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
