本文整理汇总了Python中dipper.models.Genotype.Genotype.addGeneProduct方法的典型用法代码示例。如果您正苦于以下问题：Python Genotype.addGeneProduct方法的具体用法？Python Genotype.addGeneProduct怎么用？Python Genotype.addGeneProduct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.addGeneProduct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_genes
# 需要导入模块: from dipper.models.Genotype import Genotype [as 别名]
# 或者: from dipper.models.Genotype.Genotype import addGeneProduct [as 别名]
def _process_genes(self, taxid, limit=None):
if self.test_mode:
graph = self.testgraph
else:
graph = self.graph
model = Model(graph)
geno = Genotype(graph)
raw = '/'.join((self.rawdir, self.files[taxid]['file']))
line_counter = 0
LOG.info("Processing Ensembl genes for tax %s", taxid)
with open(raw, 'r', encoding="utf8") as csvfile:
filereader = csv.reader(csvfile, delimiter='\t')
for row in filereader:
if len(row) < 4:
LOG.warning("Too few columns in: " + row)
raise ValueError("Data error for file %s", raw)
(ensembl_gene_id, external_gene_name, description, gene_biotype,
entrezgene, ensembl_peptide_id, uniprotswissprot) = row[0:7]
# in the case of human genes, we also get the hgnc id,
# and is the last col
if taxid == '9606':
hgnc_id = row[7]
else:
hgnc_id = None
if self.test_mode and entrezgene != '' and \
int(entrezgene) not in self.gene_ids:
continue
line_counter += 1
gene_id = 'ENSEMBL:' + ensembl_gene_id
peptide_curie = 'ENSEMBL:{}'.format(ensembl_peptide_id)
uniprot_curie = 'UniProtKB:{}'.format(uniprotswissprot)
entrez_curie = 'NCBIGene:{}'.format(entrezgene)
if description == '':
description = None
gene_biotype = gene_biotype.strip()
gene_type_id = self.resolve(gene_biotype, False)
if gene_type_id == gene_biotype.strip(): # did not resolve
gene_type_id = self.globaltt['polypeptide']
model.addClassToGraph(
gene_id, external_gene_name, gene_type_id, description)
model.addIndividualToGraph(peptide_curie, None, gene_type_id)
model.addIndividualToGraph(uniprot_curie, None, gene_type_id)
if entrezgene != '':
if taxid == '9606':
# Use HGNC for eq in human data
model.addXref(gene_id, entrez_curie)
else:
model.addEquivalentClass(gene_id, entrez_curie)
if hgnc_id is not None and hgnc_id != '':
model.addEquivalentClass(gene_id, hgnc_id)
geno.addTaxon('NCBITaxon:'+taxid, gene_id)
if ensembl_peptide_id != '':
geno.addGeneProduct(gene_id, peptide_curie)
if uniprotswissprot != '':
geno.addGeneProduct(gene_id, uniprot_curie)
model.addXref(peptide_curie, uniprot_curie)
if not self.test_mode and limit is not None and line_counter > limit:
break
return示例2: _process_genes
# 需要导入模块: from dipper.models.Genotype import Genotype [as 别名]
# 或者: from dipper.models.Genotype.Genotype import addGeneProduct [as 别名]
def _process_genes(self, taxid, limit=None):
if self.testMode:
g = self.testgraph
else:
g = self.graph
model = Model(g)
geno = Genotype(g)
raw = '/'.join((self.rawdir, self.files[taxid]['file']))
line_counter = 0
logger.info("Processing Ensembl genes for tax %s", taxid)
with open(raw, 'r', encoding="utf8") as csvfile:
filereader = csv.reader(csvfile, delimiter='\t')
for row in filereader:
if len(row) < 4:
raise ValueError("Data error for file %s", raw)
(ensembl_gene_id, external_gene_name,
description, gene_biotype, entrezgene,
peptide_id, uniprot_swissprot) = row[0:7]
# in the case of human genes, we also get the hgnc id,
# and is the last col
if taxid == '9606':
hgnc_id = row[7]
else:
hgnc_id = None
if self.testMode and entrezgene != '' \
and int(entrezgene) not in self.gene_ids:
continue
line_counter += 1
gene_id = 'ENSEMBL:' + ensembl_gene_id
peptide_curie = 'ENSEMBL:{}'.format(peptide_id)
uniprot_curie = 'UniProtKB:{}'.format(uniprot_swissprot)
entrez_curie = 'NCBIGene:{}'.format(entrezgene)
if description == '':
description = None
# gene_type_id = self._get_gene_type(gene_biotype)
gene_type_id = None
model.addClassToGraph(
gene_id, external_gene_name, gene_type_id, description)
model.addIndividualToGraph(peptide_curie, None, self._get_gene_type("polypeptide"))
model.addIndividualToGraph(uniprot_curie, None, self._get_gene_type("polypeptide"))
if entrezgene != '':
model.addEquivalentClass(gene_id, entrez_curie)
if hgnc_id is not None and hgnc_id != '':
model.addEquivalentClass(gene_id, hgnc_id)
geno.addTaxon('NCBITaxon:'+taxid, gene_id)
if peptide_id != '':
geno.addGeneProduct(gene_id, peptide_curie)
if uniprot_swissprot != '':
geno.addGeneProduct(gene_id, uniprot_curie)
model.addXref(peptide_curie, uniprot_curie)
if not self.testMode \
and limit is not None and line_counter > limit:
break
return