SNP位点上下游序列查找1.0 2020-9-27

换账号重新发布orz

/*
 * Author：Henriette-L（luanxito＠163.com）
 * Date： 2020-9-27
 * Introduction: （等我有空补）简单来说给定SNP序列的Excel文件，在源序列txt文件中查找SNP位点的上下游300个序列并且定位。
 */
 
package demo;

public class Bean {

	private String fiveSource;
	private String fiveTarget;
	private String fiveStartNum;
	private String threeSource;
	private String threeTarget;
	private String threeStartNum;
	
	public String getFiveSource() {
		return fiveSource;
	}
	public void setFiveSource(String fiveSource) {
		this.fiveSource = fiveSource;
	}
	public String getFiveTarget() {
		return fiveTarget;
	}
	public void setFiveTarget(String fiveTarget) {
		this.fiveTarget = fiveTarget;
	}
	public String getFiveStartNum() {
		return fiveStartNum;
	}
	public void setFiveStartNum(String fiveStartNum) {
		this.fiveStartNum = fiveStartNum;
	}
	public String getThreeSource() {
		return threeSource;
	}
	public void setThreeSource(String threeSource) {
		this.threeSource = threeSource;
	}
	public String getThreeTarget() {
		return threeTarget;
	}
	public void setThreeTarget(String threeTarget) {
		this.threeTarget = threeTarget;
	}
	public String getThreeStartNum() {
		return threeStartNum;
	}
	public void setThreeStartNum(String threeStartNum) {
		this.threeStartNum = threeStartNum;
	}	
	
}



package demo;

import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;

import org.apache.poi.ss.usermodel.Cell;
import org.apache.poi.ss.usermodel.CellType;
import org.apache.poi.ss.usermodel.Row;
import org.apache.poi.ss.usermodel.Sheet;
import org.apache.poi.ss.usermodel.Workbook;
import org.apache.poi.xssf.usermodel.XSSFCell;
import org.apache.poi.xssf.usermodel.XSSFRow;
import org.apache.poi.xssf.usermodel.XSSFSheet;
import org.apache.poi.xssf.usermodel.XSSFWorkbook;

        public class demo {

            public static void main(String[] args) throws IOException {
                List<Bean> list = new ArrayList<>();
                System.out.println("1");
                getExcelData(list);
                System.out.println("2");
                getTargetList(list);
                System.out.println("3");
                getTargetDataFromTXT(list);//时间较长
                System.out.println("4");
                setTargetDataToExcel(list);
                System.out.println("end");
            }
            /**
             * 将目标写入到excel
             * @throws IOException
             */
            public static void setTargetDataToExcel(List<Bean> list) throws IOException {
                Workbook workbook = new XSSFWorkbook();
                String [] title = {"序号","5'端起始数字","5’端前300数据","3'端起始数字","3'端后300数据"};
                //设置sheet
                String sheetName = "目标数据";
                Sheet sheet = workbook.createSheet(sheetName);
                //获取表投行
                Row titleRow = sheet.createRow(0);
                //创建单元格
                Cell cell =null;
                for(int i=0;i<title.length;i++) {
                    cell = titleRow.createCell(i);
                    cell.setCellValue(title[i]);
                }
                Row row = null;
                for (int i = 0; i < list.size(); i++) {
                    //创建list.size()行数据
                    row = sheet.createRow(i + 1);
                    //把值一一写进单元格里
                    //设置第一列为自动递增的序号
                    row.createCell(0).setCellValue(i + 1);
                    row.createCell(1).setCellValue(list.get(i).getFiveStartNum());
                    row.createCell(2).setCellValue(list.get(i).getFiveTarget());
                    row.createCell(3).setCellValue(list.get(i).getThreeStartNum());
                    row.createCell(4).setCellValue(list.get(i).getThreeTarget());
                }
                //设置单元格宽度自适应，在此基础上把宽度调至1.5倍
                for (int i = 0; i < title.length; i++) {
                    sheet.autoSizeColumn(i, true);
                    //sheet.setColumnWidth(i, sheet.getC
                    //上述列宽报错
                    //Throws：java.lang.lllegalArgumentException-if width>255*256(the maximum column width in Excel is 255characters)
                    //结合上述微软注意规范可知未考虑边界情况，不是String的问题是org.apache.pol.xssf.usermode.XSSFSheet的问题
                 
	    //写入到excel
		//修改生成文件名修改下面绿色的路径
	    String exportFilePath = "E:\\结果分析.xlsx";
	    File exportFile = new File(exportFilePath);
	    if(!exportFile.exists()) {
	    	exportFile.createNewFile();
	    }
	    OutputStream fileOut = new FileOutputStream(exportFile);
	    workbook.write(fileOut);
	    fileOut.close();
	}
	
