Mercurial > repos > jankanis > blast2html
annotate blast2html.py @ 54:d6c7b5de2833 draft
minor fix
| author | Jan Kanis <jan.code@jankanis.nl> |
|---|---|
| date | Wed, 21 May 2014 18:39:51 +0200 |
| parents | b15a20c2372a |
| children | 4217bb9cf1d3 |
| rev | line source |
|---|---|
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1 #!/usr/bin/env python3 |
| 52 | 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 |
| 52 | 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 |
| 53 | 16 import six |
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17 import argparse |
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18 from lxml import objectify |
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19 import jinja2 |
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20 |
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21 |
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22 |
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23 _filters = {} |
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24 def filter(func_or_name): |
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25 "Decorator to register a function as filter in the current jinja environment" |
| 53 | 26 if isinstance(func_or_name, six.string_types): |
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27 def inner(func): |
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28 _filters[func_or_name] = func.__name__ |
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29 return func |
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30 return inner |
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31 else: |
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32 _filters[func_or_name.__name__] = func_or_name.__name__ |
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33 return func_or_name |
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34 |
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35 |
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36 def color_idx(length): |
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37 if length < 40: |
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38 return 0 |
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39 elif length < 50: |
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40 return 1 |
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41 elif length < 80: |
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42 return 2 |
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43 elif length < 200: |
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44 return 3 |
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45 return 4 |
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46 |
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47 @filter |
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48 def fmt(val, fmt): |
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49 return format(float(val), fmt) |
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50 |
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51 @filter |
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52 def firsttitle(hit): |
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53 return hit.Hit_def.text.split('>')[0] |
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54 |
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55 @filter |
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56 def othertitles(hit): |
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57 """Split a hit.Hit_def that contains multiple titles up, splitting out the hit ids from the titles.""" |
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58 id_titles = hit.Hit_def.text.split('>') |
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59 |
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60 titles = [] |
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61 for t in id_titles[1:]: |
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62 fullid, title = t.split(' ', 1) |
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63 hitid, id = fullid.split('|', 2)[1:3] |
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64 titles.append(dict(id = id, |
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65 hitid = hitid, |
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66 fullid = fullid, |
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67 title = title)) |
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68 return titles |
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69 |
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70 @filter |
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71 def hitid(hit): |
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72 hitid = hit.Hit_id.text |
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73 s = hitid.split('|', 2) |
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74 if len(s) >= 2: |
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75 return s[1] |
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76 return hitid |
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77 |
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78 @filter |
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79 def seqid(hit): |
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80 hitid = hit.Hit_id.text |
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81 s = hitid.split('|', 2) |
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82 if len(s) >= 3: |
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83 return s[2] |
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84 return hitid |
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85 |
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86 |
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87 @filter |
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88 def alignment_pre(hsp): |
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89 return ( |
| 17 | 90 "Query {:>7s} {} {}\n".format(hsp['Hsp_query-from'].text, hsp.Hsp_qseq, hsp['Hsp_query-to']) + |
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91 " {:7s} {}\n".format('', hsp.Hsp_midline) + |
| 17 | 92 "Subject{:>7s} {} {}".format(hsp['Hsp_hit-from'].text, hsp.Hsp_hseq, hsp['Hsp_hit-to']) |
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93 ) |
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94 |
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95 @filter('len') |
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96 def blastxml_len(node): |
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97 if node.tag == 'Hsp': |
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98 return int(node['Hsp_align-len']) |
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99 elif node.tag == 'Iteration': |
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100 return int(node['Iteration_query-len']) |
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101 raise Exception("Unknown XML node type: "+node.tag) |
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102 |
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103 |
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104 @filter |
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105 def asframe(frame): |
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106 if frame == 1: |
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107 return 'Plus' |
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108 elif frame == -1: |
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109 return 'Minus' |
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110 raise Exception("frame should be either +1 or -1") |
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111 |
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112 def genelink(hit, type='genbank', hsp=None): |
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113 if not isinstance(hit, str): |
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114 hit = hitid(hit) |
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115 link = "http://www.ncbi.nlm.nih.gov/nucleotide/{}?report={}&log$=nuclalign".format(hit, type) |
