Mercurial > repos > jankanis > blast2html
annotate blast2html.py @ 50:bfc82a8aa3c9
unicodify python sources
| author | Jan Kanis <jan.code@jankanis.nl> |
|---|---|
| date | Wed, 21 May 2014 18:17:03 +0200 |
| parents | 4e6ac737ba17 |
| children | b15a20c2372a |
| rev | line source |
|---|---|
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1 #!/usr/bin/env python3 |
| 50 | 2 # -*- coding: utf-8 -*- |
| 3 # | |
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4 # Actually runs under either python 2 or 3 |
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5 |
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6 # Copyright The Hyve B.V. 2014 |
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7 # License: GPL version 3 or higher |
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8 |
| 50 | 9 from __future__ import unicode_literals |
| 10 | |
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11 import sys |
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12 import math |
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13 import warnings |
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14 from os import path |
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15 from itertools import repeat |
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16 import argparse |
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17 from lxml import objectify |
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18 import jinja2 |
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19 |
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20 |
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21 |
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22 _filters = {} |
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23 def filter(func_or_name): |
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24 "Decorator to register a function as filter in the current jinja environment" |
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25 if isinstance(func_or_name, str): |
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26 def inner(func): |
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27 _filters[func_or_name] = func.__name__ |
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28 return func |
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29 return inner |
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30 else: |
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31 _filters[func_or_name.__name__] = func_or_name.__name__ |
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32 return func_or_name |
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33 |
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34 |
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35 def color_idx(length): |
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36 if length < 40: |
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37 return 0 |
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38 elif length < 50: |
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39 return 1 |
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40 elif length < 80: |
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41 return 2 |
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42 elif length < 200: |
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43 return 3 |
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44 return 4 |
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45 |
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46 @filter |
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47 def fmt(val, fmt): |
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48 return format(float(val), fmt) |
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49 |
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50 @filter |
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51 def firsttitle(hit): |
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52 return hit.Hit_def.text.split('>')[0] |
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53 |
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54 @filter |
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55 def othertitles(hit): |
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56 """Split a hit.Hit_def that contains multiple titles up, splitting out the hit ids from the titles.""" |
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57 id_titles = hit.Hit_def.text.split('>') |
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58 |
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59 titles = [] |
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60 for t in id_titles[1:]: |
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61 fullid, title = t.split(' ', 1) |
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62 hitid, id = fullid.split('|', 2)[1:3] |
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63 titles.append(dict(id = id, |
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64 hitid = hitid, |
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65 fullid = fullid, |
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66 title = title)) |
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67 return titles |
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68 |
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69 @filter |
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70 def hitid(hit): |
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71 hitid = hit.Hit_id.text |
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72 s = hitid.split('|', 2) |
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73 if len(s) >= 2: |
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74 return s[1] |
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75 return hitid |
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76 |
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77 @filter |
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78 def seqid(hit): |
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79 hitid = hit.Hit_id.text |
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80 s = hitid.split('|', 2) |
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81 if len(s) >= 3: |
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82 return s[2] |
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83 return hitid |
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84 |
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85 |
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86 @filter |
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87 def alignment_pre(hsp): |
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88 return ( |
| 15 | 89 "Query {:>7s} {} {}\n".format(hsp['Hsp_query-from'].text, hsp.Hsp_qseq, hsp['Hsp_query-to']) + |
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90 " {:7s} {}\n".format('', hsp.Hsp_midline) + |
| 15 | 91 "Subject{:>7s} {} {}".format(hsp['Hsp_hit-from'].text, hsp.Hsp_hseq, hsp['Hsp_hit-to']) |
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92 ) |
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93 |
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94 @filter('len') |
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95 def blastxml_len(node): |
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96 if node.tag == 'Hsp': |
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97 return int(node['Hsp_align-len']) |
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98 elif node.tag == 'Iteration': |
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99 return int(node['Iteration_query-len']) |
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100 raise Exception("Unknown XML node type: "+node.tag) |
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101 |
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102 |
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103 @filter |
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104 def asframe(frame): |
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105 if frame == 1: |
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106 return 'Plus' |
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107 elif frame == -1: |
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108 return 'Minus' |
