinkageMethod="average", #"single", "complete", "average", "weighted"
Bootstrap=True,
N_Bootstrap=10,
Bootstrap_method="booster", #"booster", "sumtrees"
Bootstrap_N_CPUs=20,
Heatmap=False,
Heatmap_VirusOrderScheme=None, #"Filename",
Heatmap_WithDendrogram=True,
Heatmap_DendrogramFile=None,
Heatmap_DendrogramSupport_Cutoff=0.75,
VirusGrouping=True,
):
print "################################################################################"
print "#Generate GRAViTy dendrogram and heat map #"
print "################################################################################"
'''
Generate GRAViTy dendrogram and heat map
---------------------------------------------
'''
################################################################################
print "- Define dir/file paths"
################################################################################
print "\tto program output shelve"
#-------------------------------------------------------------------------------
VariableShelveDir = ShelveDir + "/Shelves"
if Dendrogram == True:
print "\t\tto virus dendrogram file"
#-------------------------------------------------------------------------------
VirusDendrogramFile = VariableShelveDir + "/Dendrogram.IncompleteGenomes=%s.Scheme=%s.Method=%s.p=%s.nwk" % (
str(int(IncludeIncompleteGenomes)), SimilarityMeasurementScheme,
Dendrogram_LinkageMethod, p)
if Bootstrap == True:
print "\t\tto dendrogram distribution file"
#-------------------------------------------------------------------------------
VirusDendrogramDistFile = VariableShelveDir + "/DendrogramDist.IncompleteGenomes=%s.Scheme=%s.Method=%s.p=%s.nwk" % (
str(int(IncludeIncompleteGenomes)),
SimilarityMeasurementScheme, Dendrogram_LinkageMethod, p)
if os.path.isfile(VirusDendrogramDistFile):
os.remove(VirusDendrogramDistFile)
print "\t\tto bootstrapped dendrogram file"
#-------------------------------------------------------------------------------
BootstrappedVirusDendrogramFile = VariableShelveDir + "/BootstrappedDendrogram.IncompleteGenomes=%s.Scheme=%s.Method=%s.p=%s.nwk" % (
str(int(IncludeIncompleteGenomes)),
SimilarityMeasurementScheme, Dendrogram_LinkageMethod, p)
if os.path.isfile(BootstrappedVirusDendrogramFile):
os.remove(BootstrappedVirusDendrogramFile)
if Heatmap == True:
print "\t\tto heat map file"
#-------------------------------------------------------------------------------
HeatmapFile = VariableShelveDir + "/Heatmap.IncompleteGenomes=%s.Scheme=%s.p=%s.pdf" % (
str(int(IncludeIncompleteGenomes)), SimilarityMeasurementScheme, p)
if Heatmap_WithDendrogram == True:
print "\t\tto heat map with dendrogram file"
#-------------------------------------------------------------------------------
HeatmapWithDendrogramFile = VariableShelveDir + "/HeatmapWithDendrogram.IncompleteGenomes=%s.Scheme=%s.Method=%s.p=%s.support_cutoff=%s.pdf" % (
str(int(IncludeIncompleteGenomes)), SimilarityMeasurementScheme,
Dendrogram_LinkageMethod, p, Heatmap_DendrogramSupport_Cutoff)
if Heatmap_DendrogramFile == None:
if Dendrogram == True:
if Bootstrap == True:
Heatmap_DendrogramFile = BootstrappedVirusDendrogramFile
elif Bootstrap == False:
Heatmap_DendrogramFile = VirusDendrogramFile
else:
raise SystemExit("The dendrogram file is missing.")
