my ($in,$gene,$out)=@ARGV;
open(IN,"<$in");
open(GENE,"<$gene");
open(OUT,">$out");

my %hash;
my $a=<GENE>;
foreach(<GENE>){
   chomp;
   my @g;
   @g=split/\t/,$_;
   $hash{$g[1].",".($g[2]-1).",".$g[3]}=$g[4]."\t".$g[7]."\t".$g[9]."\t".$g[15]."\t".$g[18];

}

chomp(my $head=<IN>);
@name=split/\t/,$head;
my @ctl;
@ctl=grep{$name[$_]=~'_Ctrl_'} 0..$#name;
my @con1=split/_/,$name[10];
my @con2=split/_/,$name[$ctl[1]];
my $condition1=$con1[0]."_".$con1[2]."_".$con1[4]."_".$con1[5]."_".$con1[6];
my $condition2=$con2[0]."_".$con2[2]."_".$con2[4]."_".$con2[5]."_".$con2[6];

foreach(<IN>){
  chomp;
  my $term;
  my @num;
  @num=split/\t/,$_;
  $term=$num[0]."\t".$num[1]."\t".$num[2]."\t".$num[3]."\t".$num[4]."\t".$num[5]."\t".$num[6]."\t".$num[7]."\t".$num[8]."\t".$num[9];
  my $n=$ctl[0]-1;
  for(10..$n){
     print OUT $term."\t".$condition1."\t".$num[$_]."\t".$hash{$num[4]}."\n";
  }
  foreach(@ctl){
     print OUT $term."\t".$condition2."\t".$num[$_]."\t".$hash{$num[4]}."\n";
  }

}