resolve issue 1682

qiime/workflow/upstream.py

@@ -332,7 +332,7 @@ def run_pick_closed_reference_otus(
     # confirm that a valid otu picking method was supplied before doing
     # any work
     reference_otu_picking_methods = ['blast', 'uclust_ref', 'usearch61_ref',
-                                     'sortmerna']
+                                     'usearch_ref', 'sortmerna']
 
     try:
         otu_picking_method = params['pick_otus']['otu_picking_method']

qiime_test_data/pick_closed_reference_otus/usearch5.2_params.txt

@@ -0,0 +1,2 @@
+pick_otus:otu_picking_method usearch_ref
+pick_otus:suppress_reference_chimera_detection True

scripts/pick_closed_reference_otus.py

@@ -50,6 +50,15 @@
      "Pick OTUs, assign taxonomy, and create an OTU table against a reference set of OTUs using usearch_ref. ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/).",
      "%prog -i $PWD/seqs.fna -r $PWD/refseqs.fna -o $PWD/otus_usearch/ -p $PWD/usearch_params.txt -t $PWD/taxa.txt"))
 
+script_info['script_usage'].append(
+    ("",
+     "Pick OTUs using usearch_ref, assign taxonomy, and create an OTU table "
+     "against a reference set of OTUs using usearch_ref. ALWAYS SPECIFY ABSOLUTE "
+     "FILE PATHS (absolute path represented here as $PWD, but will generally look "
+     "something like /home/ubuntu/my_analysis/).",
+     "%prog -i $PWD/seqs.fna -r $PWD/refseqs.fna -o $PWD/otus_usearch_ref/ "
+     "-p $PWD/usearch5.2_params.txt -t $PWD/taxa.txt"))
+
 script_info['script_usage'].append(
     ("",
      "Pick OTUs, assign taxonomy, and create an OTU table against a "
@@ -64,7 +73,8 @@
     '$PWD/otus/',
     '$PWD/otus_w_tax/',
     '$PWD/otus_usearch/',
-    '$PWD/otus_sortmerna/']
+    '$PWD/otus_sortmerna/',
+    '$PWD/otus_usearch_ref/']
 
 script_info['output_description'] = ""
 

tests/test_workflow/test_upstream.py

@@ -44,7 +44,7 @@ def setUp(self):
         self.test_out = mkdtemp(dir=tmp_dir,
                                 prefix='core_qiime_analyses_test_',
                                 suffix='')
-        self.dirs_to_remove.append(self.test_out)
+        self.dirs_to_remove.append("self.test_out")
 
         self.qiime_config = load_qiime_config()
         self.params = parse_qiime_parameters([])
@@ -159,6 +159,59 @@ def test_run_pick_closed_reference_otus_parallel(self):
         log_fp = glob(join(self.test_out, 'log*.txt'))[0]
         self.assertTrue(getsize(log_fp) > 0)
 
+    def test_run_pick_closed_reference_otus_usearch(self):
+        """run_pick_closed_reference_otus generates expected results
+            using usearch_ref"""
+
+        self.params['pick_otus']['otu_picking_method'] = "usearch_ref"
+        self.params['pick_otus']['suppress_reference_chimera_detection'] = ""
+
+        run_pick_closed_reference_otus(
+            self.test_data['seqs'][0],
+            self.test_data['refseqs'][0],
+            self.test_out,
+            self.test_data['refseqs_tax'][0],
+            call_commands_serially,
+            self.params,
+            self.qiime_config,
+            parallel=False,
+            status_update_callback=no_status_updates)
+
+        input_file_basename = splitext(split(self.test_data['seqs'][0])[1])[0]
+        otu_map_fp = join(self.test_out, 'usearch_ref_picked_otus',
+                          '%s_otus.txt' % input_file_basename)
+        otu_table_fp = join(self.test_out, 'otu_table.biom')
+        otu_table = load_table(otu_table_fp)
+        expected_sample_ids = ['f1', 'f2', 'f3', 'f4', 'p1', 'p2', 't1', 't2']
+        self.assertItemsEqual(otu_table.ids(), expected_sample_ids)
+
+        # Number of OTUs matches manually confirmed result
+        otu_map_lines = list(open(otu_map_fp))
+        num_otus = len(otu_map_lines)
+        otu_map_otu_ids = [o.split()[0] for o in otu_map_lines]
+        self.assertEqual(num_otus, 2)
+
+        # parse the otu table
+        otu_table = load_table(otu_table_fp)
+        expected_sample_ids = ['f1', 'f2', 'f3', 'f4', 'p1', 'p2', 't1', 't2']
+        # sample IDs are as expected
+        self.assertItemsEqual(otu_table.ids(), expected_sample_ids)
+        # otu ids are as expected
+        self.assertItemsEqual(otu_table.ids(axis='observation'),
+                              otu_map_otu_ids)
+
+        # expected number of sequences in OTU table
+        number_seqs_in_otu_table = sum([v.sum()
+                                       for v in otu_table.iter_data()])
+        self.assertEqual(number_seqs_in_otu_table, 116)
+
+        # One tax assignment per otu
+        self.assertEqual(len(otu_table.metadata(axis='observation')), 2)
+
+        # Check that the log file is created and has size > 0
+        log_fp = glob(join(self.test_out, 'log*.txt'))[0]
+        self.assertTrue(getsize(log_fp) > 0)
+
     def test_run_pick_closed_reference_otus_sortmerna(self):
         """run_pick_closed_reference_otus generates expected results
            using sortmerna