Change mutation notation

klebgenomics · Aug 17, 2020 · adf8939 · adf8939
1 parent 2f80d6f
commit adf8939
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/kleborate/resBLAST.py b/kleborate/resBLAST.py
@@ -150,7 +150,7 @@ def blast_against_all(seqs, min_cov, min_ident, contigs, gene_info, min_spurious
                 hit_allele += trunc_suffix
 
             if class_changing_muts:
-                hit_allele += '-' + '-'.join(class_changing_muts)
+                hit_allele += ' +' + ' +'.join(class_changing_muts)
 
             # If the hit is decent (above the min coverage and identity thresholds), it goes in the
             # column for the class.

diff --git a/test/test_shv.py b/test/test_shv.py
@@ -50,7 +50,7 @@ class to ESBL, so the mutation is included in the
         """
         results = get_resistance_results(self.data_dir, 'test/test_shv/02.fasta', self.args,
                                          self.res_headers, True)
-        self.assertEqual(results['Bla_ESBL_acquired'], 'SHV-1*-238Y')
+        self.assertEqual(results['Bla_ESBL_acquired'], 'SHV-1* +238Y')
         self.assertEqual(results['SHV_mutations'], '238Y')
 
     def test_shv_03(self):
@@ -59,7 +59,7 @@ def test_shv_03(self):
         """
         results = get_resistance_results(self.data_dir, 'test/test_shv/03.fasta', self.args,
                                          self.res_headers, True)
-        self.assertEqual(results['Bla_ESBL_acquired'], 'SHV-1*-238Y')
+        self.assertEqual(results['Bla_ESBL_acquired'], 'SHV-1* +238Y')
         self.assertEqual(results['SHV_mutations'], '238Y')
 
     def test_shv_04(self):
@@ -87,7 +87,7 @@ def test_shv_06(self):
         """
         results = get_resistance_results(self.data_dir, 'test/test_shv/06.fasta', self.args,
                                          self.res_headers, True)
-        self.assertEqual(results['Bla_ESBL_inhR_acquired'], 'SHV-29*-234Y')
+        self.assertEqual(results['Bla_ESBL_inhR_acquired'], 'SHV-29* +234Y')
         self.assertEqual(results['SHV_mutations'], '234Y;238A;35Q')
 
     def test_shv_07(self):
@@ -115,7 +115,7 @@ def test_shv_09(self):
         """
         results = get_resistance_results(self.data_dir, 'test/test_shv/09.fasta', self.args,
                                          self.res_headers, True)
-        self.assertEqual(results['Bla_ESBL_acquired'], 'SHV-1*-174R')
+        self.assertEqual(results['Bla_ESBL_acquired'], 'SHV-1* +174R')
         self.assertEqual(results['SHV_mutations'], '174R;omega-loop=RWETELNEALRGDARD')
 
     def test_bla_class_01(self):