elif not os.path.isfile(Heatmap_DendrogramFile):
raise SystemExit("Can't find %s." % Heatmap_DendrogramFile)
if VirusGrouping == True:
VirusGroupingFile = VariableShelveDir + "/VirusGrouping.IncompleteGenomes=%s.Scheme=%s.p=%s.txt" % (
str(int(IncludeIncompleteGenomes)), SimilarityMeasurementScheme, p)
################################################################################
print "- Retrieve variables"
################################################################################
if IncludeIncompleteGenomes == True:
print "\tfrom ReadGenomeDescTable.AllGenomes.shelve"
#-------------------------------------------------------------------------------
VariableShelveFile = VariableShelveDir + "/ReadGenomeDescTable.AllGenomes.shelve"
elif IncludeIncompleteGenomes == False:
print "\tfrom ReadGenomeDescTable.CompleteGenomes.shelve"
#-------------------------------------------------------------------------------
VariableShelveFile = VariableShelveDir + "/ReadGenomeDescTable.CompleteGenomes.shelve"
#VariableShelveFile = VariableShelveDir+"/ReadGenomeDescTable.shelve"
Parameters = shelve.open(VariableShelveFile)
for key in [
"SeqIDLists",
"FamilyList",
"GenusList",
"VirusNameList",
"TaxoGroupingList",
]:
globals()[key] = Parameters[key]
print "\t\t" + key
Parameters.close()
if IncludeIncompleteGenomes == True:
print "\tfrom RefVirusAnnotator.AllGenomes.shelve"
#-------------------------------------------------------------------------------
VariableShelveFile = VariableShelveDir + "/RefVirusAnnotator.AllGenomes.shelve"
elif IncludeIncompleteGenomes == False:
print "\tfrom RefVirusAnnotator.CompleteGenomes.shelve"
#-------------------------------------------------------------------------------
VariableShelveFile = VariableShelveDir + "/RefVirusAnnotator.CompleteGenomes.shelve"
#VariableShelveFile = VariableShelveDir+"/RefVirusAnnotator.shelve"
Parameters = shelve.open(VariableShelveFile)
for key in [
"PPHMMSignatureTable",
"PPHMMLocationTable",
"PPHMMSignatureTable_coo",
"PPHMMLocationTable_coo",
"GOMIDList",
"GOMSignatureTable",
]:
try:
globals()[key] = Parameters[key]
print "\t\t" + key
except KeyError:
pass
Parameters.close()
if "PPHMMSignatureTable_coo" in globals().keys():
globals()["PPHMMSignatureTable"] = PPHMMSignatureTable_coo.toarray()
if "PPHMMLocationTable_coo" in globals().keys():
globals()["PPHMMLocationTable"] = PPHMMLocationTable_coo.toarray()
################################################################################
print "- Estimate virus pairwise distances"
################################################################################
SimMat = SimilarityMat_Constructor(
PPHMMSignatureTable=PPHMMSignatureTable,
GOMSignatureTable=GOMSignatureTable,
PPHMMLocationTable=PPHMMLocationTable,
SimilarityMeasurementScheme=SimilarityMeasurementScheme,
p=p,
)
DistMat = 1 - SimMat
DistMat[DistMat < 0] = 0
if Dendrogram == True:
################################################################################
print "- Estimate the GRAViTy dendrogram"
################################################################################
#Make TaxoLabelList
#---------------------------------------------------------------------
TaxoLabelList = TaxoLabel_Constructor(SeqIDLists=SeqIDLists,
FamilyList=FamilyList,
GenusList=GenusList,
VirusNameList=VirusNameList)
#Make dendrogram
#---------------------------------------------------------------------
VirusDendrogram = DistMat2Tree(
DistMat=DistMat,
LeafList=TaxoLabelList,
Dendrogram_LinkageMethod=Dendrogram_LinkageMethod)
with open(VirusDendrogramFile, "w") as VirusDendrogram_txt:
VirusDendrogram_txt.write(VirusDendrogram)
if Bootstrap == True:
################################################################################
print "- Compute bootstrap support"
################################################################################
N_PPHMMs = PPHMMSignatureTable.shape[1]
for Bootstrap_i in range(0, N_Bootstrap):
