xz: Compressing and uncompressing text files

In micropan: Microbial Pan-Genome Analysis

Description

These functions are adapted from the R.utils package from gzip to xz. Internally xzfile() (see connections) is used to read (write) chunks to (from) the xz file. If the process is interrupted before completed, the partially written output file is automatically removed.

Usage

xzcompress(
  filename,
  destname = sprintf("%s.xz", filename),
  temporary = FALSE,
  skip = FALSE,
  overwrite = FALSE,
  remove = TRUE,
  BFR.SIZE = 1e+07,
  compression = 6,
  ...
)

xzuncompress(
  filename,
  destname = gsub("[.]xz$", "", filename, ignore.case = TRUE),
  temporary = FALSE,
  skip = FALSE,
  overwrite = FALSE,
  remove = TRUE,
  BFR.SIZE = 1e+07,
  ...
)

Arguments

filename	Path name of input file.
destname	Pathname of output file.
temporary	If TRUE, the output file is created in a temporary directory.
skip	If TRUE and the output file already exists, the output file is returned as is.
overwrite	If TRUE and the output file already exists, the file is silently overwritting, otherwise an exception is thrown (unless skip is TRUE).
remove	If TRUE, the input file is removed afterward, otherwise not.
BFR.SIZE	The number of bytes read in each chunk.
compression	The compression level used (1-9).
...	Not used.

Value

Returns the pathname of the output file. The number of bytes processed is returned as an attribute.

Author(s)

Kristian Hovde Liland.

Examples

# Creating small file
tf <- tempfile()
cat(file=tf, "Hello world!")

# Compressing
tf.xz <- xzcompress(tf)
print(file.info(tf.xz))

# Uncompressing
tf <- xzuncompress(tf.xz)
print(file.info(tf))
file.remove(tf)

micropan documentation built on July 15, 2020, 5:08 p.m.