Mercurial > repos > sagun98 > micropita
view galaxy_micropita/src/breadcrumbs/src/circlader/circlader.py @ 3:8fb4630ab314 draft default tip
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author | sagun98 |
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date | Thu, 03 Jun 2021 17:07:36 +0000 |
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#!/usr/bin/env python #----------------------------------------------------------------------------- # NAME: circlader.py # DESCRIPTION: Circlader (circular cladogram buider) is a python script for # creating images of circular cladogram starting from any guide # tree in tabular or Newick format # # Author: Nicola Segata # email: nsegata@hsph.harvard.edu # # Copyright: (c) 2011 # Licence: <your licence> # #----------------------------------------------------------------------------- import os import sys,argparse import circlader_lib as cir def read_params(args): parser = argparse.ArgumentParser(description='Circlader') parser.add_argument('tree_file', nargs='?', default=None, type=str, help= "the input tree in Newick format (unless --tf is specified)" "[stdin if not present]") parser.add_argument('out_image', nargs='?', default=None, type=str, help= "the output image (the format is guessed from the extension " "[windows visualization if not present]") parser.add_argument('--tree_format', choices=['newick','tabular'], default='newick', type=str, help= "specifies the input tree format (default \"newick\", " "other choice is \"tabular\")") parser.add_argument('--style_file', nargs='?', default=os.getcwd()+"/default_styles/style.txt", type=str, help= "set the style file (default_styles/style.txt if not specified)") parser.add_argument('--color_file', nargs='?', default=None, type=str, help= "set the color file (default_styles/colors.txt if not specified)") parser.add_argument('--highlight_file', nargs='?', default=None, type=str, help= "set the highlight file (default none)") parser.add_argument('--tick_file', nargs='?', default=None, type=str, help= "set the label file for level's names (default none)") parser.add_argument('--size_file', nargs='?', default=None, type=str, help= "set the file containing the dimentison of the circles (default none)") parser.add_argument('--circle_file', nargs='?', default=None, type=str, help= "set the external circles file (default none) [BETA FEATURE]") parser.add_argument('--format', choices=['png','pdf','ps','eps','svg'], default=None, type=str, help= "set the format of the output image (default none " "meaning that the format is guessed from the output " "file extension)") parser.add_argument('--dpi', default=300, type=int ) return vars(parser.parse_args()) params = read_params(sys.argv) cladogram = cir.Tree() cladogram.read_colors(params['color_file']) cladogram.read_style(params['style_file']) cladogram.read_sizes(params['size_file']) cladogram.read_circles(params['circle_file']) cladogram.read_highlights(params['highlight_file']) cladogram.read_tick_labels(params['tick_file']) if params['tree_format'] == 'newick': cladogram.load_newick(params['tree_file']) else: cladogram.load_lefse(params['tree_file']) cladogram.pos_rad_leaves() cladogram.set_pos() cladogram.draw(params['out_image'],outformat=params['format'],dpi=params['dpi'])