def load_ncbi_info(self):
if not self.ncbi_id:
return
info = GeneInfoDB().select_gene_info(self.ncbi_id)
for attr, value in zip(self.__slots__, info):
if attr == 'db_refs':
value = parse_sources(value)
elif attr == 'synonyms':
value = parse_synonyms(value)
setattr(self, attr, value)
def _init_gene_info(self, organism):
for gene in GeneInfoDB().select_genes_by_organism(organism):
gene_obj = Gene()
for attr, value in zip(gene_obj.__slots__, gene):
if attr == 'db_refs':
value = parse_sources(value)
elif attr == 'synonyms':
value = parse_synonyms(value)
setattr(gene_obj, attr, value)
self[gene_obj.gene_id] = gene_obj
def load_ncbi_info(self):
""" Populate :class:`Gene` with data from NCBI gene database
"""
if not self.ncbi_id:
return
info = GeneInfoDB().select_gene_info(self.ncbi_id)
for attr, value in zip(self.__slots__, info):
if attr == 'db_refs':
value = parse_sources(value)
elif attr == 'synonyms':
value = parse_synonyms(value)
setattr(self, attr, value)
def parse_gene_record(parent_tax, mapper, gene_record):
gene = gene_matcher_tuple(parent_tax, gene_record[gene_id],
gene_record[symbol],
parse_synonyms(gene_record[synonyms]),
parse_sources(gene_record[source]),
gene_record[locus_tag])
# construct gene mapper
mapper[MAP_SYMBOLS][gene.symbol].append(gene)
mapper[MAP_LOCUS][gene.locus_tag].append(gene)
mapper[MAP_GENE_IDS][gene.gene_id].append(gene)
for gene_synonym in gene.synonyms:
mapper[MAP_SYNONYMS][gene_synonym].append(gene)
for source_id in gene.sources.values():
mapper[MAP_SOURCES][source_id].append(gene)
def parse_gene_record(parent_tax, mapper, gene_record):
gene = {MAP_TAX_ID: parent_tax,
MAP_GENE_ID: gene_record[gene_id],
MAP_SYMBOL: gene_record[symbol],
MAP_SYNONYMS: parse_synonyms(gene_record[synonyms]),
MAP_SOURCES: parse_sources(gene_record[sources]),
MAP_LOCUS: gene_record[locus_tag],
MAP_NOMENCLATURE: gene_record[nomenclature]
}
# construct gene mapper
mapper[MAP_SYMBOL][gene[MAP_SYMBOL]].append(gene)
mapper[MAP_LOCUS][gene[MAP_LOCUS]].append(gene)
mapper[MAP_GENE_ID][gene[MAP_GENE_ID]].append(gene)
mapper[MAP_NOMENCLATURE][gene[MAP_NOMENCLATURE]].append(gene)
for gene_synonym in gene[MAP_SYNONYMS]:
mapper[MAP_SYNONYMS][gene_synonym].append(gene)
for source_id in gene[MAP_SOURCES].values():
mapper[MAP_SOURCES][source_id].append(gene)
