Mercurial > repos > jankanis > blast2html2

annotate visualise.py @ 10:2fbdf2eb27b4

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All data is displayed now, still some formatting to do
author Jan Kanis <jan.code@jankanis.nl>
date Fri, 09 May 2014 18:16:48 +0200
parents 9e7927673089
children 7660519f2dc9
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1 #!/usr/bin/env python3
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2
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3 # Copyright The Hyve B.V. 2014
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4 # License: GPL version 3 or higher
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5
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6 import sys
7
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7 import math
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8 import warnings
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9 from itertools import repeat
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10 from lxml import objectify
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11 import jinja2
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12
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13
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14 blast = objectify.parse('blast xml example1.xml').getroot()
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15 loader = jinja2.FileSystemLoader(searchpath='.')
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16 environment = jinja2.Environment(loader=loader, lstrip_blocks=True, trim_blocks=True, autoescape=True)
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17
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18 def filter(func_or_name):
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19 if isinstance(func_or_name, str):
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20 def inner(func):
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21 environment.filters[func_or_name] = func
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22 return func
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23 return inner
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24 else:
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25 environment.filters[func_or_name.__name__] = func_or_name
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26 return func_or_name
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28
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29 def color_idx(length):
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30 if length < 40:
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31 return 0
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32 elif length < 50:
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33 return 1
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34 elif length < 80:
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35 return 2
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36 elif length < 200:
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37 return 3
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38 return 4
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39
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40 colors = ['black', 'blue', 'green', 'magenta', 'red']
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41
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42 environment.filters['color'] = lambda length: match_colors[color_idx(length)]
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43
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44 @filter
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45 def fmt(val, fmt):
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46 return format(float(val), fmt)
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47
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48 @filter
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49 def firsttitle(hit):
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50 return hit.Hit_def.text.split('>')[0]
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51
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52 @filter
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53 def othertitles(hit):
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54 """Split a hit.Hit_def that contains multiple titles up, splitting out the hit ids from the titles."""
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55 id_titles = hit.Hit_def.text.split('>')
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56
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57 titles = []
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58 for t in id_titles[1:]:
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59 fullid, title = t.split(' ', 1)
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60 id = fullid.split('|', 2)[2]
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61 titles.append(dict(id = id,
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62 fullid = fullid,
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63 title = title))
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64 return titles
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65
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66 @filter
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67 def hitid(hit):
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68 return hit.Hit_id.text.split('|', 2)[1]
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69
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70 @filter
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71 def seqid(hit):
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72 return hit.Hit_id.text.split('|', 2)[2]
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73
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74 @filter
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75 def alignment_pre(hsp):
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76 return (
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77 "Query {:>7s} {} {}\n".format(hsp['Hsp_query-from'], hsp.Hsp_qseq, hsp['Hsp_query-to']) +
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78 " {:7s} {}\n".format('', hsp.Hsp_midline) +
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79 "Subject {:>7s} {} {}".format(hsp['Hsp_hit-from'], hsp.Hsp_hseq, hsp['Hsp_hit-to']))
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80
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81 @filter('len')
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82 def hsplen(node):
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83 return int(node['Hsp_align-len'])
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84
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85 @filter
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86 def asframe(frame):
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87 if frame == 1:
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88 return 'Plus'
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89 elif frame == -1:
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90 return 'Minus'
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91 raise Exception("frame should be either +1 or -1")
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92
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93
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94 query_length = int(blast["BlastOutput_query-len"])
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95
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96 hits = blast.BlastOutput_iterations.Iteration.Iteration_hits.Hit
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97 # sort hits by longest hotspot first
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98 ordered_hits = sorted(hits,
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99 key=lambda h: max(hsplen(hsp) for hsp in h.Hit_hsps.Hsp),
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100 reverse=True)
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101
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102 def match_colors():
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103 """
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104 An iterator that yields lists of length-color pairs.
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105 """
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106
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107 percent_multiplier = 100 / query_length
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108
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109 for hit in hits:
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110 # sort hotspots from short to long, so we can overwrite index colors of
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111 # short matches with those of long ones.
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112 hotspots = sorted(hit.Hit_hsps.Hsp, key=lambda hsp: hsplen(hsp))
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113 table = bytearray([255]) * query_length
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114 for hsp in hotspots:
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115 frm = hsp['Hsp_query-from'] - 1
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116 to = int(hsp['Hsp_query-to'])
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117 table[frm:to] = repeat(color_idx(hsplen(hsp)), to - frm)
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118
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119 matches = []
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120 last = table[0]
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121 count = 0
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122 for i in range(query_length):
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123 if table[i] == last:
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124 count += 1
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125 continue
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126 matches.append((count * percent_multiplier, colors[last] if last != 255 else 'none'))
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127 last = table[i]
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128 count = 1
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129 matches.append((count * percent_multiplier, colors[last] if last != 255 else 'none'))
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130
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131 yield dict(colors=matches, link="#hit"+hit.Hit_num.text, defline=firsttitle(hit))
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132
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133
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134 def queryscale():
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135 max_labels = 10
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136 skip = math.ceil(query_length / max_labels)
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137 percent_multiplier = 100 / query_length
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138 for i in range(1, query_length+1):
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139 if i % skip == 0:
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140 yield dict(label = i, width = skip * percent_multiplier)
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141 if query_length % skip != 0:
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142 yield dict(label = query_length, width = (query_length % skip) * percent_multiplier)
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143
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144
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145 def hit_info():
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146
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147 for hit in ordered_hits:
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148 hsps = hit.Hit_hsps.Hsp
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149
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150 cover = [False] * query_length
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151 for hsp in hsps:
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152 cover[hsp['Hsp_query-from']-1 : int(hsp['Hsp_query-to'])] = repeat(True, hsplen(hsp))
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153 cover_count = cover.count(True)
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154
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155 def hsp_val(path):
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156 return (hsp[path] for hsp in hsps)
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157
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158 yield dict(title = firsttitle(hit),
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159 link_id = hit.Hit_num,
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160 maxscore = "{:.1f}".format(float(max(hsp_val('Hsp_bit-score')))),
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161 totalscore = "{:.1f}".format(float(sum(hsp_val('Hsp_bit-score')))),
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162 cover = "{:.0%}".format(cover_count / query_length),
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163 e_value = "{:.4g}".format(float(min(hsp_val('Hsp_evalue')))),
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164 # FIXME: is this the correct formula vv?
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165 ident = "{:.0%}".format(float(min(hsp.Hsp_identity / hsplen(hsp) for hsp in hsps))),
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166 accession = hit.Hit_accession)
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167
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168
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169 def main():
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170 template = environment.get_template('visualise.html.jinja')
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171
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172 params = (('Query ID', blast["BlastOutput_query-ID"]),
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173 ('Query definition', blast["BlastOutput_query-def"]),
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174 ('Query length', blast["BlastOutput_query-len"]),
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175 ('Program', blast.BlastOutput_version),
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176 ('Database', blast.BlastOutput_db),
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177 )
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178
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179 if len(blast.BlastOutput_iterations.Iteration) > 1:
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180 warnings.warn("Multiple 'Iteration' elements found, showing only the first")
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181
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182 sys.stdout.write(template.render(blast=blast,
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183 length=query_length,
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184 hits=blast.BlastOutput_iterations.Iteration.Iteration_hits.Hit,
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185 colors=colors,
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186 match_colors=match_colors(),
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187 queryscale=queryscale(),
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188 hit_info=hit_info(),
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189 params=params))
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190
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191 main()