Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/fileIO/CopyFiles.java @ 68:5028fdace37b

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
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67:0e9998148a16 68:5028fdace37b
1 package fileIO;
2
3 import java.io.File;
4
5
6 public class CopyFiles {
7
8
9 public static void main(String[] args){
10 for(String s : args){
11 renameFiles(s);
12 }
13 }
14
15
16 public static void renameFiles(String path){
17 File f=new File(path);
18 renameFiles(f);
19 }
20
21 public static void renameFiles(File path){
22
23 if(path.isDirectory()){
24 File[] array=path.listFiles();
25 for(File f : array){renameFiles(f);}
26 }else{
27 rename(path);
28 }
29
30 }
31
32 public static void rename(File in){
33 assert(in.exists());
34 assert(in.isFile());
35 String abs=in.getAbsolutePath();
36
37
38 int dot=abs.lastIndexOf('.');
39 int slash=abs.lastIndexOf('/');
40
41 // String[] split=Person.parsePath(abs.substring(0, slash));
42 // String name=split[0];
43 // String out=abs.substring(0, dot)+"_"+name+".txt";
44
45
46
47 String fname=abs.substring(slash+1);
48
49 // System.out.println(fname);
50
51
52 if(fname.startsWith("chr") && fname.endsWith(".txt")){
53
54 String out=abs.replace(".txt", ".flow");
55 assert(!out.equals(abs)) : out+", "+abs;
56
57 System.out.println("Renaming "+abs+" to "+out);
58 ReadWrite.copyFile(abs, out);
59 }
60 }
61
62 }