gc_count.java

import java.io.IOException;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.Map;
import java.util.stream.Collectors;

import static java.nio.file.Files.lines;
import static java.util.stream.Collectors.groupingBy;

public class gc_count {
    public static boolean accept(int value) {
        if (value == 'C' || value == 'G') {
            return true;
        } else if (value == 'A' || value == 'T') {
            return true;
        }
        return false;
    }

    public static void main(String... args) throws IOException {

        long start = System.currentTimeMillis();

        Path path = Paths.get("Homo_sapiens.GRCh37.67.dna_rm.chromosome.Y.fa");
        Map<Integer,Long> result = lines(path).map(line -> line)
                .collect(Collectors.joining("")).chars().
                        filter(c -> accept(c)).boxed().
                        collect(groupingBy(Integer::intValue, Collectors.counting()));

        long at = result.get(65) + result.get(84);
        long gc = result.get(67) + result.get(71);

        System.out.printf("GC count %f\n", gc / (double) (at + gc));
        System.out.printf("Elapsed %d ms\n", System.currentTimeMillis() - start);


    }
}