use strict;    #a good habit to start your prog
use warnings;
use Bio::SeqIO;

#load your codes.txt into an array
open(my $fh, "<","codes.txt") or die("could not open codes.txt $!"); #a more proper way to opening files

my @codes=<$fh>;    #slurping codes.txt into an array

my $obj=Bio::SeqIO->new(     #Bio::SeqIO for input
	-file=>"fasta.fa",
	-format=>"fasta"
	);

my $out_obj=Bio::SeqIO->new(  #Bio::SeqIO for output
	-file=>">matching.fa",
	-format=>"fasta"
	);
while(my $seq=$obj->next_seq){
	foreach my $element (@codes){
		chomp $element;
		if($seq->id=~/$element*?/gi){    #regular-expression based matching 
			$out_obj->write_seq($seq); #output written to matching.fa
			}
		}
	}