Merge pull request #70 from sanger-pathogens/various_fixes

Various fixes

ariba/summary.py

@@ -114,6 +114,36 @@ def _gather_output_rows(self):
         return rows
 
 
+    @classmethod
+    def _filter_clusters(cls, rows):
+        '''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()
+
+        for filename in rows:
+            for cluster in rows[filename]:
+                if first_filename:
+                    all_clusters.add(cluster)
+
+                if cluster in found_a_yes:
+                    continue
+
+                if rows[filename][cluster]['assembled'] == 'yes':
+                    found_a_yes.add(cluster)
+
+            first_filename = False
+
+        to_delete = all_clusters.difference(found_a_yes)
+
+        for filename in rows:
+            for cluster in to_delete:
+                del rows[filename][cluster]
+
+        return rows, len(found_a_yes)
+
+
     @classmethod
     def _write_csv(cls, filenames, rows, outfile, phandango=False):
         lines = []
@@ -223,6 +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

@@ -120,6 +120,40 @@ def test_gather_output_rows(self):
         self.assertEqual(expected, got)
 
 
+    def test_filter_clusters(self):
+        '''Test _filter_clusters'''
+        rows = {
+            'file1': {
+                'cluster1': {'assembled': 'yes'},
+                'cluster2': {'assembled': 'yes'},
+                'cluster3': {'assembled': 'no'},
+                'cluster4': {'assembled': 'no'},
+            },
+            'file2': {
+                'cluster1': {'assembled': 'yes'},
+                'cluster2': {'assembled': 'no'},
+                'cluster3': {'assembled': 'yes'},
+                'cluster4': {'assembled': 'no'},
+            }
+        }
+
+        expected = {
+            'file1': {
+                'cluster1': {'assembled': 'yes'},
+                'cluster2': {'assembled': 'yes'},
+                'cluster3': {'assembled': 'no'},
+            },
+            'file2': {
+                'cluster1': {'assembled': 'yes'},
+                'cluster2': {'assembled': 'no'},
+                'cluster3': {'assembled': 'yes'},
+            }
+        }
+
+        got = summary.Summary._filter_clusters(rows)
+        self.assertEqual((expected, 3), got)
+
+
     def test_write_csv(self):
         '''Test _write_csv'''
         tmp_out = 'tmp.out.tsv'