Merge pull request #179 from martinghunt/card_1.1.8

Card 1.1.8

ariba/card_record.py

@@ -61,10 +61,17 @@ def _dna_seqs_and_genbank_ids(gene_dict):
                 genbank_id = seq_dict['dna_sequence']['accession']
                 start = seq_dict['dna_sequence']['fmin']
                 end = seq_dict['dna_sequence']['fmax']
-                gi = seq_dict['protein_sequence']['GI']
+
+                # Card version <=1.1.7 has 'GI', but 1.1.8 has 'accession' instead
+                if 'GI' in seq_dict['protein_sequence']:
+                    gi = seq_dict['protein_sequence']['GI']
+                else:
+                    gi = seq_dict['protein_sequence']['accession']
+
                 protein_seq = seq_dict['protein_sequence']['sequence']
             except:
                 print('Missing data from', key, file=sys.stderr)
+                pprint.pprint(seq_dict)
                 continue
 
             assert gi != 'NA'

ariba/tests/card_record_test.py

@@ -81,6 +81,9 @@ def test_dna_seqs_and_genbank_ids(self):
         d['model_sequences']['sequence']['foo']['protein_sequence']['sequence'] = 'III'
         expected = [('foo', '123456789', 'ABC123', '42', '4242', 'ACGT', 'III')]
         self.assertEqual(expected, card_record.CardRecord._dna_seqs_and_genbank_ids(d))
+        del d['model_sequences']['sequence']['foo']['protein_sequence']['GI']
+        d['model_sequences']['sequence']['foo']['protein_sequence']['accession'] = '123456789'
+        self.assertEqual(expected, card_record.CardRecord._dna_seqs_and_genbank_ids(d))
 
         d['model_sequences']['sequence']['bar'] = {
             'dna_sequence': {

setup.py

@@ -55,7 +55,7 @@
 setup(
     ext_modules=[minimap_mod, fermilite_mod, vcfcall_mod],
     name='ariba',
-    version='2.9.3',
+    version='2.9.4',
     description='ARIBA: Antibiotic Resistance Identification By Assembly',
     packages = find_packages(),
     package_data={'ariba': ['test_run_data/*']},