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109 raise Exception("frame should be either +1 or -1") |
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110 |
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111 def genelink(hit, type='genbank', hsp=None): |
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112 if not isinstance(hit, str): |
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113 hit = hitid(hit) |
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114 link = "http://www.ncbi.nlm.nih.gov/nucleotide/{}?report={}&log$=nuclalign".format(hit, type) |
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115 if hsp != None: |
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116 link += "&from={}&to={}".format(hsp['Hsp_hit-from'], hsp['Hsp_hit-to']) |
| 16 | 117 return link |
| 118 | |
| 119 | |
| 120 # javascript escape filter based on Django's, from https://github.com/dsissitka/khan-website/blob/master/templatefilters.py#L112-139 | |
| 121 # I've removed the html escapes, since html escaping is already being performed by the template engine. | |
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122 |
| 16 | 123 _base_js_escapes = ( |
| 124 ('\\', r'\u005C'), | |
| 125 ('\'', r'\u0027'), | |
| 126 ('"', r'\u0022'), | |
| 127 # ('>', r'\u003E'), | |
| 128 # ('<', r'\u003C'), | |
| 129 # ('&', r'\u0026'), | |
| 130 # ('=', r'\u003D'), | |
| 131 # ('-', r'\u002D'), | |
| 132 # (';', r'\u003B'), | |
| 133 # (u'\u2028', r'\u2028'), | |
| 134 # (u'\u2029', r'\u2029') | |
| 135 ) | |
| 136 | |
| 137 # Escape every ASCII character with a value less than 32. This is | |
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138 # needed a.o. to prevent html parsers from jumping out of javascript |
| 16 | 139 # parsing mode. |
| 140 _js_escapes = (_base_js_escapes + | |
| 141 tuple(('%c' % z, '\\u%04X' % z) for z in range(32))) | |
| 142 | |
| 143 @filter | |
| 144 def js_string_escape(value): | |
| 145 """Escape javascript string literal escapes. Note that this only works | |
| 146 within javascript string literals, not in general javascript | |
| 147 snippets.""" | |
| 148 | |
| 149 value = str(value) | |
| 150 | |
| 151 for bad, good in _js_escapes: | |
| 152 value = value.replace(bad, good) | |
| 153 | |
| 154 return value | |
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155 |
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156 @filter |
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157 def hits(result): |
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158 # sort hits by longest hotspot first |
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159 return sorted(result.Iteration_hits.findall('Hit'), |
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160 key=lambda h: max(blastxml_len(hsp) for hsp in h.Hit_hsps.Hsp), |
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161 reverse=True) |
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162 |
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163 |
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164 |
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165 class BlastVisualize: |
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166 |
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167 colors = ('black', 'blue', 'green', 'magenta', 'red') |
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168 |
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169 max_scale_labels = 10 |
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170 |
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171 def __init__(self, input, templatedir, templatename): |
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172 self.input = input |
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173 self.templatename = templatename |
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174 |
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175 self.blast = objectify.parse(self.input).getroot() |
| 50 | 176 self.loader = jinja2.FileSystemLoader(searchpath=templatedir, encoding='utf-8') |
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177 self.environment = jinja2.Environment(loader=self.loader, |
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178 lstrip_blocks=True, trim_blocks=True, autoescape=True) |
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179 |
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180 self._addfilters(self.environment) |
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181 |
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182 |
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183 def _addfilters(self, environment): |
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184 for filtername, funcname in _filters.items(): |
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185 try: |
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186 environment.filters[filtername] = getattr(self, funcname) |
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187 except AttributeError: |
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188 environment.filters[filtername] = globals()[funcname] |
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189 |
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190 def render(self, output): |
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191 template = self.environment.get_template(self.templatename) |
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192 |
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193 params = (('Query ID', self.blast["BlastOutput_query-ID"]), |
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194 ('Query definition', self.blast["BlastOutput_query-def"]), |
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195 ('Query length', self.blast["BlastOutput_query-len"]), |
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196 ('Program', self.blast.BlastOutput_version), |
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197 ('Database', self.blast.BlastOutput_db), |
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198 ) |
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199 |
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200 output.write(template.render(blast=self.blast, |
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201 iterations=self.blast.BlastOutput_iterations.Iteration, |
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202 colors=self.colors, |
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203 # match_colors=self.match_colors(), |
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204 # hit_info=self.hit_info(), |
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205 genelink=genelink, |
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206 params=params)) |
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207 |
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208 @filter |
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209 def match_colors(self, result): |
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210 """ |
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211 An iterator that yields lists of length-color pairs. |
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212 """ |
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213 |
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214 query_length = blastxml_len(result) |
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215 |
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216 percent_multiplier = 100 / query_length |
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217 |
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218 for hit in hits(result): |
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219 # sort hotspots from short to long, so we can overwrite index colors of |
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220 # short matches with those of long ones. |
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221 hotspots = sorted(hit.Hit_hsps.Hsp, key=lambda hsp: blastxml_len(hsp)) |
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222 table = bytearray([255]) * query_length |
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223 for hsp in hotspots: |
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224 frm = hsp['Hsp_query-from'] - 1 |
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225 to = int(hsp['Hsp_query-to']) |
