Rosalind Java| Computing GC Content_gccontentdesktop-优快云博客

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Rosalind编程问题之计算GC含量。

Computing GC Content

Problem
The GC-content of a DNA string is given by the percentage of symbols in the string that are ‘C’ or ‘G’. For example, the GC-content of “AGCTATAG” is 37.5%. Note that the reverse complement of any DNA string has the same GC-content.

DNA strings must be labeled when they are consolidated into a database. A commonly used method of string labeling is called FASTA format. In this format, the string is introduced by a line that begins with ‘>’, followed by some labeling information. Subsequent lines contain the string itself; the first line to begin with ‘>’ indicates the label of the next string.

In Rosalind’s implementation, a string in FASTA format will be labeled by the ID “Rosalind_xxxx”, where “xxxx” denotes a four-digit code between 0000 and 9999.

Given: At most 10 DNA strings in FASTA format (of length at most 1 kbp each).
Sample input：

>Rosalind_6404
CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCC
TCCCACTAATAATTCTGAGG
>Rosalind_5959
CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCT
ATATCCATTTGTCAGCAGACACGC
>Rosalind_0808
CCACCCTCGTGGTATGGCTAGGCATTCAGGAACCGGAGAACGCTTCAGACCAGCCCGGAC
TGGGAACCTGCGGGCAGTAGGTGGAAT

Return: The ID of the string having the highest GC-content, followed by the GC-content of that string. Rosalind allows for a default error of 0.001 in all decimal answers unless otherwise stated; please see the note on absolute error below.
Sample output：

Rosalind_0808
60.919540

GC含量是在所研究的对象的全基因组中，鸟嘌呤（Guanine）和胞嘧啶（Cytosine）在全部碱基中所占的比例。能够决定DNA的稳定性。本道题需要我们读取含有多序列的fasta文件，并且挨个计算GC含量，最终输出GC含量最高的序列开头注释信息以及其GC含量值。** 解题思路如下：

1.逐行读取fasta文件，消掉序列信息中的换行符。
2.计算每条序列的GC含量。
3.各条序列的GC含量进行对比，并获得最大GC含量。
4.输出GC含量最高的序列及其标签

因此，小编分别定义了三个子方法：

子方法1BufferedReader用来读取fasta文件并且去掉其中的序列换行符。详情请见：解决Java逐行读取带有行缩进的fasta文件
子方法2FindMaxCount获取GC含量最高值。
子方法3FindIndex获取最大的GC含量序列引索值，用以输出其对应的开头注释信息。以下是全部代码。

import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;

public class Computing_GC_Content {
    public static void main(String[] args) {
        //1.逐行读取fasta文件
        ArrayList<String> fasta = BufferedReader("C:/Users/Administrator/Desktop/rosalind_gc.txt", "fasta");//设置返回值是碱基序列。
        ArrayList<String> tag = BufferedReader("C:/Users/Administrator/Desktop/rosalind_gc.txt", "tag");//设置返回值是标签名称。
        //2.计算每条序列的GC含量
        float[] GCratio = new float[fasta.size()];//定义数组存储每条fasta序列的GC比例
        int[] GCcount = new int[fasta.size()];//定义数组存储每条fasta序列的GC含量
        for (int i = 0; i < fasta.size(); i++) {
            for (int j = 0; j < fasta.get(i).length(); j++) {
                if (fasta.get(i).charAt(j) == 'G' || fasta.get(i).charAt(j) == 'C') {
                    //fasta.get(i).charAt(j)=='G'||'C' Java不支持此类型的判断语句
                    GCcount[i]++;
                }
            }
            GCratio[i] = (float) GCcount[i] / fasta.get(i).length();
        }
        //3.各条序列的GC含量进行对比，并获得最大GC含量
        float maxcount = (float) (Math.round(FindMaxCount(GCratio) * 100000000)) / 1000000;
        int maxIndex = FindIndex(GCratio);
        //4.输出GC含量最高的序列及其标签
        System.out.println(tag.get(maxIndex));
        System.out.println(maxcount);
    }

    //子方法1.读取fasta文件并且分别存储到fasta集合和tag集合中。
    public static ArrayList<String> BufferedReader(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);
                    //第一个循环开始时StringBuilder为空，需要添加判断以排除此特例。
                    if (sb.length()!=0){
                        String seq = sb.toString();//定义字符串变量seq保存删除换行符的序列信息
                        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);//循环结束还要再次输出序列，否则会丢失一条序列。
            reader.close();
        } catch (IOException e) {
            e.printStackTrace();
        }
        if (choose.equals("tag")){
            return tag;
        }
        return fasta;
    }

    //子方法2：获取最大的GC含量数字
    public static float FindMaxCount(float[] arr) {
        float max = arr[0];
        for (int x = 1; x < arr.length; x++) {
            if (max < arr[x]) {
                max = arr[x];
            }
        }
        return max;
    }

    //子方法3：获取最大的GC含量序列引索
    public static int FindIndex(float[] arr) {
        float max = arr[0];
        int maxValIndex = 0;
        for (int x = 1; x < arr.length; x++) {
            if (max < arr[x]) {
                max = arr[x];
                maxValIndex = x;
            }
        }
        return maxValIndex;
    }

}