print "\tRound %d" % (Bootstrap_i + 1)
#-------------------------------------------------------------------------------
print "\t\tConstruct bootstrapped PPHMMSignatureTable and PPHMMLocationTable"
#-------------------------------------------------------------------------------
PPHMM_IndexList = np.random.choice(range(N_PPHMMs),
N_PPHMMs,
replace=True)
BootstrappedPPHMMSignatureTable = PPHMMSignatureTable[:,
PPHMM_IndexList]
BootstrappedPPHMMLocationTable = PPHMMLocationTable[:,
PPHMM_IndexList]
BootstrappedGOMSignatureTable = None
if "G" in SimilarityMeasurementScheme:
print "\t\tConstruct bootstrapped GOMSignatureTable"
#-------------------------------------------------------------------------------
BootstrappedGOMDB = GOMDB_Constructor(
TaxoGroupingList=TaxoGroupingList,
PPHMMLocationTable=BootstrappedPPHMMLocationTable,
GOMIDList=GOMIDList)
BootstrappedGOMSignatureTable = GOMSignatureTable_Constructor(
PPHMMLocationTable=BootstrappedPPHMMLocationTable,
GOMDB=BootstrappedGOMDB,
GOMIDList=GOMIDList)
print "\t\tConstruct a dendrogram from the bootstrapped data"
#-------------------------------------------------------------------------------
BootstrappedSimMat = SimilarityMat_Constructor(
PPHMMSignatureTable=BootstrappedPPHMMSignatureTable,
GOMSignatureTable=BootstrappedGOMSignatureTable,
PPHMMLocationTable=BootstrappedPPHMMLocationTable,
SimilarityMeasurementScheme=SimilarityMeasurementScheme,
p=p,
)
BootstrappedDistMat = 1 - BootstrappedSimMat
BootstrappedDistMat[BootstrappedDistMat < 0] = 0
BootstrappedVirusDendrogram = DistMat2Tree(
DistMat=BootstrappedDistMat,
LeafList=TaxoLabelList,
Dendrogram_LinkageMethod=Dendrogram_LinkageMethod)
with open(VirusDendrogramDistFile,
"a") as VirusDendrogramDist_txt:
VirusDendrogramDist_txt.write(BootstrappedVirusDendrogram +
"\n")
print "\tCreat a bootstrapped dendrogram"
#-------------------------------------------------------------------------------
if Bootstrap_method == "booster":
_ = subprocess.Popen(
"booster -i %s -b %s -o %s -@ %d " %
(VirusDendrogramFile, VirusDendrogramDistFile,
BootstrappedVirusDendrogramFile, Bootstrap_N_CPUs),
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True)
out, err = _.communicate()
elif Bootstrap_method == "sumtrees":
_ = subprocess.Popen(
"sumtrees.py --decimals=2 --no-annotations --preserve-underscores --force-rooted --output-tree-format=newick --output-tree-filepath=%s --target=%s %s"
% (BootstrappedVirusDendrogramFile, VirusDendrogramFile,
VirusDendrogramDistFile),
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True)
out, err = _.communicate()
else:
print "'Bootstrap_method' can either be 'booster' or 'sumtrees'."
if Heatmap == True:
################################################################################
print "- Construct GRAViTy heatmap"
################################################################################
#Determine virus order
#-------------------------------------------------------------------------------
N_Viruses = len(DistMat)
if Heatmap_VirusOrderScheme == None:
VirusOrder = range(N_Viruses)
elif os.path.isfile(Heatmap_VirusOrderScheme):
with open(Heatmap_VirusOrderScheme,
"r") as Heatmap_VirusOrderScheme_txt:
VirusOrder = [
int(Virus_i.split("\r\n")[0].split("\n")[0])
for Virus_i in Heatmap_VirusOrderScheme_txt
]
else:
VirusOrder = range(N_Viruses)
#Re-order the distance matrix
#-------------------------------------------------------------------------------
OrderedDistMat = DistMat[VirusOrder][:, VirusOrder]
#Labels, label positions, and ticks
#-------------------------------------------------------------------------------
#ClassLabelList = np.array([TaxoGrouping.split("_")[1] if TaxoGrouping.startswith("_") else TaxoGrouping for TaxoGrouping in TaxoGroupingList[VirusOrder]])
ClassLabelList = np.array([
re.split("_|\*", TaxoGrouping)[1] if TaxoGrouping.startswith(
("_", "*")) else TaxoGrouping
