#!usr/bin/perl
open(IN, "HMOX2_1000genomes") || die "can't open HMOX1_1000genomes";
open(IN2, "positions_mostfreq") || die "can't open position coordinates";
open(OUT,">210distibution_HMOX2.xls");
@a = @coord = ();
while (<IN>){ chomp $_; push (@a,$_);}
while (<IN2>){ chomp $_; push (@coord,$_);}
for $n (0..$#a){ if ($a[$n] =~m/^#CHROM/){ $start = $n; }}
$x = 0; $k = 1; @{'SNP'.$k} = ();
for $n ($start..$#a){ @{'line'.$x} = split(/\t/,$a[$n]); $x++ unless $n == $#a;}
print OUT "INDIV\t";
for $n (0..$#coord){
        for $y (1..$x){
                if (${'line'.$y}[1] =~m/^($coord[$n])/){
                        print OUT "${'line'.$y}[1](${'line'.$y}[3]-${'line'.$y}[4])\t";
                        for $z (0..$#{'line'.$y}){
                                if (${'line'.$y}[$z] =~m/^(\d)\|(\d)/){
                                        if ($1 == 0 && $2 == 0){ push (@{'SNP'.$k}, 0);}
                                        if ($1 == 0 && $2 == 1){ push (@{'SNP'.$k}, 1);}
                                        if ($1 == 1 && $2 == 0){ push (@{'SNP'.$k}, 1);}
                                        if ($1 == 1 && $2 == 1){ push (@{'SNP'.$k}, 2);}
                                }
                        }
                }
        }
        $k++ unless $n == $#coord;
}
print OUT "\n";
$p = 0;
for $z (9..$#line0){
        print OUT "$line0[$z]\t";
        for $n (1..$k){ print OUT "${'SNP'.$n}[$p]\t";}
        $p++ unless $p == $#{'SNP'.$n};
        print OUT "\n";
}