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  1. or download this
    die "Usage: $0 InputFile1 InputFile2 OutputFile\n"
    unless @ARGV==3;
my ($InputFile1, $InputFile2, $OutputFile3) = @ARGV;
# ... rest of the code here
  2. or download this
    sub process_files {
    my ($InputFile1, $InputFile2, $OutputFile3) = @_;
    # ... rest of your code here
}
  3. or download this
    my @filesets = (
    { input1 => "edited_archaea_master_list.txt",
...
    process_files( $fileset->{input1}, $fileset->{input2},
        $fileset->{output} );
}