def build_database(connection):
"""Build the hpo database
Args:
conn (sqlite3.connect): A database connection object
"""
logger.info("Fetching disease to gene file")
disease_to_genes = getreader('utf-8')(gzip.open(disease_to_genes_path),
errors='replace')
logger.info("Fetching phenotypes file")
phenotype_to_genes = getreader('utf-8')(gzip.open(phenotypes_path),
errors='replace')
logger.info("Fetching genes file")
genes = getreader('utf-8')(gzip.open(genes_path), errors='replace')
logger.info("Parsing phenotypes to gene file")
phenotypes = parse_phenotypes(phenotype_to_genes)
logger.info("Parsing disease to gene file")
diseases = parse_diseases(disease_to_genes)
logger.info("Parsing genes file")
genes = parse_genes(genes)
logger.info("Populating hpo table")
populate_hpo(connection=connection, hpo_terms=phenotypes)
logger.debug("Hpo table populated")
logger.info("Populating disease table")
populate_disease(connection=connection, disease_terms=diseases)
logger.debug("Disease table populated")
logger.info("Populating gene table")
populate_genes(connection=connection, genes=genes)
logger.debug("Gene table populated")
def hpo_terms(request):
"""Get hpo terms"""
hpo_lines = [
"#Format: HPO-ID<tab>HPO-Name<tab>Gene-ID<tab>Gene-Name",
"HP:0003295\tImpaired FSH and LH secretion",
"HP:0003564\tFolate-dependent fragile site at Xq28",
"HP:0003565\tElevated erythrocyte sedimentation rate",
"HP:0003562\tAbnormal metaphyseal vascular invasion",
"HP:0003563\tHypobetalipoproteinemia",
"HP:0003292\tDecreased serum leptin",
"HP:0003561\tBirth length less than 3rd percentile",
"HP:0001403\tMacrovesicular hepatic steatosis",
"HP:0003298\tSpina bifida occulta",
"HP:0003296\tHyperthreoninuria",
"HP:0003568\tDecreased glucosephosphate isomerase activity",
"HP:0012393\tAllergy",
"HP:0003297\tHyperlysinuria",
"HP:0001153\tSeptate v****a",
"HP:0001152\tSaccadic smooth pursuit",
"HP:0030012\tAbnormal female reproductive system physiology",
"HP:0003560\tMuscular dystrophy",
"HP:0000767\tPectus excavatum",
"HP:0003042\tElbow dislocation",
"HP:0005280\tDepressed nasal bridge",
"HP:0001363\tCraniosynostosis",
"HP:0000772\tAbnormality of the ribs",
"HP:0001195\tSingle umbilical artery",
"HP:0002987\tElbow flexion contracture"
]
return parse_phenotypes(hpo_lines)
def build_database(connection):
"""Build the hpo database
Args:
conn (sqlite3.connect): A database connection object
"""
logger.info("Fetching disease to gene file")
disease_to_genes = getreader('utf-8')(
gzip.open(disease_to_genes_path), errors='replace')
logger.info("Fetching phenotypes file")
phenotype_to_genes = getreader('utf-8')(
gzip.open(phenotypes_path), errors='replace')
logger.info("Fetching genes file")
genes = getreader('utf-8')(
gzip.open(genes_path), errors='replace')
logger.info("Parsing phenotypes to gene file")
phenotypes = parse_phenotypes(phenotype_to_genes)
logger.info("Parsing disease to gene file")
diseases = parse_diseases(disease_to_genes)
logger.info("Parsing genes file")
genes = parse_genes(genes)
logger.info("Populating hpo table")
populate_hpo(
connection=connection,
hpo_terms=phenotypes
)
logger.debug("Hpo table populated")
logger.info("Populating disease table")
populate_disease(
connection=connection,
disease_terms=diseases
)
logger.debug("Disease table populated")
logger.info("Populating gene table")
populate_genes(
connection=connection,
genes=genes
)
logger.debug("Gene table populated")
