3b_collate_phasing_stats.R

###################################
### Collection of phasing stats ###
###################################

# load config
if (!(exists("config_file"))) {config_file <- "./config.txt"}
source(config_file)


phasing_prep <- read.csv(csv_file_with_phasing_prep_info, header=T)
#as.vector(t(phasing_prep[,1+1:((length(phasing_prep)-1)/2)*2]))

if(folder_for_phasing_stats==""){folder_for_phasing_stats <- file.path(path_to_phasing_folder,"phasing_stats/")}
stats_files <- list.files(folder_for_phasing_stats)

# generate empty table (ref_names x samples)

used_reference_abbr <- unique(as.vector(t(phasing_prep[,1+1:((length(phasing_prep)-1)/2)*2])))
if(length(which(is.na(used_reference_abbr)|used_reference_abbr==""))>0){
  used_reference_abbr <- used_reference_abbr[-which(is.na(used_reference_abbr)|used_reference_abbr=="")]
}



tab_phasing_stats <- matrix(nrow = length(stats_files), ncol = length(used_reference_abbr))
rownames(tab_phasing_stats) <- gsub("_phasing-stats.txt","",stats_files)
colnames(tab_phasing_stats) <- used_reference_abbr


# fill table with results from the stats files
for(i in 1:length(stats_files)){
  
  stats_file <- stats_files[i]
  
  p_unamb <- read.delim(file.path(folder_for_phasing_stats, stats_file))[,1:2]
  
  for(j in 1:length(p_unamb[,1])){
    tab_phasing_stats[i,match(p_unamb[j,1], colnames(tab_phasing_stats))] <- round(p_unamb[j,2]/100,5)
  }

}


# save output
write.csv(tab_phasing_stats, file=file.path(path_to_phasing_folder,"Table_phasing_stats.csv"), na = "")