In jensenlab/modifile: Manipulate filenames in R.

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
library(modifile)

modifile

Manipulate filenames in R.

Installation

devtools::install_github("jensenlab/modifile")

Splitting filenames into paths, names, and extensions

The split_filename function splits a filename into a path (directory location), the name of the file, and the file's extension.

split_filename("/path/to/file/myfile.fastq")

The join_filename function does the opposite.

join_filename("/path/to/file", "myfile", "fastq")

All functions in modifile are vectorized over their inputs.

split_filename(c("/path/to/file/myfile1.fastq", "/path/to/file/myfile2.fastq"))
join_filename("/path/to/file", c("myfile1","myfile2"), "fastq")

A file's extensions includes all suffixes to allow for compressed files.

split_filename("file.fasta.gz")

Modifying filenames

The modify_filename function can change the path, name, or extension of filenames.

test_filenames <- c("./file.fastq", "file.fq", "/path/to/file/file.fastq.gz")
modify_filename(test_filenames, new_path="newdir")
modify_filename(test_filenames, new_name="newfile")
modify_filename(test_filenames, new_ext="bam")

Remove the path, name, or extension by setting the new value to an empty string.

modify_filename(test_filenames, new_ext="")

You can also add test before or after each part of the filename.

modify_filename("/path/file.ext", 
                before_path="<BEFORE_PATH>", after_path="<AFTER_PATH>",
                before_name="<BEFORE_NAME>", after_name="<AFTER_NAME>",
                before_ext="<BEFORE_EXT>", after_ext="<AFTER_EXT>")

The after_path test is treated as a subdirectory, and before_ext is inserted after the . but before the rest of the extension.

Concatenating filenames

The concat_filenames function joins two sets of filenames. By default, only the names of the files are joined.

concat_filenames("path1/name1.fastq", "path2/name2.fa.gz")

You can choose to join the path, name, extension or any combination. Setting the path, name, and ext arguments to:

• 0 drops the part of the filename
• 1 uses the part from filename1
• 2 uses the part from filename2
• 1+2 combines the part from filename1 and filename2 using the separator in sep

concat_filenames("path1/name1.fastq", "path2/name2.fa.gz",
                 path=2, name=1+2, ext=1, sep="@")

jensenlab/modifile documentation built on May 7, 2019, 12:52 a.m.