def test_query_disease(database):
"""docstring for query_term"""
term = 'OMIM:600920'
result = query_disease([term], connection=database)
cursor = database.cursor()
hpo_terms = set()
for res in result:
hpo_terms.add(res['hpo_term'])
assert "HP:0000767" in hpo_terms
assert "HP:0003042" in hpo_terms
def test_query_disease(database):
"""docstring for query_term"""
term = 'OMIM:600920'
result = query_disease([term], connection=database)
cursor = database.cursor()
hpo_terms = set()
for res in result:
hpo_terms.add(res['hpo_term'])
assert "HP:0000767" in hpo_terms
assert "HP:0003042" in hpo_terms
def query(ctx, config, hpo_term, mim_term, outfile, to_json, chrom, start,
stop):
"""Query the hpo database.\n
Print the result in csv format as default.
"""
if not (hpo_term or mim_term or chrom):
logger.error("Please provide at least one hpo- or mim term")
logger.info("Exiting")
sys.exit(1)
database = phizz_db
if config:
config = ConfigObj(config)
database = config['database']
logger.info("Using database {0}".format(database))
header = "#{0}\t{1}".format('hpo_id', 'description')
results = []
if chrom and start and stop:
for hgnc_symbol in query_gene_symbol(chrom, start, stop):
results.append(hgnc_symbol)
header = "#hgnc_symbol"
if hpo_term:
try:
for result in query_hpo(hpo_terms=hpo_term, database=database):
results.append(result)
except ValueError:
logger.info("Exiting")
sys.exit(1)
if mim_term:
try:
for result in query_disease(disease_terms=mim_term,
database=database):
results.append(result)
except ValueError:
logger.info("Exiting")
sys.exit(1)
if to_json:
if outfile:
json.dump(results, outfile)
else:
print(json.dumps(results))
else:
if outfile:
outfile.write(header + '\n')
else:
print(header)
for result in results:
if chrom:
print_line = result
else:
print_line = "{0}\t{1}".format(result['hpo_term'],
result['description'])
if outfile:
outfile.write(print_line + '\n')
else:
print(print_line)
def test_query_non_existing_term(database):
"""docstring for query_term"""
term = 'OMIM:1'
result = query_disease([term], connection=database)
assert result == []
def test_query_wrong_term(database):
"""docstring for query_term"""
term = 'MIM'
with pytest.raises(ValueError):
result = query_disease([term], connection=database)
def test_query_non_existing_term(database):
"""docstring for query_term"""
term = 'OMIM:1'
result = query_disease([term], connection=database)
assert result == []
def test_query_wrong_term(database):
"""docstring for query_term"""
term = 'MIM'
with pytest.raises(ValueError):
result = query_disease([term], connection=database)
def query(ctx, config, hpo_term, mim_term, outfile, to_json, chrom, start, stop):
"""Query the hpo database.\n
Print the result in csv format as default.
"""
if not (hpo_term or mim_term or chrom):
logger.error("Please provide at least one hpo- or mim term")
logger.info("Exiting")
sys.exit(1)
database = phizz_db
if config:
config = ConfigObj(config)
database = config["database"]
logger.info("Using database {0}".format(database))
header = "#{0}\t{1}".format("hpo_id", "description")
results = []
if chrom and start and stop:
for hgnc_symbol in query_gene_symbol(chrom, start, stop):
results.append(hgnc_symbol)
header = "#hgnc_symbol"
if hpo_term:
try:
for result in query_hpo(hpo_terms=hpo_term, database=database):
results.append(result)
except ValueError:
logger.info("Exiting")
sys.exit(1)
if mim_term:
try:
for result in query_disease(disease_terms=mim_term, database=database):
results.append(result)
except ValueError:
logger.info("Exiting")
sys.exit(1)
if to_json:
if outfile:
json.dump(results, outfile)
else:
print(json.dumps(results))
else:
if outfile:
outfile.write(header + "\n")
else:
print(header)
for result in results:
if chrom:
print_line = result
else:
print_line = "{0}\t{1}".format(result["hpo_term"], result["description"])
if outfile:
outfile.write(print_line + "\n")
else:
print(print_line)
