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 -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 checkgithub源码安装wget -O ete3.20160719.zip

unzip ete3.20160719.zip

python setup.py install

yum install python-six.noarch

ete3 upgrade-external-toolsETE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 5totally 4 parts included as stated above, multiple sequence alignment, trimming MSA results, select best model, use appropriate softwares to build tree.- represents command separatornone 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_bootstrapete3 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alignerete3 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_fasttreeETE: 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 xvfbwrapperExternal 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

The most simple way of showing a tree.

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 filet.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);'

t = Tree(t_str)ts = TreeStyle()ts.show_leaf_name = Truets.show_branch_length = Truets.show_branch_support = Truet.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'clockts.arc_span = 180t.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 = Truets.show_branch_length = Truets.show_branch_support = True# Draws nodes as small red spheres of diameter equal to 10 pixelsfor 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"] = 30t.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 = Falsets.show_branch_length = Truets.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 = mylayoutt.img_style["size"] = 30t.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 = Falsets.show_branch_length = Truets.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 = mylayoutt.img_style["size"] = 30t.img_style["fgcolor"] = "black"t.render(file_name="%%inline",tree_style=ts)

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 attributedef 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 = Falsets.show_branch_length = Truets.show_branch_support = Truesetup_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 = Falsets.show_branch_length = Truets.show_branch_support = Truets.layout_fn = mylayout_onlysetup_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\tcol7A\t-1.23\t-0.81\t1.79\t0.78\t-0.42\t-0.69\t0.58B\t-1.76\t-0.94\t1.16\t0.36\t0.41\t-0.35\t1.12C\t-2.19\t0.13\t0.65\t-0.51\t0.52\t1.04\t0.36D\t-1.22\t-0.98\t0.79\t-0.76\t-0.29\t1.54\t0.93E\t-1.47\t-0.83\t0.85\t0.07\t-0.81\t1.53\t0.65F\t-1.04\t-1.11\t0.87\t-0.14\t-0.80\t1.74\t0.48G\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 colorDclan_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()

ReferenceETE tutorial googlegroup link

原文链接