Merge branch 'develop' into bugfix/DEVSU-2477-filter-gkb_matches

pori_python/graphkb/genes.py

@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 from typing import Any, Dict, List, Sequence, Set, Tuple, cast
+from typing_extensions import deprecated
 
 from pori_python.types import IprGene, Ontology, Record, Statement, Variant
 
@@ -256,6 +257,7 @@ def get_preferred_gene_name(
     return gene_names[0]
 
 
+@deprecated("Use get_gene_linked_cancer_predisposition_info instead")
 def get_cancer_predisposition_info(
     conn: GraphKBConnection, source: str = PREFERRED_GENE_SOURCE_NAME
 ) -> Tuple[List[str], Dict[str, str]]:
@@ -360,6 +362,7 @@ def get_gene_linked_cancer_predisposition_info(
     return sorted(genes), variants
 
 
+@deprecated("Use get_gene_linked_pharmacogenomic_info instead")
 def get_pharmacogenomic_info(
     conn: GraphKBConnection, source: str = PREFERRED_GENE_SOURCE_NAME
 ) -> Tuple[List[str], Dict[str, str]]:

pori_python/graphkb/match.py

@@ -31,7 +31,12 @@
     looks_like_rid,
     stringifyVariant,
 )
-from .vocab import get_equivalent_terms, get_term_tree, get_terms_set
+from .vocab import (
+    get_equivalent_terms,
+    get_term_by_name,
+    get_term_tree,
+    get_terms_set,
+)
 
 FEATURES_CACHE: Set[str] = set()
 
@@ -275,7 +280,55 @@ def positions_overlap(
     return start is None or pos == start
 
 
+def equivalent_types(
+    conn: GraphKBConnection,
+    type1: str,
+    type2: str,
+    strict: bool = False,
+) -> bool:
+    """
+    Compare 2 variant types to determine if they should match
+
+    Args:
+        conn: the graphkb connection object
+        type1: type from the observed variant we want to match to the DB
+        type2: type from the DB variant
+        strict: wether or not only the specific-to-generic ones are considered.
+                By default (false), not only specific types can match more generic ones,
+                but generic types can also match more specific ones.
+
+    Returns:
+        bool: True if the types can be matched
+    """
+
+    # Convert rid to displayName if needed
+    if looks_like_rid(type1):
+        type1 = conn.get_records_by_id([type1])[0]['displayName']
+    if looks_like_rid(type2):
+        type2 = conn.get_records_by_id([type2])[0]['displayName']
+
+    # Get type terms from observed variant
+    terms1 = []
+    if strict:
+        try:
+            terms1.append(get_term_by_name(conn, type1)['@rid'])
+        except:
+            pass
+    else:
+        terms1 = get_terms_set(conn, [type1])
+
+    # Get type terms from DB variant
+    terms2 = get_terms_set(conn, [type2])
+
+    # Check for intersect
+    if len(terms2.intersection(terms1)) == 0:
+        return False
+
+    return True
+
+
 def compare_positional_variants(
+    conn: GraphKBConnection,
     variant: Union[PositionalVariant, ParsedVariant],
     reference_variant: Union[PositionalVariant, ParsedVariant],
     generic: bool = True,
@@ -378,6 +431,11 @@ def compare_positional_variants(
         elif len(variant["refSeq"]) != len(reference_variant["refSeq"]):  # type: ignore
             return False
 
+    # Equivalent types
+    if variant.get('type') and reference_variant.get('type'):
+        if not equivalent_types(conn, variant["type"], reference_variant["type"]):
+            return False
+
     return True
 
 
@@ -598,10 +656,14 @@ def match_positional_variant(
     ):
         # TODO: Check if variant and reference_variant should be interchanged
         if compare_positional_variants(
-            variant=parsed, reference_variant=cast(PositionalVariant, row), generic=True
+            conn,
+            variant=parsed,
+            reference_variant=cast(PositionalVariant, row),
+            generic=True,
         ):
             filtered_similarAndGeneric.append(row)
             if compare_positional_variants(
+                conn,
                 variant=parsed,
                 reference_variant=cast(PositionalVariant, row),
                 generic=False,  # Similar variants only

tests/test_graphkb/test_match.py

@@ -269,80 +269,95 @@ def test_known_increased_expression(self, conn):
 class TestComparePositionalVariants:
     def test_nonspecific_altseq(self):
         assert match.compare_positional_variants(
-            {"break1Start": {"pos": 1}}, {"break1Start": {"pos": 1}}
+            conn, {"break1Start": {"pos": 1}}, {"break1Start": {"pos": 1}}
         )
         # null matches anything
         assert match.compare_positional_variants(
-            {"break1Start": {"pos": 1}, "untemplatedSeq": "T"}, {"break1Start": {"pos": 1}}
+            conn, {"break1Start": {"pos": 1}, "untemplatedSeq": "T"}, {"break1Start": {"pos": 1}}
         )
         assert match.compare_positional_variants(
-            {"break1Start": {"pos": 1}}, {"break1Start": {"pos": 1}, "untemplatedSeq": "T"}
+            conn, {"break1Start": {"pos": 1}}, {"break1Start": {"pos": 1}, "untemplatedSeq": "T"}
         )
 
