How to rename files with a specific pattern in R?

Question

There are some .fcs files in a data.000X format (where X = 1, 2, 3...) in a directory.

I want to rename every n file to the following format: exp.fcs (where exp is a text from a vector) if the file to be renamed is an .fcs file.

in other words: I want to rename files to exp.txt, where exp is a text and not a consecutive letter(s) i.e. F, cA, K, etc.

For example, from:

data.0001, data.0002, data.0003, data.0004, data.0005, data.0006...  

to

textF_a.fcs, textF_b.fcs, textF_c.fcs, textVv_a.fcs, textVv_b.fcs, textVv_c.fcs ...  

I tried to do it with file.rename(from, to) but failed as the arguments have different lengths (and I don't know what it means):

a <- list.files(path = ".", pattern = "data.*$")  
b <- paste("data", 1:1180, ".fcs", sep = "")  
file.rename(a, b)

Answer 1

Based on your comments, one issue is that your first file isn't named "data.001" - it's named "data.1". Use this:

b <- sprintf("data%.4d.fcs", seq(a)) 

It prepends up to 3 0s (since it seems you have 1000+ files, this may be better) to indices < 1000, so that all names have the same width. If you really just want to see things like "data.001", then use %.3d in the command.

Answer 2

Your code "works" on my machine ("works" in the sense that, when I created a set of files and followed your procedure, the renaming happened correctly). The error is likely that the number of files that you have (length(a)) is different from the number of new names that you give (length(b)). Post back if it turns out that these objects do have the same length.

Answer 3

As with the (very similar) question here, this function might be of use to you. I wrote it to allow regex find and replace in R. If you're on a mac it can detect and use the frontmost Finder window as a target. Also supports test runs, over-write control, and filtering large folders.

umxRenameFile <- function(baseFolder = "Finder", findStr = NA, replaceStr = NA, listPattern = NA, test = T, overwrite = F) {
    # uppercase = u$1
    if(baseFolder == "Finder"){
        baseFolder = system(intern = T, "osascript -e 'tell application \"Finder\" to get the POSIX path of (target of front window as alias)'")
        message("Using front-most Finder window:", baseFolder)
    } else if(baseFolder == "") {
        baseFolder = paste(dirname(file.choose(new = FALSE)), "/", sep = "") ## choose a directory
        message("Using selected folder:", baseFolder)
    }
    if(is.na(listPattern)){
        listPattern = findStr
    }
    a = list.files(baseFolder, pattern = listPattern)
    message("found ", length(a), " possible files")
    changed = 0
    for (fn in a) {
        findB = grepl(pattern = findStr, fn) # returns 1 if found
        if(findB){
            fnew = gsub(findStr, replace = replaceStr, fn) # replace all instances
            if(test){
                message("would change ", fn, " to ", fnew)  
            } else {
                if((!overwrite) & file.exists(paste(baseFolder, fnew, sep = ""))){
                    message("renaming ", fn, "to", fnew, "failed as already exists. To overwrite set T")
                } else {
                    file.rename(paste(baseFolder, fn, sep = ""), paste(baseFolder, fnew, sep = ""))
                    changed = changed + 1;
                }
            }
        }else{
            if(test){
                # message(paste("bad file",fn))
            }
        }
    }
    message("changed ", changed)
}