Do not assume cluster representative comes first

ariba/cdhit.py

@@ -56,8 +56,8 @@ def _get_ids(self, infile):
     @staticmethod
     def _parse_cluster_info_file(infile, cluster_representatives):
         f = pyfastaq.utils.open_file_read(infile)
-        clusters = {}
-        current_cluster = None
+        cluster_sets = {}
+        found_representatives = {}  # store cluster number -> representative name
 
         for line in f:
             data = line.rstrip().split()
@@ -66,21 +66,24 @@ def _parse_cluster_info_file(infile, cluster_representatives):
                 raise Error('Unexpected format of line from cdhit output file "' + infile + '". Line is:\n' + line)
             seqname = seqname[1:-3]
 
-            if data[3] == '*':
-                current_cluster = seqname
-                assert current_cluster not in clusters
-                clusters[current_cluster] = {current_cluster}
-            else:
-                assert current_cluster in clusters
-                if seqname in clusters[current_cluster]:
-                    raise Error('Duplicate name "' + seqname + '" found in cluster ' + current_cluster)
+            cluster_number = int(data[0]) # this is the cluster number used by cdhit
+            if cluster_number not in cluster_sets:
+                cluster_sets[cluster_number] = set()
 
-                clusters[current_cluster].add(seqname)
+            cluster_sets[cluster_number].add(seqname)
+
+            if data[3] == '*':
+                found_representatives[cluster_number] = seqname
 
         pyfastaq.utils.close(f)
-        if set(clusters.keys()) != cluster_representatives:
+
+        if set(found_representatives.values()) != cluster_representatives:
             raise Error('Mismatch in cdhit output sequence names between fasta file and clusters file. Cannot continue')
 
+        clusters = {}
+        for cluster_number, cluster_name in found_representatives.items():
+            clusters[cluster_name] = cluster_sets[cluster_number]
+
         return clusters
 
 

ariba/tests/cdhit_test.py

@@ -25,12 +25,13 @@ def test_get_ids(self):
 
     def test_parse_cluster_info_file(self):
         '''test _parse_cluster_info_file'''
-        cluster_representatives = {'seq1', 'seq4'}
+        cluster_representatives = {'seq1', 'seq4', 'seq6'}
         infile = os.path.join(data_dir, 'cdhit_test_parse_cluster_info_file.infile')
         got_clusters = cdhit.Runner._parse_cluster_info_file(infile, cluster_representatives)
         expected_clusters = {
             'seq1': {'seq1', 'seq2', 'seq3'},
-            'seq4': {'seq4'}
+            'seq4': {'seq4'},
+            'seq6': {'seq5', 'seq6'},
         }
         self.assertEqual(expected_clusters, got_clusters)
 

ariba/tests/data/cdhit_test_parse_cluster_info_file.infile

@@ -2,3 +2,5 @@
 0	499aa, >seq2... at 99.40%
 0	499aa, >seq3... at 98.40%
 1	500aa, >seq4... *
+2	300aa, >seq5... at 90.42%
+2	301aa, >seq6... *