From 5e3076c8e5a9945dec4256809af70b7644b35887 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 13 Aug 2024 15:02:15 -0500
Subject: Bug: cross reference with NULL cM when "gmap" file is absent

The "gmap" file might not exist in some bundles. In those instances,
cross-reference the data without including the genotypes' physical
positions (cM).
---
 scripts/rqtl2/install_genotypes.py | 23 +++++++++++++----------
 1 file changed, 13 insertions(+), 10 deletions(-)

(limited to 'scripts/rqtl2/install_genotypes.py')

diff --git a/scripts/rqtl2/install_genotypes.py b/scripts/rqtl2/install_genotypes.py
index 966728f..08fc0ba 100644
--- a/scripts/rqtl2/install_genotypes.py
+++ b/scripts/rqtl2/install_genotypes.py
@@ -154,16 +154,19 @@ def cross_reference_genotypes(
         (tuple(), tuple(), {}))
 
     with dbconn.cursor(cursorclass=DictCursor) as cursor:
-        paramstr = ", ".join(["%s"] * len(markers))
-        insertparams = (speciesid,) + markers
-        selectquery = ("SELECT Id, Name FROM Geno "
-                 f"WHERE SpeciesId=%s AND Name IN ({paramstr})")
-        _logger.debug(
-            "The select query was\n\t%s\n\nwith the parameters\n\t%s",
-            selectquery,
-            (speciesid,) + markers)
-        cursor.execute(selectquery, insertparams)
-        markersdict = {row["Id"]: row["Name"] for row in cursor.fetchall()}
+        markersdict = {}
+        if len(markers) > 0:
+            paramstr = ", ".join(["%s"] * len(markers))
+            insertparams = (speciesid,) + markers
+            selectquery = ("SELECT Id, Name FROM Geno "
+                     f"WHERE SpeciesId=%s AND Name IN ({paramstr})")
+            _logger.debug(
+                "The select query was\n\t%s\n\nwith the parameters\n\t%s",
+                selectquery,
+                (speciesid,) + markers)
+            cursor.execute(selectquery, insertparams)
+            markersdict = {row["Id"]: row["Name"] for row in cursor.fetchall()}
+
         insertquery = (
             "INSERT INTO GenoXRef(GenoFreezeId, GenoId, DataId, cM) "
             "VALUES(%(datasetid)s, %(markerid)s, %(dataid)s, %(pos)s) "
-- 
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