Added getref feature for NCBI's Bacterial Antimicrobial Resistance Reference Gene Database

[schultzm]

Hi ARIBA team,

With this pull request, the user can now do ariba getref ncbi ncbi.getref to download the Bacterial Antimicrobial Resistance Reference Gene Database of over 4000 curated AMR genes. Unitests have been put in place, which can be run for the new feature doing python3 ariba/ariba/tests/ncbi_getter_test.py . I have updated the version number to 2.14.0.

Cheers,

Mark

[kpepper]

Hi @schultzm, thanks for the PR. Should be able to merge early next week.

[kpepper]

Could you try changing the python version from 3.5 to 3.6 in .travis.yml and commit that to the PR. Hopefully that will allow the Travis build to pass, as matplotlib requires 3.6. Also, could you add the ncbi option into the help text at line 65 of scripts/ariba. Thanks.

[schultzm]

@kpepper changes made as requested. Travis build now passes. Thanks.

[kpepper]

Hi @schultzm,
Was there any particular reason for removing the following line from the MANIFEST.in:
recursive-include third_party *.h
I think it's causing the PyPi/Bioconda builds to fall over as the compiler can't find "bseq.h" - the PyPi tar is missing the .h files.
Thanks.