ranemone

Installation

You can install the development version from GitHub:

# install.packages("pak")
pak::pak("heavywatal/ranemone")

Use the same command from time to time to update the package.

Usage

library(ranemone)

Download data

ranemone provides a function to download data files recursively from ANEMONE DB in the same way as instructed on the website. Use ranemone.directory_prefix option to specify an existing data tree or a new destination for downloading.

options(ranemone.directory_prefix = "~/db")
ranemone::directory_prefix()

Authentication requires your username and a temporary password generated in ANEMONE DB.

options(ranemone.user = "your-username")
options(ranemone.password = "generated-password") # not yours

ranemone::wget_recursive("dist/MiFish/ANEMONE/")

This command tries not to overwrite existing files.

Read files

ANEMONE DB consists of many small files. It can take time to list and read them all. This package provides a caching mechanism to speed up the process for repeated use. You can check and change the cache directory as follows:

ranemone::cache_dir()
options(ranemone.cache_dir = "~/.cache/ranemone")
ranemone::cache_dir()

Read all files with the given file name recursively in directory_prefix().

sample_df = ranemone::read_tsv_xz("sample.tsv.xz")
experiment_df = ranemone::read_tsv_xz("experiment.tsv.xz")
community_df = ranemone::read_tsv_xz("community_qc3nn_target.tsv.xz")

The results are cached in cache_dir(), which makes subsequent calls faster.

fs::dir_ls(ranemone::cache_dir())