欢迎大家来到IT世界,在知识的湖畔探索吧!
ETE能做什么
A Python framework for construction, analysis and visualization of trees.
安装和使用
- conda安装
- # Install Minconda (you can ignore this step if you already have Anaconda/Miniconda)
wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O Miniconda-latest-Linux-x86_64.sh
bash Miniconda-latest-Linux-x86_64.sh -b -p ~/anaconda/
export PATH=~/anaconda/bin:$PATH;
# Install ETE
conda install -c etetoolkit ete3 ete3_external_apps
# Check installation
ete3 version
ete3 build check - github源码安装
- wget https://github.com/etetoolkit/ete/archive/master.zip -O ete3.20160719.zip
unzip ete3.20160719.zip
python setup.py install
yum install python-six.noarch
ete3 upgrade-external-tools
ETE运行
- 输入序列
- 输入序列为标准的fasta格式文件，名字可以为任意形式
- 如果需要在序列名字中区分物种信息，fasta序列名需满足SpeciesCode_SequenceName例如HUMAN_p53 = HUMAN, p53。 可以通过参数–spname-delimiter指定使用其它字符作为分隔符。
- ete预先定义了多个流程用以完成从原始fasta序列到后续进化树生成的各个步骤。
- 运行以下命令可以列出系统自带的流程及其解释
- ete3 build workflows genetree
- 使用既定流程最简单运行
- -w指定所用的流程，-a指定输入序列，–tools-dir指定安装的外部程序的路径
- ete3 build -w standard_fasttree -a diTPS.prot.fa -o standard_fasttree
–tools-dir /root/.etetoolkit/ext_apps-latest/ - 自己定制流程
- 查看已有分析模块的定义
- ete3 build show phyml_default
[phyml_default]
_desc = Phyml tree using +G+I+F, 4 classes and aLRT branch supports. Default models JTT/GTR
_app = phyml
_aa_model = JTT
-nt_model = GTR
–pinv = e
–alpha = e
–nclasses = 4
-o = tlr
-f = m
–bootstrap = –2 - 修改部分定义获得新的模块
- ete3 build show phyml_default >customized.config
## 修改后的customized.config
[phyml_bootstrap_100]
_desc = Phyml tree using +G+I+F, 4 classes and aLRT branch supports. Default models JTT/GTR
_app = phyml
_aa_model = JTT
-nt_model = GTR
–pinv = e
–alpha = e
–nclasses = 4
-o = tlr
-f = m
–bootstrap = 100
[trimal_auto]
_desc = trimal alignment cleaning using auto algorithm
_app = trimal
-automated1 =
## 使用新定义的模块
ete3 build -a diTPS.prot.fa –clearall -o phyml_bootstrap_100 -w
mafft_einsi-trimal_auto-none-phyml_bootstrap_100 -c customized.cfg –cpu 5 - totally 4 parts included as stated above, multiple sequence alignment, trimming MSA results, select best model, use appropriate softwares to build tree.
- – represents command separator
- none represents skipping related operations
- 获取可以定制的各部分命令
- ete3 build apps
- 选择预定义好的模块，如tree builders: phyml_default_bootstrap, aligners: mafft_einsi, model testers: pmodeltest_full_slow, alg cleaners:trimal_gappyout.
