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package driver;
import java.io.File;
import java.io.PrintStream;
import java.util.ArrayList;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import fileIO.TextFile;
import shared.Parse;
import shared.PreParser;
import shared.Shared;
import shared.Timer;
/**
* Renames files based on their headers
* @author Brian Bushnell
* @date May 19, 2016
*
*/
public class RenameByHeader {
public static void main(String[] args){
Timer t=new Timer();
RenameByHeader x=new RenameByHeader(args);
x.process(t);
//Close the print stream if it was redirected
Shared.closeStream(x.outstream);
}
public RenameByHeader(String[] args){
{//Preparse block for help, config files, and outstream
PreParser pp=new PreParser(args, getClass(), false);
args=pp.args;
outstream=pp.outstream;
}
ReadWrite.USE_PIGZ=false;
ReadWrite.USE_UNPIGZ=false;
ReadWrite.USE_UNBGZIP=false;
for(int i=0; i<args.length; i++){
String arg=args[i];
String[] split=arg.split("=");
String a=split[0].toLowerCase();
String b=split.length>1 ? split[1] : null;
File f=(b==null ? new File(arg) : null);
if(f!=null && f.exists()){
if(f.isDirectory()){
for(File f2 : f.listFiles()){
String name=f2.getAbsolutePath();
if(f2.isFile() && FileFormat.hasFastqOrFastqExtension(name)){
list.add(name);
}
}
}else{
list.add(f.getAbsolutePath());
}
}else if(a.equals("verbose")){
verbose=Parse.parseBoolean(b);
ReadWrite.verbose=verbose;
}else{
outstream.println("Unknown parameter "+args[i]);
assert(false) : "Unknown parameter "+args[i];
// throw new RuntimeException("Unknown parameter "+args[i]);
}
}
}
void process(Timer t){
for(String s : list){
processFile(s);
}
}
void processFile(String path){
TextFile tf=new TextFile(path);
String line=tf.nextLine();
tf.close();
if(line==null){return;}
StringBuilder sb=new StringBuilder();
File f=new File(path);
String dir=f.getParent();
if(dir!=null){sb.append(dir).append('/');}
try {
String[] split=line.substring(1).replace(",", "").split(" ");
sb.append(split[1]);
sb.append('_');
sb.append(split[2]);
sb.append('_');
if(split[2].equals("sp.")){
sb.append(split[3]);
sb.append('_');
}
} catch (Exception e) {
// TODO Auto-generated catch block
System.err.println(path);
e.printStackTrace();
return;
}
if(sb.length()>0){
String name=f.getName();
sb.append(name);
f.renameTo(new File(sb.toString()));
}
}
/*--------------------------------------------------------------*/
private ArrayList<String> list=new ArrayList<String>();
private PrintStream outstream=System.err;
private static boolean verbose=false;
}
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