Change assembly_Ns to ambiguous_bases

Author: rrwick

kleborate/contig_stats.py

@@ -16,11 +16,11 @@
 
 
 def get_contig_stat_results(contigs):
-    contig_count, n50, longest_contig, contains_n = get_contig_stats(contigs)
+    contig_count, n50, longest_contig, ambiguous_bases = get_contig_stats(contigs)
     return {'contig_count': str(contig_count),
             'N50': str(n50),
             'largest_contig': str(longest_contig),
-            'assembly_Ns': contains_n}
+            'ambiguous_bases': ambiguous_bases}
 
 
 def get_contig_stats(assembly):
@@ -29,11 +29,17 @@ def get_contig_stats(assembly):
     """
     fasta = load_fasta(assembly)
 
-    contains_n = 'no'
+    characters = set()
     for _, seq in fasta:
-        if 'N' in seq:
-            contains_n = 'yes'
-            break
+        characters |= set(b for b in seq)
+    characters.discard('A')
+    characters.discard('C')
+    characters.discard('G')
+    characters.discard('T')
+    if characters:
+        ambiguous_bases = 'yes'
+    else:
+        ambiguous_bases = 'no'
 
     contig_lengths = sorted([len(x[1]) for x in fasta])
     if not contig_lengths:
@@ -51,4 +57,4 @@ def get_contig_stats(assembly):
     else:
         n50 = 0
 
-    return len(contig_lengths), n50, longest, contains_n
+    return len(contig_lengths), n50, longest, ambiguous_bases

kleborate/kleborate.py

@@ -185,7 +185,8 @@ def get_output_headers(args, data_folder):
     stdout_header = ['strain', 'species']
     full_header = ['strain', 'species', 'species_match']
     stdout_header += ['ST', 'virulence_score']
-    full_header += ['contig_count', 'N50', 'largest_contig', 'assembly_Ns', 'ST', 'virulence_score']
+    full_header += ['contig_count', 'N50', 'largest_contig', 'ambiguous_bases', 'ST',
+                    'virulence_score']
 
     if args.resistance:
         stdout_header.append('resistance_score')

test/sequences/contig_stats_3.fasta

@@ -0,0 +1,6 @@
+>1
+agggggggaagggtttcgta
+>2
+attaggccgtggagccttcctgccgggttcgaaaagtagt
+>3
+aaatgtaatgcttgtgtttttgggctaagtgctaccattaacaggcgtcagcggatcggcttagttagttgccttggtccaacccaaattttctttaggcggcccgaagactccaactctgctgcataccccgttgtcagctatcatgtcactaaaaatgcacctataagacagtactagaaccacacagacatgacagg

test/sequences/contig_stats_4.fasta

@@ -0,0 +1,6 @@
+>1
+AGGGGGGGAAGGGTTTCGTA
+>2
+ATTAGGCCGTGGAGCCTTCCTGCCGGGTTCGAAAAGTAGT
+>3
+AAATGTAATGCTTGTGTTTTTGGGCTAAGTGCTACCATTAACAGGCGTCAGCGGATCGGCTTAGTTAGTTGCCTTGGTCCAACCCAAATTTTCTTTAGGCGGCCCGAAGACTCCAACTCTGCTGCATACCCCGTTGTCAGCTATCATGTCACTAAAAATGCACCTATAAGACAGTACTAGAADCACACAGACATGACAGG

test/test_contig_stats.py

@@ -43,10 +43,19 @@ def test_longest_2(self):
         _, _, longest_contig, _ = get_contig_stats('test/sequences/contig_stats_2.fasta')
         self.assertEqual(longest_contig, 200)
 
-    def test_n_1(self):
-        _, _, _, contains_n = get_contig_stats('test/sequences/contig_stats_1.fasta')
-        self.assertEqual(contains_n, 'no')
+    def test_ambiguous_bases_1(self):
+        _, _, _, ambiguous_bases = get_contig_stats('test/sequences/contig_stats_1.fasta')
+        self.assertEqual(ambiguous_bases, 'no')
+
+    def test_ambiguous_bases_2(self):
+        _, _, _, ambiguous_bases = get_contig_stats('test/sequences/contig_stats_2.fasta')
+        self.assertEqual(ambiguous_bases, 'yes')
+
+    def test_ambiguous_bases_3(self):
+        _, _, _, ambiguous_bases = get_contig_stats('test/sequences/contig_stats_3.fasta')
+        self.assertEqual(ambiguous_bases, 'no')
+
+    def test_ambiguous_bases_4(self):
+        _, _, _, ambiguous_bases = get_contig_stats('test/sequences/contig_stats_4.fasta')
+        self.assertEqual(ambiguous_bases, 'yes')
 
-    def test_n_2(self):
-        _, _, _, contains_n = get_contig_stats('test/sequences/contig_stats_2.fasta')
-        self.assertEqual(contains_n, 'yes')