- 流程定制模板: 顺序为aligner-trimmer-model_tester-builder
- 基于我们的选择定制的流程mafft_einsi-trimal_gappyout-pmodeltest_full_slow-phyml_default_bootstrap
- ete3 build -w mafft_einsi-trimal_gappyout-pmodeltest_full_slow-phyml_default_bootstrap
-a diTPS.prot.fa -o custom_phymltree - -w可以接受多个流程(空格分开)，进而得到不同的比对工具、处理方式和建树工具 输出的多个结果，可以通过ete3 compare比较这些结果的吻合度, 比如Robinson-Foulds距离等。
- ete3 compare -r newtree1.nwq -t “tree2.nw tree3.nw tree4.nw” –unrooted
# Tree file can be got using find
find custom_phymltree -name *.nw - 定制不同的分析模块
- 氨基酸比对指导核苷酸比对的进化树构建 (要求氨基酸序列与核苷酸序列名字一一对应，核苷酸序列可以含有终止密码子，最终获得的核苷酸比对序列存储在*.used_alg.fa文件中。)
- ete3 build -a diTPS.prot.fa -n diTPS.nucl.fa -o aa2nt
-w standard_fasttree –clearall –nt-switch-threshold 0.9
-C 20 - 使用预先比对好的序列, 使用none代替aligner
- ete3 build -a diTPS.prot.aln.fa -w none-none-none-fasttree
-o manual_alg –clearall - 设置树的根节点
- from ete3 import Tree
tree = Tree(‘tree.nw’)
root = ‘one_node_name’
tree.set_outgroup(root)
#use mid-point as root
mid = tree.get_midpoint_outgroup()
tree.set_outgroup(mid)
tree.write(‘tree.rooted.nw’)
tree.render(‘tree.rooted.pdf’)
问题解决
- ETE: cannot connect to X server 如果程序运行出现错误ETE: cannot connect to X server则安装Xvfb， 并运行 xvfb-run ete3取代ete3, 后面的代码不变。
- yum install xorg-x11-server-Xvfb.x86_64
xvfb-run ete3 build -w standard_fasttree -a diTPS.prot.fa -o standard_fasttree - ETE: cannot connect to X server (solve in python script or jupyter ref)
- # Add the following 4 lines at the beginning of python code
# or the first cell in Jupyter
from xvfbwrapper import Xvfb
vdisplay = Xvfb()
vdisplay.start()
# launch stuff inside virtual display here
# other python codes here
# Add this line at the end of python code
# or the last cell in Jupyter
vdisplay.stop() - Install xvfbwrapper using pip install xvfbwrapper
- External applications directory are not found 指定ETE使用的工具的安装路径；一般发生在普通用户使用根用户编译的ETE时。
- –tools-dir /root/.etetoolkit/ext_apps-latest/
Tree annotation
# A virtual X-server XVFB is used in case you do not have X-serverfrom xvfbwrapper import Xvfbvdisplay = Xvfb()vdisplay.start()# launch stuff inside virtual display here#vdisplay.stop()from ete3 import Tree, faces, TreeStyle, NodeStylefrom ete3 import ClusterTree, RectFace, AttrFace, ProfileFace, TextFacefrom ete3.treeview.faces import add_face_to_nodeimport pandas as pdimport numpy as npimport colorsys欢迎大家来到IT世界,在知识的湖畔探索吧!
The most simple way of showing a tree.
欢迎大家来到IT世界,在知识的湖畔探索吧!t = Tree()
t.populate(7,names_library=['A','B','C','D','E','F','G'])
## %%liline is used for showing plots in ipythonnotebook.
## t.render(file_name="tree.pdf") # will save tree into pdf file
t.render(file_name="%%inline")
Get the randomly generated tree in newick format and save to a string variable which can be read using Tree() function.
t_str = t.write(outfile=None, format=0)
t_str
'(((B:1,A:1)1:1,(G:1,F:1)1:1)1:1,(E:1,(D:1,C:1)1:1)1:1);'欢迎大家来到IT世界,在知识的湖畔探索吧!t = Tree(t_str)
ts = TreeStyle()
ts.show_leaf_name = True
ts.show_branch_length = True
ts.show_branch_support = True
t.render(file_name="%%inline", tree_style=ts)
Get the randomly generated tree in newick format and save to file which can also be read using Tree() function.
t.write(outfile="tree.nw", format=0)
t = Tree("tree.nw")
ts.mode = "c"
ts.arc_start = -180 # 0 degrees = 3 o'clock
ts.arc_span = 180
t.render(file_name="%%inline", w=500, tree_style=ts)设置根节点、叶节点和中间节点的属性
ts = TreeStyle()
ts.show_leaf_name = True
ts.show_branch_length = True
ts.show_branch_support = True
# Draws nodes as small red spheres of diameter equal to 10 pixels
for n in t.traverse(): # Traverse each node and set attribute for each type of nodes
if n.is_leaf(): # Decide if leaf node
nstyle = NodeStyle()
nstyle["shape"] = "sphere"
nstyle["size"] = 10
nstyle["fgcolor"] = "darkred"
n.set_style(nstyle)
else:
nstyle = NodeStyle()
nstyle["shape"] = "square"
nstyle["size"] = 15
nstyle["fgcolor"] = "orange"
n.set_style(nstyle)
t.img_style["size"] = 30
t.img_style["fgcolor"] = "blue"
t.render(file_name="%%inline", w=500, tree_style=ts)修改节点的名字
t = Tree(t_str)
nameMap = {'A': 'American', 'B': 'Britain', 'C':'China',
'D':'Dutch', 'E':'Egypt','F':'France','G':'German'}
ts = TreeStyle()
