use strict;
use warnings;

while ( my $file = glob '*.txt' ) { 

    print "Debug: found file $file\n";
    open my $fh, '<', $file or die "Cannot open file $file: $!";
    my $headers = grep /^>/, <$fh>;

    if ($headers <= 3) {
        unlink $file or die "Cannot unlink file $file: $!";
    } else {
        print "Debug: file $file only has $headers headers - skipping\n";
    }
}