Mercurial > repos > iuc > virannot_otu

annotate rps2tree_html.py @ 4:adcf06db3030 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
author iuc
date Tue, 13 May 2025 11:52:27 +0000
parents c9dac9b2e01c
children
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c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
1 #!/usr/bin/env python3
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
2 import argparse
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
3 import csv
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
4 import logging
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
5 import sys
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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6
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
7
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
8 logging.basicConfig(level=logging.INFO)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
9 logger = logging.getLogger(__name__)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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10
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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11
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
12 def main():
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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13 options = _set_options()
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
14 data, headers = _read_map_file(options.map)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
15 html = _print_html(data, headers, options.out)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
16 index_file = options.out + '/index.html'
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
17 fh = open(index_file, mode='w')
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
18 fh.write(html)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
19 fh.close()
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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20
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
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21
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
22 def _get_google_script_headers(data, headers, out_dir):
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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23 html = '<script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
24 html += '<script type="text/javascript">' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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25 html += 'google.charts.load(\'current\', {\'packages\':[\'table\']});' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
26 chart_names, java_scripts = _get_google_js(data, headers, out_dir)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
27 for i in range(0, len(chart_names)):
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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28 html += 'google.charts.setOnLoadCallback(' + chart_names[i].replace('-', '_') + ');' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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29 html += 'function ' + chart_names[i].replace('-', '_') + '() {' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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30 html += java_scripts[i] + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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31 html += '}' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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32 html += '</script>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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33 return html
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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34
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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35
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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36 def _get_google_js(data, headers, out_dir):
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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37 java_scripts = []
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
38 chart_names = []
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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39 for cdd in data:
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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40 chart_names.append(cdd['cdd_id'] + '_' + cdd['description'])
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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41 js = 'var data = new google.visualization.DataTable();' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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42 mat, head = _parse_csv(out_dir + '/' + cdd['cluster_nb_reads_files'])
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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43 for el in head:
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
44 if el == '#OTU_name':
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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45 js += 'data.addColumn(\'string\', \'' + el + '\');' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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46 elif el == 'taxonomy':
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
47 js += 'data.addColumn(\'string\', \'' + el + '\');' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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48 elif el == 'contigs_list' or el == 'seq_list':
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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49 js += 'data.addColumn(\'string\', \'' + el + '\');' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
50 else:
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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51 js += 'data.addColumn(\'number\', \'' + el + '\');' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
52 js += 'data.addRows([' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
53 for j in range(0, len(mat)):
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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54 js += '[\'' + mat[j][head[0]] + '\''
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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55 for i in range(1, len(head) - 2):
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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56 js += ',' + mat[j][head[i]]
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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57 js += ',\'' + mat[j][head[len(head) - 2]] + '\''
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
58 js += ',\'' + mat[j][head[len(head) - 1]] + '\''
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
59 js += ']'
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
60 if j != (len(mat) - 1):
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
61 js += ','
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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62 js += "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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63 js += ']);' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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64 js += 'var table = new google.visualization.Table(document.getElementById(\'' + (cdd['cdd_id'] + '_' + cdd['description']).replace('-', '_') + '_div' + '\'));' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
65 js += 'table.draw(data, {showRowNumber: false, width: \'70%\', height: \'70%\'});' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
66 java_scripts.append(js)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
67 return chart_names, java_scripts
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
68
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
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69
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
70 def _parse_csv(file):
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
71 fh = open(file)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
72 reader = csv.reader(fh, delimiter="\t")
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
73 data = list(reader)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
74 headers = data[0]
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
75 matrix = []
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
76 for i in range(1, len(data)):
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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77 dict = {}
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
78 for j in range(0, len(data[i])):
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
79 if data[i][j] == '':
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
80 dict[headers[j]] = None
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
81 elif data[i][j] == 'null':
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
82 dict[headers[j]] = None
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
83 else:
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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84 dict[headers[j]] = data[i][j]
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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85 matrix.append(dict)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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86 return matrix, headers
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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87
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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88
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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89 def _print_html(data, headers, out_dir):
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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90 html = '<html>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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91 html += '<head>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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92 html += '<title>' + 'rps2tree' + '</title>'
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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93 html += _get_google_script_headers(data, headers, out_dir)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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94 html += '</head>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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95 html += '<div style="text-align:center">' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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96 html += '<h1 align=center>rps2tree</h1>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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97 html += '<body>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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98 html += _print_data(data, headers)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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99 html += '</body>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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100 html += '</div>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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101 html += '</html>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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102 return html
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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103
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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104
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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105 def _print_data(data, headers):
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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106 html = ''
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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107 for cdd in data:
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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108 html += '<h2>' + cdd['cdd_id'] + ' ' + cdd['description'] + '</h2>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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109 html += '<p>' + cdd['full_description'] + '</br>' + '</p>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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110 html += '<div id="' + (cdd['cdd_id'] + '_' + cdd['description']).replace('-', '_') + '_div' + '"></div>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
111 html += '</br>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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112 html += '</br>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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113 html += '<img src=' + cdd['tree_files'] + ' href="' + cdd['tree_files'] + '">' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
114 html += '</br>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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115 html += '<a href="' + cdd['align_files'] + '">' + cdd['align_files'] + '</a>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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116 html += '</br>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
117 html += '<a href="' + cdd['cluster_files'] + '">' + cdd['cluster_files'] + '</a>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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118 html += '</br>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
119 html += '<a href="' + cdd['cluster_nb_reads_files'] + '">' + cdd['cluster_nb_reads_files'] + '</a>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
120 html += '</br>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
121 html += '<a href="' + cdd['pairwise_files'] + '">' + cdd['pairwise_files'] + '</a>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
122 html += '</br>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
123 html += '</br>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
124 html += '<hr>' + "\n"
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
125 return html
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
126
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
diff changeset
127
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
diff changeset
128 def _read_map_file(file):
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
129 reader = csv.reader(file, delimiter="\t")
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
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130 data = list(reader)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
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131 headers = data[0]
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
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132 headers[0] = headers[0][1:]
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
diff changeset
133 map_obj = []
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
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134 for i in range(1, len(data)):
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
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135 dict = {}
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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136 if len(data[i]) != len(headers):
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
137 sys.exit('line and headers not the same length.')
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
138 for j in range(0, len(headers)):
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
139 dict[headers[j]] = data[i][j]
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
140 map_obj.append(dict)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
diff changeset
141 return map_obj, headers
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
diff changeset
142
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
diff changeset
143
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
diff changeset
144 def _set_options():
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
145 parser = argparse.ArgumentParser()
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
146 parser.add_argument('-m', '--map', help='The map file produced by rps2tree.pl script.', action='store', type=argparse.FileType('r'), required=True)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
diff changeset
147 parser.add_argument('-o', '--out', help='The title for the HTML page.', action='store', type=str, default='./')
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
diff changeset
148 args = parser.parse_args()
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
diff changeset
149 return args
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
diff changeset
150
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
diff changeset
151
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
diff changeset
152 if __name__ == "__main__":
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
153 main()