[med-svn] [Git][med-team/ariba][master] 3 commits: New upstream version 2.14.6+ds

[Sascha Steinbiss]

Sascha Steinbiss pushed to branch master at Debian Med / ariba


Commits:
65895acf by Sascha Steinbiss at 2020-09-13T18:30:27+02:00
New upstream version 2.14.6+ds
- - - - -
6c13d984 by Sascha Steinbiss at 2020-09-13T18:30:35+02:00
Update upstream source from tag 'upstream/2.14.6+ds'

Update to upstream version '2.14.6+ds'
with Debian dir 68512f1670550c5c2eb3ec3908e5b16ad93ed131
- - - - -
280aced8 by Sascha Steinbiss at 2020-09-14T08:56:47+02:00
new upstream release

- - - - -


6 changed files:

- CHANGELOG.md
- ariba/pubmlst_getter.py
- ariba/ref_genes_getter.py
- debian/changelog
- debian/patches/add-testdata.patch
- 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)')


=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+ariba (2.14.6+ds-1) unstable; urgency=medium
+
+  * New upstream release.
+
+ -- Sascha Steinbiss <satta at debian.org>  Sun, 13 Sep 2020 18:34:46 +0200
+
 ariba (2.14.5+ds-3) unstable; urgency=medium
 
   * Only build-depend on spades on amd64.


=====================================
debian/patches/add-testdata.patch
=====================================
@@ -4,7 +4,7 @@ Last-Update: 2019-09-09
 --- a/setup.py
 +++ b/setup.py
 @@ -57,7 +57,43 @@
-     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/*']},


=====================================
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/-/compare/e2ed8ac021b503644386e17aa075c6aef13ba79d...280aced86a10937b97a28e889feee79c19dc9482

-- 
View it on GitLab: https://salsa.debian.org/med-team/ariba/-/compare/e2ed8ac021b503644386e17aa075c6aef13ba79d...280aced86a10937b97a28e889feee79c19dc9482
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