Mercurial > repos > iuc > qiime_split_libraries_fastq
diff jackknifed_beta_diversity_output_management.py @ 0:20194da2549d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
| author | iuc |
|---|---|
| date | Fri, 19 May 2017 03:54:05 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/jackknifed_beta_diversity_output_management.py Fri May 19 03:54:05 2017 -0400 @@ -0,0 +1,99 @@ +#!/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)