CODEWITHSUNDEEP
r
Achal Neupane
Achal Neupane

Reputation: 5729

How to loop over each file in multiple directories in R

I have an object called wanted.bam with the list of wanted file names for all the .bam (is the extension) files in three of my directories path1,path2,path3. I am looping over all these directories to search for the wanted files. What I am trying to do is look for wanted files by looping over each directory and implement a FUNCTION in each file. This loop works for all the matched file in the first directory, but as it progresses to another directory, it breaks giving an error: 

Error in value[[3L]](cond) : 
  failed to open BamFile: file(s) do not exist:
  'sort.bam'

my code:

bam.dir<- c("path1","path2","path3")
    for (j in 1:length(bam.dir)){
    all.bam.files <- list.files(bam.dir[j])
    all.bam.files <- grep(wanted.names, all.bam.files, value=TRUE)           
    print(paste("The wanted number of bam files in this directory:", (length(all.bam.files))))     
      if(length(all.bam.files)==0){
        next
      }else{
    setwd(bam.dir[j])
    }
    print(paste("The working directory number:",j,":",(getwd())))

    ## ****using another loop here for each file to implement a function*****
    all.FAD<- {}
    for(i in 1:length(all.bam.files)){
    output<- FUNCTION(all.bam.files[i])
    }
  }

Upvotes: 0

Views: 1794

Answers (1)

Rorschach
Rorschach

Reputation: 32466

You probably don't want to be changing working directory like this. Instead, use the option in list.files, full.names=TRUE, to return the full path of your files. Then, you can just use read.csv, or whatever, on the full path name without need to change directory. Your code is failing because after you set directory, the relative path to the next directory is changed.

If you want to keep changing directories, just make sure you set the directory back to the base directory at the end of the loop.

Upvotes: 4

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