jpayne@68: package tax;
jpayne@68: 
jpayne@68: import java.io.File;
jpayne@68: import java.util.ArrayList;
jpayne@68: 
jpayne@68: import fileIO.ByteFile;
jpayne@68: import fileIO.ReadWrite;
jpayne@68: import shared.Parse;
jpayne@68: import shared.Shared;
jpayne@68: import shared.Tools;
jpayne@68: import structures.IntList;
jpayne@68: 
jpayne@68: /**
jpayne@68:  * @author Brian Bushnell
jpayne@68:  * @date Mar 10, 2015
jpayne@68:  *
jpayne@68:  */
jpayne@68: public class GiToTaxidInt {
jpayne@68: 	
jpayne@68: 	public static void main(String[] args){
jpayne@68: 		ReadWrite.USE_UNPIGZ=true;
jpayne@68: 		ReadWrite.USE_PIGZ=true;
jpayne@68: 		ReadWrite.ZIPLEVEL=9;
jpayne@68: 		ReadWrite.PIGZ_BLOCKSIZE=256;
jpayne@68: //		ReadWrite.PIGZ_ITERATIONS=30;
jpayne@68: 		
jpayne@68: 		for(String arg : args){
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: 			shared.Parser.parseZip(arg, a, b);
jpayne@68: 		}
jpayne@68: //		if(args.length>2 && false){//Run a test
jpayne@68: //			test(args);
jpayne@68: //		}else 
jpayne@68: 		if(args.length>=2){//Write array
jpayne@68: 			initialize(args[0]);
jpayne@68: 			ReadWrite.write(array, args[1], true);
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static void test(String[] args){
jpayne@68: 		System.err.println(getID(1000));
jpayne@68: 		System.err.println(getID(10000));
jpayne@68: 		System.err.println(getID(10001));
jpayne@68: 		System.err.println(getID(10002));
jpayne@68: 		System.err.println(getID(10003));
jpayne@68: 		System.err.println(getID(10004));
jpayne@68: 		System.err.println(getID(10005));
jpayne@68: 		System.err.println(getID(100000));
jpayne@68: 		System.err.println(getID(1000000));
jpayne@68: 		System.err.println(getID(10000000));
jpayne@68: 		
jpayne@68: 		TaxTree tree=null;
jpayne@68: 		if(args.length>1){
jpayne@68: 			tree=TaxTree.loadTaxTree(args[0], System.err, true, true);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		System.err.println("Strings:");
jpayne@68: 		int x;
jpayne@68: 		x=getID("gi|18104025|emb|AJ427095.1| Ceratitis capitata centromeric or pericentromeric satellite DNA, clone 44");
jpayne@68: 		System.err.println(x);
jpayne@68: 		if(tree!=null){
jpayne@68: 			System.err.println(tree.getNode(x));
jpayne@68: 			tree.incrementRaw(x, 30);
jpayne@68: 		}
jpayne@68: 		x=getID("gi|15982920|gb|AY057568.1| Arabidopsis thaliana AT5g43500/MWF20_22 mRNA, complete cds");
jpayne@68: 		System.err.println(x);
jpayne@68: 		if(tree!=null){
jpayne@68: 			System.err.println(tree.getNode(x));
jpayne@68: 			tree.incrementRaw(x, 40);
jpayne@68: 		}
jpayne@68: 		x=getID("gi|481043749|gb|KC494054.1| Plesiochorus cymbiformis isolate ST05-58 internal transcribed spacer 2, partial sequence");
jpayne@68: 		System.err.println(x);
jpayne@68: 		if(tree!=null){
jpayne@68: 			System.err.println(tree.getNode(x));
jpayne@68: 			tree.incrementRaw(x, 20);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		if(tree!=null){
jpayne@68: 			tree.percolateUp();
jpayne@68: 			ArrayList<TaxNode> nodes=tree.gatherNodesAtLeastLimit(35);
jpayne@68: 			for(TaxNode n : nodes){
jpayne@68: 				System.err.println(n);
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static int parseGiToTaxid(String s){return parseGiToTaxid(s, '|');}
jpayne@68: 	public static int parseGiToTaxid(String s, char delimiter){
jpayne@68: 		int x=parseGiNumber(s, delimiter);
jpayne@68: 		assert(x>=0) : s;
jpayne@68: 		assert(array!=null) : "To use gi numbers, you must load a gi table.";
jpayne@68: //		if(x>=array.length || array[x]<0){x=(int)(Math.random()*array.length);} //Test to make sure array is nonempty.
jpayne@68: 		if(x>=0 && x<array.length){return array[x];}
jpayne@68: 		assert(x<array.length) : "The GI number "+x+" is too big.\n"
jpayne@68: 				+ "Please update the gi table with the latest version from NCBI as per the instructions in gitable.sh.\n"
jpayne@68: 				+ "To ignore this problem, please run with the -da flag.\n";
jpayne@68: 		return -1;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 
jpayne@68: 	public static int parseGiToTaxid(byte[] s){return parseGiToTaxid(s, '|');}
jpayne@68: 	public static int parseGiToTaxid(byte[] s, char delimiter){
jpayne@68: 		long x=parseGiNumber(s, delimiter);
jpayne@68: 		if(x>=0 && x<array.length){return array[(int)x];}
jpayne@68: 		if(x<0){return -1;}
jpayne@68: 		assert(false) : x;
jpayne@68: 		return -1;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Parse a gi number, or return -1 if formatted incorrectly. */
jpayne@68: 	static int parseGiNumber(String s, char delimiter){
jpayne@68: 		if(s==null || s.length()<4){return -1;}
jpayne@68: //		System.err.println("a");
jpayne@68: 		if(s.charAt(0)=='>'){return getID(s.substring(1), delimiter);}
jpayne@68: //		System.err.println("b");
jpayne@68: 		if(!s.startsWith("gi")){return -1;}
jpayne@68: //		System.err.println("c");
jpayne@68: //		System.err.println("d");
jpayne@68: 		int initial=s.indexOf(delimiter);
jpayne@68: //		System.err.println("e");
jpayne@68: 		if(initial<0){
jpayne@68: 			if(delimiter!='~'){
jpayne@68: 				delimiter='~';
jpayne@68: 				initial=s.indexOf(delimiter);
jpayne@68: 			}
jpayne@68: 			if(initial<0){
jpayne@68: 				delimiter='_';
jpayne@68: 				initial=s.indexOf(delimiter);
jpayne@68: 			}
jpayne@68: 			if(initial<0){return -1;}
jpayne@68: //			System.err.println("f");
jpayne@68: //			System.err.println("g");
jpayne@68: 		}
jpayne@68: //		System.err.println("h");
jpayne@68: 		if(!Tools.isDigit(s.charAt(initial+1))){return -1;}
jpayne@68: //		System.err.println("i");
jpayne@68: 		
jpayne@68: 		int number=0;
jpayne@68: 		for(int i=initial+1; i<s.length(); i++){
jpayne@68: 			char c=s.charAt(i);
jpayne@68: 			if(c==delimiter){break;}
jpayne@68: 			assert(Tools.isDigit(c));
jpayne@68: 			number=(number*10)+(c-'0');
jpayne@68: 		}
jpayne@68: //		System.err.println("j: "+number);
jpayne@68: 		return number;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Parse a ncbi number, or return -1 if formatted incorrectly. */
jpayne@68: 	public static int parseTaxidNumber(String s, char delimiter){
jpayne@68: 		if(s==null || s.length()<5){return -1;}
jpayne@68: 		if(s.charAt(0)=='>'){return parseTaxidNumber(s.substring(1), delimiter);}
jpayne@68: 		if(!s.startsWith("ncbi") && !s.startsWith("tid")){return -1;}
jpayne@68: 		int initial=s.indexOf(delimiter);
jpayne@68: 		if(initial<0){
jpayne@68: 			delimiter='_';
jpayne@68: 			initial=s.indexOf(delimiter);
jpayne@68: 			if(initial<0){return -1;}
jpayne@68: 		}
jpayne@68: 		if(!Tools.isDigit(s.charAt(initial+1))){return -1;}
jpayne@68: 		
jpayne@68: 		int number=0;
jpayne@68: 		for(int i=initial+1; i<s.length(); i++){
jpayne@68: 			char c=s.charAt(i);
jpayne@68: 			if(c==delimiter || c==' '){break;}
jpayne@68: 			assert(Tools.isDigit(c)) : c+"\n"+s;
jpayne@68: 			number=(number*10)+(c-'0');
jpayne@68: 		}
jpayne@68: 		return number;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 
