|
3
|
1 #!/usr/bin/env python
|
|
|
2
|
|
|
3 #-----------------------------------------------------------------------------
|
|
|
4 # NAME: circlader.py
|
|
|
5 # DESCRIPTION: Circlader (circular cladogram buider) is a python script for
|
|
|
6 # creating images of circular cladogram starting from any guide
|
|
|
7 # tree in tabular or Newick format
|
|
|
8 #
|
|
|
9 # Author: Nicola Segata
|
|
|
10 # email: nsegata@hsph.harvard.edu
|
|
|
11 #
|
|
|
12 # Copyright: (c) 2011
|
|
|
13 # Licence: <your licence>
|
|
|
14 #
|
|
|
15 #-----------------------------------------------------------------------------
|
|
|
16
|
|
|
17
|
|
|
18 import os
|
|
|
19 import sys,argparse
|
|
|
20 import circlader_lib as cir
|
|
|
21
|
|
|
22 def read_params(args):
|
|
|
23 parser = argparse.ArgumentParser(description='Circlader')
|
|
|
24
|
|
|
25 parser.add_argument('tree_file', nargs='?', default=None, type=str,
|
|
|
26 help= "the input tree in Newick format (unless --tf is specified)"
|
|
|
27 "[stdin if not present]")
|
|
|
28 parser.add_argument('out_image', nargs='?', default=None, type=str,
|
|
|
29 help= "the output image (the format is guessed from the extension "
|
|
|
30 "[windows visualization if not present]")
|
|
|
31 parser.add_argument('--tree_format', choices=['newick','tabular'],
|
|
|
32 default='newick', type=str,
|
|
|
33 help= "specifies the input tree format (default \"newick\", "
|
|
|
34 "other choice is \"tabular\")")
|
|
|
35 parser.add_argument('--style_file', nargs='?', default=os.getcwd()+"/default_styles/style.txt", type=str,
|
|
|
36 help= "set the style file (default_styles/style.txt if not specified)")
|
|
|
37 parser.add_argument('--color_file', nargs='?', default=None, type=str,
|
|
|
38 help= "set the color file (default_styles/colors.txt if not specified)")
|
|
|
39 parser.add_argument('--highlight_file', nargs='?', default=None, type=str,
|
|
|
40 help= "set the highlight file (default none)")
|
|
|
41 parser.add_argument('--tick_file', nargs='?', default=None, type=str,
|
|
|
42 help= "set the label file for level's names (default none)")
|
|
|
43 parser.add_argument('--size_file', nargs='?', default=None, type=str,
|
|
|
44 help= "set the file containing the dimentison of the circles (default none)")
|
|
|
45 parser.add_argument('--circle_file', nargs='?', default=None, type=str,
|
|
|
46 help= "set the external circles file (default none) [BETA FEATURE]")
|
|
|
47 parser.add_argument('--format', choices=['png','pdf','ps','eps','svg'], default=None, type=str,
|
|
|
48 help= "set the format of the output image (default none "
|
|
|
49 "meaning that the format is guessed from the output "
|
|
|
50 "file extension)")
|
|
|
51 parser.add_argument('--dpi', default=300, type=int )
|
|
|
52
|
|
|
53 return vars(parser.parse_args())
|
|
|
54
|
|
|
55 params = read_params(sys.argv)
|
|
|
56
|
|
|
57 cladogram = cir.Tree()
|
|
|
58 cladogram.read_colors(params['color_file'])
|
|
|
59 cladogram.read_style(params['style_file'])
|
|
|
60 cladogram.read_sizes(params['size_file'])
|
|
|
61 cladogram.read_circles(params['circle_file'])
|
|
|
62 cladogram.read_highlights(params['highlight_file'])
|
|
|
63 cladogram.read_tick_labels(params['tick_file'])
|
|
|
64 if params['tree_format'] == 'newick':
|
|
|
65 cladogram.load_newick(params['tree_file'])
|
|
|
66 else:
|
|
|
67 cladogram.load_lefse(params['tree_file'])
|
|
|
68 cladogram.pos_rad_leaves()
|
|
|
69 cladogram.set_pos()
|
|
|
70 cladogram.draw(params['out_image'],outformat=params['format'],dpi=params['dpi'])
|
