refpkgContents: Read the contents of a collection of reference sequences...

In clstutils: Tools for performing taxonomic assignment.

Description

Read the manifest file from a refpackage and return a list containing the package contents.

Usage

refpkgContents(path, manifest = "CONTENTS.json")

Arguments

path	path to a refpkg directory
manifest	name of the manifest file

Value

Returns a list of lists. Run example(refpkgContents) for details.

Author(s)

Noah Hoffman

References

The decsription and specification for a reference package can be found in the project repository in github: https://github.com/fhcrc/taxtastic

Scripts and tools for creating reference packages are provided in the python package taxonomy, also available from the taxtastic project site.

See Also

taxonomyFromRefpkg

Examples

archive <- 'vaginal_16s.refpkg.tar.gz'
destdir <- tempdir()
system(gettextf('tar -xzf %s --directory="%s"',
                system.file('extdata',archive,package='clstutils'),
                destdir))
refpkg <- file.path(destdir, sub('.tar.gz','',archive))
contents <- refpkgContents(refpkg)
str(refpkg)

clstutils documentation built on Nov. 8, 2020, 5:23 p.m.