from graphkb import GraphKBConnection
from graphkb.constants import BASE_RETURN_PROPERTIES, GENERIC_RETURN_PROPERTIES
from graphkb.match import match_positional_variant
from graphkb.util import convert_to_rid_list
from graphkb.vocab import get_term_tree
GKB_API_URL = 'https://pori-demo.bcgsc.ca/graphkb-api/api'
GKB_USER = '******'
GKB_PASSWORD = '******'
graphkb_conn = GraphKBConnection(GKB_API_URL, use_global_cache=False)
graphkb_conn.login(GKB_USER, GKB_PASSWORD)
variant_name = 'KRAS:p.G12D'
variant_matches = match_positional_variant(graphkb_conn, variant_name)
for match in variant_matches:
print(variant_name, 'will match', match['displayName'])
# return properties should be customized to the users needs
return_props = (BASE_RETURN_PROPERTIES +
['sourceId', 'source.name', 'source.displayName'] +
[f'conditions.{p}' for p in GENERIC_RETURN_PROPERTIES] +
[f'subject.{p}' for p in GENERIC_RETURN_PROPERTIES] +
[f'evidence.{p}' for p in GENERIC_RETURN_PROPERTIES] +
[f'relevance.{p}' for p in GENERIC_RETURN_PROPERTIES] +
[f'evidenceLevel.{p}' for p in GENERIC_RETURN_PROPERTIES])
statements = graphkb_conn.query({
'target': 'Statement',
'filters': {
def genes() -> List[Dict]:
graphkb_conn = GraphKBConnection()
graphkb_conn.login(os.environ['IPR_USER'], os.environ['IPR_PASS'])
return get_gene_information(graphkb_conn,
['kras', 'cdkn2a', 'blargh-monkeys', 'ewsr1'])
def conn():
conn = GraphKBConnection()
conn.login(os.environ['GRAPHKB_USER'], os.environ['GRAPHKB_PASS'])
return conn
def test_login_ok():
conn = GraphKBConnection()
conn.login(os.environ['GRAPHKB_USER'], os.environ['GRAPHKB_PASS'])
assert conn.token is not None
parser.add_argument('--graphkb_user',
default='colab_demo',
help='The username for logging in to GraphKB')
parser.add_argument('--graphkb_pass',
default='colab_demo',
help='The password for logging in to GraphKB')
parser.add_argument(
'--include_unmatched',
default=False,
action='store_true',
help='Include lines for variants that did not match any statements',
)
args = parser.parse_args()
graphkb_conn = GraphKBConnection(args.graphkb_url, use_global_cache=True)
graphkb_conn.login(args.graphkb_user, args.graphkb_pass)
# read the input files
inputs = []
for filename in args.inputs:
print(f'reading: {filename}')
temp_df = pd.read_csv(filename, sep='\t')
temp_df['filename'] = os.path.basename(filename)
inputs.append(temp_df)
input_df = pd.concat(inputs)
# generate the variant list df
def get_variant(row):
if not pd.isnull(row['ANN[*].HGVS_P']):
return row['ANN[*].GENE'] + ':' + row['ANN[*].HGVS_P']