def hpo_genes(phenotype_ids, username, password):
"""Return list of HGNC symbols matching HPO phenotype ids.
Args:
phenotype_ids (list): list of phenotype ids
username (str): username to connect to phenomizer
password (str): password to connect to phenomizer
Returns:
query_result: a list of dictionaries on the form
{
'p_value': float,
'gene_id': str,
'omim_id': int,
'orphanet_id': int,
'decipher_id': int,
'any_id': int,
'mode_of_inheritance': str,
'description': str,
'raw_line': str
}
"""
if phenotype_ids:
try:
results = query_phenomizer.query(username, password, phenotype_ids)
return [
result for result in results if result['p_value'] is not None
]
except SystemExit, RuntimeError:
pass
def hpo_diseases(username, password, hpo_ids, p_value_treshold=1):
"""Return the list of HGNC symbols that match annotated HPO terms.
Args:
username (str): username to use for phenomizer connection
password (str): password to use for phenomizer connection
Returns:
query_result: a generator of dictionaries on the form
{
'p_value': float,
'disease_source': str,
'disease_nr': int,
'gene_symbols': list(str),
'description': str,
'raw_line': str
}
"""
# skip querying Phenomizer unless at least one HPO terms exists
try:
results = query_phenomizer.query(username, password, *hpo_ids)
diseases = [result for result in results if result["p_value"] <= p_value_treshold]
return diseases
except SystemExit:
return None
def hpo_diseases(username, password, hpo_ids, p_value_treshold=1):
"""Return the list of HGNC symbols that match annotated HPO terms.
Args:
username (str): username to use for phenomizer connection
password (str): password to use for phenomizer connection
Returns:
query_result: a generator of dictionaries on the form
{
'p_value': float,
'disease_source': str,
'disease_nr': int,
'gene_symbols': list(str),
'description': str,
'raw_line': str
}
"""
# skip querying Phenomizer unless at least one HPO terms exists
try:
results = query_phenomizer.query(username, password, *hpo_ids)
diseases = [result for result in results
if result['p_value'] <= p_value_treshold]
return diseases
except SystemExit:
return None
def hpo_genes(phenotype_terms):
"""Return the list of HGNC symbols that match annotated HPO terms.
Returns:
query_result: a list of dictionaries on the form
{
'p_value': float,
'gene_id': str,
'omim_id': int,
'orphanet_id': int,
'decipher_id': int,
'any_id': int,
'mode_of_inheritance': str,
'description': str,
'raw_line': str
}
"""
hpo_terms = [phenotype_term.phenotype_id for phenotype_term in phenotype_terms]
# skip querying Phenomizer unless at least one HPO terms exists
if hpo_terms:
try:
results = query_phenomizer.query(hpo_terms)
return [result for result in results if result['p_value'] is not None]
except SystemExit:
return None
else:
return None
def hpo_genes(phenotype_ids, username, password):
"""Return list of HGNC symbols matching HPO phenotype ids.
Args:
phenotype_ids (list): list of phenotype ids
username (str): username to connect to phenomizer
password (str): password to connect to phenomizer
Returns:
query_result: a list of dictionaries on the form
{
'p_value': float,
'gene_id': str,
'omim_id': int,
'orphanet_id': int,
'decipher_id': int,
'any_id': int,
'mode_of_inheritance': str,
'description': str,
'raw_line': str
}
"""
if phenotype_ids:
try:
results = query_phenomizer.query(username, password, phenotype_ids)
return [result for result in results
if result['p_value'] is not None]
except SystemExit, RuntimeError:
pass
def hpo_genes(phenotype_terms):
"""Return the list of HGNC symbols that match annotated HPO terms.
