Merge pull request #282 from sanger-pathogens/argannot_issue281

Fixed GitHub issue #281 - ARG-ANNOT Fails to Download

CHANGELOG.md

@@ -1,5 +1,12 @@
 # Change Log
 
+[v2.14.4](https://github.com/sanger-pathogens/ariba/tree/v2.14.4) (2019-09-24)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.14.3...v2.14.4)
+
+**Fixed bugs:**
+
+- ARGannot download fails [\#281](https://github.com/sanger-pathogens/ariba/issues/281)
+
 [v2.14.3](https://github.com/sanger-pathogens/ariba/tree/v2.14.3) (2019-08-23)
 [Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.14.2...v2.14.3)
 

ariba/ref_genes_getter.py

@@ -277,13 +277,12 @@ def _get_from_argannot(self, outprefix):
         except:
             raise Error('Error mkdir/chdir ' + tmpdir)
 
-        zipfile = 'arg-annot-database_doc.zip'
-        common.download_file('http://www.mediterranee-infection.com/arkotheque/client/ihumed/_depot_arko/articles/304/arg-annot-database_doc.zip', zipfile, max_attempts=self.max_download_attempts, sleep_time=self.sleep_time, verbose=True)
-        common.syscall('unzip ' + zipfile)
+        downloadfile = 'arg-annot-database_doc'
+        common.download_file('https://www.mediterranee-infection.com/wp-content/uploads/2019/09/ARG-ANNOT_NT_V6_July2019.txt', downloadfile, max_attempts=self.max_download_attempts, sleep_time=self.sleep_time, verbose=True)
         os.chdir(current_dir)
         print('Extracted files.')
 
-        genes_file = os.path.join(tmpdir, 'Database Nt Sequences File.txt')
+        genes_file = os.path.join(tmpdir, downloadfile)
         final_fasta = outprefix + '.fa'
         final_tsv = outprefix + '.tsv'
 

setup.py

@@ -55,7 +55,7 @@
 setup(
     ext_modules=[minimap_mod, fermilite_mod, vcfcall_mod],
     name='ariba',
-    version='2.14.3',
+    version='2.14.4',
     description='ARIBA: Antibiotic Resistance Identification By Assembly',
     packages = find_packages(),
     package_data={'ariba': ['test_run_data/*', 'tb_data/*']},