How do I rename all the files within a directory?-CodePudding

My bamFiles are currently "11.bam" "114.bam" "132.bam" "60.bam". I want to add chr16_ to the front of each file. These names should be back into the bamFiles character vector.

Code:

bamPath = "C:/Users/User/Downloads/chr16_bam"
for(f in bamPath){file.rename(list.files(pattern=".bam$", all.files=F, full.names=F), paste("chr16", sep="_", f))}

Traceback:

Error in file.rename(list.files(pattern = ".bam$", all.files = F, full.names = F),  : 
  'from' and 'to' are of different lengths

Expected output:

"chr16_11.bam"  "chr16_114.bam" "chr16_132.bam" "chr16_60.bam"

CodePudding user response：

Try This Solution, It's working perfectly at my end, now its your turn

> library(reproducible) 
> bamPath = "C:/Users/User/Downloads/chr16_bam"
> files <- list.files(bampath ,pattern = "*.bam",full.names = T)
> sapply(files,FUN=function(eachPath){ 
  file.rename(from=eachPath,to= .prefix(eachPath, "chr16_"))
})

Console Logs Should be like this

C:/Documents/Sample/16_161.bam                                                                                                              
TRUE 

C:/Documents/Sample/16_162.bam                                                                                                              
TRUE

C:/Documents/Sample/16_163.bam                                                                                                              
TRUE

If your getting "TRUE"then its renamed successfully also check folder where your files kept

Thanks....!

CodePudding user response：

Maybe I am not getting something here. If your issue is just to rename a bunch of files, this should do the trick.

I added to my home folder exactly the files you mentioned: 11.bam, 114.bam, 132.bam, 60.bam.

> oldfiles = list.files("~/", pattern = "*.bam")
> oldfiles
# [1] "11.bam"  "114.bam" "32.bam"  "60.bam" 
> 
> newfiles = paste0("chr16_", oldfiles)
> newfiles
# [1] "chr16_11.bam"  "chr16_114.bam" "chr16_32.bam"  "chr16_60.bam" 
> 
> file.rename(oldfiles, newfiles)
# [1] TRUE TRUE TRUE TRUE
> 
> list.files("~/", pattern = "*.bam")
# [1] "chr16_11.bam"  "chr16_114.bam" "chr16_32.bam"  "chr16_60.bam"