def labelForPaml(unlabelledTreeAsString,listOfNodes, tree):
t = EvolTree(unlabelledTreeAsString)
marks = []
count = 1
for i in listOfNodes:
marks.append("#"+str(count))
count+=1
t.mark_tree(listOfNodes, marks=marks)
print(t.write())
outfile = tree+"."+"_".join(listOfNodes)
with open(outfile, 'w') as out:
out.write(t.write())
def showAlignmentWithTree(unlabelledTreeAsString,alignment):
t = EvolTree(unlabelledTreeAsString, alignment,alg_format="paml")
t.link_to_alignment(alignment, alg_format="paml")
for node in t.traverse():
print(node)
print(node.node_id, node.name)
print(t.write())
#print(t)
t.show() #layout=evol_clean_layout)
def labelForPamlRegex(unlabelledTreeAsString, regex, tree):
pattern = re.compile(regex)
t = EvolTree(unlabelledTreeAsString)
marks = []
count = 1
outfiles = []
#nsFG=TreeStyle()
nsMatch = NodeStyle() #match
nsMatch["fgcolor"] = "blue"
nsMatch["size"] = 10
nsBG = NodeStyle()
nsBG["fgcolor"] = "black"
nsBG["size"] = 0
nsFG = []
tolabelreg = []
for i in range(0,MAX_PARENT):
nsFG.append( NodeStyle())
nsFG[i]["size"] = 10
nsFG[i]["fgcolor"] = NODE_COLORS[i]
isroot=True
for node in t.traverse():
node.set_style(nsBG)
if node.is_root():
print("root")
node.unroot()
node._support = None
for node in t.get_descendants():
node.add_face(TextFace(node.node_id), column=0)
#traverse and match
for node in t.traverse():
if re.match(pattern, node.name):
print("MATCH", node.name, node.node_id)
node.set_style(nsMatch)
n = node
try:
for i in range(0,MAX_PARENT):
n = n.up
n.set_style(nsFG[i])
marks.append("#"+str(count))
print(count)
t.mark_tree([str(count)], marks=marks)
#just label everything with #1
print(t.write())
tolabelreg.append(str(n.node_id))
outfile = tree+"."+"_".join([str(n.node_id)])
with open(outfile, 'w') as out:
out.write(t.write())
outfiles.append(outfile)
except AttributeError:
pass
marks.append("#"+str(count))
print(count)
t.mark_tree([str(count)], marks=marks)
#just label everything with #1
print(t.write())
outfile = tree+"."+"_".join([str(node.node_id)])
with open(outfile, 'w') as out:
out.write(t.write())
outfiles.append(outfile)
#t.show()
t.render(tree+".png")
return(outfiles, tolabelreg)
from ete2 import EvolTree
from ete2 import NodeStyle
tree = EvolTree ("data/S_example/measuring_S_tree.nw")
tree.link_to_alignment ('data/S_example/alignment_S_measuring_evol.fasta')
print tree
print 'Tree and alignment loaded.'
raw_input ('Tree will be mark in order to contrast Gorilla and Chimpanzee as foreground \nspecies.')
marks = ['1', 3, '7']
tree.mark_tree (marks, ['#1'] * 3)
print tree.write ()
# display marked branches in orange
for node in tree.traverse ():
if not hasattr (node, 'mark'):
continue
if node.mark == '':
continue
node.img_style = NodeStyle()
node.img_style ['bgcolor'] = '#ffaa00'
tree.show()
print '''now running branch-site models C and D that represents
the addition of one class of sites in on specific branch.
These models must be compared to null models M1 and M3.
def label_regex(unlabeled_tree, regex, treefile, depth=4,
model_list=None, paml_msa=None, outfile=None):
pattern = re.compile(regex)
t = EvolTree(unlabeled_tree)
marks = []
count = 1
outfiles = []
ts = TreeStyle()
ts.mode = "c"
nsMatch = NodeStyle() # match
nsMatch["fgcolor"] = "blue"
nsMatch["size"] = 10
nsBG = NodeStyle()
nsBG["fgcolor"] = "black"
nsBG["size"] = 0
nsFG = []
tolabelreg = []
for i in range(0, depth):
nsFG.append(NodeStyle())
nsFG[i]["size"] = 10
nsFG[i]["fgcolor"] = "blue"
#isroot = True
#for node in t.traverse():
# node.set_style(nsBG)
# if node.is_root():
# print("root")
# node.unroot()
# node._support = None
for node in t.get_descendants():
node.add_face(TextFace(node.node_id), column=0)
# traverse and match
for node in t.traverse():
if re.match(pattern, node.name):
node.set_style(nsMatch)
n = node
try:
for i in range(0, depth):
n = n.up
n.set_style(nsFG[i])
marks.append("#" + str(count))
#print(count)
t.mark_tree([str(count)], marks=marks)
#just label everything with #1
tolabelreg.append(str(n.node_id))
outfile = treefile + "." + "_".join([str(n.node_id)])
with open(outfile, 'w') as out:
out.write(t.write())
outfiles.append(outfile)
except AttributeError:
pass
else:
node.set_style(nsBG)
for f in tolabelreg:
print(f,"FFF")
for m in model_list:
generateCtl(model=m, treefile=treefile+"."+f, seqfile=paml_msa, outfile=treefile+"."+f,
generateOther=False)
t = fakeUnroot(t)
t.render(treefile+".png", tree_style=ts)
return outfiles, tolabelreg