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116 if hsp != None: |
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117 link += "&from={}&to={}".format(hsp['Hsp_hit-from'], hsp['Hsp_hit-to']) |
| 18 | 118 return link |
| 119 | |
| 120 | |
| 121 # javascript escape filter based on Django's, from https://github.com/dsissitka/khan-website/blob/master/templatefilters.py#L112-139 | |
| 122 # I've removed the html escapes, since html escaping is already being performed by the template engine. | |
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123 |
| 18 | 124 _base_js_escapes = ( |
| 125 ('\\', r'\u005C'), | |
| 126 ('\'', r'\u0027'), | |
| 127 ('"', r'\u0022'), | |
| 128 # ('>', r'\u003E'), | |
| 129 # ('<', r'\u003C'), | |
| 130 # ('&', r'\u0026'), | |
| 131 # ('=', r'\u003D'), | |
| 132 # ('-', r'\u002D'), | |
| 133 # (';', r'\u003B'), | |
| 134 # (u'\u2028', r'\u2028'), | |
| 135 # (u'\u2029', r'\u2029') | |
| 136 ) | |
| 137 | |
| 138 # Escape every ASCII character with a value less than 32. This is | |
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139 # needed a.o. to prevent html parsers from jumping out of javascript |
| 18 | 140 # parsing mode. |
| 141 _js_escapes = (_base_js_escapes + | |
| 142 tuple(('%c' % z, '\\u%04X' % z) for z in range(32))) | |
| 143 | |
| 144 @filter | |
| 145 def js_string_escape(value): | |
| 146 """Escape javascript string literal escapes. Note that this only works | |
| 147 within javascript string literals, not in general javascript | |
| 148 snippets.""" | |
| 149 | |
| 150 value = str(value) | |
| 151 | |
| 152 for bad, good in _js_escapes: | |
| 153 value = value.replace(bad, good) | |
| 154 | |
| 155 return value | |
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156 |
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157 @filter |
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158 def hits(result): |
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159 # sort hits by longest hotspot first |
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160 return sorted(result.Iteration_hits.findall('Hit'), |
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161 key=lambda h: max(blastxml_len(hsp) for hsp in h.Hit_hsps.Hsp), |
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162 reverse=True) |
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163 |
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164 |
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165 |
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166 class BlastVisualize: |
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167 |
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168 colors = ('black', 'blue', 'green', 'magenta', 'red') |
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169 |
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170 max_scale_labels = 10 |
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171 |
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172 def __init__(self, input, templatedir, templatename): |
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173 self.input = input |
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174 self.templatename = templatename |
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175 |
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176 self.blast = objectify.parse(self.input).getroot() |
| 52 | 177 self.loader = jinja2.FileSystemLoader(searchpath=templatedir, encoding='utf-8') |
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178 self.environment = jinja2.Environment(loader=self.loader, |
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179 lstrip_blocks=True, trim_blocks=True, autoescape=True) |
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180 |
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181 self._addfilters(self.environment) |
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182 |
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183 |
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184 def _addfilters(self, environment): |
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185 for filtername, funcname in _filters.items(): |
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186 try: |
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187 environment.filters[filtername] = getattr(self, funcname) |
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188 except AttributeError: |
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189 environment.filters[filtername] = globals()[funcname] |
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190 |
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191 def render(self, output): |
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192 template = self.environment.get_template(self.templatename) |
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193 |
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194 params = (('Query ID', self.blast["BlastOutput_query-ID"]), |
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195 ('Query definition', self.blast["BlastOutput_query-def"]), |
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196 ('Query length', self.blast["BlastOutput_query-len"]), |
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197 ('Program', self.blast.BlastOutput_version), |
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198 ('Database', self.blast.BlastOutput_db), |
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199 ) |
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200 |
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201 output.write(template.render(blast=self.blast, |
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202 iterations=self.blast.BlastOutput_iterations.Iteration, |
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203 colors=self.colors, |
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204 # match_colors=self.match_colors(), |
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205 # hit_info=self.hit_info(), |
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206 genelink=genelink, |
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207 params=params)) |
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208 |
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209 @filter |
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210 def match_colors(self, result): |
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211 """ |
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212 An iterator that yields lists of length-color pairs. |
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213 """ |
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214 |
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215 query_length = blastxml_len(result) |
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216 |
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217 percent_multiplier = 100 / query_length |
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218 |
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219 for hit in hits(result): |
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220 # sort hotspots from short to long, so we can overwrite index colors of |
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221 # short matches with those of long ones. |
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222 hotspots = sorted(hit.Hit_hsps.Hsp, key=lambda hsp: blastxml_len(hsp)) |
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223 table = bytearray([255]) * query_length |
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224 for hsp in hotspots: |
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225 frm = hsp['Hsp_query-from'] - 1 |
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226 to = int(hsp['Hsp_query-to']) |
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227 table[frm:to] = repeat(color_idx(blastxml_len(hsp)), to - frm) |
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228 |
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229 matches = [] |
