Mercurial > repos > iuc > qiime_plot_taxa_summary
diff beta_diversity_through_plots_html_generation.py @ 0:78b8aba19876 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
| author | iuc |
|---|---|
| date | Thu, 18 May 2017 09:29:27 -0400 |
| parents | |
| children | c6d84b3ad9db |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/beta_diversity_through_plots_html_generation.py Thu May 18 09:29:27 2017 -0400 @@ -0,0 +1,63 @@ +#!/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)