from ete_dev import TreeStyle
from ete_dev import EvolTree
from ete_dev import faces
tree = EvolTree("data/S_example/measuring_S_tree.nw")
tree.link_to_alignment('data/S_example/alignment_S_measuring_evol.fasta')
print tree
print '\n Running free-ratio model with calculation of ancestral sequences...'
tree.run_model('fb_anc')
#tree.link_to_evol_model('/tmp/ete2-codeml/fb_anc/out', 'fb_anc')
I = TreeStyle()
I.force_topology = False
I.draw_aligned_faces_as_table = True
I.draw_guiding_lines = True
I.guiding_lines_type = 2
I.guiding_lines_color = "#CCCCCC"
for n in sorted(tree.get_descendants() + [tree], key=lambda x: x.node_id):
if n.is_leaf(): continue
anc_face = faces.SequenceFace(n.sequence, 'aa', fsize=10, bg_colors={})
I.aligned_foot.add_face(anc_face, 1)
I.aligned_foot.add_face(
faces.TextFace('node_id: #%d ' % (n.node_id), fsize=8), 0)
print 'display result of bs_anc model, with ancestral amino acid sequences.'
tree.show(tree_style=I)
print '\nThe End.'
from ete_dev import faces
tree = EvolTree ("data/S_example/measuring_S_tree.nw")
tree.link_to_alignment ('data/S_example/alignment_S_measuring_evol.fasta')
print tree
print '\n Running free-ratio model with calculation of ancestral sequences...'
tree.run_model ('fb_anc')
#tree.link_to_evol_model('/tmp/ete2-codeml/fb_anc/out', 'fb_anc')
I = TreeStyle()
I.force_topology = False
I.draw_aligned_faces_as_table = True
I.draw_guiding_lines = True
I.guiding_lines_type = 2
I.guiding_lines_color = "#CCCCCC"
for n in sorted (tree.get_descendants()+[tree],
key=lambda x: x.node_id):
if n.is_leaf(): continue
anc_face = faces.SequenceFace (n.sequence, 'aa', fsize=10, bg_colors={})
I.aligned_foot.add_face(anc_face, 1)
I.aligned_foot.add_face(faces.TextFace('node_id: #%d '%(n.node_id),
fsize=8), 0)
print 'display result of bs_anc model, with ancestral amino acid sequences.'
tree.show(tree_style=I)
print '\nThe End.'
def draw_tree(tree, conf, outfile):
try:
from ete_dev import (add_face_to_node, AttrFace, TextFace, TreeStyle, RectFace, CircleFace,
SequenceFace, random_color, SeqMotifFace)
except ImportError as e:
print e
return
def ly_basic(node):
if node.is_leaf():
node.img_style['size'] = 0
else:
node.img_style['size'] = 0
node.img_style['shape'] = 'square'
if len(MIXED_RES) > 1 and hasattr(node, "tree_seqtype"):
if node.tree_seqtype == "nt":
node.img_style["bgcolor"] = "#CFE6CA"
ntF = TextFace("nt", fsize=6, fgcolor='#444', ftype='Helvetica')
add_face_to_node(ntF, node, 10, position="branch-bottom")
if len(NPR_TREES) > 1 and hasattr(node, "tree_type"):
node.img_style['size'] = 4
node.img_style['fgcolor'] = "steelblue"
node.img_style['hz_line_width'] = 1
node.img_style['vt_line_width'] = 1
def ly_leaf_names(node):
if node.is_leaf():
spF = TextFace(node.species, fsize=10, fgcolor='#444444', fstyle='italic', ftype='Helvetica')
add_face_to_node(spF, node, column=0, position='branch-right')
if hasattr(node, 'genename'):
geneF = TextFace(" (%s)" %node.genename, fsize=8, fgcolor='#777777', ftype='Helvetica')
add_face_to_node(geneF, node, column=1, position='branch-right')
def ly_supports(node):
if not node.is_leaf() and node.up:
supFace = TextFace("%0.2g" %(node.support), fsize=7, fgcolor='indianred')
add_face_to_node(supFace, node, column=0, position='branch-top')
def ly_tax_labels(node):
if node.is_leaf():
c = LABEL_START_COL
largest = 0
for tname in TRACKED_CLADES:
if hasattr(node, "named_lineage") and tname in node.named_lineage:
linF = TextFace(tname, fsize=10, fgcolor='white')
linF.margin_left = 3
linF.margin_right = 2
linF.background.color = lin2color[tname]
add_face_to_node(linF, node, c, position='aligned')
c += 1
for n in xrange(c, len(TRACKED_CLADES)):
add_face_to_node(TextFace('', fsize=10, fgcolor='slategrey'), node, c, position='aligned')
c+=1
def ly_full_alg(node):
pass
def ly_block_alg(node):
if node.is_leaf():
if 'sequence' in node.features:
seqFace = SeqMotifFace(node.sequence, [])
# [10, 100, "[]", None, 10, "black", "rgradient:blue", "arial|8|white|domain Name"],
motifs = []
last_lt = None
for c, lt in enumerate(node.sequence):
if lt != '-':
if last_lt is None:
last_lt = c
if c+1 == len(node.sequence):
start, end = last_lt, c
motifs.append([start, end, "()", 0, 12, "slategrey", "slategrey", None])
last_lt = None
elif lt == '-':
if last_lt is not None:
start, end = last_lt, c-1
motifs.append([start, end, "()", 0, 12, "grey", "slategrey", None])
last_lt = None
seqFace = SeqMotifFace(node.sequence, motifs,
intermotif_format="line",
seqtail_format="line", scale_factor=ALG_SCALE)
add_face_to_node(seqFace, node, ALG_START_COL, aligned=True)
TRACKED_CLADES = ["Eukaryota", "Viridiplantae", "Fungi",
"Alveolata", "Metazoa", "Stramenopiles", "Rhodophyta",
"Amoebozoa", "Crypthophyta", "Bacteria",
"Alphaproteobacteria", "Betaproteobacteria", "Cyanobacteria",
"Gammaproteobacteria",]
# ["Opisthokonta", "Apicomplexa"]
colors = random_color(num=len(TRACKED_CLADES), s=0.45)
lin2color = dict([(ln, colors[i]) for i, ln in enumerate(TRACKED_CLADES)])
NAME_FACE = AttrFace('name', fsize=10, fgcolor='#444444')
LABEL_START_COL = 10
ALG_START_COL = 40
ts = TreeStyle()
ts.draw_aligned_faces_as_table = False
ts.draw_guiding_lines = False
ts.show_leaf_name = False
ts.show_branch_support = False
ts.scale = 160
ts.layout_fn = [ly_basic, ly_leaf_names, ly_supports, ly_tax_labels]
MIXED_RES = set()
MAX_SEQ_LEN = 0
NPR_TREES = []
for n in tree.traverse():
if hasattr(n, "tree_seqtype"):
MIXED_RES.add(n.tree_seqtype)
if hasattr(n, "tree_type"):
NPR_TREES.append(n.tree_type)
seq = getattr(n, "sequence", "")
MAX_SEQ_LEN = max(len(seq), MAX_SEQ_LEN)
if MAX_SEQ_LEN:
ALG_SCALE = min(1, 1000./MAX_SEQ_LEN)
ts.layout_fn.append(ly_block_alg)
if len(NPR_TREES) > 1:
rF = RectFace(4, 4, "steelblue", "steelblue")
rF.margin_right = 10
rF.margin_left = 10
ts.legend.add_face(rF, 0)
ts.legend.add_face(TextFace(" NPR node"), 1)
ts.legend_position = 3
if len(MIXED_RES) > 1:
rF = RectFace(20, 20, "#CFE6CA", "#CFE6CA")
rF.margin_right = 10
rF.margin_left = 10
ts.legend.add_face(rF, 0)
ts.legend.add_face(TextFace(" Nucleotide based alignment"), 1)
ts.legend_position = 3
try:
tree.set_species_naming_function(spname)
annotate_tree_with_ncbi(tree)
a = tree.search_nodes(species='Dictyostelium discoideum')[0]
b = tree.search_nodes(species='Chondrus crispus')[0]
#out = tree.get_common_ancestor([a, b])
#out = tree.search_nodes(species='Haemophilus parahaemolyticus')[0].up
tree.set_outgroup(out)
tree.swap_children()
except Exception:
pass
tree.render(outfile, tree_style=ts, w=170, units='mm', dpi=150)
tree.render(outfile+'.svg', tree_style=ts, w=170, units='mm', dpi=150)
tree.render(outfile+'.pdf', tree_style=ts, w=170, units='mm', dpi=150)
def draw(t, draw_alg=True):
def ly(node):
node.img_style['vt_line_width'] = 1
node.img_style['hz_line_width'] = 1
if node.is_leaf():
add_face_to_node(TextFace(
' (%s)' % node.name.split()[0].replace("/exon2", ""),
fsize=10,
fgcolor='slategrey',
tight_text=False),
node,
1,
position='branch-right')
add_face_to_node(TextFace(node.species,
fsize=12,
fgcolor='black',
fstyle='italic',
tight_text=False),
node,
0,
position='branch-right')
c = 1
for tname in tracked_clades:
if tname in node.named_lineage:
linF = TextFace(tname, fsize=10, fgcolor='white')
linF.margin_left = 3
linF.background.color = lin2color[tname]
add_face_to_node(linF, node, c, position='aligned')
c += 1
for n in xrange(1, 20 - (c - 1)):
add_face_to_node(TextFace('', fsize=10, fgcolor='slategrey'),
node,
c,
position='aligned')
c += 1
if draw_alg and 'sequence' in node.features:
#seqFace = SequenceFace(node.sequence,"aa",13)
seqFace = SeqMotifFace(node.sequence, [])
# [10, 100, "[]", None, 10, "black", "rgradient:blue", "arial|8|white|domain Name"],
motifs = []
last_lt = None
