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#!/usr/bin/env python
from ete3 import Tree, TreeStyle, NodeStyle, TextFace, AttrFace, faces
from pathlib import Path
import argparse
import csv
import os
import sys
out_stem = "etefmt" # not actual default
out_format = "pdf" # not actual default
names = {}
def layout(node):
if node.is_leaf():
pretty_name = names[node.name] if node.name in names else node.name
# derp = AttrFace("name", fsize=10, ftype="Arial", fgcolor="black")
pretty_name_face = faces.TextFace(pretty_name)
pretty_name_face.margin_left = 5
faces.add_face_to_node(pretty_name_face, node, column=0)
def read_tree(file_name):
if file_name == "-":
file_name = "/dev/stdin"
t = Tree(file_name);
# ignore any errors with midpoint rooting
R = t.get_midpoint_outgroup()
try:
t.set_outgroup(R)
except Exception as e:
pass
t.ladderize(direction=1)
return t
def main(file_name):
t = read_tree(file_name)
nstyle = NodeStyle()
nstyle["size"] = 0
ts = TreeStyle()
ts.show_leaf_name = False
ts.scale = 25000 # pixels per branch length unit
ts.layout_fn = layout
for n in t.traverse():
n.set_style(nstyle)
# t.show(tree_style=ts)
t.render(out_stem + "." + out_format, tree_style=ts)
def read_names(names_file):
global names
with open(names_file) as csvfile:
namesreader = csv.reader(csvfile, delimiter=',')
for row in namesreader:
names[row[0]] = row[1]
return names
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='Render a phylogeny to an image.')
parser.add_argument('file', nargs='?', help='Name of file with phylogeny')
parser.add_argument('-o', dest='image_file', help='Image file name')
parser.add_argument('-r', dest='names_file', help='File with ID and real name (CSV)')
args = parser.parse_args()
if args.names_file:
read_names(args.names_file)
# parse output file name
if args.image_file:
# split arg
out_stem = Path(args.image_file).stem
out_format = Path(args.image_file).suffix[1:]
else:
# split input file name
print(args.file)
inputfile = Path(args.file if args.file else "etefmt.pdf")
out_stem = Path(inputfile).stem
out_format = "pdf"
if args.file:
main(args.file)
elif not os.isatty(0):
main("-")
else:
parser.print_help()
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