Rosalind Java|k-Mer Composition

Rosalind编程问题之统计DNA序列上由ACTG组成的K(4)-mers出现的次数。

k-Mer Composition

Problem：
For a fixed positive integer k, order all possible k-mers taken from an underlying alphabet lexicographically.

Then the k-mer composition of a string s can be represented by an array A for which A[m] denotes the number of times that the mth k-mer (with respect to the lexicographic order) appears in s.
Given: A DNA string s in FASTA format (having length at most 100 kbp).
Sample input：

Rosalind_6431
CTTCGAAAGTTTGGGCCGAGTCTTACAGTCGGTCTTGAAGCAAAGTAACGAACTCCACGG
CCCTGACTACCGAACCAGTTGTGAGTACTCAACTGGGTGAGAGTGCAGTCCCTATTGAGT
TTCCGAGACTCACCGGGATTTTCGATCCAGCCTCAGTCCAGTCTTGTGGCCAACTCACCA
AATGACGTTGGAATATCCCTGTCTAGCTCACGCAGTACTTAGTAAGAGGTCGCTGCAGCG
GGGCAAGGAGATCGGAAAATGTGCTCTATATGCGACTAAAGCTCCTAACTTACACGTAGA
CTTGCCCGTGTTAAAAACTCGGCTCACATGCTGTCTGCGGCTGGCTGTATACAGTATCTA
CCTAATACCCTTCAGTTCGCCGCACAAAAGCTGGGAGTTACCGCGGAAATCACAG

Return: The 4-mer composition of s.
Sample output：

4 1 4 3 0 1 1 5 1 3 1 2 2 1 2 0 1 1 3 1 2 1 3 1 1 1 1 2 2 5 1 3 0 2 2 1 1 1 1 3 1 0 0 1 5 5 1 5 0 2 0 2 1 2 1 1 1 2 0 1 0 0 1 1 3 2 1 0 3 2 3 0 0 2 0 8 0 0 1 0 2 1 3 0 0 0 1 4 3 2 1 1 3 1 2 1 3 1 2 1 2 1 1 1 2 3 2 1 1 0 1 1 3 2 1 2 6 2 1 1 1 2 3 3 3 2 3 0 3 2 1 1 0 0 1 4 3 0 1 5 0 2 0 1 2 1 3 0 1 2 2 1 1 0 3 0 0 4 5 0 3 0 2 1 1 3 0 3 2 2 1 1 0 2 1 0 2 2 1 2 0 2 2 5 2 2 1 1 2 1 2 2 2 2 1 1 3 4 0 2 1 1 0 1 2 2 1 1 1 5 2 0 3 2 1 1 2 2 3 0 3 0 1 3 1 2 3 0 2 1 2 2 1 2 3 0 1 2 3 1 1 3 1 0 1 1 3 0 2 1 2 2 0 2 1 1

---

题目给出我们一段序列，需要我们统计序列中各个4-mers出现的次数，以空格分隔输出到屏幕。

解题思路如下：
1.采用IO流读取待统计kmers的序列。
2.ArrayList存放ACTG组成的256种4-mers。
3.LinkedHashMap存入刚生成的4-mers，即ArrayList元素转化为LinkedHashMap键。
4.在DNA序列的4-mer子集中进行遍历比对。每当DNA的4-mer子集出现，就在Map中对应的键处将值累加1，依次遍历完全部DNA。

下面是实现代码：

public class kMer_Composition {
    public static void main(String[] args) {
        //1.获取ATCG全排列组合
        String alphabet = "ACGT";
        List<String> Order = new ArrayList<>();
        kmers(alphabet, Order, 4, 0);
        //2.产生ATCG全排列组合的集合并保存刚刚产生的kmers进map集合
        //ArrayList元素转化为LinkedHashMap标签
        Map<String, Integer> maps = new LinkedHashMap<>();
        for (int i = 0; i < Order.size(); i++) {
            maps.put(Order.get(i), 0);
        }
        //3.输入待统计kmers的序列
        ArrayList<String> fasta = BufferedReader2("C:/Users/Administrator/Desktop/rosalind_kmer.txt", "fasta");
        String DNA = fasta.get(0);
        for (int i = 0; i <= DNA.length() - 4; i++) {
            String ch = DNA.substring(i, i + 4);
            if (maps.containsKey(ch)){
                maps.put(ch, maps.get(ch)+1);
            }
        }
		
		//遍历HashMap值进行输出
        Set<String> keys = maps.keySet();
        for (String key : keys) {
            int value = maps.get(key);
            System.out.print(value + " ");
        }

    }

    //方法1.获取ATCG全排列组合
    public static void kmers(String alphabet, List<String> Order, int n, int i) {//初始默认i为0，意为从第一个字母开始遍历产生kmers
        while (i < n) {
            i += 1;
            //从第二轮循环开始向原有元素累加新字符
            if (i != 1) {
                int size = Order.size();
                for (int k = 0; k < size; k++) {
                    for (int j = 0; j < alphabet.length(); j++) {
                        Order.add(Order.get(k) + alphabet.charAt(j));
                    }
                }

                //使用列表迭代器循环删除元素
                ListIterator<String> lit = Order.listIterator();
                while (lit.hasNext()) {
                    String s = lit.next();
                    if (s.length() < i) {
                        lit.remove();//迭代器删除，可以防止删除改变ArrayList大小改变导致的并发修改异常。
                    }
                }


            } else {//第一轮循环直接添加元素进数组
                for (int j = 0; j < alphabet.length(); j++) {
                    Order.add(String.valueOf(alphabet.charAt(j)));
                }
            }

        }
    }
    
	//IO流读取fasta序列
    public static ArrayList<String> BufferedReader2(String path,String choose) {//返回值类型是新建集合大类，此处是Set而非哈希。
        BufferedReader reader;
        ArrayList<String> tag = new java.util.ArrayList<String>();
        ArrayList<String> fasta = new java.util.ArrayList<String>();
        try {
            reader = new BufferedReader(new FileReader(path));
            String line = reader.readLine();
            StringBuilder sb = new StringBuilder();
            while (line != null) {//多次匹配带有“>”的行，\w代表0—9A—Z_a—z，需要转义。\W代表非0—9A—Z_a—z。
                if (line.matches(">[\\w*|\\W*]*")){
                    tag.add(line);
                    //定义字符串变量seq保存删除换行符的序列信息
                    if (sb.length()!=0){
                        String seq = sb.toString();
                        fasta.add(seq);
                        sb.delete(0, sb.length());//清空StringBuilder中全部元素
                    }

                }else{
                    sb.append(line);//重新向StringBuilder添加元素
                }
                // read next line
                line = reader.readLine();
            }
            String seq = sb.toString();
            fasta.add(seq);

            reader.close();
        } catch (IOException e) {
            e.printStackTrace();
        }
        if (choose.equals("tag")){
            return tag;
        }
        return fasta;
    }
}