Merge pull request #46 from genenetwork/partial-correlations

Partial correlations

1 files changed, 31 insertions, 0 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