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package driver;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.util.Arrays;
import fileIO.ReadWrite;
import fileIO.TextFile;
import fileIO.TextStreamWriter;
import shared.Timer;
public class ConcatenateFiles {
public static void main(String[] args){
Timer t=new Timer();
final String in=args[0];
final String out=(args.length>1 ? args[1] : null);
if(new File(in).isDirectory()){
try {
concatenateDirectory(in, out);
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}else{
concatenatePattern(in, out);
}
t.stop();
System.err.println(t);
}
public static void concatenatePattern(final String basename, final String out){
assert(false) : "This is human-specific.";
String outname=(out==null ? basename.replace("#", "ALL") : out);
TextStreamWriter tsw=new TextStreamWriter(outname, true, false, true);
tsw.start();
for(int chrom=1; chrom<26; chrom++){
String fname=basename.replace("#", ""+chrom);
TextFile tf=new TextFile(fname, false);
tsw.print(">chr"+chrom+"\n");
for(String s=tf.nextLine(); s!=null; s=tf.nextLine()){
char c=s.charAt(0);
if(c!='>' && c!=';'){
tsw.println(s);
}
}
System.err.print(".");
}
tsw.poisonAndWait();
}
public static void concatenateDirectory(final String in, String out) throws IOException{
if(out==null){out="stdout";}
final byte[] buf=new byte[32768];
final File dir=new File(in);
final File[] files=dir.listFiles();
Arrays.sort(files);
final File outfile=new File(out);
final OutputStream os=ReadWrite.getOutputStream(out, false, true, true);
for(File f : files){
if(f!=null && f.isFile() && !f.equals(outfile)){
String fname=f.getAbsolutePath();
System.err.println("Processing "+fname);
InputStream is=ReadWrite.getInputStream(fname, false, false);
for(int lim=is.read(buf); lim>0; lim=is.read(buf)){
os.write(buf, 0, lim);
}
is.close();
System.err.print(".");
}
}
ReadWrite.close(os);
}
}
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