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package driver;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import shared.Tools;
public class MoveFiles {
public static void main(String[] args){
String root=args[0].replace('\\', '/');
File dir=new File(root);
assert(dir.exists());
assert(dir.isDirectory());
File[] files=dir.listFiles();
for(int chrom=1; chrom<=22; chrom++){
String key="chr"+chrom;
File dest=new File(root+"/"+key);
if(!dest.exists()){
dest.mkdir();
}
for(File f : files){
String name=f.getName();
if(name.contains("/")){
name=name.substring(name.lastIndexOf("/")+1);
}
final String name2=name;
if(name.contains(".")){
name=name.substring(0,name.lastIndexOf("."));
}
while(name.length()>1 && !Tools.isDigit(name.charAt(name.length()-1))){
name=name.substring(0, name.length()-1);
}
name=name.toLowerCase();
if(f.isFile() && name.endsWith("chr"+chrom)){
copyFile(f.getAbsolutePath(), dest.getAbsolutePath()+"/"+name2);
}
}
}
}
/**
* @param srFile
* @param dtFile
* {@link from http://www.roseindia.net/java/beginners/CopyFile.shtml}
*/
private static void copyFile(String src, String dst){
// assert(false) : src+" -> "+dst;
try{
File f1 = new File(src);
File f2 = new File(dst);
InputStream in = new FileInputStream(f1);
//For Append the file.
// OutputStream out = new FileOutputStream(f2,true);
//For Overwrite the file.
OutputStream out = new FileOutputStream(f2);
byte[] buf = new byte[16384];
int len;
while ((len = in.read(buf)) > 0){
out.write(buf, 0, len);
}
in.close();
out.close();
}catch(FileNotFoundException e){
throw new RuntimeException(e);
}catch(IOException e){
throw new RuntimeException(e);
}
}
}
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