properly deal with [None] returned by parkour (#211)

maxplanck-ie · Dec 12, 2024 · 79c0b6a · 79c0b6a
2 parents 6cbbe80 + 9a7cbd4
commit 79c0b6a
Showing 1 changed file with 5 additions and 3 deletions.
diff --git a/src/dissectBCL/fakeNews.py b/src/dissectBCL/fakeNews.py
@@ -442,9 +442,11 @@ def gatherFinalMetrics(outLane, flowcell):
         # samples with 0 reads still make an empty report.
         # hence the try / except.
         # 'mouse (GRCm39)' -> 'mouse'
-        parkourOrg = str(  # To string since NA is a float
-                ssdf[ssdf["Sample_ID"] == sampleID]['Organism'].values[0][0]
-            ).split(' ')[0]
+        # Since the ['organism', 'substr', 'yamlstr'], 'nonetypes' are [None]
+        try:
+            parkourOrg = ssdf[ssdf["Sample_ID"] == sampleID]['Organism'].values[0][0]
+        except TypeError:
+            parkourOrg = "NA"
         try:
             screenDF = pd.read_csv(
                 screen, sep='\t', header=None