for TaxoGrouping in TaxoGroupingList[VirusOrder]
])
LineList = np.where(ClassLabelList[0:-1] != ClassLabelList[1:])[0]
ClassLabelList = np.hstack(
(ClassLabelList[LineList], ClassLabelList[-1]))
LineList = LineList + 0.5
TickLocList = np.array(
map(np.mean,
(zip(np.hstack(([-0.5], LineList)),
np.hstack((LineList, [len(TaxoGroupingList) - 0.5]))))))
#Plot configuration
#-------------------------------------------------------------------------------
Heatmap_width = float(12)
Heatmap_height = Heatmap_width
TaxoLable_space = 1.00
CBar_Heatmap_gap = 0.05
CBar_width = Heatmap_width
CBar_height = 0.25
CBarLable_space = 0.25
Outer_margin = 0.5
FontSize = 6
Fig_width = Outer_margin + Heatmap_width + TaxoLable_space + Outer_margin
Fig_height = Outer_margin + CBarLable_space + CBar_height + CBar_Heatmap_gap + Heatmap_height + TaxoLable_space + Outer_margin
ax_Heatmap_L = (Outer_margin + TaxoLable_space) / Fig_width
ax_Heatmap_B = (Outer_margin + CBarLable_space + CBar_height +
CBar_Heatmap_gap) / Fig_height
ax_Heatmap_W = Heatmap_width / Fig_width
ax_Heatmap_H = Heatmap_height / Fig_height
ax_CBar_L = (Outer_margin + TaxoLable_space) / Fig_width
ax_CBar_B = (Outer_margin + CBarLable_space) / Fig_height
ax_CBar_W = CBar_width / Fig_width
ax_CBar_H = CBar_height / Fig_height
#Plot the heat map
#-------------------------------------------------------------------------------
fig = plt.figure(figsize=(Fig_width, Fig_height), dpi=300)
ax_Heatmap = fig.add_axes(
[ax_Heatmap_L, ax_Heatmap_B, ax_Heatmap_W, ax_Heatmap_H],
frame_on=True,
facecolor="white")
Heatmap_Graphic = ax_Heatmap.imshow(OrderedDistMat,
cmap='magma',
aspect='auto',
vmin=0,
vmax=1,
interpolation='none')
for l in LineList:
ax_Heatmap.axvline(l, color='k', lw=0.2)
ax_Heatmap.axhline(l, color='k', lw=0.2)
ax_Heatmap.set_xticks(TickLocList)
ax_Heatmap.set_xticklabels(ClassLabelList, rotation=90, size=FontSize)
ax_Heatmap.set_yticks(TickLocList)
ax_Heatmap.set_yticklabels(ClassLabelList, rotation=0, size=FontSize)
ax_Heatmap.tick_params(top='on',
bottom='off',
left='off',
right='on',
labeltop='on',
labelbottom='off',
labelleft='off',
labelright='on',
direction='out')
ax_CBar = fig.add_axes([ax_CBar_L, ax_CBar_B, ax_CBar_W, ax_CBar_H],
frame_on=True,
facecolor="white")
CBar_Graphic = fig.colorbar(Heatmap_Graphic,
cax=ax_CBar,
orientation="horizontal",
ticks=[0, 0.25, 0.50, 0.75, 1])
CBar_Graphic.ax.set_xticklabels(
['0.00', '0.25', '0.50', '0.75', '1.00'], size=FontSize)
CBar_Graphic.ax.set_xlabel('Distance', rotation=0, size=FontSize + 2)
CBar_Graphic.ax.tick_params(top='off',
bottom='on',
left='off',
right='off',
labeltop='off',
labelbottom='on',
labelleft='off',
labelright='off',
direction='out')
#Save the plot to file
#-------------------------------------------------------------------------------
plt.savefig(HeatmapFile, format="pdf")
if Heatmap_WithDendrogram == True:
################################################################################
print "- Construct GRAViTy heat map with dendrogram"
################################################################################
N_Viruses = len(DistMat)
#Load the tree
#-------------------------------------------------------------------------------
VirusDendrogram = Phylo.read(Heatmap_DendrogramFile, "newick")
#Determine virus order
#-------------------------------------------------------------------------------
TaxoLabelList = TaxoLabel_Constructor(SeqIDLists=SeqIDLists,
FamilyList=FamilyList,
GenusList=GenusList,
VirusNameList=VirusNameList)
_ = VirusDendrogram.ladderize(reverse=True)
OrderedTaxoLabelList = [
Clade.name for Clade in VirusDendrogram.get_terminals()
]
VirusOrder = [
TaxoLabelList.index(TaxoLabel)
for TaxoLabel in OrderedTaxoLabelList
]
#Re-order the distance matrix
#-------------------------------------------------------------------------------
OrderedDistMat = DistMat[VirusOrder][:, VirusOrder]
#Remove clade support values that are < Heatmap_DendrogramSupport_Cutoff
