def query_gene(ensembl_id=None, hgnc_symbol=None, database=None, connection=None):
"""Query with gene symbols, either hgnc or ensembl
If no database is given use the one that follows with package
Args:
ensemb_id (str): A ensembl gene id
hgnc_symbol (str): A hgnc symbol
database (str): Path to database
Returns:
answer (iterator)
"""
cursor = get_cursor(
path_to_database=database,
connection=connection
)
result = []
if not (ensembl_id or hgnc_symbol):
raise SyntaxError("Use gene identifier to query")
if ensembl_id:
if not ensembl_id.startswith("ENSG"):
raise ValueError("invalid format for ensemb id")
logger.debug("Querying genes with ensembl id {0}".format(ensembl_id))
result = cursor.execute("SELECT * FROM gene WHERE"\
" ensembl_id = ?" , (ensembl_id,)).fetchall()
else:
logger.debug("Querying genes with hgnc symbol {0}".format(hgnc_symbol))
result = cursor.execute("SELECT * FROM gene WHERE"\
" hgnc_symbol = ?" , (hgnc_symbol,)).fetchall()
return result
def test_populate_genes(connection, genes):
populate_genes(
connection=connection,
genes=genes,
)
cursor = get_cursor(connection=connection)
cursor.execute("SELECT * from gene where ensembl_id = 'ENSG00000070814'")
for row in cursor.fetchmany():
assert row['hgnc_symbol'] == "TCOF1"
def test_populate_genes(connection, genes):
populate_genes(
connection=connection,
genes=genes,
)
cursor = get_cursor(connection=connection)
cursor.execute("SELECT * from gene where ensembl_id = 'ENSG00000070814'")
for row in cursor.fetchmany():
assert row['hgnc_symbol'] == "TCOF1"
def test_populate_hpo(connection, hpo_terms, mim_terms):
"""docstring for test_populate_hpo"""
populate_hpo(
connection=connection,
hpo_terms=hpo_terms,
)
cursor = get_cursor(connection=connection)
cursor.execute("SELECT * from hpo where hpo_id = '1459'")
for row in cursor.fetchmany():
assert row['description'] == "1-3 toe syndactyly"
assert row['name'] == "HP:0001459"
def test_populate_hpo(connection, hpo_terms, mim_terms):
"""docstring for test_populate_hpo"""
populate_hpo(
connection=connection,
hpo_terms=hpo_terms,
)
cursor = get_cursor(connection=connection)
cursor.execute("SELECT * from hpo where hpo_id = '1459'")
for row in cursor.fetchmany():
assert row['description'] == "1-3 toe syndactyly"
assert row['name'] == "HP:0001459"
def test_get_hpo_from_omim(connection, hpo_terms, mim_terms):
"""docstring for test_get_description"""
populate_disease(
connection=connection,
disease_terms=mim_terms,
)
cursor = get_cursor(connection=connection)
cursor.execute("SELECT * FROM disease WHERE mim_nr = '600920'")
hpo_ids = set()
for row in cursor.fetchall():
hpo_ids.add(row['mim_hpo'])
assert hpo_ids == set([767, 3042, 5280, 1363, 772, 1195, 2987])
def test_get_hpo_from_omim(connection, hpo_terms, mim_terms):
"""docstring for test_get_description"""
populate_disease(
connection=connection,
disease_terms=mim_terms,
)
cursor = get_cursor(connection=connection)
cursor.execute("SELECT * FROM disease WHERE mim_nr = '600920'")
hpo_ids = set()
for row in cursor.fetchall():
hpo_ids.add(row['mim_hpo'])
assert hpo_ids == set([767, 3042,5280,1363,772,1195,2987])
def query_disease(disease_terms, database=None, connection=None):
"""Query with diseae terms
If no databse is given use the one that follows with package
Args:
hpo_terms (iterator): An iterator with hpo terms
database (str): Path to database
Returns:
answer (list): A list of dictionaries where each dictionary
represents a hpo term on the form {'hpo_term': <hpo_term>,
'description':<description>}
"""
cursor = get_cursor(
path_to_database=database,
connection=connection
)
answer = []
for disease_term in disease_terms:
try:
disease_term = int(disease_term.lstrip('OMIM:'))
logger.debug("Querying diseases with {0}".format(disease_term))
except ValueError as e:
logger.error("{0} is not a valid OMIM term".format(disease_term))
raise e
result = cursor.execute("SELECT hpo.name, hpo.description"\
" FROM hpo, disease WHERE"\
" hpo.hpo_id = disease.mim_hpo"\
" AND disease.mim_nr = ?", (str(disease_term),)).fetchall()
for hpo_row in result:
answer.append({
'hpo_term': hpo_row['name'],
'description': hpo_row['description']
})
return answer
def query_hpo(hpo_terms, database=None, connection=None):
"""Query with hpo terms
If no databse is given use the one that follows with package
Args:
hpo_terms (iterator): An iterator with hpo terms
database (str): Path to database
Returns:
answer (list): A list of dictionaries where each dictionary
represents a hpo term on the form {'hpo_term': <hpo_term>,
'description':<description>}
"""
cursor = get_cursor(
path_to_database=database,
connection=connection
)
answer = []
for hpo_term in hpo_terms:
try:
hpo_term = int(hpo_term.lstrip('HP:'))
except ValueError as e:
logger.error("{0} is not a valid HPO term".format(hpo_term))
raise e
hpo_result = cursor.execute("SELECT * FROM hpo"\
" WHERE hpo_id = '{0}'".format(hpo_term)).fetchall()
for row in hpo_result:
answer.append({
'hpo_term': row['name'],
'description': row['description']
})
return answer