#!/usr/bin/perl -w

use strict;
use warnings;

my $infile = '/path/to/infile.fa';
my $outfile = '/out/outfile.txt';
my %single_hash;

open(INFILE,"<$infile") or die $!;
while(my $line = <INFILE>){
  chomp $line;
  $single_hash{$line} = 1;
}
close INFILE;

open(OUTFILE,">$outfile") or die $!;
for my $key(keys(%single_hash)){
  print OUTFILE $key,"\n";
}
close OUTFILE;