#!/usr/bin/env Rscript                                                  
#########################################################
# TASK: To calculate Allele Frequency and
# Odds Ratio from master data
#########################################################
# working dir 
setwd("~/git/LSHTM_analysis/scripts")
getwd()

# load libraries
#source("Header_TT.R")
require("getopt", quietly = TRUE) # cmd parse arguments

# load functions
source("functions/plotting_globals.R")
source("functions/mychisq_or.R")
source("functions/myaf_or_calcs.R")

#############################################################
# command line args
#********************
spec = matrix(c(
  "drug"          ,"d",  1, "character",
  "gene"          ,"g",  1, "character",
  "master_data"   ,"m",  2, "character", 
  "gene_data"     ,"G",  2, "character", 
  "outfile"       ,"o",  2, "character",
  "idcol"         ,"I",  2, "character",
  "drmuts_col"    ,"D",  2, "character", 
  "othermuts_col" ,"O",  2, "character"
  
), byrow = TRUE, ncol = 4)

opt = getopt(spec)

drug            = opt$drug
gene            = opt$gene
infile_master   = opt$master_data
infile_metadata = opt$gene_data
outfile         = opt$outfile
idcol           = opt$idcol
dr_muts_col     = opt$drmuts_col
other_muts_col  = opt$othermuts_col

if(is.null(drug)|is.null(gene)) {
  stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
}

# import_dirs()
import_dirs(drug, gene)

# setting sensible defaults for opt args

#----------------------------
# input file 1: master data
#----------------------------
#class(infile_master)
if (is.null(infile_master)){
#if (!is.character(infile) && exists("gene")){
  #in_filename_master  = 'original_tanushree_data_v2.csv' #19K
  in_filename_master  = 'mtb_gwas_meta_v6.csv' #35k
  infile_master = paste0(datadir, in_filename_master)
  cat("\nInput file 1 not specified, assuming filename: ", infile_master)
  cat(paste0("\nReading infile 1 i.e raw data: ", infile_master) )
} 

#---------------------------------------------------
# input file 2: gene associated meta
# data file to extract valid snps and add calcs to.
#---------------------------------------------------
if (is.null(infile_metadata)){
  # This is outfile_metadata from data_extraction.py
  in_filename_metadata =  paste0(tolower(gene), '_metadata.csv')
  infile_metadata = paste0(outdir, '/', in_filename_metadata)
  cat("\nInput file 2 not specified, assuming filename: ", infile_metadata)
  cat(paste0("\nReading infile 2 i.e gene associated metadata:", infile_metadata))
}

#-------------------------------------------
# outfile: csv file containing AF and OR
#-------------------------------------------
if (is.null(outfile)){  
  # out_filename_af_or = paste0(tolower(gene), '_meta_data_with_AF_OR.csv')
  out_filename_af_or = paste0(tolower(gene), '_af_or.csv')
  outfile = paste0(outdir, '/', out_filename_af_or)
  cat("\nOutfile not specified, assuming filename: ", outfile)
  cat(paste0('\nOutput file with full path:', outfile))
}

#-------------------------------------------
# idcol: column name "id"
#-------------------------------------------
if (is.null(idcol)){
  idcol = "id"
}

#-------------------------------------------
# dr-and-others muts cols: comes from plotting_globals.R
# colnames that can be constructed using drug 
# (dr_mutations_<drug>), (other_mutations_<drug>)
#-------------------------------------------
if (is.null(dr_muts_col)){
  dr_muts_col 
  cat("\ndrug and other mut colnames not specified, sourcing from globals: "
  ,  dr_muts_col, "\n")
}

if (is.null(other_muts_col)){
 other_muts_col 
    cat("\ndrug and other mut colnames not specified, sourcing from globals: "
      , other_muts_col, "\n")
}

# Informing the user of the sensible defaults being used:
cat("======================"
, "\nParameters passed:"
, "\n======================"
, "\nDRUG name: ", drug, "\n"
, "\nGENE name: ", gene, "\n"
, "\nReading infile 1 i.e raw data: ", infile_master, "\n"
, "\nReading infile 2 i.e gene associated metadata:", infile_metadata, "\n"
, '\nOutput file with full path:', outfile, "\n"
, "\nColumn name of id:", idcol, "\n"
, "\ndr mutation colname:", dr_muts_col, "\n"
, "\nother mutation colname:", other_muts_col, "\n")

#=======================================================================
#============================
# call function: my_afor()
#=============================
my_afor(  drug
         , gene
         , infile_master
         , infile_metadata
         , outfile
         , idcol
         , dr_muts_col 
         , other_muts_col
         )
#=======================================================================