jpayne@68: 	public static int getID(String s){return getID(s, '|');}
jpayne@68: 	/** Get the taxID from a header starting with a taxID or gi number */
jpayne@68: 	public static int getID(String s, char delimiter){
jpayne@68: 		int x=parseTaxidNumber(s, delimiter);
jpayne@68: 		if(x>=0){return x;}
jpayne@68: 		x=parseGiNumber(s, delimiter);
jpayne@68: 		if(x>=0){return array[x];}
jpayne@68: 		return -1;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Parse a gi number, or return -1 if formatted incorrectly. */
jpayne@68: 	static int parseGiNumber(byte[] s, char delimiter){
jpayne@68: 		if(s==null || s.length<4){return -1;}
jpayne@68: 		if(!Tools.startsWith(s, "gi") && !Tools.startsWith(s, ">gi")){return -1;}
jpayne@68: 		int initial=Tools.indexOf(s, (byte)delimiter);
jpayne@68: 		if(initial<0){
jpayne@68: 			delimiter='_';
jpayne@68: 			initial=Tools.indexOf(s, (byte)delimiter);
jpayne@68: 			if(initial<0){return -1;}
jpayne@68: 		}
jpayne@68: 		if(!Tools.isDigit(s[initial+1])){return -1;}
jpayne@68: 		
jpayne@68: 		long number=0;
jpayne@68: 		for(int i=initial+1; i<s.length; i++){
jpayne@68: 			byte c=s[i];
jpayne@68: 			if(c==delimiter){break;}
jpayne@68: 			assert(Tools.isDigit(c));
jpayne@68: 			number=(number*10)+(c-'0');
jpayne@68: 		}
jpayne@68: 		return (int)number;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Parse a gi number, or return -1 if formatted incorrectly. */
jpayne@68: 	static int parseNcbiNumber(byte[] s, char delimiter){
jpayne@68: 		if(s==null || s.length<3){return -1;}
jpayne@68: 		if(!Tools.startsWith(s, "ncbi") && !Tools.startsWith(s, ">ncbi") && !Tools.startsWith(s, "tid") && !Tools.startsWith(s, ">tid")){return -1;}
jpayne@68: 		int initial=Tools.indexOf(s, (byte)delimiter);
jpayne@68: 		if(initial<0){
jpayne@68: 			delimiter='_';
jpayne@68: 			initial=Tools.indexOf(s, (byte)delimiter);
jpayne@68: 			if(initial<0){return -1;}
jpayne@68: 		}
jpayne@68: 		if(!Tools.isDigit(s[initial+1])){return -1;}
jpayne@68: 		
jpayne@68: 		int number=0;
jpayne@68: 		for(int i=initial+1; i<s.length; i++){
jpayne@68: 			byte c=s[i];
jpayne@68: 			if(c==delimiter){break;}
jpayne@68: 			assert(Tools.isDigit(c));
jpayne@68: 			number=(number*10)+(c-'0');
jpayne@68: 		}
jpayne@68: 		return number;
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	public static int getID(byte[] s){return getID(s, '|');}
jpayne@68: 	/** Get the taxID from a header starting with a taxID or gi number */
jpayne@68: 	public static int getID(byte[] s, char delimiter){
jpayne@68: 		int x=parseGiNumber(s, delimiter);
jpayne@68: 		if(x>=0){return array[x];}
jpayne@68: 		return parseNcbiNumber(s, delimiter);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Get the taxID from a gi number */
jpayne@68: 	public static int getID(long gi){
jpayne@68: 		assert(gi>=0) : gi;
jpayne@68: 		assert(gi<Integer.MAX_VALUE) : gi+" > "+Integer.MAX_VALUE;
jpayne@68: 		assert(gi<array.length) : gi+", "+array.length;
jpayne@68: 		return array[(int)gi];
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static void initialize(String fname){
jpayne@68: 		assert(fname!=null);
jpayne@68: 		if(fileString==null || !fileString.equals(fname)){
jpayne@68: 			synchronized(GiToTaxid.class){
jpayne@68: 				if(!initialized || fileString==null || !fileString.equals(fname)){
jpayne@68: 					fileString=fname;
