Mercurial > repos > sagun98 > micropita_v2
comparison src/breadcrumbs/src/circlader/circlader.py @ 0:0de566f21448 draft default tip
v2
| author | sagun98 |
|---|---|
| date | Thu, 03 Jun 2021 18:13:32 +0000 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:0de566f21448 |
|---|---|
| 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']) |