#-------------------------------------------------------------------------------
N_InternalNodes = len(VirusDendrogram.get_nonterminals())
for InternalNode_i in range(N_InternalNodes):
if VirusDendrogram.get_nonterminals(
)[InternalNode_i].confidence < Heatmap_DendrogramSupport_Cutoff or np.isnan(
VirusDendrogram.get_nonterminals()
[InternalNode_i].confidence):
VirusDendrogram.get_nonterminals(
)[InternalNode_i].confidence = ""
else:
VirusDendrogram.get_nonterminals(
)[InternalNode_i].confidence = round(
VirusDendrogram.get_nonterminals()
[InternalNode_i].confidence, 2)
#Labels, label positions, and ticks
#-------------------------------------------------------------------------------
Taxo2ClassDict = {
TaxoLabel: TaxoGrouping
for TaxoLabel, TaxoGrouping in zip(TaxoLabelList, TaxoGroupingList)
}
ClassDendrogram = copy(VirusDendrogram)
for Clade in ClassDendrogram.find_clades(terminal=True):
Clade.name = Taxo2ClassDict[Clade.name]
ClassLabelList = []
LineList = [-1]
TerminalNodeList = [
TerminalNode for TerminalNode in ClassDendrogram.get_terminals()
]
while len(TerminalNodeList) != 0:
FarLeftNode = TerminalNodeList[0]
for Clade in ([ClassDendrogram] +
ClassDendrogram.get_path(FarLeftNode)):
DescendantNodeList = Clade.get_terminals()
DescendantClassLabelList = list(
set(map(lambda c: c.name, DescendantNodeList)))
if len(DescendantClassLabelList) == 1:
ClassLabelList.append(DescendantClassLabelList[0])
LineList.append(LineList[-1] + len(DescendantNodeList))
TerminalNodeList = TerminalNodeList[len(DescendantNodeList
):]
break
ClassLabelList = np.array(ClassLabelList)
LineList = np.array(LineList) + 0.5
TickLocList = np.array(map(np.mean, zip(LineList[0:-1], LineList[1:])))
#Plot configuration
#-------------------------------------------------------------------------------
Heatmap_width = float(12)
Heatmap_height = Heatmap_width
TaxoLable_space = 1.00
CBar_Heatmap_gap = 0.05
CBar_width = Heatmap_width
CBar_height = 0.25
CBarLable_space = 0.25
Dendrogram_width = Heatmap_width / 3
Dendrogram_height = Heatmap_height
Dendrogram_Heatmap_gap = 0.1
ScaleBar_Dendrogram_gap = CBar_Heatmap_gap
ScaleBar_width = Dendrogram_width
ScaleBar_height = CBar_height
ScaleBarLable_space = CBarLable_space
Outer_margin = 0.5
FontSize = 6
Fig_width = Outer_margin + Dendrogram_width + Dendrogram_Heatmap_gap + Heatmap_width + TaxoLable_space + Outer_margin
Fig_height = Outer_margin + CBarLable_space + CBar_height + CBar_Heatmap_gap + Heatmap_height + TaxoLable_space + Outer_margin
ax_Dendrogram_L = Outer_margin / Fig_width
ax_Dendrogram_B = (Outer_margin + ScaleBarLable_space + ScaleBar_height
+ ScaleBar_Dendrogram_gap) / Fig_height
ax_Dendrogram_W = Dendrogram_width / Fig_width
ax_Dendrogram_H = Dendrogram_height / Fig_height
ax_ScaleBar_L = Outer_margin / Fig_width
ax_ScaleBar_B = (Outer_margin + ScaleBarLable_space) / Fig_height
ax_ScaleBar_W = ScaleBar_width / Fig_width
ax_ScaleBar_H = ScaleBar_height / Fig_height
ax_Heatmap_L = (Outer_margin + Dendrogram_width +
Dendrogram_Heatmap_gap) / Fig_width
ax_Heatmap_B = (Outer_margin + CBarLable_space + CBar_height +
CBar_Heatmap_gap) / Fig_height
ax_Heatmap_W = Heatmap_width / Fig_width
ax_Heatmap_H = Heatmap_height / Fig_height
ax_CBar_L = (Outer_margin + Dendrogram_width +
Dendrogram_Heatmap_gap) / Fig_width
ax_CBar_B = (Outer_margin + CBarLable_space) / Fig_height
ax_CBar_W = CBar_width / Fig_width
ax_CBar_H = CBar_height / Fig_height
#Plot the heat map
#-------------------------------------------------------------------------------
fig = plt.figure(figsize=(Fig_width, Fig_height), dpi=300)
ax_Dendrogram = fig.add_axes([
ax_Dendrogram_L, ax_Dendrogram_B, ax_Dendrogram_W, ax_Dendrogram_H
],
frame_on=False,
facecolor="white")
Phylo.draw(VirusDendrogram,
label_func=lambda x: "",
do_show=False,
axes=ax_Dendrogram)
VirusDendrogramDepth = max(
[v for k, v in VirusDendrogram.depths().iteritems()])
