Mercurial > repos > immuneml > immuneml_tools

annotate test.py @ 2:9bf78cb6b91d draft

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"planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
author immuneml
date Thu, 01 Jul 2021 14:43:41 +0000
parents 629e7e403e19
children
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immuneml
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1 import argparse
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immuneml
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2 import os
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3 from shutil import copyfile
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4
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immuneml
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5 #immuneml --inputs file1 file2 file3 --output_dir /some/path --yaml_path abc.yml --metadata abc.csv --tool galaxy_yaml_tool
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6
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7 def get_args():
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8 parser = argparse.ArgumentParser(description='Tool for detecting known and novel MicroRNAs')
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immuneml
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9 parser.add_argument('-o', '--output_dir', help='Output directory', default='.', required=True)
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immuneml
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10 parser.add_argument('-i', '--inputs', help='Input directory', default='.', required=True, nargs='+')
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immuneml
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11 parser.add_argument('-y', '--yaml', help='Yaml input', default='.', required=True)
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12 parser.add_argument('-m', '--metadata', help='Metadata input', default='.', required=False)
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13 parser.add_argument('-t', '--tool', help='Tool', default='.', required=False)
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14
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15 return parser.parse_args()
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17
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18 def main():
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19 print('main')
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20 args = get_args()
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21
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22 print(args.output_dir)
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23 print(args.inputs)
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24
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25 #os.mkdir(args.output_dir)
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immuneml
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26 i = 0
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27 html_files_links = ''
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28 for f in args.inputs:
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29 filename = str(i) + '.txt'
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30 copyfile(f, os.path.join(args.output_dir, str(i) + '.txt'))
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31 i += 1
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32 html_files_links += '<li><a href="' + filename + '" title="' + filename + '">Input file ' + str(i) + '</a></li>'
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33
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34 copyfile(args.yaml, os.path.join(args.output_dir, 'yaml_file.txt'))
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immuneml
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35 copyfile(args.metadata, os.path.join(args.output_dir, 'metadata_file.txt'))
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immuneml
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36 copyfile('pipout.txt', os.path.join(args.output_dir, 'pipout.txt'))
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immuneml
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37 copyfile('immuneout.txt', os.path.join(args.output_dir, 'immuneout.txt'))
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immuneml
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38 html_files_links += '<li><a href="yaml_file.txt" title="YAML file">YAML file</a></li>'
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immuneml
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39 html_files_links += '<li><a href="metadata_file.txt" title="Metadata file">Metadata file</a></li>'
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immuneml
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40 html_files_links += '<li><a href="pipout.txt" title="Pip output">Pip output</a></li>'
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immuneml
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41 html_files_links += '<li><a href="immuneout.txt" title="ImmuneML output">ImmuneML output</a></li>'
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42
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43 html_output = open(os.path.join(args.output_dir, 'output.html'), 'w')
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45 html_test = '''<nav>
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46 <ul>'''
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47
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48 html_test += html_files_links
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49 html_test += '''</ul>
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50 </nav>'''
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51 html_output.write(html_test)
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52 html_output.close()
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55 if __name__ == '__main__':
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56 main()
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