     @pytest.mark.parametrize("seq1", ["T", "X", "?"])
     @pytest.mark.parametrize("seq2", ["T", "X", "?"])
     def test_ambiguous_altseq(self, seq1, seq2):
         # ambiguous AA matches anything the same length
         assert match.compare_positional_variants(
+            conn,
             {"break1Start": {"pos": 1}, "untemplatedSeq": seq1},
             {"break1Start": {"pos": 1}, "untemplatedSeq": seq2},
         )
 
     def test_altseq_length_mismatch(self):
         assert not match.compare_positional_variants(
+            conn,
             {"break1Start": {"pos": 1}, "untemplatedSeq": "??"},
             {"break1Start": {"pos": 1}, "untemplatedSeq": "T"},
         )
         assert not match.compare_positional_variants(
+            conn,
             {"break1Start": {"pos": 1}, "untemplatedSeq": "?"},
             {"break1Start": {"pos": 1}, "untemplatedSeq": "TT"},
         )
 
     def test_nonspecific_refseq(self):
         # null matches anything
         assert match.compare_positional_variants(
-            {"break1Start": {"pos": 1}, "refSeq": "T"}, {"break1Start": {"pos": 1}}
+            conn, {"break1Start": {"pos": 1}, "refSeq": "T"}, {"break1Start": {"pos": 1}}
         )
         assert match.compare_positional_variants(
-            {"break1Start": {"pos": 1}}, {"break1Start": {"pos": 1}, "refSeq": "T"}
+            conn, {"break1Start": {"pos": 1}}, {"break1Start": {"pos": 1}, "refSeq": "T"}
         )
 
     @pytest.mark.parametrize("seq1", ["T", "X", "?"])
     @pytest.mark.parametrize("seq2", ["T", "X", "?"])
     def test_ambiguous_refseq(self, seq1, seq2):
         # ambiguous AA matches anything the same length
         assert match.compare_positional_variants(
-            {"break1Start": {"pos": 1}, "refSeq": seq1}, {"break1Start": {"pos": 1}, "refSeq": seq2}
+            conn,
+            {"break1Start": {"pos": 1}, "refSeq": seq1},
+            {"break1Start": {"pos": 1}, "refSeq": seq2},
         )
 
     def test_refseq_length_mismatch(self):
         assert not match.compare_positional_variants(
-            {"break1Start": {"pos": 1}, "refSeq": "??"}, {"break1Start": {"pos": 1}, "refSeq": "T"}
+            conn,
+            {"break1Start": {"pos": 1}, "refSeq": "??"},
+            {"break1Start": {"pos": 1}, "refSeq": "T"},
         )
         assert not match.compare_positional_variants(
-            {"break1Start": {"pos": 1}, "refSeq": "?"}, {"break1Start": {"pos": 1}, "refSeq": "TT"}
+            conn,
+            {"break1Start": {"pos": 1}, "refSeq": "?"},
+            {"break1Start": {"pos": 1}, "refSeq": "TT"},
         )
 
     def test_diff_altseq(self):
         assert not match.compare_positional_variants(
+            conn,
             {"break1Start": {"pos": 1}, "untemplatedSeq": "M"},
             {"break1Start": {"pos": 1}, "untemplatedSeq": "R"},
         )
 
     def test_same_altseq_matches(self):
         assert match.compare_positional_variants(
+            conn,
             {"break1Start": {"pos": 1}, "untemplatedSeq": "R"},
             {"break1Start": {"pos": 1}, "untemplatedSeq": "R"},
         )
 
     def test_diff_refseq(self):
         assert not match.compare_positional_variants(
-            {"break1Start": {"pos": 1}, "refSeq": "M"}, {"break1Start": {"pos": 1}, "refSeq": "R"}
+            conn,
+            {"break1Start": {"pos": 1}, "refSeq": "M"},
+            {"break1Start": {"pos": 1}, "refSeq": "R"},
         )
 
     def test_same_refseq_matches(self):
         assert match.compare_positional_variants(
-            {"break1Start": {"pos": 1}, "refSeq": "R"}, {"break1Start": {"pos": 1}, "refSeq": "R"}
+            conn,
+            {"break1Start": {"pos": 1}, "refSeq": "R"},
+            {"break1Start": {"pos": 1}, "refSeq": "R"},
         )
 
     def test_range_vs_sub(self):
@@ -364,8 +379,8 @@ def test_range_vs_sub(self):
             "refSeq": "G",
             "untemplatedSeq": "VV",
         }
-        assert not match.compare_positional_variants(sub, range_variant)
-        assert not match.compare_positional_variants(range_variant, sub)
+        assert not match.compare_positional_variants(conn, sub, range_variant)
+        assert not match.compare_positional_variants(conn, range_variant, sub)
 
 
 class TestMatchPositionalVariant: