#!/usr/bin/env Rscript                                                  
#require('compare')
require('getopt', quietly=TRUE) # We need to be able to parse arguments
#########################################################
# TASK: To calculate Allele Frequency and
# Odds Ratio from master data
# and add the calculated params to meta_data extracted from
# data_extraction.py
#########################################################
#getwd()
setwd('~/git/LSHTM_analysis/scripts')
cat(c(getwd(),'\n'))

# Command line args
spec = matrix(c(
  "drug"   , "d", 1, "character",
  "gene"   , "g", 1, "character"
), byrow = TRUE, ncol = 4)

opt = getopt(spec);

drug = opt$drug
gene = opt$gene

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

#options(scipen = 999) #disabling scientific notation in R.
#options(scipen = 4)  

#%% variable assignment: input and output paths & filenames
drug = 'pyrazinamide'
gene = 'pncA'
gene_match = paste0(gene,'_p.')
cat(gene_match)

#===========
# input
#===========
# infile1: Raw data
#indir = 'git/Data/pyrazinamide/input/original'
indir = paste0('~/git/Data')
in_filename  = 'original_tanushree_data_v2.csv'
#in_filename  = 'mtb_gwas_v3.csv'
infile = paste0(indir, '/', in_filename)
cat(paste0('Reading infile1: raw data', ' ', infile) )

# infile2: gene associated meta data file to extract valid snps and add calcs to.
# This is outfile3 from data_extraction.py
indir_metadata = paste0('~/git/Data', '/', drug, '/', 'output')
in_filename_metadata = 'pnca_metadata.csv'
infile_metadata = paste0(indir_metadata, '/', in_filename_metadata)
cat(paste0('Reading infile2: gene associated metadata:', infile_metadata))

#===========
# output
#===========
# outdir = 'git/Data/pyrazinamide/output'
outdir = paste0('~/git/Data', '/', drug, '/', 'output')
#out_filename = paste0(tolower(gene), '_meta_data_with_AF_OR.csv')
out_filename = paste0(tolower(gene), '_af_or.csv')
outfile = paste0(outdir, '/', out_filename)
cat(paste0('Output file with full path:', outfile))
#%% end of variable assignment for input and output files

#########################################################
# 1: Read master/raw data stored in Data/
#########################################################
raw_data_all = read.csv(infile, stringsAsFactors = F)

# building cols to extract
dr_muts_col = paste0('dr_mutations_', drug)
other_muts_col = paste0('other_mutations_', drug)

cat('Extracting columns based on variables:\n'
      , drug
      , '\n'
      , dr_muts_col
      , '\n'
      , other_muts_col
      , '\n===============================================================')

raw_data = raw_data_all[,c("id"
                     , drug
                     , dr_muts_col
                     , other_muts_col)]
rm(raw_data_all)

rm(indir, in_filename, infile)

#===========
# 1a: exclude na
#===========
raw_data = raw_data[!is.na(raw_data[[drug]]),]

total_samples = length(unique(raw_data$id))
cat(paste0('Total samples without NA in', ' ', drug, 'is:', total_samples))

# sanity check: should  be true
is.numeric(total_samples) 

#===========
# 1b: combine the two mutation columns
#===========
all_muts_colname = paste0('all_mutations_', drug)
#raw_data$all_mutations_pyrazinamide = paste(raw_data$dr_mutations_pyrazinamide, raw_data$other_mutations_pyrazinamide)
raw_data[[all_muts_colname]] = paste(raw_data[[dr_muts_col]], raw_data[[other_muts_col]])
head(raw_data[[all_muts_colname]])

#===========
# 1c: create yet another column that contains all the mutations but in lower case
#===========
head(raw_data[[all_muts_colname]])
raw_data$all_muts_gene = tolower(raw_data[[all_muts_colname]]) 
head(raw_data$all_muts_gene)

# sanity checks
#table(grepl("gene_p",raw_data$all_muts_gene))
cat(paste0('converting gene match:', gene_match, ' ', 'to lowercase'))
gene_match = tolower(gene_match)

table(grepl(gene_match,raw_data$all_muts_gene))

# sanity check: should be TRUE
#sum(table(grepl("gene_p",raw_data$all_muts_gene))) == total_samples
# sanity check
if(sum(table(grepl(gene_match, raw_data$all_muts_gene))) == total_samples){
  cat('PASS: Total no. of samples match')
} else{
  cat('FAIL: No. of samples mismatch')
}

#########################################################
# 2: Read valid snps for which OR 
# can be calculated
#########################################################
cat(paste0('Reading metadata infile:', infile_metadata))

gene_metadata = read.csv(infile_metadata
                         #, file.choose()
                         , stringsAsFactors = F
                         , header = T)


# clear variables
rm(in_filename_metadata, infile_metadata)

# count na in pyrazinamide column
tot_pza_na = sum(is.na(gene_metadata$pyrazinamide))
expected_rows = nrow(gene_metadata) - tot_pza_na

# drop na from the pyrazinamide colum
gene_snps_or = gene_metadata[!is.na(gene_metadata[[drug]]),]

# sanity check
if(nrow(gene_snps_or) == expected_rows){
  cat('PASS: no. of rows match with expected_rows')
} else{
  cat('FAIL: nrows mismatch.')
}

