#!/usr/bin/perl

if(@ARGV<6) { print "usage: $0 final.iFVKM_file mapping_stat_file gene2symbol_file factor_col sample_name iLVKM_file\n"; exit; }
my ($iFVKM_file,$mapping_stat_file,$gene2symbol_file,$factor_col,$sample_name,$iLVKM_file) = @ARGV;

open STAT, $mapping_stat_file or die "Can't open mapping stat file $mapping_stat_file\n";
<STAT>; #discard header
while(<STAT>){
  chomp;
  next if !/\S/;
  my ($sample,$factor) = (split/\t/)[0,$factor_col];
  $norm_factor1{$sample} = $factor/1000000;
  if($factor==0) { die "Error: Total reads is zero. Please check datatype option. Use option 'E' if your reference doesn't contain 'NM' prefix for mRNA.\n"; }

}
close STAT;

open GENE2SYM, $gene2symbol_file or die "can't open gene2symbol file $gene2symbol_file\n";
while(<GENE2SYM>){
 chomp;
 split/\t/;
 $gene2symbol{$_[0]}=$_[1];
}
close GENE2SYM;


$"="\t";
open OUT1, ">$iLVKM_file" or die "Can't write to norm1outfile $iLVKM_file\n";
print OUT1 "gene.id\tgene.symbol\tisoform.id\tiLVKM\tiFVKM\tfinal.iFVK\torig.iFVK\tiFVKM.factor\tiEUMA\t#isoforms\t#measured_isoforms\n";

open IFVKM, $iFVKM_file or die "Can't open iFVKM file $iFVKM_file\n";
<IFVKM>;  #discard header
while(<IFVKM>){
  chomp;
  my @line = split/\t/;
  my $gene_id = shift @line;
  my $isoform_id = shift @line;
  my $gene_symbol = $gene2symbol{$gene_id};
  $norm1=$line[0]/$norm_factor1{$sample_name};
  $norm2=log($norm1+1)/log(2);
  printf OUT1 "$gene_id\t$gene_symbol\t$isoform_id\t%.3f\t%.3f\t@line\n",$norm2,$norm1,;
}
close IFVKM;


close OUT1;