jpayne@68: 					if(fname.contains(".int1d")){
jpayne@68: 						array=ReadWrite.read(int[].class, fname, true);
jpayne@68: 					}else{
jpayne@68: 						array=makeArray(fname);
jpayne@68: 					}
jpayne@68: 				}
jpayne@68: 				initialized=true;
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static boolean isInitialized(){return initialized;}
jpayne@68: 	
jpayne@68: 	public static synchronized void unload(){
jpayne@68: 		array=null;
jpayne@68: 		fileString=null;
jpayne@68: 		initialized=false;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private static int[] makeArray(String fnames){
jpayne@68: 		String[] split;
jpayne@68: 		if(new File(fnames).exists()){split=new String[] {fnames};}
jpayne@68: 		else if(fnames.indexOf(',')>=0){split=fnames.split(",");}
jpayne@68: 		else if(fnames.indexOf('#')>=0){
jpayne@68: 			assert(fnames.indexOf("/")<0) : "Note: Wildcard # only works for relative paths in present working directory.";
jpayne@68: 			File dir=new File(System.getProperty("user.dir"));
jpayne@68: 			String prefix=fnames.substring(0, fnames.indexOf('#'));
jpayne@68: 			String suffix=fnames.substring(fnames.indexOf('#')+1);
jpayne@68: 			
jpayne@68: 			File[] array=dir.listFiles();
jpayne@68: 			StringBuilder sb=new StringBuilder();
jpayne@68: 			String comma="";
jpayne@68: 			for(File f : array){
jpayne@68: 				String s=f.getName();
jpayne@68: 				if(s.startsWith(prefix) && s.startsWith(suffix)){
jpayne@68: 					sb.append(comma);
jpayne@68: 					sb.append(s);
jpayne@68: 					comma=",";
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 			split=sb.toString().split(",");
jpayne@68: 		}else{
jpayne@68: 			throw new RuntimeException("Invalid file: "+fnames);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		IntList list=new IntList();
jpayne@68: //		assert(max<Integer.MAX_VALUE) : "Overflow.";
jpayne@68: //		int[] x=new int[(int)max+1];
jpayne@68: //		Arrays.fill(x, -1);
jpayne@68: 		
jpayne@68: 		long total=0;
jpayne@68: 		for(String s : split){
jpayne@68: 			long count=addToList(s, list);
jpayne@68: 			total+=count;
jpayne@68: 		}
jpayne@68: 		return list.shrink().array;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private static long addToList(String fname, IntList list){
jpayne@68: 		boolean warned=false;
jpayne@68: 		ByteFile bf=ByteFile.makeByteFile(fname, true);
jpayne@68: 		long count=0, invalid=0;
jpayne@68: 		byte[] line=bf.nextLine();
jpayne@68: 		while(line!=null){
jpayne@68: 			if(line.length>0 && Tools.isDigit(line[line.length-1])){//Invalid lines will end with tab or na
jpayne@68: 				count++;
jpayne@68: 				int tab2=Tools.indexOfNth(line, '\t', 2);
jpayne@68: 				int tab3=Tools.indexOfNth(line, '\t', 1, tab2+1);
jpayne@68: 				assert(tab2>0 && (tab2<tab3) && tab3<line.length) : tab2+", "+tab3+", "+line.length;
jpayne@68: 				assert(tab2<line.length && line[tab2]=='\t') : tab2+", "+tab3+", '"+new String(line)+"'";
jpayne@68: 				assert(tab3<line.length && line[tab3]=='\t') : tab2+", "+tab3+", '"+new String(line)+"'";
jpayne@68: //				assert(false) : tab2+", "+tab3+", '"+new String(line)+"'";
jpayne@68: 				int tid=Parse.parseInt(line, tab2+1, tab3);
jpayne@68: 				int gi=Parse.parseInt(line, tab3+1, line.length);
jpayne@68: 				if(gi>=Shared.MAX_ARRAY_LEN || gi<0){//A gi over 2.5b was observed May 3, 2021.
