get_eupath_pkgnames: Generate standardized package names for the various eupathdb...

In khughitt/EuPathDB: Provides access to pathogen annotation resources available on EuPathDB databases

Generate standardized package names for the various eupathdb species.

Description

This is a surprisingly difficult problem. Many species names in the eupathdb have odd characters in the species suffix which defines the strain ID. Many of these peculiarities result in packages which are non-viable for installation. Thus this function attempts to filter them out and result in consistent, valid package names. They are not exactly the same in format as other orgdb/txdb/etc packages, as I include in them a field for the eupathdb version used; but otherwise they should be familiar to any user of the sqlite based organism packages.

Usage

get_eupath_pkgnames(entry, eu_version = NULL, column = "TaxonUnmodified")

Arguments

entry	A metadatum entry.
eu_version	Choose a specific version of the eupathdb, only really useful when downloading files.
column	Which column to query to get the species name?

Details

The default argument for this function shows the funniest one I have found so far thanks to the hash character in the strain definition.

Value

List of package names and some booleans to see if they have already been installed.

Author(s)

atb

khughitt/EuPathDB documentation built on Nov. 4, 2023, 4:19 a.m.