checks to prevent qc to fail on empty samples

proost · Aug 29, 2016 · a5e859c · a5e859c
1 parent f4e354e
commit a5e859c
Showing 1 changed file with 5 additions and 3 deletions.
diff --git a/pipeline/check/quality.py b/pipeline/check/quality.py
@@ -53,14 +53,16 @@ def check_htseq(filename, cutoff=0, log=None):
             else:
                 values[gene] = int(value)
 
-        total = sum([mapped_reads, values['__no_feature'], values['__ambiguous']])
+        total = sum([mapped_reads,
+                     values['__no_feature'] if '__no_feature' in values.keys() else 0,
+                     values['__ambiguous'] if '__ambiguous' in values.keys() else 0])
 
-        percentage_mapped = (mapped_reads*100)/total
+        percentage_mapped = ((mapped_reads*100)/total) if total > 0 else 0
 
         if percentage_mapped >= cutoff:
             return True
         else:
-             if log is not None:
+            if log is not None:
                 print('WARNING:', filename, 'didn\'t pass HTSEQ-Count Quality check!', percentage_mapped
                       , 'reads mapped. Cutoff,', cutoff, file=log)