Report error if all columns get removed

ariba/summary.py

@@ -116,7 +116,8 @@ def _gather_output_rows(self):
 
     @classmethod
     def _filter_clusters(cls, rows):
-        '''Removes any cluster where every sample has assembled == "no"'''
+        '''Removes any cluster where every sample has assembled == "no".
+           Returns tuple: (filtered rows, number of remaining columns)'''
         found_a_yes = set()
         first_filename = True
         all_clusters = set()
@@ -131,7 +132,6 @@ def _filter_clusters(cls, rows):
 
                 if rows[filename][cluster]['assembled'] == 'yes':
                     found_a_yes.add(cluster)
-                    break
 
             first_filename = False
 
@@ -141,7 +141,7 @@ def _filter_clusters(cls, rows):
             for cluster in to_delete:
                 del rows[filename][cluster]
 
-        return rows
+        return rows, len(found_a_yes)
 
 
     @classmethod
@@ -253,6 +253,11 @@ def run(self):
         self._check_files_exist()
         self.samples = self._load_input_files(self.filenames, self.min_id)
         self.rows = self._gather_output_rows()
+        self.rows, remaining_clusters = Summary._filter_clusters(self.rows)
+        if remaining_clusters == 0:
+            print('No clusters found that are present in any sample. Will not write any output files', file=sys.stderr)
+            sys.exit(1)
+
         Summary._write_csv(self.filenames, self.rows, self.outprefix + '.csv', phandango=False)
 
         if len(self.samples) > 1:

ariba/tests/summary_test.py

@@ -151,7 +151,7 @@ def test_filter_clusters(self):
         }
 
         got = summary.Summary._filter_clusters(rows)
-        self.assertEqual(expected, got)
+        self.assertEqual((expected, 3), got)
 
 
     def test_write_csv(self):