Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/fileIO/CopyFiles.java @ 68:5028fdace37b
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 16:23:26 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| jpayne@68 | 1 package fileIO; |
| jpayne@68 | 2 |
| jpayne@68 | 3 import java.io.File; |
| jpayne@68 | 4 |
| jpayne@68 | 5 |
| jpayne@68 | 6 public class CopyFiles { |
| jpayne@68 | 7 |
| jpayne@68 | 8 |
| jpayne@68 | 9 public static void main(String[] args){ |
| jpayne@68 | 10 for(String s : args){ |
| jpayne@68 | 11 renameFiles(s); |
| jpayne@68 | 12 } |
| jpayne@68 | 13 } |
| jpayne@68 | 14 |
| jpayne@68 | 15 |
| jpayne@68 | 16 public static void renameFiles(String path){ |
| jpayne@68 | 17 File f=new File(path); |
| jpayne@68 | 18 renameFiles(f); |
| jpayne@68 | 19 } |
| jpayne@68 | 20 |
| jpayne@68 | 21 public static void renameFiles(File path){ |
| jpayne@68 | 22 |
| jpayne@68 | 23 if(path.isDirectory()){ |
| jpayne@68 | 24 File[] array=path.listFiles(); |
| jpayne@68 | 25 for(File f : array){renameFiles(f);} |
| jpayne@68 | 26 }else{ |
| jpayne@68 | 27 rename(path); |
| jpayne@68 | 28 } |
| jpayne@68 | 29 |
| jpayne@68 | 30 } |
| jpayne@68 | 31 |
| jpayne@68 | 32 public static void rename(File in){ |
| jpayne@68 | 33 assert(in.exists()); |
| jpayne@68 | 34 assert(in.isFile()); |
| jpayne@68 | 35 String abs=in.getAbsolutePath(); |
| jpayne@68 | 36 |
| jpayne@68 | 37 |
| jpayne@68 | 38 int dot=abs.lastIndexOf('.'); |
| jpayne@68 | 39 int slash=abs.lastIndexOf('/'); |
| jpayne@68 | 40 |
| jpayne@68 | 41 // String[] split=Person.parsePath(abs.substring(0, slash)); |
| jpayne@68 | 42 // String name=split[0]; |
| jpayne@68 | 43 // String out=abs.substring(0, dot)+"_"+name+".txt"; |
| jpayne@68 | 44 |
| jpayne@68 | 45 |
| jpayne@68 | 46 |
| jpayne@68 | 47 String fname=abs.substring(slash+1); |
| jpayne@68 | 48 |
| jpayne@68 | 49 // System.out.println(fname); |
| jpayne@68 | 50 |
| jpayne@68 | 51 |
| jpayne@68 | 52 if(fname.startsWith("chr") && fname.endsWith(".txt")){ |
| jpayne@68 | 53 |
| jpayne@68 | 54 String out=abs.replace(".txt", ".flow"); |
| jpayne@68 | 55 assert(!out.equals(abs)) : out+", "+abs; |
| jpayne@68 | 56 |
| jpayne@68 | 57 System.out.println("Renaming "+abs+" to "+out); |
| jpayne@68 | 58 ReadWrite.copyFile(abs, out); |
| jpayne@68 | 59 } |
| jpayne@68 | 60 } |
| jpayne@68 | 61 |
| jpayne@68 | 62 } |