<regex_correction

[Farm]

#I would wish that my snippet is corrected. many thanks

#Example of filename in a directory:: 02_ZR66_042_FRT1008.fcs

# Function to rename files
rename_files <- function(directory) {
  # Retrieve the basenames of the files in the directory
  files <- list.files(directory, full.names = TRUE) 
  filenames <- basename(files)
  
  ## Regular expression pattern to remove the initial part
  pattern <- "\\d{2}_ZR\\d{2}_\\d{3}_"
  ## Regular expression pattern to extract the desired substring
  pattern2 <- "[A-Za-z0-9]{8}"
  
  ## Apply renaming to each file
  for (file in filenames) {
    # Extracting the desired substring from the file name
    result <- str_remove(file, pattern)
    result2 <- str_extract(result, pattern2)
    
    # Ensure the extension is maintained
    new_file_name <- paste0(directory, result2, ".fcs")
      
     # Renaming the file
    file.rename(file.path(directory, file), file.path(directory, new_file_name))
  }
}

## Apply the renaming function to the specified directory
rename_files(“directory”)


#output 
#Warning messages:
#1: In file.rename(file.path(directory, file), file.path(directory,  :
#  cannot rename '..../.fcs' to '..../NA.fcs’ , reason 'No such file or directory'

[dromano]

@Farm

"[A-Za-z0-9]{8}"

Your example has only seven characters before the .fcs file extension — could that be the problem?

[Farm]

Changing it to 7 didn’t solve the problem

[M_AcostaCH]

Hi @Farm , maybe is better is you provide a better example of the file names.

Try to paste the a df when you get list.files().

files_list <- data.frame(folder_path=list.files(path = 'D:\\Put_you_path\\Desktop\\folder_name',
                                                recursive = TRUE, 
                                                full.names = TRUE,
                                                pattern = '\\.fcs))

[dromano]

@M_AcostaCH

files_list <- data.frame(folder_path=list.files(path = ...
                                                recursive = TRUE, ...
                                                ...
 

Not sure a data frame is necessary, but a simple copy-paste of the directory contents — or at least enough so it includes file names that trigger an error — would be helpful.

[Farm]

I made the following changes and it all works now.

library(stringr)
#Function to rename files
rename_files <- function() {
  
  files_list <- list.files(path = "directory",
                           recursive = TRUE, 
                           full.names = TRUE,
                           pattern = '\\.fcs')
                                      
  # Convert list of files into a one-column data frame
  files_df <- data.frame(folder_path = files_list)
  
  #Regular expression pattern to remove the initial part
  pattern <- "\\d{2}_TA\\d{2}_\\d{3}_"
  #Regular expression pattern to extract the desired substring
  pattern2 <- "[A-Za-z0-9]{7}"
  
  #Apply renaming to each file
  for (file in files_df$folder_path) {
    
    #Extracting the desired substring from the file name
    result <- str_remove(basename(file), pattern)
    result2 <- str_extract(result, pattern2)
    
    #Ensure the extension is maintained
    new_file_name <- paste0(result2, ".fcs")
    
    # Renaming the file, in the proper directory
    file.rename(file, new_file_name)
  }
}

#Apply the renaming function to the specified directory
rename_files()
  }
}

directory= “actual_directory"
rename_files("directory")

[nirgrahamuk]

You seem to have an issue with unusual quotation marks

your first use of them ; consider the first quote mark symbol
It should be :
path = "directory"
what you have :
path = “directory"
which I wouldnt expect to run

In my view of the code formatting on this forum (I use darkmode) I can see the code is white text, and where there is text within quotations its highlighted in pink, and after the section I highlighted to you everything goes pink...

[Farm]

Thanks for pointing that out