ts.show_leaf_name = False
ts.show_branch_length = True
ts.show_branch_support = True
# Creates my own layout function. I will use all previously created
# faces and will set different node styles depending on the type of
# node.
def mylayout(node):
# If node is a leaf, add the nodes name and a its scientific
# name
if node.is_leaf():
# We can also create faces on the fly
newName = nameMap.get(node.name, node.name)
newNameFace = faces.TextFace(newName)
faces.add_face_to_node(newNameFace, node, column=1, aligned=True)
# Sets the style of leaf nodes
node.img_style["size"] = 12
node.img_style["shape"] = "sphere"
node.img_style["fgcolor"] = "blue"
#If node is an internal node
else:
# Sets the style of internal nodes
node.img_style["size"] = 1
node.img_style["shape"] = "circle"
node.img_style["fgcolor"] = "darkred"
ts.layout_fn = mylayout
t.img_style["size"] = 30
t.img_style["fgcolor"] = "black"
t.render(file_name="%%inline", w=600, tree_style=ts)不同的节点设置不同的背景色，树枝的颜色
t = Tree(t_str)
nameMap = {'A': 'American', 'B': 'Britain', 'C':'China',
'D':'Dutch', 'E':'Egypt','F':'France','G':'German'}
colorMap = { 'American': '#ACFFFF',
'Britain': '#ACACFF',
'China': '#ACACAC',
'Dutch': '#59ACAC',
'Egypt': '#5959AC',
'France': '#595959',
'German': '#065959'}
ts = TreeStyle()
ts.show_leaf_name = False
ts.show_branch_length = True
ts.show_branch_support = True
# Creates my own layout function. I will use all previously created
# faces and will set different node styles depending on the type of
# node.
def mylayout(node):
#Change branch color
node.img_style["hz_line_color"] = 'orange' # change horizontal branch color
node.img_style["vt_line_color"] = 'red' # Change vertical branch color
# If node is a leaf, add the nodes name and a its scientific
# name
if node.is_leaf():
# We can also create faces on the fly
newName = nameMap.get(node.name, node.name)
newNameFace = faces.TextFace(newName)
faces.add_face_to_node(newNameFace, node, column=1, aligned=True)
# Sets the style of leaf nodes
node.img_style["size"] = 12
node.img_style["shape"] = "sphere"
node.img_style["fgcolor"] = "blue"
node.img_style["bgcolor"] = colorMap[newName]
node.img_style["hz_line_color"] = 'blue' # change branch color
#If node is an internal node
else:
# Sets the style of internal nodes
node.img_style["size"] = 1
node.img_style["shape"] = "circle"
node.img_style["fgcolor"] = "darkred"
ts.layout_fn = mylayout
t.img_style["size"] = 30
t.img_style["fgcolor"] = "black"
t.render(file_name="%%inline",tree_style=ts)树+热图（自定义颜色+列名字）
自定义热图函数，同时该函数也支持替换或新增节点的名字。
nameFace = AttrFace("name", fsize=12) #Set leaf node attribute
def setup_heatmap(tree, tree_style, header, center_value=0.0, nameMap ={}, nameLabel = '',
color_up=0.7, color_down=0.2, color_center="white"):
DEFAULT_COLOR_SATURATION = 0.5
BASE_LIGHTNESS = 0.7
def gradient_color(value, max_value, saturation=0.5, hue=0.1):
def rgb2hex(rgb):
return '#%02x%02x%02x' % rgb
def hls2hex(h, l, s):
return rgb2hex( tuple(map(lambda x: int(x*255),
colorsys.hls_to_rgb(h, l, s))))
lightness = 1 - (value * BASE_LIGHTNESS) / max_value
