Mercurial > repos > iuc > qiime_align_seqs
comparison beta_diversity_through_plots_html_generation.py @ 0:56adf8db7ce7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
| author | iuc |
|---|---|
| date | Thu, 18 May 2017 09:33:27 -0400 |
| parents | |
| children | 2a132ceae8a8 |
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| -1:000000000000 | 0:56adf8db7ce7 |
|---|---|
| 1 #!/usr/bin/env python | |
| 2 # -*- coding: utf-8 -*- | |
| 3 | |
| 4 import argparse | |
| 5 import os | |
| 6 import re | |
| 7 | |
| 8 | |
| 9 def generate_index_html(dir_list, args): | |
| 10 with open(args.html_file, 'w') as index_html_file: | |
| 11 s = "" | |
| 12 s += '<html>\n' | |
| 13 s += '\t<head><title>PCoA beta diversity results</title></head>\n' | |
| 14 s += '\t<body>\n' | |
| 15 s += '\t\t<a href="http://www.qiime.org" target="_blank">' | |
| 16 s += '<img src="http://qiime.org/_static/wordpressheader.png" ' | |
| 17 s += 'alt="www.qiime.org""/></a>\n' | |
| 18 s += '\t\t<p>\n' | |
| 19 s += '\t\t\tBeta diversity metrics\n' | |
| 20 s += '\t\t\t<ul>\n' | |
| 21 | |
| 22 for directory in dir_list: | |
| 23 regexp_result = re.search( | |
| 24 '([a-zA-Z\_]*)_emperor_pcoa_plot', | |
| 25 directory) | |
| 26 metric = regexp_result.group(1) | |
| 27 s += '\t\t\t\t<li>' + metric + ': ' | |
| 28 s += '<a href="' + directory | |
| 29 s += '/index.html">PCoA results</a></td>\n' | |
| 30 s += '\t\t\t\t</li>\n' | |
| 31 | |
| 32 s += '\t\t\t</ul>\n' | |
| 33 s += '\t\t</p>\n' | |
| 34 s += '\t</body>\n' | |
| 35 s += '</html>\n' | |
| 36 | |
| 37 index_html_file.write(s) | |
| 38 | |
| 39 | |
| 40 def build_html(args): | |
| 41 os.mkdir(args.html_dir) | |
| 42 | |
| 43 dir_list = [name for name in os.listdir(args.data_directory) | |
| 44 if os.path.isdir(os.path.join( | |
| 45 args.data_directory, | |
| 46 name))] | |
| 47 | |
| 48 generate_index_html(dir_list, args) | |
| 49 | |
| 50 for directory in dir_list: | |
| 51 input_path = os.path.join(args.data_directory, directory) | |
| 52 cmd = 'cp -r ' + input_path + ' ' + args.html_dir | |
| 53 os.system(cmd) | |
| 54 | |
| 55 | |
| 56 if __name__ == '__main__': | |
| 57 parser = argparse.ArgumentParser() | |
| 58 parser.add_argument('--data_directory', required=True) | |
| 59 parser.add_argument('--html_file', required=True) | |
| 60 parser.add_argument('--html_dir', required=True) | |
| 61 args = parser.parse_args() | |
| 62 | |
| 63 build_html(args) |