ax_Dendrogram.set_xlim([(VirusDendrogramDepth - 1),
VirusDendrogramDepth])
ax_Dendrogram.set_ylim([N_Viruses + 0.5, 0.5])
ax_Dendrogram.set_axis_off()
ax_ScaleBar = fig.add_axes(
[ax_ScaleBar_L, ax_ScaleBar_B, ax_ScaleBar_W, ax_ScaleBar_H],
frame_on=False,
facecolor="white")
ax_ScaleBar.plot([0, 1], [0, 0], 'k-')
ScaleBarTicks = [0, 0.25, 0.5, 0.75, 1]
for Tick in ScaleBarTicks:
ax_ScaleBar.plot([Tick, Tick], [-0.05, 0.05], 'k-')
ax_ScaleBar.set_xlim([1, 0])
ax_ScaleBar.set_xticks(ScaleBarTicks)
ax_ScaleBar.set_xticklabels(map(str, ScaleBarTicks),
rotation=0,
size=FontSize)
ax_ScaleBar.set_xlabel('Distance', rotation=0, size=FontSize + 2)
ax_ScaleBar.xaxis.set_label_position('bottom')
ax_ScaleBar.tick_params(top='off',
bottom='off',
left='off',
right='off',
labeltop='off',
labelbottom='on',
labelleft='off',
labelright='off',
direction='out')
ax_Heatmap = fig.add_axes(
[ax_Heatmap_L, ax_Heatmap_B, ax_Heatmap_W, ax_Heatmap_H],
frame_on=True,
facecolor="white")
Heatmap_Graphic = ax_Heatmap.imshow(OrderedDistMat,
cmap='magma',
aspect='auto',
vmin=0,
vmax=1,
interpolation='none')
for l in LineList:
ax_Heatmap.axvline(l, color='k', lw=0.2)
ax_Heatmap.axhline(l, color='k', lw=0.2)
ax_Heatmap.set_xticks(TickLocList)
ax_Heatmap.set_xticklabels(ClassLabelList, rotation=90, size=FontSize)
ax_Heatmap.set_yticks(TickLocList)
ax_Heatmap.set_yticklabels(ClassLabelList, rotation=0, size=FontSize)
ax_Heatmap.tick_params(top='on',
bottom='off',
left='off',
right='on',
labeltop='on',
labelbottom='off',
labelleft='off',
labelright='on',
direction='out')
ax_CBar = fig.add_axes([ax_CBar_L, ax_CBar_B, ax_CBar_W, ax_CBar_H],
frame_on=True,
facecolor="white")
CBar_Graphic = fig.colorbar(Heatmap_Graphic,
cax=ax_CBar,
orientation="horizontal",
ticks=[0, 0.25, 0.50, 0.75, 1])
CBar_Graphic.ax.set_xticklabels(['0', '0.25', '0.50', '0.75', '1'],
rotation=0,
size=FontSize)
CBar_Graphic.ax.set_xlabel('Distance', rotation=0, size=FontSize + 2)
CBar_Graphic.ax.tick_params(top='off',
bottom='on',
left='off',
right='off',
labeltop='off',
labelbottom='on',
labelleft='off',
labelright='off',
direction='out')
#Save the plot to file
#-------------------------------------------------------------------------------
plt.savefig(HeatmapWithDendrogramFile, format="pdf")
if VirusGrouping == True:
################################################################################
print "- Virus grouping"
################################################################################
from GRAViTy.Utilities.OrderedSet import OrderedSet
from GRAViTy.Utilities.VirusGrouping_Estimator import VirusGrouping_Estimator
(VirusGroupingList, OptDistance_Cutoff, CorrelationScore,
Theils_u_TaxoGroupingListGivenPred,
Theils_u_PredGivenTaxoGroupingList) = VirusGrouping_Estimator(
DistMat, Dendrogram_LinkageMethod, TaxoGroupingList)
np.savetxt(
fname=VirusGroupingFile,
X=np.column_stack((
map(", ".join, SeqIDLists),
FamilyList,
GenusList,
VirusNameList,
TaxoGroupingList,
VirusGroupingList,
)),
fmt='%s',
delimiter="\t",
header=
"Sequence identifier\tFamily\tGenus\tVirus name\tClass\tGrouping")
with open(VirusGroupingFile, "a") as VirusGrouping_txt:
VirusGrouping_txt.write(
"\n" + "Distance cut off: %s\n" % OptDistance_Cutoff +
"Theil's uncertainty correlation for the reference assignments given the predicted grouping U(Ref|Pred): %s\n"
% Theils_u_TaxoGroupingListGivenPred +
"Theil's uncertainty correlation for the predicted grouping given the reference assignments U(Pred|Ref): %s\n"
% Theils_u_PredGivenTaxoGroupingList +
"Symmetrical Theil's uncertainty correlation between the reference assignments and the predicted grouping U(Ref, Pred): %s\n"
% CorrelationScore +
"U(X|Y) == 1 means that knowing Y implies a perfect knowledge of X, but not vice-versa\n"
+
"U(X,Y) == 1 means that knowing Y implies a perfect knowledge of X and vice-versa\n"
)
def test_int_labels(self):
"""Read newick formatted tree with numeric labels."""