return hls2hex(hue, lightness, DEFAULT_COLOR_SATURATION)
# Calculate max gradient value from the ClusterTree matrix
maxv = abs(center_value - tree.arraytable._matrix_max)
minv = abs(center_value - tree.arraytable._matrix_min)
if center_value <= tree.arraytable._matrix_min:
MAX_VALUE = minv + maxv
else:
MAX_VALUE = max(maxv, minv)
# Add heatmap colors to tree
cols_add_before_heat = 0
if nameMap:
cols_add_before_heat = 1
for lf in tree:
if nameMap:
longNameFace = faces.TextFace(nameMap.get(lf.name, lf.name))
lf.add_face(longNameFace, column=0, position="aligned")
for i, value in enumerate(getattr(lf, "profile", [])):
if value > center_value:
color = gradient_color(abs(center_value - value), MAX_VALUE,
hue=color_up)
elif value < center_value:
color = gradient_color(abs(center_value - value), MAX_VALUE,
hue=color_down)
else:
color = color_center
lf.add_face(RectFace(20, 20, color, color), position="aligned",
column=i+cols_add_before_heat)
# Uncomment to add numeric values to the matrix
#lf.add_face(TextFace("%0.2f "%value, fsize=5), position="aligned", column=i)
lf.add_face(nameFace, column=i+cols_add_before_heat+1, position="aligned")
if nameMap and nameLabel:
nameF = TextFace(nameLabel, fsize=7)
#nameF.rotation = -90
tree_style.aligned_header.add_face(nameF, column=0)
# Add header
for i, name in enumerate(header):
nameF = TextFace(name, fsize=7)
nameF.rotation = -90
tree_style.aligned_header.add_face(nameF, column=i+cols_add_before_heat)
#-------------END setup_heatmap----------------------------------------------读入矩阵 （可把文后的测试矩阵存储到文件中读入）
矩阵需满足三个条件：
- 矩阵为TAB键分割，第一行是每列的名字
- 矩阵每一行第一列为行名字，与树的节点对应
- 矩阵可以存储与一个文件中，也可以是如下的字符串
data = pd.read_table("matrix", header=0, index_col=0)
data.index.name = "#Names" #修改第一行的名字使其符合ETE的要求
data_mat = data.to_csv(None, sep="\t", float_format="%.2f")
header = list(data.columns.values) #获取列的名字用于标记
data|
col1 |
col2 |
col3 |
col4 |
col5 |
col6 |
col7 |
|
|
#Names |
|||||||
|
A |
-1.23 |
-0.81 |
1.79 |
0.78 |
-0.42 |
-0.69 |
0.58 |
|
B |
-1.76 |
-0.94 |
1.16 |
0.36 |
0.41 |
-0.35 |
1.12 |
|
C |
-2.19 |
0.13 |
0.65 |
-0.51 |
0.52 |
1.04 |
0.36 |
|
D |
-1.22 |
-0.98 |
0.79 |
-0.76 |
-0.29 |
1.54 |
0.93 |
|
E |
-1.47 |
-0.83 |
0.85 |
0.07 |
-0.81 |
1.53 |
0.65 |
|
F |
-1.04 |
-1.11 |
0.87 |
-0.14 |
-0.80 |
1.74 |
0.48 |
|
G |
-1.57 |
-1.17 |
1.29 |
0.23 |
-0.20 |
1.17 |
0.26 |
data_mat'#Names\tcol1\tcol2\tcol3\tcol4\tcol5\tcol6\tcol7\nA\t-1.23\t-0.81\t1.79\t0.78\t-0.42\t-0.69\t0.58\nB\t-1.76\t-0.94\t1.16\t0.36\t0.41\t-0.35\t1.12\nC\t-2.19\t0.13\t0.65\t-0.51\t0.52\t1.04\t0.36\nD\t-1.22\t-0.98\t0.79\t-0.76\t-0.29\t1.54\t0.93\nE\t-1.47\t-0.83\t0.85\t0.07\t-0.81\t1.53\t0.65\nF\t-1.04\t-1.11\t0.87\t-0.14\t-0.80\t1.74\t0.48\nG\t-1.57\t-1.17\t1.29\t0.23\t-0.20\t1.17\t0.26\n'header['col1', 'col2', 'col3', 'col4', 'col5', 'col6', 'col7']调用函数绘制热图
t = ClusterTree(t_str, data_mat)
ts = TreeStyle()
ts.show_leaf_name = False
ts.show_branch_length = True
ts.show_branch_support = True
setup_heatmap(t, ts, header, center_value=0, color_up=0.9, color_down=0.3, color_center="white")
