#!/usr/bin/perl-w
use strict;
my %barcode_clinical;
open IN,"<$ARGV[0]" or die "can't open the file: $ARGV[0]\n";# Clinical File
while(<IN>){
chomp;
my @array=split/\t/;
my $barcode=join "\-",$array[0],"01";
next if $array[1]!~/^Stage/;
$array[1]=~s/A$//g;
$array[1]=~s/B$//g;
$array[1]=~s/C$//g;
my $clinical=$array[1];
$barcode_clinical{$barcode}=$clinical;
}
close IN;
##############################################################################################################
my %hash;
my @position;
my (@I_position,@II_position,@III_position,@IV_position);
my @barcode;
open IN,"<$ARGV[1]" or die "can't open this file:$ARGV[1]\n";#Merge Methylation File
while(<IN>){
next if $_!~/^Key/;
chomp;
my @array=split/\t/,$_;
shift @array;
@barcode=@array;
foreach my $i(@array){
my @bar=split/\_/,$i;
# print "$bar[0]\n";
$barcode_clinical{$i} ="HC" if $bar[0]=~/\-11$/;
if($barcode_clinical{$bar[0]}){
$hash{$i}=$barcode_clinical{$bar[0]};
}else{
$hash{$i}="Tumor";
}
}
# map{print "$_\t$hash{$_}\n";}@array;
my $hc=grep{$hash{$_} eq "HC";}@array;
my $i=grep{$hash{$_} eq "Stage I";}@array;
my $ii=grep{$hash{$_} eq "Stage II";}@array;
my $iii=grep{$hash{$_} eq "Stage III";}@array;
my $iv=grep{$hash{$_} eq "Stage IV";}@array;
@position=sort{$hash{$array[$a]} cmp $hash{$array[$b]}} 0 .. $#array;
@I_position=@position[0 .. ($hc+$i-1)];
@II_position=@position[0 .. ($hc-1),($hc+$i) .. ($hc+$i+$ii-1)];
@III_position=@position[0 .. ($hc-1),($hc+$i+$ii) ..($hc+$i+$ii+$iii-1)];
@IV_position=@position[0 .. ($hc-1),($hc+$i+$ii+$iii) .. ($i+$ii+$iii+$iv+$hc-1)];
}
print "@III_position\n";
open OUT1,">sample_file_1.txt";
open OUT2,">sample_file_2.txt";
open OUT3,">sample_file_3.txt";
open OUT4,">sample_file_4.txt";
for my$i (@I_position){
print OUT1 "$barcode[$i]\t$hash{$barcode[$i]}\n";
}
for my $i(@II_position){
print OUT2 "$barcode[$i]\t$hash{$barcode[$i]}\n";
}
for my $i(@III_position){
print OUT3 "$barcode[$i]\t$hash{$barcode[$i]}\n";
}
for my $i(@IV_position){
print OUT4 "$barcode[$i]\t$hash{$barcode[$i]}\n";
}
close OUT1;
close OUT2;
close OUT3;
close OUT4;
open OUT1,">methy_stage1.txt";
open OUT2,">methy_stage2.txt";
open OUT3,">methy_stage3.txt";
open OUT4,">methy_stage4.txt";close IN;open IN,"<$ARGV[1]";while(){
chomp;
my @array=split/\t/;
my $SiteID=shift @array;
# print "$SiteID\n";
if($SiteID=~/^Key/){
$SiteID = "SiteID";
}
print OUT1 "$SiteID";
map{print OUT1 "\t$array[$_]";}@I_position;
print OUT1 "\n";
print OUT2 "$SiteID";
map{print OUT2 "\t$array[$_]";}@II_position;
print OUT2 "\n";
print OUT3 "$SiteID";
map{print OUT3 "\t$array[$_]";}@III_position;
print OUT3 "\n";
print OUT4 "$SiteID";
map{print OUT4 "\t$array[$_]";}@IV_position;
print OUT4 "\n";
}
close IN;
close OUT1;
close OUT2;
close OUT3;
close OUT4;
