Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/gff/GbffFile.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 gff;
2
3 import java.util.ArrayList;
4
5 import fileIO.ByteFile;
6 import fileIO.ByteStreamWriter;
7 import fileIO.FileFormat;
8 import shared.Shared;
9 import shared.Tools;
10
11 public class GbffFile {
12
13 public static void main(String[] args){
14 String gbff=args[0];
15 String gff=(args.length>1 ? args[1] : "stdout.gff");
16
17 if(gbff.indexOf('=')>=0){gbff=gbff.split("=")[1];}
18 if(gff.indexOf('=')>=0){gff=gff.split("=")[1];}
19
20 FileFormat ffin=FileFormat.testInput(gbff, ".gbff", true);
21 FileFormat ffout=FileFormat.testOutput(gff, FileFormat.GFF, null, true, true, false, false);
22 GbffFile file=new GbffFile(ffin);
23 ByteStreamWriter bsw=new ByteStreamWriter(ffout);
24 bsw.start();
25 file.toGff(bsw, true);
26 bsw.poisonAndWait();
27 }
28
29
30 // ##gff-version 3
31 // #!gff-spec-version 1.21
32 // #!processor NCBI annotwriter
33 // #!genome-build IMG-taxon 2724679794 annotated assembly
34 // #!genome-build-accession NCBI_Assembly:GCF_900182635.1
35 // #!annotation-date 07/14/2019 01:52:19
36 // #!annotation-source NCBI RefSeq
37 // ##sequence-region NZ_FXTD01000001.1 1 528269
38 // ##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=413815
39
40 public void toGff(ByteStreamWriter bsw, boolean printHeader){
41 if(printHeader){
42 bsw.println("##gff-version 3".getBytes());
43 bsw.println(("#BBTools "+Shared.BBMAP_VERSION_STRING+" GbffToGff").getBytes());
44 bsw.println("#seqid source type start end score strand phase attributes".getBytes());
45 }
46 for(GbffLocus locus=nextLocus(); locus!=null; locus=nextLocus()){
47 locus.toGff(bsw);
48 }
49 }
50
51 public GbffFile(FileFormat ff_) {
52 ff=ff_;
53 assert(ff.format()==FileFormat.GBFF) : ff;
54 reset();
55 }
56
57 public synchronized void reset(){
58 if(bf!=null){
59 bf.close();
60 bf=null;
61 }
62 bf=ByteFile.makeByteFile(ff, FileFormat.GBFF);
63 line=bf.nextLine();
64 if(line==null){bf.close();}//empty
65 }
66
67 public GbffLocus nextLocus(){
68 assert(bf!=null);
69 if(line==null){return null;}
70 assert(Tools.startsWith(line, "LOCUS ")) : "Expecting: 'LOCUS ...'\nGot: '"+new String(line)+"'";
71 ArrayList<byte[]> lines=new ArrayList<byte[]>();
72 lines.add(line);
73 boolean sequence=false;
74 for(line=bf.nextLine(); line!=null && (line.length==0 || line[0]!='L' || !Tools.startsWith(line, "LOCUS ")); line=bf.nextLine()){
75 if(line.length>0){
76 final byte b=line[0];
77 if(b=='/'){
78 //skip
79 }else if(b=='O' && Tools.startsWith(line, "ORIGIN ")){
80 sequence=true;
81 }else if(b==' ' && sequence){
82 //do nothing
83 }else{
84 sequence=false;
85 lines.add(line);
86 }
87 }
88 }
89 if(line==null){bf.close();}
90 return new GbffLocus(lines);
91 }
92
93 private final FileFormat ff;
94 private ByteFile bf;
95 private byte[] line=null;
96
97 }