jpayne@68: package gff;
jpayne@68: 
jpayne@68: import java.io.PrintStream;
jpayne@68: import java.util.ArrayList;
jpayne@68: import java.util.HashMap;
jpayne@68: import java.util.Locale;
jpayne@68: import java.util.Map.Entry;
jpayne@68: 
jpayne@68: import fileIO.ByteFile;
jpayne@68: import fileIO.FileFormat;
jpayne@68: import fileIO.ReadWrite;
jpayne@68: import prok.ProkObject;
jpayne@68: import shared.Parse;
jpayne@68: import shared.Parser;
jpayne@68: import shared.PreParser;
jpayne@68: import shared.Shared;
jpayne@68: import shared.Timer;
jpayne@68: import shared.Tools;
jpayne@68: import structures.StringNum;
jpayne@68: 
jpayne@68: /**
jpayne@68:  * Compares gff files for the purpose of grading gene-calling.
jpayne@68:  * @author Brian Bushnell
jpayne@68:  * @date October 3, 2018
jpayne@68:  *
jpayne@68:  */
jpayne@68: public class CompareGff {
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------        Initialization        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	/**
jpayne@68: 	 * Code entrance from the command line.
jpayne@68: 	 * @param args Command line arguments
jpayne@68: 	 */
jpayne@68: 	public static void main(String[] args){
jpayne@68: 		//Start a timer immediately upon code entrance.
jpayne@68: 		Timer t=new Timer();
jpayne@68: 		
jpayne@68: 		//Create an instance of this class
jpayne@68: 		CompareGff x=new CompareGff(args);
jpayne@68: 		
jpayne@68: 		//Run the object
jpayne@68: 		x.process(t);
jpayne@68: 		
jpayne@68: 		//Close the print stream if it was redirected
jpayne@68: 		Shared.closeStream(x.outstream);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/**
jpayne@68: 	 * Constructor.
jpayne@68: 	 * @param args Command line arguments
jpayne@68: 	 */
jpayne@68: 	public CompareGff(String[] args){
jpayne@68: 		
jpayne@68: 		{//Preparse block for help, config files, and outstream
jpayne@68: 			PreParser pp=new PreParser(args, getClass(), false);
jpayne@68: 			args=pp.args;
jpayne@68: 			outstream=pp.outstream;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		//Set shared static variables prior to parsing
jpayne@68: 		ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=true;
jpayne@68: 		ReadWrite.MAX_ZIP_THREADS=Shared.threads();
jpayne@68: 		
jpayne@68: 		{//Parse the arguments
jpayne@68: 			final Parser parser=parse(args);
jpayne@68: 			overwrite=parser.overwrite;
jpayne@68: 			append=parser.append;
jpayne@68: 			
jpayne@68: 			in=parser.in1;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		fixExtensions(); //Add or remove .gz or .bz2 as needed
jpayne@68: 		checkFileExistence(); //Ensure files can be read and written
jpayne@68: 		checkStatics(); //Adjust file-related static fields as needed for this program
jpayne@68: 
jpayne@68: 		ffin=FileFormat.testInput(in, FileFormat.GFF, null, true, true);
jpayne@68: 		ffref=FileFormat.testInput(ref, FileFormat.GFF, null, true, true);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------    Initialization Helpers    ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	/** Parse arguments from the command line */
jpayne@68: 	private Parser parse(String[] args){
jpayne@68: 		
jpayne@68: 		Parser parser=new Parser();
jpayne@68: 		for(int i=0; i<args.length; i++){
jpayne@68: 			String arg=args[i];
jpayne@68: 			String[] split=arg.split("=");
jpayne@68: 			String a=split[0].toLowerCase();
jpayne@68: 			String b=split.length>1 ? split[1] : null;
jpayne@68: 			if(b!=null && b.equalsIgnoreCase("null")){b=null;}
jpayne@68: 
jpayne@68: 			if(a.equals("ref")){
jpayne@68: 				ref=b;
jpayne@68: 			}else if(a.equals("lines")){
jpayne@68: 				maxLines=Long.parseLong(b);
jpayne@68: 				if(maxLines<0){maxLines=Long.MAX_VALUE;}
