How to edit multiple file names at once? - linux

Question

I have directory full of .txt files (2000 files). they have very long name. I want to edit their name and just keep certain letter from inside of their name as file name.
like this :
UNCID_279113.TCGA-A6-2683-01A-01R-0821-07.100902_UNC7-RDR3001641_00025_FC_62EPOAAXX.1.trimmed.annotated.gene.quantification.txt
I want eliminate this long names and just keep the name starting from TCGA and ending after three - ; for example, my new file name would be : TCGA-A6-2683-01A
does anybody knows how can I do this for whole files in one directory?

Answer 1

Assuming the files are in the current directory:
library(gsubfn)
pat <- "TCGA-[^-]*-[^-]*-[^-]*"
file.names <- dir(pattern = pat)
new.names <- strapplyc(file.names, pat, simplify = TRUE)
file.rename(file.names, new.names)
Create a shell/batch script Here is a variation. It produces a UNIX shell file or a Windows batch file. You can then review the file and run it:
# UNIX
writeLines(paste("mv", file.names, new.names), con = "tcga_rename.sh")
shell("tcga_rename.sh")
or on Windows:
# Windows
writeLines(paste("rename", file.names, new.names), con = "tcga_rename.bat")
shell("tcga_rename.bat")
REVISED: Factored out pat, simplified and added variations.

Answer 2

Assuming your files are in the current working directory, try
library(stringr)
files <- list.files(".", pattern=".txt")
file.rename(files, str_extract(files, "TCGA(-\\w+){3}"))

Answer 3

You can do something like this:
pattern <- ".*(TCGA-[^-]+-[^-]+-[^-]*).*"
file.rename(
list.files("."),
sub(pattern, "\\1", list.files("."))
)
But be super careful that the sub command does what you think it will do before you run the full thing (i.e. just run the sub piece). Hard to be sure this won't cause a problem without knowing what patterns you have in your file names.
Also, in this case replace list.files(".") with your directory. Note you don't need to filter our the files that match the pattern in the first place since sub will only modify the file names that do match the pattern (not super efficient if you have a lot of files that don't match the pattern, but easier to write, if a concern, you can use the pattern argument as Greg Snow does).

Answer 4

You cane use list.files() to get a list of the filenames in the directory, then use substitute with regular expressions to edit the names, then file.rename to actually do the renaming.
Something like (untested):
curfiles <- list.files(pattern='TCGA') # only grab files with TCGA in them
newfiles <- sub("^.*(TCGA-[a-zA-z0-9]+-[a-zA-Z0-9]+-[a-zA-Z0-9]+).*$", "\\1", curfiles)
file.rename(curfiles,newfiles)