for c, lt in enumerate(node.sequence):
if lt != '-':
if last_lt is None:
last_lt = c
if c + 1 == len(node.sequence):
start, end = last_lt, c
w = end - start
motifs.append([
start, end, "[]", w, 13, "slategrey",
"slategrey", None
])
last_lt = None
elif lt == '-':
if last_lt is not None:
start, end = last_lt, c - 1
w = end - start
motifs.append([
start, end, "[]", w, 13, "slategrey",
"slategrey", None
])
last_lt = None
if not motifs:
print node, node.sequence
seqFace = SeqMotifFace(node.sequence,
motifs,
intermotif_format="line",
seqtail_format="line",
scale_factor=1)
add_face_to_node(seqFace, node, 20, aligned=True)
else:
if node.up:
add_face_to_node(TextFace('% 3g' % node.support,
fsize=11,
fgcolor='indianred'),
node,
0,
position='branch-top')
if hasattr(node, "support2") and node.up:
add_face_to_node(TextFace('% 3g' % float(node.support2),
fsize=11,
fgcolor='steelblue'),
node,
0,
position='branch-bottom')
node.img_style['size'] = 0
node.img_style['hz_line_color'] = 'black'
node.img_style['vt_line_color'] = 'black'
colors = random_color(num=len(tracked_clades))
lin2color = dict([(ln, colors[i]) for i, ln in enumerate(tracked_clades)])
ts = TreeStyle()
ts.draw_aligned_faces_as_table = False
ts.draw_guiding_lines = False
ts.show_leaf_name = False
ts.show_branch_support = False
ts.layout_fn = ly
print 'Rendering tree.pdf'
t.render('tree.svg', tree_style=ts)
t.render('tree.png', tree_style=ts)
def draw(t, draw_alg=True):
def ly(node):
node.img_style['vt_line_width'] = 1
node.img_style['hz_line_width'] = 1
if node.is_leaf():
add_face_to_node(TextFace(' (%s)' %node.name.split()[0].replace("/exon2", ""), fsize=10, fgcolor='slategrey', tight_text=False), node, 1, position='branch-right')
add_face_to_node(TextFace(node.species, fsize=12, fgcolor='black', fstyle='italic', tight_text=False), node, 0, position='branch-right')
c = 1
for tname in tracked_clades:
if tname in node.named_lineage:
linF = TextFace(tname, fsize=10, fgcolor='white')
linF.margin_left = 3
linF.background.color = lin2color[tname]
add_face_to_node(linF, node, c, position='aligned')
c += 1
for n in xrange(1, 20-(c-1)):
add_face_to_node(TextFace('', fsize=10, fgcolor='slategrey'), node, c, position='aligned')
c+=1
if draw_alg and 'sequence' in node.features:
#seqFace = SequenceFace(node.sequence,"aa",13)
seqFace = SeqMotifFace(node.sequence, [])
# [10, 100, "[]", None, 10, "black", "rgradient:blue", "arial|8|white|domain Name"],
motifs = []
last_lt = None
for c, lt in enumerate(node.sequence):
if lt != '-':
if last_lt is None:
last_lt = c
if c+1 == len(node.sequence):
start, end = last_lt, c
w = end-start
motifs.append([start, end, "[]", w, 13, "slategrey", "slategrey", None])
last_lt = None
elif lt == '-':
if last_lt is not None:
start, end = last_lt, c-1
w = end-start
motifs.append([start, end, "[]", w, 13, "slategrey", "slategrey", None])
last_lt = None
if not motifs:
print node, node.sequence
seqFace = SeqMotifFace(node.sequence, motifs,
intermotif_format="line",
seqtail_format="line", scale_factor=1)
add_face_to_node(seqFace, node, 20, aligned=True)
else:
if node.up:
add_face_to_node(TextFace('% 3g' %node.support, fsize=11, fgcolor='indianred'), node, 0, position='branch-top')
if hasattr(node, "support2") and node.up:
add_face_to_node(TextFace('% 3g' %float(node.support2), fsize=11, fgcolor='steelblue'), node, 0, position='branch-bottom')
node.img_style['size'] = 0
node.img_style['hz_line_color'] = 'black'
node.img_style['vt_line_color'] = 'black'
colors = random_color(num=len(tracked_clades))
lin2color = dict([(ln, colors[i]) for i, ln in enumerate(tracked_clades)])
ts = TreeStyle()
ts.draw_aligned_faces_as_table = False
ts.draw_guiding_lines = False
ts.show_leaf_name = False
ts.show_branch_support = False
ts.layout_fn = ly
print 'Rendering tree.pdf'
t.render('tree.svg', tree_style=ts)
t.render('tree.png', tree_style=ts)