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230 last = table[0] |
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231 count = 0 |
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232 for i in range(query_length): |
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233 if table[i] == last: |
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234 count += 1 |
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235 continue |
| 18 | 236 matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent')) |
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237 last = table[i] |
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238 count = 1 |
| 18 | 239 matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent')) |
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240 |
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241 yield dict(colors=matches, link="#hit"+hit.Hit_num.text, defline=firsttitle(hit)) |
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242 |
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243 @filter |
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244 def queryscale(self, result): |
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245 query_length = blastxml_len(result) |
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246 skip = math.ceil(query_length / self.max_scale_labels) |
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247 percent_multiplier = 100 / query_length |
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248 for i in range(1, query_length+1): |
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249 if i % skip == 0: |
| 25 | 250 yield dict(label = i, width = skip * percent_multiplier) |
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251 if query_length % skip != 0: |
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252 yield dict(label = query_length, |
| 25 | 253 width = (query_length % skip) * percent_multiplier) |
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254 |
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255 @filter |
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256 def hit_info(self, result): |
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257 |
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258 query_length = blastxml_len(result) |
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259 |
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260 for hit in hits(result): |
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261 hsps = hit.Hit_hsps.Hsp |
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262 |
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263 cover = [False] * query_length |
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264 for hsp in hsps: |
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265 cover[hsp['Hsp_query-from']-1 : int(hsp['Hsp_query-to'])] = repeat(True, blastxml_len(hsp)) |
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266 cover_count = cover.count(True) |
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267 |
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268 def hsp_val(path): |
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269 return (float(hsp[path]) for hsp in hsps) |
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270 |
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271 yield dict(hit = hit, |
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272 title = firsttitle(hit), |
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273 link_id = hit.Hit_num, |
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274 maxscore = "{:.1f}".format(max(hsp_val('Hsp_bit-score'))), |
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275 totalscore = "{:.1f}".format(sum(hsp_val('Hsp_bit-score'))), |
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276 cover = "{:.0%}".format(cover_count / query_length), |
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277 e_value = "{:.4g}".format(min(hsp_val('Hsp_evalue'))), |
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278 # FIXME: is this the correct formula vv? |
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279 ident = "{:.0%}".format(float(min(hsp.Hsp_identity / blastxml_len(hsp) for hsp in hsps))), |
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280 accession = hit.Hit_accession) |
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281 |
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282 |
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283 def main(): |
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284 default_template = path.join(path.dirname(__file__), 'blast2html.html.jinja') |
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285 |
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286 parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page", |
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287 usage="{} [-i] INPUT [-o OUTPUT]".format(sys.argv[0])) |
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288 input_group = parser.add_mutually_exclusive_group(required=True) |
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289 input_group.add_argument('positional_arg', metavar='INPUT', nargs='?', type=argparse.FileType(mode='r'), |
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290 help='The input Blast XML file, same as -i/--input') |
| 52 | 291 input_group.add_argument('-i', '--input', type=argparse.FileType(mode='r', encoding='utf-8'), |
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292 help='The input Blast XML file') |
| 52 | 293 parser.add_argument('-o', '--output', type=argparse.FileType(mode='w', encoding='utf-8'), default=sys.stdout, |
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294 help='The output html file') |
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295 # We just want the file name here, so jinja can open the file |
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296 # itself. But it is easier to just use a FileType so argparse can |
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297 # handle the errors. This introduces a small race condition when |
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298 # jinja later tries to re-open the template file, but we don't |
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299 # care too much. |
| 52 | 300 parser.add_argument('--template', type=argparse.FileType(mode='r', encoding='utf-8'), default=default_template, |
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301 help='The template file to use. Defaults to blast_html.html.jinja') |
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302 |
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303 args = parser.parse_args() |
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304 if args.input == None: |
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305 args.input = args.positional_arg |
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306 if args.input == None: |
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307 parser.error('no input specified') |
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308 |
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309 templatedir, templatename = path.split(args.template.name) |
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310 args.template.close() |
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311 if not templatedir: |
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312 templatedir = '.' |
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313 |
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314 b = BlastVisualize(args.input, templatedir, templatename) |
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315 b.render(args.output) |
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316 |
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317 |
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318 if __name__ == '__main__': |
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319 main() |
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320 |