	/**
	 * 从TXT中获取目标数据
	 * @throws IOException 
	 */
	public static void getTargetDataFromTXT(List<Bean> list) throws IOException {
		//需要换数据源修改下面路径
		Path path =Paths.get("E:\\G.txt");
		byte [] data = Files.readAllBytes(path);//获取TXT数据
		String res = new String(data);
        res=res.replaceAll("\r|\n","");
		for(Bean bean : list) {
			//获取第五列目标
			int index = res.indexOf(bean.getFiveSource());
			if(index == -1) {
				bean.setFiveStartNum("-1");
				bean.setFiveTarget("不存在");
			}else {
				bean.setFiveStartNum(String.valueOf(index));
				int length = bean.getFiveSource().length();
				int start =index -300;
				if(start<0) {
					start =0;
				}
				bean.setFiveTarget(res.substring(start, index));
			}
			//获取3'端目标数据
			index = res.indexOf(bean.getThreeSource());
			if(index == -1) {
				bean.setThreeStartNum("-1");
				bean.setThreeTarget("不存在");
			}else {
				bean.setThreeStartNum(String.valueOf(index));
				int length =bean.getThreeSource().length();
				int end = index +300+ length;
				if(end>res.length()) {
					end = res.length() - 1;
				}
				bean.setThreeTarget(res.substring(index + length, end));
			}
		}
	}
	
	/**
	 * 去除[*],返回字符串
	 */
	public static void getTargetList(List<Bean> list) {
		for (int i = 0; i < list.size(); i++) {
			if(list.get(i).getFiveSource().indexOf('[') != -1) {//存在[]
				StringBuffer reStringBuffer = new StringBuffer(list.get(i).getFiveSource());
				int start = list.get(i).getFiveSource().indexOf('[');
				int end =list.get(i).getFiveSource().indexOf(']');
				reStringBuffer.replace(start, end+1, "");
				list.get(i).setFiveSource(reStringBuffer.toString());
			}
			if(list.get(i).getThreeSource().indexOf('[') != -1) {//存在[]
				StringBuffer reStringBuffer = new StringBuffer(list.get(i).getThreeSource());
				int start = list.get(i).getThreeSource().indexOf('[');
				int end =list.get(i).getThreeSource().indexOf(']');
				reStringBuffer.replace(start, end+1, "");
				list.get(i).setThreeSource(reStringBuffer.toString());
			}
		}
	}
	
	/**
	 * 获取excel数据
	 * @throws IOException 
	 */
	public static void getExcelData(List<Bean> list) throws IOException {
		//用流的方式先读取到你想要的excel文件
		//想换查找的序列修改下面路径
		String address = "C:\\芯片SNP位点.xlsx";
        FileInputStream fis=new FileInputStream(address);
        //定义工作簿
        XSSFWorkbook xssfWorkbook = new XSSFWorkbook(fis);
        //定义工作表，默认取第一个子表
        XSSFSheet xssfSheet= xssfWorkbook.getSheetAt(1);
        //定义行默认第一行为标题行，index = 0
        XSSFRow titleRow = xssfSheet.getRow(0);
        //循环每行的数据
        for (int rowIndex = 8; rowIndex < xssfSheet.getPhysicalNumberOfRows(); rowIndex++) {
            XSSFRow xssfRow = xssfSheet.getRow(rowIndex);
            if (xssfRow == null) {
                continue;
            }
            Bean bean = new Bean();
            //循环获取每个单元格(cell)的数据
            XSSFCell xssfCell5 = xssfRow.getCell(4);
            bean.setFiveSource(getString(xssfCell5));
            if("".equals(xssfCell5)) {
            	break;
            }
            XSSFCell xssfCell3 = xssfRow.getCell(5);
            bean.setThreeSource(getString(xssfCell3));
            list.add(bean);
        }
        try {
			fis.close();
		} catch (IOException e) {
			e.printStackTrace();
		}
	}
	
	/**
     * 把单元格的内容转为字符串
     * @param xssfCell 单元格
     * @return 字符串
     */
    public static String getString(XSSFCell xssfCell) {
        if (xssfCell == null) {
            return "";
        }
        if (xssfCell.getCellTypeEnum() == CellType.NUMERIC) {
            return String.valueOf(xssfCell.getNumericCellValue());
        } else if (xssfCell.getCellTypeEnum() == CellType.BOOLEAN) {
            return String.valueOf(xssfCell.getBooleanCellValue());
        } else {
            return xssfCell.getStringCellValue();
        }
    }

}