[med-svn] [ariba] 01/01: New upstream version 2.9.4+ds

[Sascha Steinbiss]

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satta pushed a commit to branch upstream
in repository ariba.

commit 3ba405862933350229216bffaa1093ed9c2bb868
Author: Sascha Steinbiss <satta at debian.org>
Date:   Mon May 29 16:58:08 2017 +0200

    New upstream version 2.9.4+ds
---
 AUTHORS                         | 2 +-
 LICENSE                         | 4 ++++
 ariba/card_record.py            | 9 ++++++++-
 ariba/tests/card_record_test.py | 3 +++
 setup.py                        | 2 +-
 5 files changed, 17 insertions(+), 3 deletions(-)

diff --git a/AUTHORS b/AUTHORS
index 711ae85..39205dc 100644
--- a/AUTHORS
+++ b/AUTHORS
@@ -1 +1 @@
-Martin Hunt (mh12 at sanger.ac.uk)
+Martin Hunt (path-help at sanger.ac.uk)
diff --git a/LICENSE b/LICENSE
index 6b156fe..4faa525 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,3 +1,7 @@
+Copyright (c) 2015 - 2017 by Genome Research Ltd.
+
+This is free software, licensed under:
+
 GNU GENERAL PUBLIC LICENSE
                        Version 3, 29 June 2007
 
diff --git a/ariba/card_record.py b/ariba/card_record.py
index f1a1f49..20d977c 100644
--- a/ariba/card_record.py
+++ b/ariba/card_record.py
@@ -61,10 +61,17 @@ class CardRecord:
                 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'
diff --git a/ariba/tests/card_record_test.py b/ariba/tests/card_record_test.py
index 6058eac..58d7546 100644
--- a/ariba/tests/card_record_test.py
+++ b/ariba/tests/card_record_test.py
@@ -81,6 +81,9 @@ class TestCardRecord(unittest.TestCase):
         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': {
diff --git a/setup.py b/setup.py
index 1f1d390..f391e55 100644
--- a/setup.py
+++ b/setup.py
@@ -55,7 +55,7 @@ vcfcall_mod = Extension(
 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/*']},

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