tree = Phylo.read(StringIO("(((0:0.1,1:0.1)0.99:0.1,2:0.1)0.98:0.0);"),
"newick")
self.assertEqual({leaf.name
for leaf in tree.get_terminals()}, {"0", "1", "2"})
def test_unicode_exception(self):
"""Read a Newick file with a unicode byte order mark (BOM)."""
with open(EX_NEWICK_BOM, encoding="utf-8") as handle:
tree = Phylo.read(handle, "newick")
self.assertEqual(len(tree.get_terminals()), 3)
def test_convert_phyloxml_binary(self):
"""Try writing phyloxml to a binary handle; fail on Py3."""
trees = Phylo.parse("PhyloXML/phyloxml_examples.xml", "phyloxml")
with tempfile.NamedTemporaryFile(mode="wb") as out_handle:
self.assertRaises(TypeError, Phylo.write, trees, out_handle,
"phyloxml")
def test_newick_read_single1(self):
"""Read first Newick file with one tree."""
tree = Phylo.read(EX_NEWICK, "newick")
self.assertEqual(len(tree.get_terminals()), 28)
def get_newick_tree_str(filename):
tree = Phylo.parse(filename, 'newick').next()
# output = StringIO.StringIO()
output = io.StringIO()
Phylo.write(tree, output, 'newick')
return output.getvalue()
def test_convert_phyloxml_text(self):
"""Write phyloxml to a text handle."""
trees = Phylo.parse("PhyloXML/phyloxml_examples.xml", "phyloxml")
with tempfile.NamedTemporaryFile(mode="w") as out_handle:
count = Phylo.write(trees, out_handle, "phyloxml")
self.assertEqual(13, count)
type=int,
default=100,
help='Resolution for numerical solution of ODE.')
parser.add_argument('-delimiter',
default=None,
help='Field separator for node names in tree.')
parser.add_argument('-position',
type=int,
default=-1,
help='Python index of field with tip date.')