Returns:
query_result: a list of dictionaries on the form
{
'p_value': float,
'gene_id': str,
'omim_id': int,
'orphanet_id': int,
'decipher_id': int,
'any_id': int,
'mode_of_inheritance': str,
'description': str,
'raw_line': str
}
"""
hpo_terms = [
phenotype_term.phenotype_id for phenotype_term in phenotype_terms
]
# skip querying Phenomizer unless at least one HPO terms exists
if hpo_terms:
try:
results = query_phenomizer.query(hpo_terms)
return [
result for result in results if result['p_value'] is not None
]
except SystemExit:
return None
else:
return None
def cli(ctx, hpo_term, check_terms, output, p_value_limit, verbose, username,
password, to_json):
"Give hpo terms either on the form 'HP:0001623', or '0001623'"
loglevel = LEVELS.get(min(verbose, 3))
configure_stream(level=loglevel)
if not hpo_term:
logger.info(
"Please specify at least one hpo term with '-t/--hpo_term'.")
ctx.abort()
if not (username and password):
logger.info("Please specify username with -u and password with -p.")
logger.info("Contact [email protected].")
ctx.abort()
hpo_list = []
for term in hpo_term:
if len(term.split(':')) < 2:
term = ':'.join(['HP', term])
hpo_list.append(term)
logger.info("HPO terms used: {0}".format(','.join(hpo_list)))
if check_terms:
for term in hpo_list:
try:
if not validate_term(username, password, term):
logger.info("HPO term : {0} does not exist".format(term))
else:
logger.info("HPO term : {0} does exist!".format(term))
except RuntimeError as err:
click.echo(err)
ctx.abort()
ctx.abort()
else:
try:
for result in query(username, password, *hpo_list):
if to_json:
click.echo(json.dumps(result))
else:
print_string = "{0}\t{1}:{2}\t{3}\t{4}".format(
result['p_value'], result['disease_source'],
result['disease_nr'], result['description'],
','.join(result['gene_symbols']))
p_value = result['p_value']
if p_value <= p_value_limit:
click.echo(print_string)
except RuntimeError as e:
click.echo(e)
ctx.abort()
def hpo_genes(phenotype_ids):
"""Return list of HGNC symbols matching HPO phenotype ids.
Returns:
query_result: a list of dictionaries on the form
{
'p_value': float,
'gene_id': str,
'omim_id': int,
'orphanet_id': int,
'decipher_id': int,
'any_id': int,
'mode_of_inheritance': str,
'description': str,
'raw_line': str
}
"""
try:
results = query_phenomizer.query(phenotype_ids)
return [result for result in results if result["p_value"] is not None]
except SystemExit:
return None
def cli(ctx, hpo_term, check_terms, output, p_value_limit, verbose, username,
password, to_json):
"""Give hpo terms either on the form 'HP:0001623', or '0001623'.
If -p is not used, a password prompt will appear instead."""
loglevel = LEVELS.get(min(verbose, 3))
configure_stream(level=loglevel)
if not hpo_term:
logger.info(
"Please specify at least one hpo term with '-t/--hpo_term'.")
ctx.abort()
if not username:
logger.info("Please specify username with -u (and password with -p).")
logger.info("Contact [email protected].")
ctx.abort()
if not password:
password = getpass("password:"******"HPO terms used: {0}".format(','.join(hpo_list)))
if check_terms:
for term in hpo_list:
try:
if not validate_term(username, password, term):
logger.info("HPO term : {0} does not exist".format(term))
else:
logger.info("HPO term : {0} does exist!".format(term))
except RuntimeError as err:
click.echo(err)
ctx.abort()
ctx.abort()
else:
try:
if output:
header = "p-value\tdisease-id\tdisease-name\tgene-symbols" + linesep # The file header.
output.write(
header.encode()) # "a bytes-like object is required"
for result in query(username, password, *hpo_list):
if to_json:
click.echo(json.dumps(result))
else:
print_string = "{0}\t{1}:{2}\t{3}\t{4}".format(
result['p_value'], result['disease_source'],
result['disease_nr'], result['description'],
','.join(result['gene_symbols']))
p_value = result['p_value']
if p_value <= p_value_limit:
if output:
print_string += linesep # Adds line separator to output.
output.write(print_string.encode()
) # "a bytes-like object is required"
else:
click.echo(print_string)
except RuntimeError as e:
click.echo(e)
ctx.abort()
finally:
if output:
output.flush()
output.close()
def test_query_unicode(username, password):
res = query(username, password, "HP:0000252")
assert res
def test_query_ataxia(ataxia, username, password):
res = query(username, password, ataxia)
assert res