def test_movel_specific_matches_general(self, conn):
novel_specific = 'CDKN2A:p.T18888888888888888888M'
matches = match.match_positional_variant(conn, novel_specific)
names = {m['displayName'] for m in matches}
assert matches
assert novel_specific not in names
assert 'CDKN2A mutation' in names
def test_match_explicit_references(self, conn):
reference1 = conn.query({'target': 'Feature', 'filters': {'name': 'BCR'}})[0]['@rid']
reference2 = conn.query({'target': 'Feature', 'filters': {'name': 'ABL1'}})[0]['@rid']
matches = match.match_positional_variant(
conn, 'fusion(e.13,e.3)', reference1=reference1, reference2=reference2
)
assert matches
def test_known_fusions(self, conn, known_variant, related_variants):
matches = match.match_positional_variant(conn, known_variant)
types_selected = [m['type']['name'] for m in matches]
assert GENERAL_MUTATION not in types_selected
names = {m['displayName'] for m in matches}
assert matches
assert known_variant in names
for variant in related_variants:
assert variant in names
def test_known_variants(self, conn, known_variant, related_variants, unrelated_variants):
matches = match.match_positional_variant(conn, known_variant)
names = {m['displayName'] for m in matches}
assert matches
assert known_variant in names
for variant in related_variants:
assert variant in names
for variant in unrelated_variants:
assert variant not in names
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 test_genomic_coordinates(self, conn):
genomic = 'X:g.100611165A>T'
match.match_positional_variant(conn, genomic)
def test_known_fusion_single_gene_no_match(self, conn):
known = '(BCR,?):fusion(e.13,e.?)'
matches = match.match_positional_variant(conn, known)
assert not matches
def test_bad_gene2_name(self, conn):
with pytest.raises(FeatureNotFoundError):
match.match_positional_variant(
conn,
'(BCR,ME-AS-A-GENE):fusion(e.13,e.3)',
)
def test_match_explicit_reference1(self, conn):
reference1 = conn.query({'target': 'Feature', 'filters': {'name': 'KRAS'}})[0]['@rid']
matches = match.match_positional_variant(conn, 'p.G12D', reference1=reference1)
assert matches
def test_uncertain_position_not_supported(self, conn):
with pytest.raises(NotImplementedError):
match.match_positional_variant(
conn,
'(BCR,ABL1):fusion(e.13_24,e.3)',
)
def test_bad_gene_name(self, conn):
with pytest.raises(FeatureNotFoundError):
match.match_positional_variant(
conn,
'ME-AS-A-GENE:p.G12D',
)
def test_error_on_duplicate_reference2(self, conn):
with pytest.raises(ValueError):
match.match_positional_variant(
conn, '(BCR,ABL1):fusion(e.13,e.3)', reference2='#123:34'
)
def test_error_on_bad_reference2(self, conn):
with pytest.raises(ValueError):
match.match_positional_variant(conn, 'KRAS:p.G12D', reference2='#123:34')
def test_error_on_duplicate_reference1(self, conn):
with pytest.raises(ValueError):
match.match_positional_variant(conn, 'KRAS:p.G12D', '#123:34')
def annotate_variant(graphkb_conn: GraphKBConnection,
raw_variant_name: str,
include_unmatched: bool = False) -> List[Dict[str, str]]:
results = []
variant_name = convert_aa_3to1(raw_variant_name)
if 'c.*' in variant_name:
results.append({
'variant':
raw_variant_name,
'error':
f'skipping unsupported notation: {variant_name}'
})
return results
print(f'processing: {variant_name}')
try:
variant_matches = match_positional_variant(graphkb_conn, variant_name)
except FeatureNotFoundError:
if include_unmatched:
results.append({'variant': raw_variant_name})
return results
except Exception as err:
results.append({'variant': raw_variant_name, 'error': str(err)})
return results
if variant_matches:
print(f'{variant_name} matches {len(variant_matches)} variant records')
# 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] + ['reviewStatus'])
statements = typing.cast(
Statement,
graphkb_conn.query({
'target': 'Statement',
'filters': {
'conditions': convert_to_rid_list(variant_matches),
'operator': 'CONTAINSANY',
},
'returnProperties': return_props,
}),
)
if not statements:
if include_unmatched:
results.append({
'variant_matches':
';'.join(sorted([v['displayName'] for v in variant_matches])),
'variant':
raw_variant_name,
})
return results
print(f'{variant_name} matches {len(statements)} statements')
for statement in statements:
row = {
'variant_matches':
';'.join(sorted([v['displayName'] for v in variant_matches])),
'variant':
raw_variant_name,
'statement.relevance':
statement['relevance']['displayName'],
'statement.@rid':
statement['@rid'],
'statement.subject':
statement['subject']['displayName'],
'statement.source':
statement['source']['displayName'] if statement['source'] else '',
'statement.evidence':
';'.join(sorted([e['displayName']
for e in statement['evidence']])),
'statement.conditions':
';'.join(
sorted([e['displayName'] for e in statement['conditions']])),
'statement.evidence_level':
';'.join(
sorted([
e['displayName']
for e in (statement['evidenceLevel'] or [])
])),
'statement.review_status':
statement['reviewStatus'],
'is_therapeutic':
bool(statement['relevance']['@rid'] in therapeutic_terms),
}
results.append(row)
return results
def annotate_positional_variants(
graphkb_conn: GraphKBConnection,
variants: List[IprVariant],
disease_name: str,
show_progress: bool = False,
) -> List[KbMatch]:
"""
Annotate variant calls with information from GraphKB and return these annotations in the IPR
alterations format
Args:
graphkb_conn (GraphKBConnection): the graphkb api connection object
variants (list.<dict>): list of variants. Defaults to [].
Returns:
list of kbMatches records for IPR
"""
errors = 0
alterations = []
problem_genes = set()
iterfunc = progressbar if show_progress else iter
for row in iterfunc(variants):
variant = row['variant']
if not row.get('gene', '') and (not row.get('gene1', '') or not row.get('gene2', '')):
# https://www.bcgsc.ca/jira/browse/GERO-56?focusedCommentId=1234791&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-1234791
# should not match single gene SVs
continue
try:
matches = match_positional_variant(graphkb_conn, variant)
for ipr_row in get_ipr_statements_from_variants(graphkb_conn, matches, disease_name):
new_row = KbMatch({'variant': row['key'], 'variantType': row['variantType']})
new_row.update(ipr_row)
alterations.append(new_row)
except FeatureNotFoundError as err:
logger.debug(f'failed to match positional variants ({variant}): {err}')
errors += 1
if 'gene' in row:
problem_genes.add(row['gene'])
elif 'gene1' in row and f"({row['gene1']})" in str(err):
problem_genes.add(row['gene1'])
elif 'gene2' in row and f"({row['gene2']})" in str(err):
problem_genes.add(row['gene2'])
elif 'gene1' in row and 'gene2' in row:
problem_genes.add(row['gene1'])
problem_genes.add(row['gene2'])
else:
raise err
except HTTPError as err:
errors += 1
logger.error(f'failed to match positional variants ({variant}): {err}')
if problem_genes:
logger.error(f'gene finding failures for {sorted(problem_genes)}')
logger.error(f'{len(problem_genes)} gene finding failures for positional variants')
if errors:
logger.error(f'skipped {errors} positional variants due to errors')
logger.info(
f'matched {len(variants)} positional variants to {len(alterations)} graphkb annotations'
)
return alterations