args = parser.parse_args()
# open and parse tree
try:
tree = Phylo.read(args.tree, 'newick')
except:
print 'ERROR: Failed to parse tree from file', args.tree
raise
tree_height = max(tree.depths().values())
tips = tree.get_terminals()
ntips = len(tips)
if args.delimiter is None:
tip_heights = [0.] * ntips
else:
maxdate = 0
tipdates = []
for tip in tips:
try:
print('Save alignment in PHYLIP formats')
fn_ali_trim = '/tmp/largest_clone_ali_trim.phy'
AlignIO.write(ali_unique, fn_ali_trim, 'phylip')
print('Infer tree')
res = sp.run(
'phyml -i {:} -d nt'.format(fn_ali_trim),
shell=True,
stdout=sp.PIPE,
)
print('Rename and bush up leaves')
fn_tree = '/tmp/largest_clone_ali_trim.phy_phyml_tree.txt'
from Bio import Phylo
tree = Phylo.read('/tmp/largest_clone_ali_trim.phy_phyml_tree.txt',
format='newick')
leaves = tree.get_terminals()
for leaf in leaves:
lid = seqs_unique[int(leaf.name.split('_')[-1]) - 1]
if len(seqs_red[lid]) == 1:
leaf.name = seqs_red[lid][0]
else:
# Grow a hanging subtree
for lid in seqs_red[lid]:
leaf.clades.append(
leaf.__class__(
branch_length=1e-9,
name=lid,
))
tree.root.name = 'root'
geneID, geneFct = [], []
outfile1 = open("single_origin.txt", "w")
outfile2 = open("double_origin.txt", "w")
for line in IDfile:
line = line.rstrip()
geneID.append(line.split('\t')[0])
geneFct.append(line.split('\t')[1])
for i in os.listdir(inDIR):
if 'best' not in i: continue
mynode, mynode1, mynode2 = False, False, False
infile = open(inDIR + i, "r")
line = infile.readline().rstrip()
handle = StringIO(line)
tree = Phylo.read(handle, "newick")
for node in tree.get_nonterminals():
subnodes = set([x.name for x in node.get_terminals()])
if subnodes == campan1:
mynode1 = True
elif subnodes == campan2:
mynode2 = True
elif subnodes == campan:
mynode = True
if mynode == True:
for x in xrange(len(geneID)):
if geneID[x] in i:
outfile1.write("%s\t%s\t%s\n" %
(geneID[x], geneFct[x], line))
def newick2phylo(self, nwk):
handle = StringIO(nwk)
phy = Phylo.read(handle, 'newick')
return phy
#!/usr/bin/env python import sys from Bio import Phylo Phylo.convert(sys.argv[1], 'newick', sys.stdout, 'nexus')
def phylo_from_str(nwk):
""" Returns a Phylo.BaseTree object given Newick string """
handle = StringIO()
handle.write(nwk)
handle.seek(0)
return Phylo.read(handle, "newick")
def build_tree_fasttree(filename_or_ali, rootname=None, VERBOSE=0):
'''Build phylogenetic tree using FastTree
Parameters:
filename_or_ali: filename of a FASTA multiple sequence alignment, or a
Biopython alignment itself
rootname (str): name of the leaf that should be the new root (outgroup)
VERBOSE (int): verbosity level
'''
import os
import subprocess as sp
import StringIO
from Bio import Phylo
import numpy as np
from ..filenames import fasttree_bin
if isinstance(filename_or_ali, basestring):
filename = filename_or_ali
else:
from Bio import AlignIO
ali = filename_or_ali
tmp_folder = os.getenv('HOME') + '/tmp/'
filename = tmp_folder + 'tmp_fasttree_' + str(
np.random.randint(1000000000)) + '.fasta'
AlignIO.write(ali, filename, 'fasta')
try:
if VERBOSE >= 3:
output = sp.check_output([fasttree_bin, '-nt', filename])
else:
output = sp.check_output([fasttree_bin, '-nt', filename],
stderr=sp.STDOUT)
tree_string = output.split('\n')[-2]
tree = Phylo.read(StringIO.StringIO(tree_string), 'newick')
tree.root.branch_length = 0.001
if rootname is not None:
if VERBOSE >= 2:
print 'Reroot'
for leaf in tree.get_terminals():
if leaf.name == rootname:
root = leaf
break
else:
raise ValueError('Initial reference not found in tree')
tree.root_with_outgroup(leaf)
finally:
if filename_or_ali != filename:
os.remove(filename)
# NOTE: nice fasttree trims sequence names at the first bracket, restore them
if VERBOSE >= 2:
print 'Check leaf labels integrity'
if filename_or_ali == filename:
from Bio import AlignIO
ali = AlignIO.read(filename_or_ali, 'fasta')
else:
ali = filename_or_ali
seq_names = set(seq.name for seq in ali)
leaves_miss = set()
for leaf in tree.get_terminals():
if leaf.name in seq_names:
seq_names.remove(leaf.name)
else:
leaves_miss.add(leaf)
if len(leaves_miss):
if VERBOSE >= 2:
print 'Correcting leaf integrity'
for leaf in leaves_miss:
for name in seq_names:
if name.split('(')[0] == leaf.name:
leaf.name = name
seq_names.remove(name)
break
else:
print 'Leaf has unexpected (truncated?) name:', leaf.name
return tree
def load_tree(tree_path: str, patient_zero: str):
"""Load a ML tree file (nwk format) into a Phylo tree object
`patient_zero` is a user-specified reference name for rooting the tree"""
tree = next(Phylo.parse(tree_path, 'newick'))
tree.root_with_outgroup(patient_zero)
return get_tree_coords(tree)