#!/usr/bin/perl -w
use strict;

open(FILE,"$ARGV[0]");
my @input=<FILE>;
close(FILE);
foreach my $line(@input){
    chomp $line;
     my @batch=();
    (my $gene, my $VAA, my $ CCDS ,my $chrposMut, my $o_acc, my $o_pos, my $o_aa1, my $o_aa2)= split(/\t/,$line);
    (my $chrpos,my $Mut)=split(/\./,$chrposMut);
    
    my ($chr,$position)=split(/\:/,$chrpos);
    my $vAA=$o_aa1 . $o_pos . $o_aa2;
    $vAA=~s/\s//g;
       
    @batch=`perl -ne 'print if /$position/' Gene_Asign.txt`; # put the text file here that contains the gene name as well as something that can be used to identify the correct row when comparing it with the polyphen outfile
    foreach my $Line(@batch)
    {
        chomp $Line;
       # (my $snp, my $str, my $gene, my $v4, my $v5, my $CCDS)=split(/\t/,$Line);
    #print $Line ."\n";
        my($Sample,$v2)= split(/\s/,$Line);
        
   
    #if($AA=~m/$vAA/){
        print $Sample . "\t" . $line . "\n";
     #   print $gene . "\t" . $vAA . "\t" . $CCDS. "\t" . $line . "\n";
       # }
    }
    
}