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226 table[frm:to] = repeat(color_idx(blastxml_len(hsp)), to - frm) |
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227 |
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228 matches = [] |
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229 last = table[0] |
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230 count = 0 |
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231 for i in range(query_length): |
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232 if table[i] == last: |
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233 count += 1 |
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234 continue |
| 16 | 235 matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent')) |
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236 last = table[i] |
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237 count = 1 |
| 16 | 238 matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent')) |
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239 |
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240 yield dict(colors=matches, link="#hit"+hit.Hit_num.text, defline=firsttitle(hit)) |
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241 |
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242 @filter |
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243 def queryscale(self, result): |
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244 query_length = blastxml_len(result) |
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245 skip = math.ceil(query_length / self.max_scale_labels) |
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246 percent_multiplier = 100 / query_length |
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247 for i in range(1, query_length+1): |
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248 if i % skip == 0: |
| 23 | 249 yield dict(label = i, width = skip * percent_multiplier) |
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250 if query_length % skip != 0: |
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251 yield dict(label = query_length, |
| 23 | 252 width = (query_length % skip) * percent_multiplier) |
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253 |
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254 @filter |
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255 def hit_info(self, result): |
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256 |
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257 query_length = blastxml_len(result) |
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258 |
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259 for hit in hits(result): |
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260 hsps = hit.Hit_hsps.Hsp |
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261 |
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262 cover = [False] * query_length |
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263 for hsp in hsps: |
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264 cover[hsp['Hsp_query-from']-1 : int(hsp['Hsp_query-to'])] = repeat(True, blastxml_len(hsp)) |
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265 cover_count = cover.count(True) |
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266 |
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267 def hsp_val(path): |
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268 return (float(hsp[path]) for hsp in hsps) |
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269 |
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270 yield dict(hit = hit, |
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271 title = firsttitle(hit), |
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272 link_id = hit.Hit_num, |
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273 maxscore = "{:.1f}".format(max(hsp_val('Hsp_bit-score'))), |
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274 totalscore = "{:.1f}".format(sum(hsp_val('Hsp_bit-score'))), |
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275 cover = "{:.0%}".format(cover_count / query_length), |
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276 e_value = "{:.4g}".format(min(hsp_val('Hsp_evalue'))), |
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277 # FIXME: is this the correct formula vv? |
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278 ident = "{:.0%}".format(float(min(hsp.Hsp_identity / blastxml_len(hsp) for hsp in hsps))), |
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279 accession = hit.Hit_accession) |
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280 |
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281 |
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282 def main(): |
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283 default_template = path.join(path.dirname(__file__), 'blast2html.html.jinja') |
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284 |
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285 parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page", |
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286 usage="{} [-i] INPUT [-o OUTPUT]".format(sys.argv[0])) |
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287 input_group = parser.add_mutually_exclusive_group(required=True) |
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288 input_group.add_argument('positional_arg', metavar='INPUT', nargs='?', type=argparse.FileType(mode='r'), |
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289 help='The input Blast XML file, same as -i/--input') |
| 50 | 290 input_group.add_argument('-i', '--input', type=argparse.FileType(mode='r', encoding='utf-8'), |
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291 help='The input Blast XML file') |
| 50 | 292 parser.add_argument('-o', '--output', type=argparse.FileType(mode='w', encoding='utf-8'), default=sys.stdout, |
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293 help='The output html file') |
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294 # We just want the file name here, so jinja can open the file |
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295 # itself. But it is easier to just use a FileType so argparse can |
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296 # handle the errors. This introduces a small race condition when |
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297 # jinja later tries to re-open the template file, but we don't |
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298 # care too much. |
| 50 | 299 parser.add_argument('--template', type=argparse.FileType(mode='r', encoding='utf-8'), default=default_template, |
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300 help='The template file to use. Defaults to blast_html.html.jinja') |
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301 |
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302 args = parser.parse_args() |
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303 if args.input == None: |
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304 args.input = args.positional_arg |
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305 if args.input == None: |
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306 parser.error('no input specified') |
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307 |
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308 templatedir, templatename = path.split(args.template.name) |
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309 args.template.close() |
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310 if not templatedir: |
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311 templatedir = '.' |
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312 |
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313 b = BlastVisualize(args.input, templatedir, templatename) |
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314 b.render(args.output) |
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315 |
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316 |
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317 if __name__ == '__main__': |
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318 main() |
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319 |