Mercurial > repos > iuc > qiime_make_phylogeny

comparison jackknifed_beta_diversity_output_management.py @ 0:e82369a926e3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
author iuc
date Thu, 18 May 2017 09:34:15 -0400
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-1:000000000000 0:e82369a926e3
1 #!/usr/bin/env python
2 # -*- coding: utf-8 -*-
3
4 import argparse
5 import os
6
7
8 def generate_index_html(dir_list, args):
9 with open(args.html_file, 'w') as index_html_file:
10 s = '<html>\n'
11 s += '\t<head>\n'
12 s += '\t\t<title>Jackknifed beta diversity results</title>\n'
13 s += '\t</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\tEmperor PCoA plot after jacknifed beta diversity\n'
20 s += '\t\t\t<ul>\n'
21
22 for directory in dir_list:
23 if directory == 'rarefaction' or directory == 'unrarefied_bdiv':
24 continue
25
26 s += '\t\t\t\t<li><a href="' + directory
27 s += '/index.html">PCoA plots</a></td></li>\n'
28
29 s += '\t\t\t</ul>\n'
30 s += '\t\t</p>\n'
31 s += '\t</body>\n'
32 s += '</html>\n'
33 index_html_file.write(s)
34
35
36 def build_html(args):
37 os.mkdir(args.html_dir)
38
39 dir_list = [name for name in os.listdir(args.data_directory)
40 if os.path.isdir(os.path.join(
41 args.data_directory,
42 name))]
43
44 generate_index_html(dir_list, args)
45
46 os.mkdir(args.data_directory + '/pcoa')
47 os.mkdir(args.data_directory + '/rare_dm')
48 os.mkdir(args.data_directory + '/rare_upgma')
49 os.mkdir(args.data_directory + '/upgma_cmp')
50 os.mkdir(args.data_directory + '/rare_upgma_consensus')
51
52 for directory in dir_list:
53 if directory == 'rarefaction' or directory == 'unrarefied_bdiv':
54 continue
55
56 input_dir = os.path.join(args.data_directory, directory)
57
58 input_path = os.path.join(input_dir, "emperor_pcoa_plots")
59 output_path = os.path.join(args.html_dir, directory)
60 cmd = 'cp -r ' + input_path + ' ' + output_path
61 os.system(cmd)
62
63 input_path = os.path.join(input_dir, "pcoa/*")
64 output_path = os.path.join(args.data_directory, "pcoa")
65 cmd = 'cp -r ' + input_path + ' ' + output_path
66 os.system(cmd)
67
68 input_path = os.path.join(input_dir, "rare_dm/*")
69 output_path = os.path.join(args.data_directory, "rare_dm")
70 cmd = 'cp -r ' + input_path + ' ' + output_path
71 os.system(cmd)
72
73 input_path = os.path.join(input_dir, "rare_upgma/*")
74 output_path = os.path.join(args.data_directory, "rare_upgma")
75 cmd = 'cp -r ' + input_path + ' ' + output_path
76 os.system(cmd)
77
78 input_path = os.path.join(input_dir, "upgma_cmp/*")
79 output_path = os.path.join(args.data_directory, "upgma_cmp")
80 cmd = 'cp -r ' + input_path + ' ' + output_path
81 os.system(cmd)
82
83 input_path = os.path.join(input_dir, "rare_upgma_consensus.tre")
84 output_path = os.path.join(
85 args.data_directory,
86 "rare_upgma_consensus",
87 directory + '.tre')
88 cmd = 'cp ' + input_path + ' ' + output_path
89 os.system(cmd)
90
91
92 if __name__ == '__main__':
93 parser = argparse.ArgumentParser()
94 parser.add_argument('--data_directory', required=True)
95 parser.add_argument('--html_file', required=True)
96 parser.add_argument('--html_dir', required=True)
97 args = parser.parse_args()
98
99 build_html(args)