refpkgContents {clstutils} | R Documentation

## Read the contents of a collection of reference sequences ("refpkg").

### 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)

[Package clstutils version 1.36.0 Index]