open (FILE1, "Mock3_SNP.txt");

##</code><code>##

while (<FILE1>) {
    chomp;
    my $input_orig = $_;

##</code><code>##

while (defined (my $input_line = <$input>)) {
  chomp $input_line;

##</code><code>##

    my @line = split /\s+/, $_;

##</code><code>##

my @line = split ' ', $input_line;

##</code><code>##

my $chr = "chr$line[1]";

##</code><code>##

    $input{$name}[0] = $name;
    $input{$name}[1] = $chr;
    $input{$name}[2] = $pos;

##</code><code>##

$input{$name} = [ $name, $chr, $pos ];

##</code><code>##

push @{$input[$chr]} => [ $name, $pos ];

##</code><code>##

push @{$input[$chr]} => { name => $name, pos => $pos };

##</code><code>##

open (OUT, "> test.txt"); ### Change if file name changes

##</code><code>##

### At the top:
my $output_file = 'test.txt'; ### Change if the file name changes

### the open is then:
open my $out, '>', $output_file or die "Can't open $output_file: $!";

##</code><code>##

    foreach my $name(keys %input) {
        if ($input{$name}[1] eq $chr) {
            if ($input{$name}[2] > $pos-1 && $input{$name}[2] < $pos+36) {

##</code><code>##

$chr =~ s/^chr//; # remove chr if it's there
### or, if chr must be there:
# substr $chr, 0, 3, ''; # removes first three characters
if (defined $input[$chr]) {
  for my $i (@{$input[$chr]}) {
    if ($pos <= $i->{pos} && $i->{pos} <= $pos+35) {

##</code><code>##

                if ($input{$name}[2] == $pos) {
                    my $fSNP = substr($seq, 0, 1);
                    print OUT "$fSNP\n";    
                }
                if ($input{$name}[2] == $pos+35) {
                    my $fSNP = substr($seq, 35,1);
                    print OUT "$fSNP\n";    
                }
                if ($input{$name}[2] != $pos+35 && $input{$name}[2] != $pos) {
                    my $SNP = substr($seq, 0, $input{$name}[2]-($pos-1));
                    my $fSNP = substr($SNP, $input{$name}[2]-$pos);        
                    print OUT "$fSNP\n";    
                }    

##</code><code>##

my $fSNP = substr($seq, $i->{pos} - $pos, 1);
print $out "$fSNP\n";