Files

Rory Nolan

2018-02-09

First let’s load the library:

library(filesstrings)
#> Loading required package: stringr

Move files around

I find it bizarre that base R has no file.move. To move a file, you have to unintuitively rename it. filesstrings provides file.move(files, destinations). This function has the nice feature that if you try to move files to a directory that doesn’t exist, it creates the directory first and then puts the files inside. Let’s create a directory and a file:

dir.create("tmp_dir")
file.create("tmp.txt")
#> [1] TRUE

Now let’s put the file into the directory:

file.move("tmp.txt", "tmp_dir")
#> 1 file moved. 0 failed.

Delete Directories

To delete directories with base R, one has to use unlink(..., recursive = TRUE). The filesstrings package gives you dir.remove() which does the same job.

dir.remove("tmp_dir")
#> 1 directory deleted. 0 failed to delete.

Remove spaces from file names

“A space in your file name is a hole in your soul.” - Jenny Bryan

remove_filename_spaces(replacement = "_") replaces them all with underscores for all files in a directory. By default, they are replaced with nothing.

file.create(c("file 1.txt", "file 2.txt"))
#> [1] TRUE TRUE
remove_filename_spaces(pattern = "txt$", replacement = "_")
#> 2 files required renaming and this was done successfully.
list.files(pattern = "txt$")
#> [1] "file_1.txt" "file_2.txt"
file.remove(list.files(pattern = "txt$"))  # clean up
#> [1] TRUE TRUE

Messed up file numbering

The microscope I use numbers files with 3 numbers by default, i.e. file001.tif, file002.tif and so on. This is a problem when the automatic numbering passes 1000, whereby we have file999.tif, file1000.tif. What’s the problem with this? Well, sometimes you need alphabetical order to reflect the true order of your files. These file numbers don’t satisfy this requirement:

file.names <- c("file999.tif", "file1000.tif")
sort(file.names)
#> [1] "file1000.tif" "file999.tif"

so file1000.tif comes before file999.tif in alphabetical order. The function nice_nums() returns the names that we’d like them to have:

nice_nums(file.names)
#> [1] "file0999.tif" "file1000.tif"

The function nice_file_nums applies such renaming to all the files in an entire directory. It wraps nice_nums.

The name of a file without the extension

before_last_dot("spreadsheet_92.csv")
#> [1] "spreadsheet_92"

Ensure that a file name has a given extension

Add a file extension if needed:

give_ext("xyz", "csv")
#> [1] "xyz.csv"

If the file name has the correct extension already, it’s left alone:

give_ext("xyz.csv", "csv")  
#> [1] "xyz.csv"

Change a file extension:

give_ext("abc.csv", "txt")  # tack the new extension onto the end
#> [1] "abc.csv.txt"
give_ext("abc.csv", "txt", replace = TRUE)  # replace the current extension
#> [1] "abc.txt"