t.render(file_name="%%inline", tree_style=ts)绘制热图时修改Layout
def mylayout_only(node):
#Change branch color
node.img_style["hz_line_color"] = 'orange' # change horizontal branch color
node.img_style["vt_line_color"] = 'red' # Change vertical branch color
# If node is a leaf, add the nodes name and a its scientific
# name
if node.is_leaf():
newName = nameMap.get(node.name)
node.img_style["size"] = 12
node.img_style["shape"] = "sphere"
node.img_style["fgcolor"] = "blue"
node.img_style["bgcolor"] = colorMap[newName]
node.img_style["hz_line_color"] = 'blue' # change branch color
#If node is an internal node
else:
# Sets the style of internal nodes
node.img_style["size"] = 1
node.img_style["shape"] = "circle"
node.img_style["fgcolor"] = "darkred"
t = ClusterTree(t_str, data_mat)
ts = TreeStyle()
ts.show_leaf_name = False
ts.show_branch_length = True
ts.show_branch_support = True
ts.layout_fn = mylayout_only
setup_heatmap(t, ts, header, center_value=0, color_up=0.9, color_down=0.3,
color_center="white", nameMap=nameMap, nameLabel="Full")
t.render(file_name="%%inline", tree_style=ts)测试矩阵
## 矩阵为TAB键分割
## 矩阵每一行第一列为行名字，与树的节点对应
## 矩阵可以存储于一个文件中，也可以是如下的字符串
matrix = """
#Names\tcol1\tcol2\tcol3\tcol4\tcol5\tcol6\tcol7
A\t-1.23\t-0.81\t1.79\t0.78\t-0.42\t-0.69\t0.58
B\t-1.76\t-0.94\t1.16\t0.36\t0.41\t-0.35\t1.12
C\t-2.19\t0.13\t0.65\t-0.51\t0.52\t1.04\t0.36
D\t-1.22\t-0.98\t0.79\t-0.76\t-0.29\t1.54\t0.93
E\t-1.47\t-0.83\t0.85\t0.07\t-0.81\t1.53\t0.65
F\t-1.04\t-1.11\t0.87\t-0.14\t-0.80\t1.74\t0.48
G\t-1.57\t-1.17\t1.29\t0.23\t-0.20\t1.17\t0.26
"""产生颜色的辅助函数，给定一个列表，这个函数会自动返回一个字典包含每个字段对应的颜色。
def hex2rgb(hexcolor):
return [(hexcolor>>16) & 0xff, (hexcolor>>8) & 0xff, hexcolor & 0xff]
def rgb2hex(rgbcolor):
r, g, b = rgbcolor
rgb = hex((r << 16) + (g << 8) +b)[2:].upper()
zero = '0'* (6-len(rgb))
return '#'+zero+rgb
#----------------------------------
def generateColor(labelL):
labelL = list(set(labelL))
labelL.sort()
colorD = {}
r = 255
g = 255
b = 255
len_label = int(len(labelL) / 3 + 1)
step = int(250 / len_label)
cnt = 1
for labels in labelL:
if cnt % 3 == 1:
r = r - step
elif cnt % 3 == 2:
g = g -step
else:
b = b - step
cnt += 1
color = rgb2hex([r, g, b])
colorD[labels] = color
return colorD
clan_colorD = generateColor(nameMap.values())
clan_colorD
{'American': '#ACFFFF',
'Britain': '#ACACFF',
'China': '#ACACAC',
'Dutch': '#59ACAC',
'Egypt': '#5959AC',
'France': '#595959',
'German': '#065959'}带有Support value的Newick树，供测试不同的属性使用
nw = """
(((Dre:0.008339,Dme:0.300613)1.000000:0.596401,
(Cfa:0.640858,Hsa:0.753230)1.000000:0.182035)1.000000:0.106234,
((Dre:0.271621,Cfa:0.046042)1.000000:0.953250,
(Hsa:0.061813,Mms:0.110769)1.000000:0.204419)1.000000:0.973467);关闭Virtual X-server
vdisplay.stop()Ipython notebook for easy usage
https://github.com/Tong-Chen/notebook/blob/master/ETE.ipynb
Reference
- ETE tutorial http://etetoolkit.org/docs/latest/tutorial/index.html
- ETE googlegroup https://groups.google.com/d/topic/etetoolkit/pXr4B71Ozt0
Blog link
原文链接 http://blog.genesino.com/2016/07/ete/
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