Mercurial > repos > iuc > qiime_beta_diversity
view jackknifed_beta_diversity_output_management.py @ 1:2f6f266d51d2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 04:05:25 -0400 |
parents | 0f76694d7591 |
children |
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#!/usr/bin/env python # -*- coding: utf-8 -*- import argparse import os def generate_index_html(dir_list, args): with open(args.html_file, 'w') as index_html_file: s = '<html>\n' s += '\t<head>\n' s += '\t\t<title>Jackknifed beta diversity results</title>\n' s += '\t</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\tEmperor PCoA plot after jacknifed beta diversity\n' s += '\t\t\t<ul>\n' for directory in dir_list: if directory == 'rarefaction' or directory == 'unrarefied_bdiv': continue s += '\t\t\t\t<li><a href="' + directory s += '/index.html">PCoA plots</a></td></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) os.mkdir(args.data_directory + '/pcoa') os.mkdir(args.data_directory + '/rare_dm') os.mkdir(args.data_directory + '/rare_upgma') os.mkdir(args.data_directory + '/upgma_cmp') os.mkdir(args.data_directory + '/rare_upgma_consensus') for directory in dir_list: if directory == 'rarefaction' or directory == 'unrarefied_bdiv': continue input_dir = os.path.join(args.data_directory, directory) input_path = os.path.join(input_dir, "emperor_pcoa_plots") output_path = os.path.join(args.html_dir, directory) cmd = 'cp -r ' + input_path + ' ' + output_path os.system(cmd) input_path = os.path.join(input_dir, "pcoa/*") output_path = os.path.join(args.data_directory, "pcoa") cmd = 'cp -r ' + input_path + ' ' + output_path os.system(cmd) input_path = os.path.join(input_dir, "rare_dm/*") output_path = os.path.join(args.data_directory, "rare_dm") cmd = 'cp -r ' + input_path + ' ' + output_path os.system(cmd) input_path = os.path.join(input_dir, "rare_upgma/*") output_path = os.path.join(args.data_directory, "rare_upgma") cmd = 'cp -r ' + input_path + ' ' + output_path os.system(cmd) input_path = os.path.join(input_dir, "upgma_cmp/*") output_path = os.path.join(args.data_directory, "upgma_cmp") cmd = 'cp -r ' + input_path + ' ' + output_path os.system(cmd) input_path = os.path.join(input_dir, "rare_upgma_consensus.tre") output_path = os.path.join( args.data_directory, "rare_upgma_consensus", directory + '.tre') cmd = 'cp ' + input_path + ' ' + output_path 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)