Homework_11

Batch Processing Homework

Purpose: Produce 1 csv file from all the peptide tables from 1 mass spec experiment.
Input: peptide csv files downloaded from GFY, one table for each sample run.
Output: 1 csv file with all the peptide tables combined

#--------------------------------------------
# Global variables
file_folder <- "GFYFiles/"
n_files <- 8
file_out <- "PeptideTablesDate.csv"
file_names <- list.files(path=file_folder)
#--------------------------------------------

# batch process by looping through individual files

for (i in seq_along(file_names)) {
  data <- read.table(file=paste(file_folder,file_names[i],sep=""),
                     sep=",",
                     header=TRUE)
  write.table(cat("# Combinded peptide tables for ",
                "Date Mass Spec","\n",
                "# timestamp: ",as.character(Sys.time()),"\n",
                "# GB","\n",
                "# ------------------------", "\n",
                "\n",
                file=file_out,
                row.names="",
                col.names="",
                sep=""))
  
  write.table(x=data,
            file=file_out,
            row.names=FALSE,
            col.names=TRUE,
            sep=",",
            append=TRUE)
}