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#!/usr/bin/env python
#Author: Duy Tin Truong (duytin.truong@unitn.it)
# at CIBIO, University of Trento, Italy
__author__ = 'Duy Tin Truong (duytin.truong@unitn.it)'
__version__ = '0.1'
__date__ = '4 May 2015'
import sys
import os
import argparse as ap
import dendropy
from StringIO import StringIO
import re
from collections import defaultdict
import ConfigParser
import matplotlib.colors as colors
import subprocess
def read_params():
p = ap.ArgumentParser()
p.add_argument('--ifn_tree',
required=True,
default=None,
type=str,
help='The input tree in newick format.')
p.add_argument('--colorized_metadata',
required=False,
default='unset',
type=str,
help='The metadata field to colorize. Default "unset".')
p.add_argument('--fig_size',
required=False,
default=8,
type=float,
help='The figure size. Default "8".')
p.add_argument('--legend_marker_size',
required=False,
default=20,
type=int,
help='The legend marker size. Default "20".'
)
p.add_argument('--legend_font_size',
required=False,
default=10,
type=int,
help='The legend font size. Default "10".'
)
p.add_argument('--legend_marker_edge_width',
required=False,
default=0.2,
type=float,
help='The legend marker edge width. Default "0.2".'
)
p.add_argument('--leaf_marker_size',
required=False,
default=20,
type=int,
help='The legend marker size. Default "20".'
)
p.add_argument('--leaf_marker_edge_width',
required=False,
default=0.2,
type=float,
help='The legend marker edge width. Default "0.2".'
)
p.add_argument('--dpi',
required=False,
default=300,
type=int,
help='The figure dpi.')
p.add_argument('--figure_extension',
required=False,
default='.png',
type=str,
help='The figure extension. Default ".png".')
p.add_argument('--ofn_prefix',
required=False,
default=None,
type=str,
help='The prefix of output files.')
return p.parse_args()
def run(cmd):
print cmd
subprocess.call(cmd.split())
def main(args):
tree = dendropy.Tree.get_from_path(args.ifn_tree, schema='newick',
preserve_underscores=True)
tree.reroot_at_midpoint()
count = 0
metadatas = set([])
node2metadata = {}
for node in tree.preorder_node_iter():
nodestr = node.get_node_str().strip("'")
if node.is_leaf():
if '.' in nodestr:
nodestr = nodestr.replace('.',',')
node.taxon = dendropy.Taxon(label=nodestr)
substrs = re.findall(
'%s-[a-zA-Z0-9.]*'%args.colorized_metadata,
nodestr)
if substrs:
md = substrs[0].replace(args.colorized_metadata + '-', '')
metadatas.add(md)
node2metadata[nodestr] = md
else:
count += 1
node.taxon = dendropy.Taxon(label='node_%d'%count)
metadatas = sorted(list(metadatas))
color_names = colors.cnames.keys()
metadata2color = {}
for i, md in enumerate(metadatas):
metadata2color[md] = color_names[i % len(color_names)]
if not args.ofn_prefix:
args.ofn_prefix = args.ifn_tree
ofn_tree = args.ofn_prefix + '.graphlantree'
tree.write_to_path(ofn_tree, 'newick')
ofn_annot = args.ofn_prefix + '.annot'
with open(ofn_annot, 'w') as ofile:
#ofile.write('clade_separation\t0\n')
ofile.write('branch_bracket_width\t0\n')
#ofile.write('clade_separation\t0.15\n')
ofile.write('branch_bracket_depth\t0\n')
#ofile.write('branch_thickness\t1.25\n')
ofile.write('annotation_background_width\t0\n')
# legend
ofile.write('#legends\n')
ofile.write('class_legend_font_size\t%d\n'%args.legend_font_size)
for md in metadata2color:
ofile.write('%s\tclade_marker_size\t%d\n'%(md, args.legend_marker_size))
ofile.write('%s\tclade_marker_color\t%s\n'%(md, metadata2color[md]))
ofile.write('%s\tclade_marker_edge_width\t%f\n'%(md, args.legend_marker_edge_width))
# remove intermedate nodes
for node in tree.preorder_node_iter():
if not node.is_leaf():
nodestr = node.get_node_str().strip("'")
ofile.write('%s\tclade_marker_size\t0\n'%(nodestr))
# colorize leaf nodes
for node in tree.seed_node.leaf_nodes():
nodestr = node.get_node_str().strip("'")
if nodestr in node2metadata:
leaf_color = metadata2color[node2metadata[nodestr]]
ofile.write('%s\tclade_marker_size\t%d\n'%(nodestr, args.leaf_marker_size))
ofile.write('%s\tclade_marker_color\t%s\n'%(nodestr, leaf_color))
ofile.write('%s\tclade_marker_edge_width\t%f\n'%(nodestr, args.leaf_marker_edge_width))
ofn_xml = args.ofn_prefix + '.xml'
cmd = 'graphlan_annotate.py --annot %s %s %s'%(ofn_annot, ofn_tree, ofn_xml)
run(cmd)
ofn_fig = args.ofn_prefix + args.figure_extension
cmd = 'graphlan.py %s %s --dpi %d --size %f'%(ofn_xml, ofn_fig, args.dpi, args.fig_size)
run(cmd)
print 'Output file: %s'%ofn_fig
if __name__ == "__main__":
args = read_params()
main(args)
#test()
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