use Bio::SeqIO;
my $input = new Bio::SeqIO(-format => 'fasta', 
                           -file   => 'inputfile');
my $output = new Bio::SeqIO(-format => 'fasta',
                            -file   => '>outputfile');
while( my $seq = $input->next_seq ) {
   # skip the whole entry if the sequence constains the 
   # pattern using Abigail-II's suggestion
   next if ( $seq->seq() =~ /\.(?:WKP|MRP)/);
   # otherwise write the sequence out to the output file
   $out->write_seq($seq);
}