From 90ed50db7385b11994dc72874aae94cc647fc855 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 15 Feb 2024 11:02:22 +0300
Subject: Filter out NULL values

---
 scripts/rqtl2/install_genotypes.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'scripts')

diff --git a/scripts/rqtl2/install_genotypes.py b/scripts/rqtl2/install_genotypes.py
index 7f3f65a..709fe0f 100644
--- a/scripts/rqtl2/install_genotypes.py
+++ b/scripts/rqtl2/install_genotypes.py
@@ -99,7 +99,7 @@ def insert_genotype_data(dbconn: mdb.Connection,
         markerids = {row["Name"]: row["Id"] for row in cursor.fetchall()}
         cursor.execute("SELECT MAX(Id) AS lastid FROM GenoData")
         lastid = cursor.fetchone()["lastid"]
-        data = tuple(
+        data = tuple(item for item in (
             {**row, "gid": gid}
             for gid, row in enumerate(
                     ({
@@ -109,6 +109,7 @@ def insert_genotype_data(dbconn: mdb.Connection,
                     } for innerrow in genotypes for marker in
                      (key for key in innerrow.keys() if key != "id")),
                     start=lastid+1))
+                     if item["value"] is not None)
         cursor.executemany(
             "INSERT INTO GenoData(Id, StrainId, value) "
             "VALUES(%(gid)s, %(indid)s, %(value)s)",
-- 
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