jpayne@68: 			}else if(a.equals("verbose")){
jpayne@68: 				verbose=Parse.parseBoolean(b);
jpayne@68: //				ByteFile1.verbose=verbose;
jpayne@68: //				ByteFile2.verbose=verbose;
jpayne@68: //				ReadWrite.verbose=verbose;
jpayne@68: 			}else if(parser.parse(arg, a, b)){
jpayne@68: 				//do nothing
jpayne@68: 			}else if(i==0 && arg.indexOf('=')<0){
jpayne@68: 				parser.in1=arg;
jpayne@68: 			}else if(i==1 && arg.indexOf('=')<0 && ref==null){
jpayne@68: 				ref=arg;
jpayne@68: 			}else{
jpayne@68: 				outstream.println("Unknown parameter "+args[i]);
jpayne@68: 				assert(false) : "Unknown parameter "+args[i];
jpayne@68: 				//				throw new RuntimeException("Unknown parameter "+args[i]);
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		return parser;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Add or remove .gz or .bz2 as needed */
jpayne@68: 	private void fixExtensions(){
jpayne@68: 		in=Tools.fixExtension(in);
jpayne@68: 		ref=Tools.fixExtension(ref);
jpayne@68: 		if(in==null || ref==null){throw new RuntimeException("Error - at least two input files are required.");}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Ensure files can be read and written */
jpayne@68: 	private void checkFileExistence(){
jpayne@68: 		
jpayne@68: 		//Ensure input files can be read
jpayne@68: 		if(!Tools.testInputFiles(true, true, in, ref)){
jpayne@68: 			throw new RuntimeException("\nCan't read some input files.\n");  
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Adjust file-related static fields as needed for this program */
jpayne@68: 	private static void checkStatics(){
jpayne@68: 		//Adjust the number of threads for input file reading
jpayne@68: 		if(!ByteFile.FORCE_MODE_BF1 && !ByteFile.FORCE_MODE_BF2 && Shared.threads()>2){
jpayne@68: 			ByteFile.FORCE_MODE_BF2=true;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: //		if(!ByteFile.FORCE_MODE_BF2){
jpayne@68: //			ByteFile.FORCE_MODE_BF2=false;
jpayne@68: //			ByteFile.FORCE_MODE_BF1=true;
jpayne@68: //		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------         Outer Methods        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	void process(Timer t){
jpayne@68: 		
jpayne@68: 		ByteFile bf=ByteFile.makeByteFile(ffin);
jpayne@68: 		
jpayne@68: 		processInner(bf);
jpayne@68: 		
jpayne@68: 		errorState|=bf.close();
jpayne@68: 		
jpayne@68: 		t.stop();
jpayne@68: 		
jpayne@68: 		outstream.println(Tools.timeLinesBytesProcessed(t, linesProcessed, bytesProcessed, 8));
jpayne@68: 		
jpayne@68: 		outstream.println();
jpayne@68: 		outstream.println("Ref count:           \t"+refCount);
jpayne@68: 		outstream.println("Query count:         \t"+queryCount);
jpayne@68: 
jpayne@68: 		outstream.println();
jpayne@68: 		outstream.println("Ref-relative counts:");
jpayne@68: 		outstream.println("True Positive Start: \t"+truePositiveStart+"\t"+(String.format(Locale.ROOT, "%.3f%%", truePositiveStart*100.0/refCount)));
jpayne@68: 		outstream.println("True Positive Stop:  \t"+truePositiveStop+"\t"+(String.format(Locale.ROOT, "%.3f%%", truePositiveStop*100.0/refCount)));
jpayne@68: //		outstream.println("False Positive Start:\t"+falsePositiveStart+"\t"+(String.format(Locale.ROOT, "%.3f%%", falsePositiveStart*100.0/refCount)));
jpayne@68: //		outstream.println("False Positive Stop: \t"+falsePositiveStop+"\t"+(String.format(Locale.ROOT, "%.3f%%", falsePositiveStop*100.0/refCount)));
jpayne@68: 		outstream.println("False Negative Start:\t"+falseNegativeStart+"\t"+(String.format(Locale.ROOT, "%.3f%%", falseNegativeStart*100.0/refCount)));
jpayne@68: 		outstream.println("False Negative Stop: \t"+falseNegativeStop+"\t"+(String.format(Locale.ROOT, "%.3f%%", falseNegativeStop*100.0/refCount)));
