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1 #!/usr/bin/env python
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2
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3 import os
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4 import re
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5 import sys
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6
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7 START = '''<html>
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8 <head>
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9 <style>
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10 a:link { text-decoration: none; color: red; }
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11 a:visited { text-decoration: none; color: blue; }
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12 a:hover { text-decoration: underline; color: green; } a:active { text-decoration: underline; color: green; }
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13 </style>
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14 </head>
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15 <body>
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16 <h1>InterProScan result summary page</h1>
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17 '''
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18
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19 END = '''
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20 </body>
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21 </html>
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22 '''
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23
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24
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25 def raw_mode(html_file, directory):
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26 with open(html_file, 'w') as h:
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27 h.write(START)
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28 h.write('<ul>')
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29 for filename in [f for f in sorted(os.listdir(directory)) if os.path.isfile(os.path.join(directory, f))]:
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30 h.write('<li><a href="%s"> %s </a></li>' % (filename, os.path.splitext(filename)[0]))
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31 h.write('</ul>')
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32 h.write(END)
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33
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34
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35 def fix_name(name):
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36 return re.sub('[&/]', '_', name)
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37
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38
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39 def cooked_mode(orfed_ids, tsv_file, html_file, directory):
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40 name_freq = {}
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41 with open(tsv_file) as f:
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42 for line in f:
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43 name = line.split("\t", 1)[0]
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44 if orfed_ids:
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45 deorfed_name = re.sub('_\\d+$', '', name)
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46 else:
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47 deorfed_name = name
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48
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49 data = name_freq.get(deorfed_name, [])
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50 if data:
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51 data[0] += 1
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52 data[1][name] = data[1].get(name, 0) + 1
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53 else:
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54 data = [1, {name: 1}]
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55 name_freq[deorfed_name] = data
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56
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57 name_freq_sorted = [(x[0], (x[1][0], sorted(x[1][1].items(), key=lambda t: t[1], reverse=True)))
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58 for x in sorted(name_freq.items(), key=lambda t: t[1][0], reverse=True)
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59 ]
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60
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61 filename_dict = {}
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62 for filename in [f for f in os.listdir(directory) if os.path.isfile(os.path.join(directory, f))]:
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63 filename_dict[os.path.splitext(filename)[0]] = filename
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64
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65 with open(html_file, 'w') as h:
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66 h.write(START)
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67 h.write('<ol>')
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68 for don, (freq, members) in name_freq_sorted:
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69 h.write('\n<li>')
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70 if len(members) == 1:
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71 fn = fix_name(members[0][0])
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72 if fn in filename_dict:
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73 h.write('<a href="%s"> %s (%d features)</a>' %
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74 (filename_dict[fn], members[0][0], members[0][1]))
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75 del filename_dict[fn]
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76 else:
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77 h.write('<a href="%s"> %s (%d features, broken link!)</a>' %
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78 (members[0][0], members[0][0], members[0][1]))
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79 else:
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80 h.write('%s (%d features)' % (don, freq))
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81 h.write('\n<ul>')
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82 for n, f in members:
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83 fn = fix_name(n)
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84 if fn in filename_dict:
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85 h.write('\n<li><a href="%s"> %s (%d features)</a></li>' % (filename_dict[fn], n, f))
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86 del filename_dict[fn]
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87 else:
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88 h.write('\n<li><a href="%s"> %s (%d features, broken link!)</a></li>' % (n, n, f))
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89 h.write('</ul>')
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90 h.write('</li>')
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91
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92 if len(filename_dict) > 0:
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93 h.write('<h2>Sequences without any features</h2>')
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94 h.write('\n<ul>')
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95 for n, p in sorted(filename_dict.items(), key=lambda t: t[0]):
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96 h.write('\n<li><a href="%s">%s</li>' % (p, n))
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97 h.write('</ul>')
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98 h.write('</ol>')
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99 h.write(END)
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100
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101
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102 def main():
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103 if len(sys.argv) == 3:
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104 raw_mode(sys.argv[1], sys.argv[2])
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105 elif len(sys.argv) == 5:
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106 cooked_mode(sys.argv[1] != '0', sys.argv[2], sys.argv[3], sys.argv[4])
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107 else:
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108 print('Args must be "html_file directory" or "[0|1] tsv_file html_file directory"')
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109 sys.exit(1)
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110
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111
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112 main()
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