use strict;
use warnings;

my $headerFile = <<DATA;
>DFHGSUEIEEK
>JKDHUEIEEOE
>KDJIEEIOIEO
DATA
my $dataFile = <<DATA;
>DFHGSUEIEEK
ACGTCGTACGATCGATCAGTACGTACGAT
>JKDHUEIEEOE
ACGATGCGTACAGTACAGTACAGTACAGT
>KDJIEEIOIEO
AGTCGTCGTAGTGTTTTACCCCCATGTCA
>HSKWJSSWWOW
AGTAGTAGTAGTAGGGGTTTTTTTTACCC
>ADJHFHIOHFO
ACGTGGGGGGGGGGTTATTACCCCCCCCA
>DTEEIJEJEOJE
TTTTTTTTTTGGGGGGGGGACCCCCCCAT
DATA

open my $FD, '<', \$headerFile;
my %headers = map {$_ => 0} <$FD>;
close $FD;

open my $FH, '<', \$dataFile;
exists $headers{$_} and print while <$FH>;
close $FH;