Merge pull request #105 from bcgsc/release/v1.13.0

Release/v1.13.0

graphkb/constants.py

@@ -60,8 +60,10 @@
 
 
 ONCOKB_SOURCE_NAME = "oncokb"
+TSO500_SOURCE_NAME = "tso500"
 ONCOGENE = "oncogenic"
 TUMOUR_SUPPRESSIVE = "tumour suppressive"
+CANCER_GENE = "cancer gene"
 FUSION_NAMES = ["structural variant", "fusion"]
 
 PHARMACOGENOMIC_SOURCE_EXCLUDE_LIST = ["cancer genome interpreter", "civic"]

graphkb/genes.py

@@ -4,6 +4,7 @@
 from . import GraphKBConnection
 from .constants import (
     BASE_THERAPEUTIC_TERMS,
+    CANCER_GENE,
     CHROMOSOMES,
     FAILED_REVIEW_STATUS,
     GENE_RETURN_PROPERTIES,
@@ -12,6 +13,7 @@
     PHARMACOGENOMIC_SOURCE_EXCLUDE_LIST,
     PREFERRED_GENE_SOURCE,
     RELEVANCE_BASE_TERMS,
+    TSO500_SOURCE_NAME,
     TUMOUR_SUPPRESSIVE,
 )
 from .match import get_equivalent_features
@@ -20,25 +22,29 @@
 from .vocab import get_terms_set
 
 
-def _get_oncokb_gene_list(
-    conn: GraphKBConnection, relevance: str, ignore_cache: bool = False
+def _get_tumourigenesis_genes_list(
+    conn: GraphKBConnection,
+    relevance: str,
+    sources: List[str],
+    ignore_cache: bool = False,
 ) -> List[Ontology]:
-    source = conn.get_source(ONCOKB_SOURCE_NAME)["@rid"]
-
     statements = cast(
         List[Statement],
         conn.query(
             {
                 "target": "Statement",
-                "filters": [
-                    {"source": source},
-                    {"relevance": {"target": "Vocabulary", "filters": {"name": relevance}}},
-                ],
+                "filters": {
+                    "AND": [
+                        {"source": {"target": "Source", "filters": {"name": sources}}},
+                        {"relevance": {"target": "Vocabulary", "filters": {"name": relevance}}},
+                    ]
+                },
                 "returnProperties": [f"subject.{prop}" for prop in GENE_RETURN_PROPERTIES],
             },
             ignore_cache=ignore_cache,
         ),
     )
+
     genes: Dict[str, Ontology] = {}
 
     for statement in statements:
@@ -58,7 +64,7 @@ def get_oncokb_oncogenes(conn: GraphKBConnection) -> List[Ontology]:
     Returns:
         gene (Feature) records
     """
-    return _get_oncokb_gene_list(conn, ONCOGENE)
+    return _get_tumourigenesis_genes_list(conn, ONCOGENE, [ONCOKB_SOURCE_NAME])
 
 
 def get_oncokb_tumour_supressors(conn: GraphKBConnection) -> List[Ontology]:
@@ -70,7 +76,21 @@ def get_oncokb_tumour_supressors(conn: GraphKBConnection) -> List[Ontology]:
     Returns:
         gene (Feature) records
     """
-    return _get_oncokb_gene_list(conn, TUMOUR_SUPPRESSIVE)
+    return _get_tumourigenesis_genes_list(conn, TUMOUR_SUPPRESSIVE, [ONCOKB_SOURCE_NAME])
+
+
+def get_cancer_genes(conn: GraphKBConnection) -> List[Ontology]:
+    """Get the list of cancer genes stored in GraphKB derived from OncoKB & TSO500.
+
+    Args:
+        conn: the graphkb connection object
+
+    Returns:
+        gene (Feature) records
+    """
+    return _get_tumourigenesis_genes_list(
+        conn, CANCER_GENE, [ONCOKB_SOURCE_NAME, TSO500_SOURCE_NAME]
+    )
 
 
 def get_therapeutic_associated_genes(graphkb_conn: GraphKBConnection) -> List[Ontology]:

setup.cfg

@@ -10,7 +10,7 @@ include_trailing_comma = true
 [metadata]
 name = graphkb
 url = https://github.com/bcgsc/pori_graphkb_python
-version = 1.12.0
+version = 1.13.0
 author_email = [email protected]
 description = python adapter for interacting with the GraphKB API
 long_description = file: README.md

tests/test_genes.py

@@ -7,6 +7,7 @@
 
 from graphkb import GraphKBConnection
 from graphkb.genes import (
+    get_cancer_genes,
     get_cancer_predisposition_info,
     get_gene_information,
     get_genes_from_variant_types,
@@ -22,6 +23,7 @@
 
 CANONICAL_ONCOGENES = ["kras", "nras", "alk"]
 CANONICAL_TS = ["cdkn2a", "tp53"]
+CANONICAL_CG = ["ercc1", "fanci", "h2bc4", "h2bc17", "acvr1b"]
 CANONICAL_FUSION_GENES = ["alk", "ewsr1", "fli1"]
 CANONICAL_STRUCTURAL_VARIANT_GENES = ["brca1", "dpyd", "pten"]
 CANNONICAL_THERAPY_GENES = ["erbb2", "brca2", "egfr"]
@@ -112,6 +114,8 @@ def test_oncogene(conn):
         assert gene in names
     for gene in CANONICAL_TS:
         assert gene not in names
+    for gene in CANONICAL_CG:
+        assert gene not in names
 
 
 def test_tumour_supressors(conn):
@@ -121,6 +125,19 @@ def test_tumour_supressors(conn):
         assert gene in names
     for gene in CANONICAL_ONCOGENES:
         assert gene not in names
+    for gene in CANONICAL_CG:
+        assert gene not in names
+
+
+def test_cancer_genes(conn):
+    result = get_cancer_genes(conn)
+    names = {row["name"] for row in result}
+    for gene in CANONICAL_CG:
+        assert gene in names
+    for gene in CANONICAL_TS:
+        assert gene not in names
+    for gene in CANONICAL_ONCOGENES:
+        assert gene not in names
 
 
 def test_get_pharmacogenomic_info(conn):