jpayne@68: 
jpayne@68: 		outstream.println();
jpayne@68: 		outstream.println("Query-relative counts:");
jpayne@68: 		outstream.println("True Positive Start: \t"+truePositiveStart2+"\t"+(String.format(Locale.ROOT, "%.3f%%", truePositiveStart2*100.0/queryCount)));
jpayne@68: 		outstream.println("True Positive Stop:  \t"+truePositiveStop2+"\t"+(String.format(Locale.ROOT, "%.3f%%", truePositiveStop2*100.0/queryCount)));
jpayne@68: 		outstream.println("False Positive Start:\t"+falsePositiveStart2+"\t"+(String.format(Locale.ROOT, "%.3f%%", falsePositiveStart2*100.0/queryCount)));
jpayne@68: 		outstream.println("False Positive Stop: \t"+falsePositiveStop2+"\t"+(String.format(Locale.ROOT, "%.3f%%", falsePositiveStop2*100.0/queryCount)));
jpayne@68: 		
jpayne@68: 		outstream.println();
jpayne@68: 		outstream.println("SNR: \t"+String.format(Locale.ROOT, "%.4f", 10*Math.log10((truePositiveStart2+truePositiveStop2+0.1)/(falsePositiveStart2+falsePositiveStop2+0.1))));
jpayne@68: 		
jpayne@68: 		if(errorState){
jpayne@68: 			throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------         Inner Methods        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	@SuppressWarnings("unchecked")
jpayne@68: 	private void processInner(ByteFile bf){
jpayne@68: 		byte[] line=bf.nextLine();
jpayne@68: 		
jpayne@68: 		{
jpayne@68: 			ArrayList<GffLine> refLines=GffLine.loadGffFile(ffref, "CDS,rRNA,tRNA", true);
jpayne@68: 
jpayne@68: 			refCount=refLines.size();
jpayne@68: 			lineMap=new HashMap<StringNum, GffLine>();
jpayne@68: 			startCountMap=new HashMap<StringNum, Integer>();
jpayne@68: 			stopCountMap=new HashMap<StringNum, Integer>();
jpayne@68: 			
jpayne@68: 			for(GffLine gline : refLines){
jpayne@68: 				final int stop=gline.trueStop();
jpayne@68: 				StringNum sn=new StringNum(gline.seqid, stop);
jpayne@68: 				lineMap.put(sn, gline);
jpayne@68: 				startCountMap.put(sn, 0);
jpayne@68: 				stopCountMap.put(sn, 0);
jpayne@68: 				assert(lineMap.get(sn)==gline);
jpayne@68: //				assert(false) : "\n\nsn='"+sn+"'\n"+lineMap.containsKey(sn)+"\n"+lineMap.keySet();
jpayne@68: 			}
jpayne@68: 			if(verbose){
jpayne@68: 				System.err.println(lineMap);
jpayne@68: 				System.err.println(startCountMap);
jpayne@68: 				System.err.println(stopCountMap);
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		while(line!=null){
jpayne@68: 			if(line.length>0){
jpayne@68: 				if(maxLines>0 && linesProcessed>=maxLines){break;}
jpayne@68: 				linesProcessed++;
jpayne@68: 				bytesProcessed+=(line.length+1);
jpayne@68: 				
jpayne@68: 				final boolean valid=(line[0]!='#');
jpayne@68: 				if(valid){
jpayne@68: 					queryCount++;
jpayne@68: 					GffLine gline=new GffLine(line);
jpayne@68: 					processLine(gline);
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 			line=bf.nextLine();
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		for(Entry<StringNum, Integer> e : startCountMap.entrySet()){
jpayne@68: 			if(e.getValue()<1){
jpayne@68: 				falseNegativeStart++;
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		for(Entry<StringNum, Integer> e : stopCountMap.entrySet()){
jpayne@68: 			if(e.getValue()<1){
jpayne@68: 				falseNegativeStop++;
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private void processLine(GffLine gline){
jpayne@68: //		boolean cds=gline.type.equals("CDS");
jpayne@68: //		boolean trna=gline.type.equals("tRNA");
jpayne@68: //		boolean rrna=gline.type.equals("rRNA");
jpayne@68: //		if(!cds && !trna && !rrna){return;}
jpayne@68: //		if(cds && !ProkObject.callCDS){return;}
jpayne@68: //		if(trna && !ProkObject.calltRNA){return;}
jpayne@68: //		if(rrna){
