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)

FWIW, the rename command in Linux supports Perl-style regular expressions (it was authored by Larry Wall). Also, the code given would be safer as seq(a). — Iterator
– Iterator, Commented Oct 23, 2011 at 16:34

Iterator · Accepted Answer · 2011-10-24 11:31:28Z

4

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.

edited Oct 24, 2011 at 11:31

answered Oct 23, 2011 at 16:41

Iterator

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4 Comments

Ben Bolker Over a year ago

I think your answer here is the solution to the question at stackoverflow.com/questions/7865177/… , not this one ... because it affects the output format, not the number of files detected

Iterator Over a year ago

@BenBolker I suspect that the file in the other question doesn't exist, because he didn't format things in the way intended. As for the argument lengths, seq(a) should ensure that b is the same length as a, no? The OP split the question, but the other question really arises because his expectations for the renaming were possibly incorrect. For the other question, I asked him to produce file.info() output. If the file really does exist, it's not from the renaming done by the OP or the other answerer. :)

Iterator Over a year ago

@stan glad to help. Does it mean your other question no longer applies?

abc Over a year ago

@Iterator: yes, thanks to all who replied to these questions :)

Charlie · Accepted Answer · 2011-10-23 03:46:48Z

4

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.

answered Oct 23, 2011 at 3:46

Charlie

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4 Comments

abc Over a year ago

Thank you @Charlie :)! Unfortunately I faced some other problems: when i type file.rename(a, b) it returns many FALSEs and after a library(flowCore') the function isFCSfile("data.001") it returns FALSE again :(... What's wrong...?

daroczig Over a year ago

@stan: please open a new question regarding your comment. BTW if you want b to be the same length, try: b <- paste("data", 1:length(a), ".fcs", sep = "")

Roman Luštrik Over a year ago

@stan if this answer appears to be correct, consider accepting it (the check at the left should turn green when you click it).

Roman Luštrik Over a year ago

@stan try giving us a reproducible example. stackoverflow.com/questions/5963269/…

Community · Accepted Answer · 2017-05-23 12:00:53Z

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) }

Please check this: meta.stackexchange.com/questions/57836/…

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