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comparison blast2html.py @ 110:e17aae23cc1c

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report query parameters for each query
author Jan Kanis <jan.code@jankanis.nl>
date Wed, 09 Jul 2014 15:04:37 +0200
parents ea3bc0b9a3d9
children 0c2a03f9740b
comparison
equal deleted inserted replaced
109:ea3bc0b9a3d9 110:e17aae23cc1c
222 # sort hits by longest hotspot first 222 # sort hits by longest hotspot first
223 return sorted(result.Iteration_hits.findall('Hit'), 223 return sorted(result.Iteration_hits.findall('Hit'),
224 key=lambda h: max(blastxml_len(hsp) for hsp in h.Hit_hsps.Hsp), 224 key=lambda h: max(blastxml_len(hsp) for hsp in h.Hit_hsps.Hsp),
225 reverse=True) 225 reverse=True)
226 226
227 @filter('params')
228 def result_params(iteration):
229 return (('Query number', iteration['Iteration_iter-num']),
230 ('Query ID', iteration['Iteration_query-ID']),
231 ('Definition line', iteration['Iteration_query-def']),
232 ('Length', blastxml_len(iteration)))
227 233
228 234
229 class BlastVisualize: 235 class BlastVisualize:
230 236
231 colors = ('black', 'blue', 'green', 'magenta', 'red') 237 colors = ('black', 'blue', 'green', 'magenta', 'red')
256 environment.filters[filtername] = getattr(builtins, funcname) 262 environment.filters[filtername] = getattr(builtins, funcname)
257 263
258 def render(self, output): 264 def render(self, output):
259 template = self.environment.get_template(self.templatename) 265 template = self.environment.get_template(self.templatename)
260 266
261 params = (('Query ID', self.blast["BlastOutput_query-ID"]), 267 params = (('Program', self.blast.BlastOutput_version),
262 ('Query definition', self.blast["BlastOutput_query-def"]),
263 ('Query length', self.blast["BlastOutput_query-len"]),
264 ('Program', self.blast.BlastOutput_version),
265 ('Database', self.blast.BlastOutput_db), 268 ('Database', self.blast.BlastOutput_db),
266 ) 269 )
267 270
268 result = template.stream(blast=self.blast, 271 result = template.stream(blast=self.blast,
269 iterations=self.blast.BlastOutput_iterations.Iteration, 272 iterations=self.blast.BlastOutput_iterations.Iteration,