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show_tree.py
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#!/usr/bin/env python
''' Author : Huy Nguyen
Program : Providing visualization of the Reconstruction. Grouping genomes
into group color
Start : 05/08/2016
End : 05/08/2016
'''
from ete3 import *
import argparse
import os
def get_arguments():
parser = argparse.ArgumentParser()
parser.add_argument("--Operon","-i", help="Operon file name")
parser.add_argument("--Group","-g", help="Color Grouping")
parser.add_argument("--Image","-o", help="Output Image")
parser.add_argument("--Space","-s",help= "Space between the leaf node", default = 100)
parser.add_argument("--Font","-f",help= "Font size", default = 50)
parser.add_argument("--Branch","-b",help= "Branch thickness", default = 10000)
args = parser.parse_args()
return args
# color group of genome
# create a dictionary, sadly this is done manually
def parse(file):
color_dic={}
group= open(file,'r')
for line in group.readlines():
key= line.split(':')[0]
color=line.split(':')[1]
value = color.split('\n')[0]
color_dic[key]=value
return color_dic
if __name__ == "__main__":
start = time.time()
args = get_arguments()
# branch thickness
thickness = int(args.Branch)
# parse the mapping file
space = int(args.Space)
font = int(args.Font)
mapping = args.Operon+'_mapping'
infile = open(mapping,'r')
dic={}
for line in infile.readlines():
line = line.strip()
line = line.split('\t')
for item in line:
item = item.split(',')
dic[item[1]]=item[0]
color_list=['green','cyan','magenta','gray','yellow','orange',
'red','lime','pink','blue','silver','maroon','mediumblue','plum']
gene_color_dic = {}
for gene in dic:
color = color_list.pop(0)
gene_color_dic[gene]= color
tree= Tree(args.Operon)
# using the color dic to color group
color_dic = parse(args.Group)
far,distance = tree.get_farthest_leaf()
for node in tree.iter_descendants("postorder"):
if not node.is_leaf():
# create face contain initial set info
genes = list(node.initial)
col = 1
for gene in genes:
if gene !="|":
gene_face = TextFace(gene,fsize = font)
gene_face.background.color = gene_color_dic[gene]
else:
gene_face = TextFace(" "*int(font/5))
gene_face.background.color = "white"
node.add_face(gene_face,col,"branch-top")
col+=1
node.add_face(TextFace(" "),col,"branch-top")
col+=1
deletion_cost = (node.deletion).split('|')[1]
dup_cost = (node.duplication).split('|')[1]
split_cost = (node.split).split('|')[1]
distances = [int(deletion_cost),int(dup_cost),int(split_cost)]
# node.add_face(TextFace(node.initial), column=0, position = "branch-top")
node.add_face(TextFace(distances,fsize= font), column=0, position = "branch-bottom")
child1,child2 = node.get_children()
color1 = child1.node_color
color2 = child2.node_color
if color1 == color2 and color1 !='mixed':
node.add_features(node_color=color1)
else:
node.add_features(node_color='mixed')
else:
name = node.name.split('_')
# modify name to be normal, and append the gene block info to it
# get accesion number
short = name[2]+'_'+name[3]
# get the color
color = color_dic[short]
node.add_features(node_color=color)
# separate the node and the text
gene_face = TextFace(" "*int(font/5))
gene_face.background.color = "white"
node.add_face(gene_face,0,"aligned")
if "Bacillus_subtilis" in node.name or "Escherichia_coli" in node.name:
node.name = name[0]+'_'+name[1]
face =TextFace(node.name,fsize= font)
face.margin_top =10
face.margin_bottom = 10
face.margin_left = 10
face.margin_right = 20
face.border.width = 10
face.hz_align = 1
face.vt_align = 1
node.add_face(face, column =1,position ="aligned")
else:
node.name = name[0]+'_'+name[1]+" "
node.add_face(TextFace(node.name,fsize= font), column =1, position ="aligned")
genes = list(node.gene_block)
# add a white column so it separate from the block
col = 2
gene_face = TextFace(" "*int(font/5))
gene_face.background.color = "white"
node.add_face(gene_face,col,"aligned")
col = 3
for gene in genes:
if gene !="|":
gene_face = TextFace(gene,fsize= font)
gene_face.background.color = gene_color_dic[gene]
else:
gene_face = TextFace(" "*int(font/5))
gene_face.background.color = "white"
node.add_face(gene_face,col,"aligned")
col+=1
node.add_face(TextFace(" "),col,"aligned")
col+=1
nstyle = NodeStyle()
# branch
nstyle.hz_line_width = thickness
nstyle.vt_line_width = thickness
if node.node_color != 'mixed':
nstyle["fgcolor"] = color
else:
nstyle["fgcolor"] = "gray"
nstyle["shape"] = "circle"
nstyle["size"] = font/2
# nstyle["vt_line_color"]=color
# nstyle["hz_line_color"]=color
node.set_style(nstyle)
### get the total cost for each event:
# get the 2 children of the tree
children= []
for child in tree.get_children():
children.append(child)
deletion_total = 0
duplication_total = 0
split_total = 0
for child in children:
deletion_total+= int(child.deletion.split('|')[1])
duplication_total+= int(child.duplication.split('|')[1])
split_total+= int(child.split.split('|')[1])
# modify tree style for better visualization
tree_style = TreeStyle()
tree_style.branch_vertical_margin = space
tree_style.show_leaf_name = False
tree_style.min_leaf_separation = 5
tree_style.extra_branch_line_type = 0
tree_style.draw_guiding_lines=True
tree_style.guiding_lines_type = 1
cost= TextFace("Deletion count: "+str(deletion_total)+
' '+"Duplication count: "+str(duplication_total)
+' '+"Split count: "+ str(split_total),fsize= font,penwidth=2)
cost.margin_top =5
cost.margin_bottom = 5
cost.margin_left = 40
cost.margin_right = 40
cost.border.width = 3
cost.border.color = "black"
tree_style.title.add_face(cost, column=1)
mystring =''
col = 2
for gene in sorted(dic):
color = gene_color_dic[gene]
mystring = TextFace(gene+":"+dic[gene],fsize= font)
mystring.margin_top =5
mystring.margin_bottom = 5
mystring.margin_left = 40
mystring.margin_right = 40
mystring.background.color = color
tree_style.title.add_face(mystring, column=col)
col+=1
# render the image
# tree.render(args.Image+'.pdf',dpi=1000,tree_style=tree_style)
tree.render(args.Image+'.png',dpi=1000,tree_style=tree_style)
# tree.render(args.Image+'.svg',dpi=1000,tree_style=tree_style)
# tree.show(tree_style=tree_style)