Commit 58b996f2fc4f9a919c7b97d42bb5949c2cbcb0e3 - ariba

Merge pull request #289 from fmaguire/master Update CARD citation message Christoph Püthe authored 3 years ago GitHub committed 3 years ago

1 changed file(s) with 2 addition(s) and 2 deletion(s). Raw diff Collapse all Expand all

-2

ariba/ref_genes_getter.py less more

182	182	print('You can use them with ARIBA like this:')
183	183	print('ariba prepareref -f', final_fasta, '-m', final_tsv, 'output_directory\n')
184	184	print('If you use this downloaded data, please cite:')
185		print('"The Comprehensive Antibiotic Resistance Database", McArthur et al 2013, PMID: 23650175')
	185	print('"CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database", Alcock et al 2020, PMID: 31665441')
186	186	print('and in your methods say that version', self.version, 'of the database was used')
187	187
188	188

658	658	print('ariba prepareref -f', final_fasta, '-m', final_tsv, 'output_directory\n')
659	659
660	660	else:
661		print(f"Nothing to do. Exiting.")
	661	print(f"Nothing to do. Exiting.")
662	662	def run(self, outprefix):
663	663	exec('self._get_from_' + self.ref_db + '(outprefix)')