[med-svn] [Git][med-team/ariba][upstream] New upstream version 2.14.6+ds

[Sascha Steinbiss]

Sascha Steinbiss pushed to branch upstream at Debian Med / ariba


Commits:
65895acf by Sascha Steinbiss at 2020-09-13T18:30:27+02:00
New upstream version 2.14.6+ds
- - - - -


4 changed files:

- CHANGELOG.md
- ariba/pubmlst_getter.py
- ariba/ref_genes_getter.py
- setup.py


Changes:

=====================================
CHANGELOG.md
=====================================
@@ -1,5 +1,20 @@
 # Change Log
 
+## [v2.14.6](https://github.com/sanger-pathogens/ariba/tree/v2.14.6) (2020-09-07)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.14.5...v2.14.6)
+
+**Closed issues:**
+
+- PubMLST URL change breaks pubmlstget [\#304](https://github.com/sanger-pathogens/ariba/issues/304)
+- get\_ref card is attempting to download RGI [\#301](https://github.com/sanger-pathogens/ariba/issues/301)
+- Reference dataset of megares cannot be downloaded  [\#287](https://github.com/sanger-pathogens/ariba/issues/287)
+
+**Merged pull requests:**
+
+- Fix for changes in PubMLST url [\#305](https://github.com/sanger-pathogens/ariba/pull/305) ([rpetit3](https://github.com/rpetit3))
+- Solution 1: for fixing CARD download [\#302](https://github.com/sanger-pathogens/ariba/pull/302) ([rpetit3](https://github.com/rpetit3))
+- Update CARD citation message [\#289](https://github.com/sanger-pathogens/ariba/pull/289) ([fmaguire](https://github.com/fmaguire))
+
 ## [v2.14.5](https://github.com/sanger-pathogens/ariba/tree/v2.14.5) (2020-05-14)
 [Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.14.4...v2.14.5)
 


=====================================
ariba/pubmlst_getter.py
=====================================
@@ -105,7 +105,7 @@ class PubmlstGetter:
         self._download_file(profile_url, profile_outfile)
 
         for fasta_url in fasta_urls:
-            outfile = os.path.join(outdir, fasta_url.split('/')[-1])
+            outfile = "{0}.tfa".format(os.path.join(outdir, fasta_url.split('/')[-2]))
             self._download_file(fasta_url, outfile + '.tmp')
             PubmlstGetter._rename_seqs_in_fasta(outfile + '.tmp', outfile)
             os.unlink(outfile + '.tmp')


=====================================
ariba/ref_genes_getter.py
=====================================
@@ -42,7 +42,7 @@ class RefGenesGetter:
     def _get_card_versions(self, tmp_file):
         print('Getting available CARD versions')
         common.download_file('https://card.mcmaster.ca/download', tmp_file, max_attempts=self.max_download_attempts, sleep_time=self.sleep_time, verbose=True)
-        p = re.compile(r'''href="(/download/.*?broad.*?v([0-9]+\.[0-9]+\.[0-9]+)\.tar\.(gz|bz2))"''')
+        p = re.compile(r'''href="(/download/0/.*?broad.*?v([0-9]+\.[0-9]+\.[0-9]+)\.tar\.(gz|bz2))"''')
         versions = {}
 
         with open(tmp_file) as f:
@@ -183,7 +183,7 @@ class RefGenesGetter:
         print('You can use them with ARIBA like this:')
         print('ariba prepareref -f', final_fasta, '-m', final_tsv, 'output_directory\n')
         print('If you use this downloaded data, please cite:')
-        print('"The Comprehensive Antibiotic Resistance Database", McArthur et al 2013, PMID: 23650175')
+        print('"CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database", Alcock et al 2020, PMID: 31665441')
         print('and in your methods say that version', self.version, 'of the database was used')
 
 
@@ -659,6 +659,6 @@ class RefGenesGetter:
                         print('ariba prepareref -f', final_fasta, '-m', final_tsv, 'output_directory\n')
 
         else:
-            print(f"Nothing to do. Exiting.")    
+            print(f"Nothing to do. Exiting.")
     def run(self, outprefix):
         exec('self._get_from_' + self.ref_db + '(outprefix)')


=====================================
setup.py
=====================================
@@ -55,7 +55,7 @@ vcfcall_mod = Extension(
 setup(
     ext_modules=[minimap_mod, fermilite_mod, vcfcall_mod],
     name='ariba',
-    version='2.14.5',
+    version='2.14.6',
     description='ARIBA: Antibiotic Resistance Identification By Assembly',
     packages = find_packages(),
     package_data={'ariba': ['test_run_data/*', 'tb_data/*']},



View it on GitLab: https://salsa.debian.org/med-team/ariba/-/commit/65895acfce631d41922b309c9220fccd8ffdd73a

-- 
View it on GitLab: https://salsa.debian.org/med-team/ariba/-/commit/65895acfce631d41922b309c9220fccd8ffdd73a
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