Esempio n. 1
0
 def _prepare_simulation(self, parameters):
     self._set_parameters(parameters)
     #recalculate PCR mixture
     mixture = self._searcher.matches_to_mixture(WorkCounter(),
                                                 self._seq_name,
                                                 self._matches_list,
                                                 self._PCR_ProductsFinder)
     if mixture is None: return None, None
     register_tmp_file(mixture)
     self._update_side_reactions(parameters)
     pcr = SinglePCR(self._abort_event, self._primers_concentrations,
                     self._elongation_time, self._polymerase,
                     self._with_exonuclease, self._num_cycles,
                     self._side_reactions, self._side_concentrations)
     ovc = compute_objective_value(pcr, self._product_bounds, self._purity)
     return ovc, mixture
Esempio n. 2
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 def _prepare_simulation(self, parameters):
     self._set_parameters(parameters)
     #recalculate PCR mixture
     mixture = self._searcher.matches_to_mixture(WorkCounter(), 
                                                 self._seq_name, 
                                                 self._matches_list,
                                                 self._PCR_ProductsFinder)
     if mixture is None: return None, None
     register_tmp_file(mixture)
     self._update_side_reactions(parameters)
     pcr = SinglePCR(self._abort_event, 
                     self._primers_concentrations, 
                     self._elongation_time, 
                     self._polymerase, 
                     self._with_exonuclease, 
                     self._num_cycles, 
                     self._side_reactions, self._side_concentrations)
     ovc = compute_objective_value(pcr, self._product_bounds, self._purity)
     return ovc, mixture
Esempio n. 3
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 def add_mixture(self, reaction_id, mixture_path):
     self._reactions_ids.add(reaction_id)
     self._PCR_mixtures[reaction_id] = mixture_path
     register_tmp_file(mixture_path)
 def add_mixture(self, reaction_id, mixture_path):
     self._reactions_ids.add(reaction_id)
     self._PCR_mixtures[reaction_id] = mixture_path
     register_tmp_file(mixture_path)