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 open in, "rep_set_ass_tax.fna"; 
 
...
    } 
 }

use strict;
use warnings;
...
 
 close IN;
 close OUT;

use strict;
use warnings;
...
 
 close IN;

>1
ATGT...
>2
ATGGTGC..

use strict; 
use warnings; 
...
  } 
} 
close IN;