Merge remote-tracking branch 'origin/master'

helper/htseq_count_stats.py

@@ -36,4 +36,5 @@
 print('sample', 'mapped_reads', 'no_feature', 'ambiguous', '% mapped', '% no_feature', '% ambiguous',  sep='\t')
 for s, m, n, a in zip(values['samples'], values['mapped_reads'], values['__no_feature'], values['__ambiguous']):
     total = sum([m, n, a])
-    print(s, m, n, a, m*100/total, n*100/total, a*100/total, sep='\t')
+    if total > 0:
+        print(s, m, n, a, m*100/total, n*100/total, a*100/total, sep='\t')

pipeline/check/quality.py

@@ -53,14 +53,17 @@ 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)