fix gather output bug (#589)

* fix gather output bug * add test for gather database filename output bug
sourmash-bio · Jan 3, 2019 · 29e5cbd · 29e5cbd
1 parent bddd23f
commit 29e5cbd
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Showing 2 changed files with 18 additions and 4 deletions.
diff --git a/sourmash/search.py b/sourmash/search.py
@@ -144,29 +144,29 @@ def find_best(dblist, query, remainder):
                     leaf_e = leaf.data.minhash
                     similarity = query.minhash.containment_ignore_maxhash(leaf_e)
                     if similarity > 0.0:
-                        results.append((similarity, leaf.data))
+                        results.append((similarity, leaf.data, filename))
             # or an LCA database
             elif filetype == 'LCA':
                 lca_db = obj
                 for x in lca_db.find(query.minhash, 0.0,
                                      containment=True, ignore_scaled=True):
                     (score, match_sig, md5, filename, name) = x
                     if score > 0.0:
-                        results.append((score, match_sig))
+                        results.append((score, match_sig, filename))
 
             # search a signature
             else:
                 for ss in obj:
                     similarity = query.minhash.containment_ignore_maxhash(ss.minhash)
                     if similarity > 0.0:
-                        results.append((similarity, ss))
+                        results.append((similarity, ss, filename))
 
         if not results:
             return None, None, None
 
         # take the best result
         results.sort(key=lambda x: (-x[0], x[1].name()))   # reverse sort on similarity, and then on name
-        best_similarity, best_leaf = results[0]
+        best_similarity, best_leaf, filename = results[0]
 
         for x in results[1:]:
             remainder.add(x[1])

diff --git a/tests/test_sourmash.py b/tests/test_sourmash.py
@@ -1178,6 +1178,20 @@ def test_gather_lca_db(c):
     assert 'NC_009665.1 Shewanella baltica OS185' in str(c)
 
 
+@utils.in_tempdir
+def test_gather_csv_output_filename_bug(c):
+    # check a bug where the database filename in the output CSV was incorrect
+    query = utils.get_test_data('lca/TARA_ASE_MAG_00031.sig')
+    lca_db_1 = utils.get_test_data('lca/delmont-1.lca.json')
+    lca_db_2 = utils.get_test_data('lca/delmont-2.lca.json')
+
+    c.run_sourmash('gather', query, lca_db_1, lca_db_2, '-o', 'out.csv')
+    with open(c.output('out.csv'), 'rt') as fp:
+        r = csv.DictReader(fp)
+        row = next(r)
+        assert row['filename'] == lca_db_1
+
+
 def test_compare_deduce_molecule():
     # deduce DNA vs protein from query, if it is unique
     with utils.TempDirectory() as location: