def result_to_dict(result): from trident.classify import get_grade result_dict = {} result_dict['microrna'] = result.microrna result_dict['chromosome'] = result.chromosome result_dict['hit_genomic_start'] = result.hit_genomic_start result_dict['hit_genomic_end'] = result.hit_genomic_end result_dict['base_type'] = result.base_type.__unicode__() result_dict['hit_score'] = result.hit_score result_dict['hit_energy'] = result.hit_energy result_dict['query_seq'] = result.query_seq result_dict['hit_string'] = result.hit_string result_dict['ref_seq'] = result.ref_seq result_dict['match_type'] = result.match_type.__unicode__() result_dict['genome'] = result.genome.__unicode__() interp = get_interpolator() if interp: result_dict["grade"] = get_grade( interp({ 'query_id': result.microrna, 'energy': result.hit_energy, 'score': result.hit_score }) ) # Supplying the necessary fields for the inerpolator as a dict (instead of full trident score dict) return result_dict
def dict(self, interp=None): result_dict = {} result_dict['microrna'] = self.microrna result_dict['chromosome'] = self.chromosome result_dict['hit_genomic_start'] = self.hit_genomic_start result_dict['hit_genomic_end'] = self.hit_genomic_end result_dict['base_type'] = self.base_type.__unicode__() result_dict['hit_score'] = self.hit_score result_dict['hit_energy'] = self.hit_energy result_dict['query_seq'] = self.query_seq result_dict['hit_string'] = self.hit_string result_dict['ref_seq'] = self.ref_seq result_dict['match_type'] = self.match_type.__unicode__() result_dict['genome'] = self.genome.__unicode__() result_dict["browser_name"] = self.genome.browser_name result_dict['id'] = self.id if interp: from trident.classify import get_grade if not hasattr(interp, "__call__"): from trident import TridentException raise TridentException("Interpolator object is not callable") result_dict["grade"] = get_grade( interp({ 'query_id': self.microrna, 'energy': self.hit_energy, 'score': self.hit_score }) ) # Supplying the necessary fields for the inerpolator as a dict (instead of full trident score dict) return result_dict
def ple_to_resultlist(parser, browser_name=None, genome=None): from views import get_interpolator interp = get_interpolator() result_list = [] for score in parser: if score is None: raise Exception("Error in trident output") score['microrna'] = "" score['chromosome'] = "" score['hit_genomic_start'] = score['ref_start'] score['hit_genomic_end'] = score['ref_end'] score['hit_score'] = score['score'] score['hit_energy'] = score['energy'] score['hit_string'] = score['match_seq'] score['ref_seq'] = score['reference_seq'] score['genome'] = "" if genome: score['genome'] = "Based on {0}".format(genome) if browser_name: if interp: from trident.classify import get_grade if not hasattr(interp,"__call__"): from trident import TridentException raise TridentException("Interpolator object is not callable") score["grade"] = get_grade(interp({'query_id': browser_name, 'energy': score['energy'], 'score': score['score']})) result_list.append(score) return result_list
def dict(self,interp = None): result_dict = {} result_dict['microrna'] = self.microrna result_dict['chromosome'] = self.chromosome result_dict['hit_genomic_start'] = self.hit_genomic_start result_dict['hit_genomic_end'] = self.hit_genomic_end result_dict['base_type'] = self.base_type.__unicode__() result_dict['hit_score'] = self.hit_score result_dict['hit_energy'] = self.hit_energy result_dict['query_seq'] = self.query_seq result_dict['hit_string'] = self.hit_string result_dict['ref_seq'] = self.ref_seq result_dict['match_type'] = self.match_type.__unicode__() result_dict['genome'] = self.genome.__unicode__() result_dict["browser_name"] = self.genome.browser_name result_dict['id'] = self.id if interp: from trident.classify import get_grade if not hasattr(interp,"__call__"): from trident import TridentException raise TridentException("Interpolator object is not callable") result_dict["grade"] = get_grade(interp({'query_id': self.microrna, 'energy': self.hit_energy,'score': self.hit_score})) # Supplying the necessary fields for the inerpolator as a dict (instead of full trident score dict) return result_dict
def result_to_dict(result): from trident.classify import get_grade result_dict = {} result_dict['microrna'] = result.microrna result_dict['chromosome'] = result.chromosome result_dict['hit_genomic_start'] = result.hit_genomic_start result_dict['hit_genomic_end'] = result.hit_genomic_end result_dict['base_type'] = result.base_type.__unicode__() result_dict['hit_score'] = result.hit_score result_dict['hit_energy'] = result.hit_energy result_dict['query_seq'] = result.query_seq result_dict['hit_string'] = result.hit_string result_dict['ref_seq'] = result.ref_seq result_dict['match_type'] = result.match_type.__unicode__() result_dict['genome'] = result.genome.__unicode__() interp = get_interpolator() if interp: result_dict["grade"] = get_grade(interp({'query_id': result.microrna, 'energy': result.hit_energy,'score': result.hit_score})) # Supplying the necessary fields for the inerpolator as a dict (instead of full trident score dict) return result_dict
def ple_to_resultlist(parser, browser_name=None, genome=None): from views import get_interpolator interp = get_interpolator() result_list = [] for score in parser: if score is None: raise Exception("Error in trident output") score['microrna'] = "" score['chromosome'] = "" score['hit_genomic_start'] = score['ref_start'] score['hit_genomic_end'] = score['ref_end'] score['hit_score'] = score['score'] score['hit_energy'] = score['energy'] score['hit_string'] = score['match_seq'] score['ref_seq'] = score['reference_seq'] score['genome'] = "" if genome: score['genome'] = "Based on {0}".format(genome) if browser_name: if interp: from trident.classify import get_grade if not hasattr(interp, "__call__"): from trident import TridentException raise TridentException( "Interpolator object is not callable") score["grade"] = get_grade( interp({ 'query_id': browser_name, 'energy': score['energy'], 'score': score['score'] })) result_list.append(score) return result_list