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package gff;
import java.util.ArrayList;
import fileIO.ByteFile;
import fileIO.ByteStreamWriter;
import fileIO.FileFormat;
import shared.Shared;
import shared.Tools;
public class GbffFile {
public static void main(String[] args){
String gbff=args[0];
String gff=(args.length>1 ? args[1] : "stdout.gff");
if(gbff.indexOf('=')>=0){gbff=gbff.split("=")[1];}
if(gff.indexOf('=')>=0){gff=gff.split("=")[1];}
FileFormat ffin=FileFormat.testInput(gbff, ".gbff", true);
FileFormat ffout=FileFormat.testOutput(gff, FileFormat.GFF, null, true, true, false, false);
GbffFile file=new GbffFile(ffin);
ByteStreamWriter bsw=new ByteStreamWriter(ffout);
bsw.start();
file.toGff(bsw, true);
bsw.poisonAndWait();
}
// ##gff-version 3
// #!gff-spec-version 1.21
// #!processor NCBI annotwriter
// #!genome-build IMG-taxon 2724679794 annotated assembly
// #!genome-build-accession NCBI_Assembly:GCF_900182635.1
// #!annotation-date 07/14/2019 01:52:19
// #!annotation-source NCBI RefSeq
// ##sequence-region NZ_FXTD01000001.1 1 528269
// ##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=413815
public void toGff(ByteStreamWriter bsw, boolean printHeader){
if(printHeader){
bsw.println("##gff-version 3".getBytes());
bsw.println(("#BBTools "+Shared.BBTOOLS_VERSION_STRING+" GbffToGff").getBytes());
bsw.println("#seqid source type start end score strand phase attributes".getBytes());
}
for(GbffLocus locus=nextLocus(); locus!=null; locus=nextLocus()){
locus.toGff(bsw);
}
}
public GbffFile(FileFormat ff_) {
ff=ff_;
assert(ff.format()==FileFormat.GBFF) : ff;
reset();
}
public synchronized void reset(){
if(bf!=null){
bf.close();
bf=null;
}
bf=ByteFile.makeByteFile(ff, FileFormat.GBFF);
line=bf.nextLine();
if(line==null){bf.close();}//empty
}
public GbffLocus nextLocus(){
assert(bf!=null);
if(line==null){return null;}
assert(Tools.startsWith(line, "LOCUS ")) : "Expecting: 'LOCUS ...'\nGot: '"+new String(line)+"'";
ArrayList<byte[]> lines=new ArrayList<byte[]>();
lines.add(line);
boolean sequence=false;
for(line=bf.nextLine(); line!=null && (line.length==0 || line[0]!='L' || !Tools.startsWith(line, "LOCUS ")); line=bf.nextLine()){
if(line.length>0){
final byte b=line[0];
if(b=='/'){
//skip
}else if(b=='O' && Tools.startsWith(line, "ORIGIN ")){
sequence=true;
}else if(b==' ' && sequence){
//do nothing
}else{
sequence=false;
lines.add(line);
}
}
}
if(line==null){bf.close();}
return new GbffLocus(lines);
}
private final FileFormat ff;
private ByteFile bf;
private byte[] line=null;
}
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