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# This program is meant to take the .csv files created by the Click1_Click2_Cut.R program and format them for use in ebFRET.
#######################################################################################################################################################################

#Create a variable that contains the full names (full paths) for each text file in your directory of interest.

path = r"(C:\Users\clark\Desktop\Documents for Thesis and Manuscript\Analysis_9.9.2022\Lifetime_of_Initial_Sampling_Event_CognateNoTig)"
setwd(path)
files <- list.files(path, pattern="*.csv", full.names=TRUE, recursive=FALSE)

b <- 1
new_file_name <- "ebFRET_formatted_traces_NearCognate_25nMTC_5uMeEF2_CoInjection_SecondaryEvents_T1_to_T2_CKH_Filtered_Traces.txt"

for (i in files){
  
  # read the file, specify the correct separator
  data <- read.csv(i, header = FALSE, sep = ",")
 
  #Add a new column to each file that specifies the ID for the file
  ID_row <- b
  formatted_table <- cbind(ID_row, data)
  
  colnames(formatted_table) <- NULL
  
  #Save the formatted files to one file where each formatted trace appended to the last trace in the file.
  write.table(formatted_table, new_file_name, row.names = FALSE, col.names = FALSE, append = TRUE)
  
  #Iterate b so that the next trace has a unique identifier.
  b = b + 1
  
}