aggregate_data_tables.R

#!/usr/bin/env Rscript
# This script is used to extract 1 column each from multiple files and report all columns
# in a single file.
# Example use case for this script is extracting raw counts from multiple per sample RSEM
# files and creating a single raw counts matrix
#
# Eg:
#
# Rscript aggregate_data_tables.R \
# 	-s KO1_resent_mutated,KO1_resent,KO1_resent_unmutated,KO1_slam_mutated \
# 	-l ./KO1_resent/KO1_resent_mutated.RSEM.genes.results,./KO1_resent/KO1_resent.RSEM.genes.results,./KO1_resent/KO1_resent_unmutated.RSEM.genes.results \
# 	-c expected_count \
# 	-i gene_id \
# 	-o rsem.raw_counts_matrix.tsv
#
suppressPackageStartupMessages(library("argparse"))
suppressPackageStartupMessages(library("sets"))

## functions
checkfile <- function(filename) {
  if (file.access(filename) == -1) {
    stop(sprintf("Specified file ( %s ) does not exist", filename))
  }
}

readfile <- function(filename, indexcols, datacol, samplename) {
  d <- read.csv(filename, header = TRUE, sep = "\t")
  cols <- colnames(d)
  reqdcols <- c(indexcols, datacol)
  if (set_is_subset(as.set(reqdcols), as.set(cols))) {
    d <- d[, reqdcols]
    cols <- colnames(d)
    cols <- gsub(pattern = datacol, replacement = samplename, cols)
    colnames(d) <- cols
    return(d)
  } else {
    stop(sprintf("Required columns: %s are missing in file %s", reqdcols, filename))
  }
}

debug <- 0



# create parser object
parser <- ArgumentParser()

# specify our desired options
# by default ArgumentParser will add an help option

parser$add_argument("-l", "--filelist",
  type = "character",
  help = "comma separated list of files",
  required = TRUE
)
parser$add_argument("-i", "--indexcols",
  type = "character",
  help = "comma separated list of columns to use as index while merging. These need to exist in all files provided in the -l option.",
  required = TRUE
)
parser$add_argument("-c", "--datacol",
  type = "character",
  help = "column to be extracted from all samples and aggregated in the outputfile. Should exist in all files provided to -l. Its name will be replaced by corresponding value in -s argument.",
  required = TRUE
)
parser$add_argument("-s", "--samplenames",
  type = "character",
  help = "comma separated list of sample names. Need to be unique. Will replace datacol (-c) when reported in the output file. ",
  required = TRUE
)
parser$add_argument("-o", "--outfile",
  type = "character",
  help = "aggregated outfile",
  required = TRUE
)


args <- parser$parse_args()

filelist <- unlist(strsplit(args$filelist, ","))
indexcols <- unlist(strsplit(args$indexcols, ","))
datacol <- args$datacol
samplenames <- unlist(strsplit(args$samplenames, ","))
outfile <- args$outfile

if (debug == 1) {
  filelist <- unlist(strsplit("/Volumes/CCBR/projects/ccbr1060/Hg38_shRNA_hybrid/HGHY2DRXY_analysis/results/596-7-2/STAR/withChimericJunctions/a.tsv,/Volumes/CCBR/projects/ccbr1060/Hg38_shRNA_hybrid/HGHY2DRXY_analysis/results/596-7-2/STAR/withChimericJunctions/b.tsv", ","))
  indexcols <- unlist(strsplit("ensemblID,gene_name,mRNA_length", ","))
  datacol <- "tpm"
  samplenames <- unlist(strsplit("A,B", ","))
  outfile <- "/Volumes/CCBR/projects/ccbr1060/Hg38_shRNA_hybrid/HGHY2DRXY_analysis/results/596-7-2/STAR/withChimericJunctions/test.tpm.tsv"
}

# 2 or more files required
if (length(filelist) <= 1) {
  stop(sprintf("Two are more comma separated files needed"))
}
# nfiles and nsamplenames should match
if (length(unique(filelist)) != length(unique(samplenames))) {
  stop(sprintf("Number of files need to match number of samplenames. Duplicate files and samplenames not allowed!"))
}

for (f in filelist) {
  checkfile(f)
}

m <- readfile(
  filename = filelist[1],
  indexcols = indexcols,
  datacol = datacol,
  samplename = samplenames[1]
)

for (i in 2:length(filelist)) {
  n <- readfile(
    filename = filelist[i],
    indexcols = indexcols,
    datacol = datacol,
    samplename = samplenames[i]
  )
  m <- merge(m, n, by = indexcols)
}

write.table(m, file = outfile, quote = FALSE, sep = "\t", row.names = FALSE)