annotate blast2html.py @ 41:637f96ffb9a4

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