2 files changed, 68 insertions, 1 deletions
diff --git a/gn3/db/species.py b/gn3/db/species.py
index 0deae4e..1e5015f 100644
--- a/gn3/db/species.py
+++ b/gn3/db/species.py
@@ -30,3 +30,34 @@ def get_chromosome(name: str, is_species: bool, conn: Any) -> Optional[Tuple]:
     with conn.cursor() as cursor:
         cursor.execute(_sql)
         return cursor.fetchall()
+
+def translate_to_mouse_gene_id(species: str, geneid: int, conn: Any) -> int:
+    """
+    Translate rat or human geneid to mouse geneid
+
+    This is a migration of the
+    `web.webqtl.correlation/CorrelationPage.translateToMouseGeneID` function in
+    GN1
+    """
+    assert species in ("rat", "mouse", "human"), "Invalid species"
+    if geneid is None:
+        return 0
+
+    if species == "mouse":
+        return geneid
+
+    with conn.cursor as cursor:
+        if species == "rat":
+            cursor.execute(
+                "SELECT mouse FROM GeneIDXRef WHERE rat = %s", geneid)
+            rat_geneid = cursor.fetchone()
+            if rat_geneid:
+                return rat_geneid[0]
+
+        cursor.execute(
+            "SELECT mouse FROM GeneIDXRef WHERE human = %s", geneid)
+        human_geneid = cursor.fetchone()
+        if human_geneid:
+            return human_geneid[0]
+
+    return 0 # default if all else fails
diff --git a/gn3/partial_correlations.py b/gn3/partial_correlations.py
index c556d10..1fb0ccc 100644
--- a/gn3/partial_correlations.py
+++ b/gn3/partial_correlations.py
@@ -6,7 +6,7 @@ GeneNetwork1.
 """
 
 from functools import reduce
-from typing import Any, Sequence
+from typing import Any, Tuple, Sequence
 
 def control_samples(controls: Sequence[dict], sampleslist: Sequence[str]):
     """
@@ -86,3 +86,39 @@ def fix_samples(primary_trait: dict, control_traits: Sequence[dict]) -> Sequence
         control_vals_vars[0],
         tuple(primary_trait[sample]["variance"] for sample in primary_samples),
         control_vals_vars[1])
+
+def find_identical_traits(
+        primary_name: str, primary_value: float, control_names: Tuple[str, ...],
+        control_values: Tuple[float, ...]) -> Tuple[str, ...]:
+    """
+    Find traits that have the same value when the values are considered to
+    3 decimal places.
+
+    This is a migration of the
+    `web.webqtl.correlation.correlationFunction.findIdenticalTraits` function in
+    GN1.
+    """
+    def __merge_identicals__(
+            acc: Tuple[str, ...],
+            ident: Tuple[str, Tuple[str, ...]]) -> Tuple[str, ...]:
+        return acc + ident[1]
+
+    def __dictify_controls__(acc, control_item):
+        ckey = "{:.3f}".format(control_item[0])
+        return {**acc, ckey: acc.get(ckey, tuple()) + (control_item[1],)}
+
+    return (reduce(## for identical control traits
+        __merge_identicals__,
+        (item for item in reduce(# type: ignore[var-annotated]
+            __dictify_controls__, zip(control_values, control_names),
+            {}).items() if len(item[1]) > 1),
+        tuple())
+            or
+            reduce(## If no identical control traits, try primary and controls
+                __merge_identicals__,
+                (item for item in reduce(# type: ignore[var-annotated]
+                    __dictify_controls__,
+                    zip((primary_value,) + control_values,
+                        (primary_name,) + control_names), {}).items()
+                 if len(item[1]) > 1),
+                tuple()))