comparison beta_diversity_through_plots_html_generation.py @ 0:a3d1104d090c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
author iuc
date Thu, 18 May 2017 09:28:39 -0400
parents
children a3b69e0b9246
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-1:000000000000 0:a3d1104d090c
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)