# extract unique snps to iterate over for AF and OR calcs
gene_snps_unique = unique(gene_snps_or$mutation) 

cat(paste0('Total no. of distinct comp snps to perform OR calcs: ', length(gene_snps_unique)))

#===========================================================================================
#########################
# custom chisq function: 
# To calculate OR
#########################
i = "pnca_p.trp68gly"
mut = grepl(i,raw_data$all_muts_gene)
mut = as.numeric(mut)

dst = raw_data[[drug]] 

#x = as.numeric(mut)
#y = dst

mychisq_or = function(x,y){
  tab = as.matrix(table(x,y))
  a = tab[2,2]
  if (a==0){ a<-0.5}
  b = tab[2,1]
  if (b==0){ b<-0.5}
  c = tab[1,2]
  if (c==0){ c<-0.5}
  d = tab[1,1]
  if (d==0){ d<-0.5}
  (a/b)/(c/d)
  
}

or_mychisq = mychisq_or(dst, mut)
print(paste0('mychisq OR:', or_mychisq ))

#=====================================
#OR calcs using the following 4
#1) chisq.test
#2) fisher
#3) modified chisq.test
#4) logistic
#5) adjusted logistic?
#6) kinship (separate script)

#======================================
# TEST FOR a few muts: sapply and df
#===============================================
snps <- gene_snps_unique # reassign so you test with subset of muts
#snps <- gene_snps_unique[1:2]
cat(paste0('Running calculations for:', length(snps), ' nssnps\n'
, 'gene: ', gene
, '\ndrug: ', drug ))

# DV: pyrazinamide 0 or 1
dst = raw_data[[drug]]

# initialise an empty df
ors_df = data.frame()

x = sapply(snps,function(m){
  
  mut = grepl(m,raw_data$all_muts_gene)
  mut = as.numeric(mut)
  cat(paste0('Running mutation:', m, '\n'))

  model<-glm(dst ~ mut, family = binomial)
  
  #-------------------
  # allele frequency
  #-------------------
  afs = mean(mut)
  
  #-------------------
  # logistic model
  #-------------------
  beta_logistic = summary(model)$coefficients[2,1]
  
  or_logistic = exp(summary(model)$coefficients[2,1])
  #print(paste0('logistic OR:', or_logistic))
  
  pval_logistic = summary(model)$coefficients[2,4]
  #print(paste0('logistic pval:', pval_logistic))
  
  se_logistic = summary(model)$coefficients[2,2]
  #print(paste0('logistic SE:', se_logistic))
  
  zval_logistic = summary(model)$coefficients[2,3]
  #print(paste0('logistic zval:', zval_logistic))
  
  ci_mod = exp(confint(model))[2,]
  #print(paste0('logistic CI:', ci_mod))
  
  ci_lower_logistic = ci_mod[["2.5 %"]]
  ci_upper_logistic = ci_mod[["97.5 %"]]
  
  #-------------------
  # custom_chisq and fisher: OR p-value and CI
  #-------------------
  or_mychisq = mychisq_or(dst, mut)
  #print(paste0('mychisq OR:', or_mychisq))
  
  odds_fisher = fisher.test(table(dst, mut))$estimate
  or_fisher = odds_fisher[[1]]
  
  pval_fisher = fisher.test(table(dst, mut))$p.value
  
  ci_lower_fisher = fisher.test(table(dst, mut))$conf.int[1]
  ci_upper_fisher = fisher.test(table(dst, mut))$conf.int[2]
  
  #-------------------
  # chi sq estimates 
  #-------------------
  estimate_chisq = chisq.test(table(dst, mut))$statistic; estimate_chisq
  est_chisq = estimate_chisq[[1]]; print(est_chisq)
  
  pval_chisq = chisq.test(table(dst, mut))$p.value                                                        
  
  # build a row to append to df
  row = data.frame(mutation = m
                   , af = afs
                   , beta_logistic = beta_logistic
                   , or_logistic = or_logistic
                   , pval_logistic = pval_logistic
                   , se_logistic = se_logistic
                   , zval_logistic = zval_logistic
                   , ci_low_logistic = ci_lower_logistic
                   , ci_hi_logistic = ci_upper_logistic
                   , or_mychisq = or_mychisq 
                   , or_fisher = or_fisher
                   , pval_fisher = pval_fisher
                   , ci_low_fisher= ci_lower_fisher
                   , ci_hi_fisher = ci_upper_fisher
                   , est_chisq = est_chisq
                   , pval_chisq = pval_chisq
  )
  #print(row)
  
  ors_df <<- rbind(ors_df, row)
  
})

#%%======================================================
# Writing file with calculated ORs and AFs
cat(paste0('writing output file: '
           , '\nFilename: ', out_filename))

write.csv(ors_df, outfile
          , row.names = F)

cat(paste0('Finished writing:'
           , outfile
           , '\nNo. of rows: ', nrow(ors_df)
           , '\nNo. of cols: ', ncol(ors_df)))
#************************************************
cat('\n======================================================================\n')
cat('End of script: calculated AF, OR, pvalues and saved file')