run multiple databases simultaneously

[pabloivan]

Hello,

I have not seen an option to run Abricate on multiple databases at once. The --db flag is uninformative on whether this is acually possible, but hints that a single database is to be used on every run (it's also a bit misleading on whether the database name should be surrounded by []or not):

--db [X] Database to use [ncbi].

Ideally I would like to use a syntax of the sort

abricate --fofn hugeFileOfFilenames.txt --db ncbi,resfinder,argannot,card,ecoh > resistanceGenesToBeCurated.txt

and then set off to curating this table.

[fmaguire]

You can always use a simple bash inline loop to do this if you need this feature right now:

for db in {ncbi,resfinder,argannot,card,ecoh}; do abricate --fofn hugeFileOfFilenames.txt --db $db --noheader >> resistanceGenesToBeCurated.txt ; done