#!/usr/bin/perl
use strict;
use warnings;

my %hash = ();
open my $fh, '<', 'sample_name_ID_hash.txt' or die "Cant open file $!";

LINE:
while (my $line = <$fh>) 
	{
    	my ($key, $value) = split /\s/, $line;
    	next LINE if not $key;
		$hash{$key} = $value;
    	chomp (%hash);
	}

close $fh;
		
@file_array = <*.nex> or die $!; #find all the files
foreach $file (@file_array)
	{
	my $prefix = $file;
	$prefix =~ s/\.nex//;
	open FH, "$file", or die $!;
	print "found $file with prefix $prefix\n";
	open OUT, ">out$prefix.nex" or die $!;

 while (<FH>)
          {
          if (/^\s+\'(\S+):(\S\d+)\|\w+\|(\d)\S+\'(.*)\n/)
               {
               $var1 = "$1";
               $var2 = "$2";
               $var3 = "$3";
               $var4 = "$4";
               print OUT "'$hash{$var1}_${var2}_$var3'$var4\n";
               }
        	elsif (/(.*)\n/)
        		{
        		print OUT "$1\n";
               }
            }
     }