💪🧬 amino acid and nucleotide filters

[TKMarkCheng]

Adding filter by a series of amino acid and/or nucleotide mutations by entering a string with comma-separated substitutions/mutations.

Also added to the README.md, as internal_query.R in addition to query.R needs to be updated for new filters to operate.

[BryanTegomoh]

certainly a useful addition to the query function

[TKMarkCheng]

@Wytamma, please can I ask if this can be built tested, and merged? R CMD check via devtools::check() worked and passed all test locally and I am bursting with excitement to contribute to this project!
use aa_substitution and nucl_mutation to filter on mutations of interest.

df <- query (credentials = credentials, aa_substitution = 'Spike_H69del, Spike_A222V, Spike_G476S, -N_P13L')
expect_equal(df$submission_date[1], "2021-04-27") #earliest is 2021-04-27

[Wytamma]

Hey @TKMarkCheng! That’s amazing thanks heaps! Sorry have been traveling will merge your PR asap!

[Wytamma]

I can’t run the tests on the PR because the worker doesn’t have access to the repo secrets. But the code looks good so I’ll just merge and run them on main.

[TKMarkCheng]

@Wytamma happy to contribute! I am in fact glad that I had an extra day to catch that incompatibility issue with load_all. Hopefully, this PR can act as a template for future contributors.

I presume the repo secrets are the GISAIDR_USERNAME and GISAIDR_PASSWORD stored on local .Renviron, so would be not fixable unless the worker itself has an equivalent to .Renviron file.

[Wytamma]

Nah it’s a security reason. GitHub prevents PRs from other people from accessing the env vars so that you can’t steal my gisaid password etc. But looks like it all worked! Congratulations and thanks again!