Mercurial > repos > iuc > virannot_blast2tsv
diff rps2tree_html.py @ 0:e889010415a1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
| author | iuc |
|---|---|
| date | Mon, 04 Mar 2024 19:55:52 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rps2tree_html.py Mon Mar 04 19:55:52 2024 +0000 @@ -0,0 +1,153 @@ +#!/usr/bin/env python3 +import argparse +import csv +import logging +import sys + + +logging.basicConfig(level=logging.INFO) +logger = logging.getLogger(__name__) + + +def main(): + options = _set_options() + data, headers = _read_map_file(options.map) + html = _print_html(data, headers, options.out) + index_file = options.out + '/index.html' + fh = open(index_file, mode='w') + fh.write(html) + fh.close() + + +def _get_google_script_headers(data, headers, out_dir): + html = '<script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>' + "\n" + html += '<script type="text/javascript">' + "\n" + html += 'google.charts.load(\'current\', {\'packages\':[\'table\']});' + "\n" + chart_names, java_scripts = _get_google_js(data, headers, out_dir) + for i in range(0, len(chart_names)): + html += 'google.charts.setOnLoadCallback(' + chart_names[i].replace('-', '_') + ');' + "\n" + html += 'function ' + chart_names[i].replace('-', '_') + '() {' + "\n" + html += java_scripts[i] + "\n" + html += '}' + "\n" + html += '</script>' + "\n" + return html + + +def _get_google_js(data, headers, out_dir): + java_scripts = [] + chart_names = [] + for cdd in data: + chart_names.append(cdd['cdd_id'] + '_' + cdd['description']) + js = 'var data = new google.visualization.DataTable();' + "\n" + mat, head = _parse_csv(out_dir + '/' + cdd['cluster_nb_reads_files']) + for el in head: + if el == '#OTU_name': + js += 'data.addColumn(\'string\', \'' + el + '\');' + "\n" + elif el == 'taxonomy': + js += 'data.addColumn(\'string\', \'' + el + '\');' + "\n" + elif el == 'contigs_list' or el == 'seq_list': + js += 'data.addColumn(\'string\', \'' + el + '\');' + "\n" + else: + js += 'data.addColumn(\'number\', \'' + el + '\');' + "\n" + js += 'data.addRows([' + "\n" + for j in range(0, len(mat)): + js += '[\'' + mat[j][head[0]] + '\'' + for i in range(1, len(head) - 2): + js += ',' + mat[j][head[i]] + js += ',\'' + mat[j][head[len(head) - 2]] + '\'' + js += ',\'' + mat[j][head[len(head) - 1]] + '\'' + js += ']' + if j != (len(mat) - 1): + js += ',' + js += "\n" + js += ']);' + "\n" + js += 'var table = new google.visualization.Table(document.getElementById(\'' + (cdd['cdd_id'] + '_' + cdd['description']).replace('-', '_') + '_div' + '\'));' + "\n" + js += 'table.draw(data, {showRowNumber: false, width: \'70%\', height: \'70%\'});' + "\n" + java_scripts.append(js) + return chart_names, java_scripts + + +def _parse_csv(file): + fh = open(file) + reader = csv.reader(fh, delimiter="\t") + data = list(reader) + headers = data[0] + matrix = [] + for i in range(1, len(data)): + dict = {} + for j in range(0, len(data[i])): + if data[i][j] == '': + dict[headers[j]] = None + elif data[i][j] == 'null': + dict[headers[j]] = None + else: + dict[headers[j]] = data[i][j] + matrix.append(dict) + return matrix, headers + + +def _print_html(data, headers, out_dir): + html = '<html>' + "\n" + html += '<head>' + "\n" + html += '<title>' + 'rps2tree' + '</title>' + html += _get_google_script_headers(data, headers, out_dir) + html += '</head>' + "\n" + html += '<div style="text-align:center">' + "\n" + html += '<h1 align=center>rps2tree</h1>' + "\n" + html += '<body>' + "\n" + html += _print_data(data, headers) + html += '</body>' + "\n" + html += '</div>' + "\n" + html += '</html>' + "\n" + return html + + +def _print_data(data, headers): + html = '' + for cdd in data: + html += '<h2>' + cdd['cdd_id'] + ' ' + cdd['description'] + '</h2>' + "\n" + html += '<p>' + cdd['full_description'] + '</br>' + '</p>' + "\n" + html += '<div id="' + (cdd['cdd_id'] + '_' + cdd['description']).replace('-', '_') + '_div' + '"></div>' + "\n" + html += '</br>' + "\n" + html += '</br>' + "\n" + html += '<img src=' + cdd['tree_files'] + ' href="' + cdd['tree_files'] + '">' + "\n" + html += '</br>' + "\n" + html += '<a href="' + cdd['align_files'] + '">' + cdd['align_files'] + '</a>' + "\n" + html += '</br>' + "\n" + html += '<a href="' + cdd['cluster_files'] + '">' + cdd['cluster_files'] + '</a>' + "\n" + html += '</br>' + "\n" + html += '<a href="' + cdd['cluster_nb_reads_files'] + '">' + cdd['cluster_nb_reads_files'] + '</a>' + "\n" + html += '</br>' + "\n" + html += '<a href="' + cdd['pairwise_files'] + '">' + cdd['pairwise_files'] + '</a>' + "\n" + html += '</br>' + "\n" + html += '</br>' + "\n" + html += '<hr>' + "\n" + return html + + +def _read_map_file(file): + reader = csv.reader(file, delimiter="\t") + data = list(reader) + headers = data[0] + headers[0] = headers[0][1:] + map_obj = [] + for i in range(1, len(data)): + dict = {} + if len(data[i]) != len(headers): + sys.exit('line and headers not the same length.') + for j in range(0, len(headers)): + dict[headers[j]] = data[i][j] + map_obj.append(dict) + return map_obj, headers + + +def _set_options(): + parser = argparse.ArgumentParser() + parser.add_argument('-m', '--map', help='The map file produced by rps2tree.pl script.', action='store', type=argparse.FileType('r'), required=True) + parser.add_argument('-o', '--out', help='The title for the HTML page.', action='store', type=str, default='./') + args = parser.parse_args() + return args + + +if __name__ == "__main__": + main()