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open (FILE1, "Mock3_SNP.txt");

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

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

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my @line = split /\s+/, $_;
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```
my @line = split ' ', $input_line;
```
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my $chr = "chr$line[1]";

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

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

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

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

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

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### 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: $!";

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    foreach my $name(keys %input) {
        if ($input{$name}[1] eq $chr) {
            if ($input{$name}[2] > $pos-1 && $input{$name}[2] < $pos+3
+6) {

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

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

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