Mercurial > repos > iuc > qiime_filter_otus_from_otu_table
view beta_diversity_through_plots_html_generation.py @ 5:e84a31935a8b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author | iuc |
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date | Sat, 05 Aug 2017 07:31:22 -0400 |
parents | 8824c27efae2 |
children | 8b42de6ad28a |
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#!/usr/bin/env python # -*- coding: utf-8 -*- import argparse import os import re def generate_index_html(dir_list, args): with open(args.html_file, 'w') as index_html_file: s = "" s += '<html>\n' s += '\t<head><title>PCoA beta diversity results</title></head>\n' s += '\t<body>\n' s += '\t\t<a href="http://www.qiime.org" target="_blank">' s += '<img src="http://qiime.org/_static/wordpressheader.png" ' s += 'alt="www.qiime.org""/></a>\n' s += '\t\t<p>\n' s += '\t\t\tBeta diversity metrics\n' s += '\t\t\t<ul>\n' for directory in dir_list: regexp_result = re.search( '([a-zA-Z\_]*)_emperor_pcoa_plot', directory) metric = regexp_result.group(1) s += '\t\t\t\t<li>' + metric + ': ' s += '<a href="' + directory s += '/index.html">PCoA results</a></td>\n' s += '\t\t\t\t</li>\n' s += '\t\t\t</ul>\n' s += '\t\t</p>\n' s += '\t</body>\n' s += '</html>\n' index_html_file.write(s) def build_html(args): os.mkdir(args.html_dir) dir_list = [name for name in os.listdir(args.data_directory) if os.path.isdir(os.path.join( args.data_directory, name))] generate_index_html(dir_list, args) for directory in dir_list: input_path = os.path.join(args.data_directory, directory) cmd = 'cp -r ' + input_path + ' ' + args.html_dir os.system(cmd) if __name__ == '__main__': parser = argparse.ArgumentParser() parser.add_argument('--data_directory', required=True) parser.add_argument('--html_file', required=True) parser.add_argument('--html_dir', required=True) args = parser.parse_args() build_html(args)