use strict; 
use wanings;

my %ids;
open my $IDS, "<", "BreastCnAPmiRNAsID.txt" or die "cannot open file BreastCnAPmiRNAsID.txt $!";
while (<$IDS>) {
    chomp;
    $ids{$_} = 1;    # populating the hash
}
close $IDS;
open my $FILECOMPARE, "<", "tarbaseData.txt" or die "cannot open tarbaseData.txt $!";
while (my $line = <$FILECOMPARE>) {
    my $id = (split /\s+/, $line)[2];    # extract the ID (third field)
    print $line if exists $ids{$id};     # print line if hash lookup is successful
}
close $FILECOMPARE;