本文整理汇总了Python中dipper.models.Genotype.Genotype.make_experimental_model_with_genotype方法的典型用法代码示例。如果您正苦于以下问题：Python Genotype.make_experimental_model_with_genotype方法的具体用法？Python Genotype.make_experimental_model_with_genotype怎么用？Python Genotype.make_experimental_model_with_genotype使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类dipper.models.Genotype.Genotype的用法示例。
在下文中一共展示了Genotype.make_experimental_model_with_genotype方法的2个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: process_disease_association
# 需要导入模块: from dipper.models.Genotype import Genotype [as 别名]
# 或者: from dipper.models.Genotype.Genotype import make_experimental_model_with_genotype [as 别名]
def process_disease_association(self, limit):
raw = '/'.join((self.rawdir, self.files['disease_assoc']['file']))
if self.testMode:
g = self.testgraph
else:
g = self.graph
gu = GraphUtils(curie_map.get())
logger.info("Processing disease models")
geno = Genotype(g, self.nobnodes)
line_counter = 0
worm_taxon = 'NCBITaxon:6239'
with open(raw, 'r') as csvfile:
filereader = csv.reader(csvfile, delimiter='\t', quotechar='\"')
for row in filereader:
if re.match(r'!', ''.join(row)): # header
continue
line_counter += 1
(db, gene_num, gene_symbol, is_not, disease_id, ref,
eco_symbol, with_or_from, aspect, gene_name, gene_synonym,
gene_class, taxon, date, assigned_by, blank, blank2) = row
if self.testMode and gene_num not in self.test_ids['gene']:
continue
# TODO add NOT phenotypes
if is_not == 'NOT':
continue
# WB WBGene00000001 aap-1 DOID:2583 PMID:19029536 IEA ENSEMBL:ENSG00000145675|OMIM:615214 D Y110A7A.10 gene taxon:6239 20150612 WB
gene_id = 'WormBase:'+gene_num
# make a variant of the gene
vl = '_'+'-'.join((gene_num, 'unspecified'))
if self.nobnodes:
vl = ':'+vl
vl_label = 'some variant of '+gene_symbol
geno.addAlleleOfGene(vl, gene_id)
animal_id = geno.make_experimental_model_with_genotype(
g, vl, vl_label, worm_taxon, 'worm')
assoc = G2PAssoc(
self.name, animal_id,
disease_id, gu.object_properties['model_of'])
ref = re.sub(r'WB_REF:', 'WormBase:', ref)
if ref != '':
assoc.add_source(ref)
eco_id = None
if eco_symbol == 'IEA':
eco_id = 'ECO:0000501' # IEA is this now
if eco_id is not None:
assoc.add_evidence(eco_id)
assoc.add_association_to_graph(g)
return示例2: process_disease_association
# 需要导入模块: from dipper.models.Genotype import Genotype [as 别名]
# 或者: from dipper.models.Genotype.Genotype import make_experimental_model_with_genotype [as 别名]
def process_disease_association(self, limit):
raw = '/'.join((self.rawdir, self.files['disease_assoc']['file']))
if self.test_mode:
graph = self.testgraph
else:
graph = self.graph
model = Model(graph)
LOG.info("Processing disease models")
geno = Genotype(graph)
line_counter = 0
worm_taxon = self.globaltt['Caenorhabditis elegans']
with open(raw, 'r') as csvfile:
filereader = csv.reader(csvfile, delimiter='\t', quotechar='\"')
for row in filereader:
if re.match(r'!', ''.join(row)): # header
continue
line_counter += 1
(db, gene_num, gene_symbol, is_not, disease_id, ref,
eco_symbol, with_or_from, aspect, gene_name, gene_synonym,
gene_class, taxon, date, assigned_by, blank, blank2) = row
if self.test_mode and gene_num not in self.test_ids['gene']:
continue
# TODO add NOT phenotypes
if is_not == 'NOT':
continue
# WB WBGene00000001 aap-1 DOID:2583 PMID:19029536 IEA ENSEMBL:ENSG00000145675|OMIM:615214 D Y110A7A.10 gene taxon:6239 20150612 WB
gene_id = 'WormBase:'+gene_num
# make a variant of the gene
vl = '_:'+'-'.join((gene_num, 'unspecified'))
vl_label = 'some variant of '+gene_symbol
geno.addAffectedLocus(vl, gene_id)
model.addBlankNodeAnnotation(vl)
animal_id = geno.make_experimental_model_with_genotype(
vl, vl_label, worm_taxon, 'worm')
assoc = G2PAssoc(
graph, self.name, animal_id,
disease_id, self.globaltt['is model of'])
ref = re.sub(r'WB_REF:', 'WormBase:', ref)
if ref != '':
assoc.add_source(ref)
assoc.add_evidence(self.resolve(eco_symbol))
assoc.add_association_to_graph()
return