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 You're receiving this email because of your account on salsa.debian.org.
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