load_microbesonline_annotations: Skip the db and download all the text annotations for a given...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Skip the db and download all the text annotations for a given species.

Description

The microbesonline publicly available mysqldb is rather more complex than I prefer. This skips that process and just grabs a tsv copy of everything and loads it into a dataframe. I have not yet figured out how to so-easily query microbesonline for species IDs, thus one will have to manually query the database to find species of interest.

Usage

load_microbesonline_annotations(species = NULL, id = NULL)

Arguments

species	Microbesonline species.
id	Microbesonline ID to query.

Details

Tested in test_70expt_spyogenes.R There is so much awesome information in microbesonline, but damn is it annoying to download. This function makes that rather easier, or so I hope at least.

Value

Dataframe containing the annotation information.

See Also

[rvest] [xml2] [readr]

Examples

 pa14_microbesonline_annot <- load_microbesonline_annotations(species = "PA14")
 colnames(pa14_microbesonline_annot)

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.