micropan: xz – R documentation

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xz

Compressing and uncompressing text files

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

Microbial Pan-Genome Analysis

v2.1

GPL-2

Authors

Lars Snipen and Kristian Hovde Liland

Initial release

2020-07-15

xz