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package fileIO;
import java.io.File;
import shared.Timer;
public class CopyFiles2 {
public static void main(String[] args){
Timer t=new Timer();
if(args.length>0){
assert(args.length==2);
inRoots=new String[] {args[0]};
outRoot=args[1];
}
for(String inRoot : inRoots){
copyFiles(inRoot, outRoot);
}
t.stop();
System.out.println("Time:\t"+t);
}
public static void copyFiles(String in, String out){
File fin=new File(in);
File fout=new File(out);
copyFiles(fin, fout);
}
public static void copyFiles(File in, File out){
String abs=in.getAbsolutePath();
for(String s : badNames){
if(abs.matches(s)){
return;
}
}
{
String temp=out.getAbsolutePath();
if(temp.endsWith("\\ASM")){
temp=temp.replace("\\ASM", "");
}else if(temp.contains("\\ASM\\")){
temp=temp.replace("\\ASM\\", "");
}
out=new File(temp);
}
if(in.isDirectory()){
// System.out.println("PATH: "+in.getAbsolutePath());
if(!out.exists()){
out.mkdir();
}
File[] array=in.listFiles();
for(File f : array){
// String outname=f.getAbsolutePath().replace(inRoot, outRoot);
String outname=out.getAbsolutePath()+"\\"+f.getName();
File f2=new File(outname);
copyFiles(f, f2);
}
}
else{
copyFile(in, out);
}
}
public static void copyFile(File in, File out){
assert(in.exists());
assert(in.isFile());
if(out.exists()){
System.out.println("Skipping existing file "+out.getAbsolutePath());
return;
}
String abs=in.getAbsolutePath();
String fname=in.getName();
boolean valid=false;
for(String s : badNames){
if(fname.matches(s)){
valid=false;
return;
}
}
for(String s : dirNames){
if(abs.contains(s)){
valid=true;
break;
}
}
for(String s : fileNames){
if(valid){break;}
if(fname.matches(s)){
valid=true;
}
}
if(!valid){return;}
if(abs.endsWith(".tsv")/* && in.length()>4000000*/){
out=new File(out.getAbsolutePath()+".zip");
}
// if(abs.endsWith(".bz2")){
// out=new File(out.getAbsolutePath().replace(".bz2", ".zip"));
// }
System.out.println("Copying file to "+out.getAbsolutePath());
ReadWrite.copyFile(in.getAbsolutePath(), out.getAbsolutePath());
}
// public static String[] inRoots={"F:\\UTSW_batch_1\\", "F:\\UTSW_batch_2\\"};
public static String[] inRoots={"F:\\UTSW_second_set\\"};
public static String outRoot="C:\\Data\\OCT_8\\";
public static final String[] dirNames={"\\CNV\\", "\\SV\\"};
public static final String[] fileNamesAbsolute={
".*\\\\gene-GS.+-ASM.*\\.tsv.*",
".*\\\\geneVarSummary-GS.+-ASM.*\\.tsv.*",
".*\\\\summary-GS.+-ASM.*\\.tsv.*",
".*\\\\var-GS.+-ASM.*\\.tsv.*",
".*\\\\manifest\\.all",
".*\\\\README\\..*",
".*\\\\version",
};
public static final String[] fileNames={
"gene-GS.+-ASM.*\\.tsv.*",
"geneVarSummary-GS.+-ASM.*\\.tsv.*",
"summary-GS.+-ASM.*\\.tsv.*",
"var-GS.+-ASM.*\\.tsv.*",
"manifest\\.all",
"README\\..*",
"version",
};
public static final String[] badNames={
".*AppleDouble.*",
".*DS_Store.*",
".*EVIDENCE.*"
};
}
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