jpayne@68: //			int type=gline.prokType();
jpayne@68: //			if(ProkObject.processType(type)){return;}
jpayne@68: //		}
jpayne@68: 		int type=gline.prokType();
jpayne@68: 		if(!ProkObject.processType(type)){return;}
jpayne@68: 		
jpayne@68: 		final int stop=gline.trueStop();
jpayne@68: 		final int start=gline.trueStart();
jpayne@68: 		
jpayne@68: //		System.err.println("Considering "+start+", "+stop);
jpayne@68: 
jpayne@68: 		StringNum sn=new StringNum(gline.seqid, stop);
jpayne@68: 		GffLine refline=lineMap.get(sn);
jpayne@68: 		
jpayne@68: 		boolean fail=(refline==null || refline.strand!=gline.strand || !refline.type.equals(gline.type));
jpayne@68: 		if(fail){
jpayne@68: 			if(verbose){
jpayne@68: 				System.err.println("Can't find "+sn+"\n"+gline+"\n"+refline);
jpayne@68: 				assert(false) : "\n\nsn='"+sn+"'\n"+lineMap.containsKey(sn)+"\n"+lineMap.keySet();
jpayne@68: 			}
jpayne@68: 			falsePositiveStart++;
jpayne@68: 			falsePositiveStop++;
jpayne@68: 			falsePositiveStart2++;
jpayne@68: 			falsePositiveStop2++;
jpayne@68: 		}else{
jpayne@68: 			assert(stop==refline.trueStop());
jpayne@68: 			truePositiveStop++;
jpayne@68: 			truePositiveStop2++;
jpayne@68: 			stopCountMap.put(sn, stopCountMap.get(sn)+1);
jpayne@68: 			if(start==refline.trueStart()){
jpayne@68: 				truePositiveStart++;
jpayne@68: 				truePositiveStart2++;
jpayne@68: 				startCountMap.put(sn, startCountMap.get(sn)+1);
jpayne@68: 			}else{
jpayne@68: 				falsePositiveStart++;
jpayne@68: 				falsePositiveStart2++;
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------            Fields            ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 
jpayne@68: 	private String in=null;
jpayne@68: 	private String ref=null;
jpayne@68: 	
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 
jpayne@68: 	private HashMap<StringNum, GffLine> lineMap;
jpayne@68: 	private HashMap<StringNum, Integer> startCountMap;
jpayne@68: 	private HashMap<StringNum, Integer> stopCountMap;
jpayne@68: 	
jpayne@68: //	private HashMap<Integer, ArrayList<GffLine>> map;
jpayne@68: //	private HashSet<Integer> stopSet;
jpayne@68: //	private HashSet<Integer> startSet;
jpayne@68: //	private HashSet<Integer> stopSetM;
jpayne@68: //	private HashSet<Integer> startSetM;
jpayne@68: 	
jpayne@68: 	private long linesProcessed=0;
jpayne@68: 	private long linesOut=0;
jpayne@68: 	private long bytesProcessed=0;
jpayne@68: 	private long bytesOut=0;
jpayne@68: 	
jpayne@68: 	private long maxLines=Long.MAX_VALUE;
jpayne@68: 
jpayne@68: 	private long falsePositiveStart=0;
jpayne@68: 	private long falsePositiveStop=0;
jpayne@68: 	private long truePositiveStart=0;
jpayne@68: 	private long truePositiveStop=0;
jpayne@68: 	private long falseNegativeStart=0;
jpayne@68: 	private long falseNegativeStop=0;
jpayne@68: 	
jpayne@68: 	private long falsePositiveStart2=0;
jpayne@68: 	private long falsePositiveStop2=0;
jpayne@68: 	private long truePositiveStart2=0;
jpayne@68: 	private long truePositiveStop2=0;
jpayne@68: 	
jpayne@68: 	private long refCount=0;
jpayne@68: 	private long queryCount=0;
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------         Final Fields         ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 
jpayne@68: 	private final FileFormat ffin;
jpayne@68: 	private final FileFormat ffref;
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------        Common Fields         ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	private PrintStream outstream=System.err;
jpayne@68: 	public static boolean verbose=false;
jpayne@68: 	public boolean errorState=false;
jpayne@68: 	private boolean overwrite=false;
jpayne@68: 	private boolean append=false;
jpayne@68: 	
jpayne@68: }