jpayne@68: 					invalid++;
jpayne@68: 				}else{
jpayne@68: 				assert(gi>=0) : "tid="+tid+", gi="+gi+", line=\n'"+new String(line)+"'";
jpayne@68: 				int old=list.get(gi);
jpayne@68: 				assert(old==0 || old==tid) : "Contradictory entries for gi "+gi+": "+old+" -> "+tid+"\n'"+new String(line)+"'\ntab2="+tab2+", tab3="+tab3;
jpayne@68: 				
jpayne@68: 				list.set(gi, tid);
jpayne@68: 				
jpayne@68: 				//assert(x[gi]==-1 || x[gi]==ncbi) : "Contradictory entries for gi "+gi+": "+x[gi]+" -> "+ncbi;
jpayne@68: //				if(x[gi]!=-1 && x[gi]!=ncbi){
jpayne@68: //					if(!warned){
jpayne@68: //						System.err.println("***WARNING*** For file "+fname+":\n"+
jpayne@68: //								("Contradictory entries for gi "+gi+": mapped to both taxID "+x[gi]+" and taxID "+ncbi)+
jpayne@68: //								"\nThis may be an error from NCBI and you may wish to report it, but it is\n"
jpayne@68: //								+ "being suppressed because NCBI data is known to contain multi-mapped gi numbers,\n"
jpayne@68: //								+ "at least between nucleotide and protein, and gi numbers are deprecated anyway.");
jpayne@68: //						warned=true;
jpayne@68: //					}
jpayne@68: //				}else{
jpayne@68: //					x[gi]=ncbi;
jpayne@68: //				}
jpayne@68: 				}
jpayne@68: 			}else{
jpayne@68: 				if(line.length==0){System.err.println(fname+", "+count);}//debug
jpayne@68: 				invalid++;
jpayne@68: 			}
jpayne@68: 			line=bf.nextLine();
jpayne@68: 		}
jpayne@68: 		if(verbose){System.err.println("Count: "+count+"; \tInvalid: "+invalid);}
jpayne@68: 		bf.close();
jpayne@68: 		return count;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: //	private static int[] makeArrayOld(String fnames){
jpayne@68: //		String[] split;
jpayne@68: //		if(new File(fnames).exists()){split=new String[] {fnames};}
jpayne@68: //		else{split=fnames.split(",");}
jpayne@68: //		
jpayne@68: //		long max=0;
jpayne@68: //		for(String s : split){
jpayne@68: //			max=Tools.max(max, findMaxID(s));
jpayne@68: //		}
jpayne@68: //		
jpayne@68: //		assert(max<Integer.MAX_VALUE) : "Overflow.";
jpayne@68: //		int[] x=new int[(int)max+1];
jpayne@68: //		Arrays.fill(x, -1);
jpayne@68: //		
jpayne@68: //		long total=0;
jpayne@68: //		for(String s : split){
jpayne@68: //			long count=fillArray(s, x);
jpayne@68: //			total+=count;
jpayne@68: //		}
jpayne@68: //		return x;
jpayne@68: //	}
jpayne@68: //	
jpayne@68: //	private static long findMaxID(String fname){
jpayne@68: //		ByteFile bf=ByteFile.makeByteFile(fname, true);
jpayne@68: //		long count=0, max=0;
jpayne@68: //		byte[] line=bf.nextLine();
jpayne@68: //		while(line!=null){
jpayne@68: //			count++;
jpayne@68: //			int tab=Tools.indexOf(line, (byte)'\t');
jpayne@68: //			long gi=Parse.parseLong(line, 0, tab);
jpayne@68: //			max=Tools.max(max, gi);
jpayne@68: //			line=bf.nextLine();
jpayne@68: //		}
jpayne@68: //		bf.close();
jpayne@68: //		return max;
jpayne@68: //	}
jpayne@68: //	
jpayne@68: //	private static long fillArray(String fname, int[] x){
jpayne@68: //		boolean warned=false;
jpayne@68: //		ByteFile bf=ByteFile.makeByteFile(fname, true);
jpayne@68: //		long count=0;
jpayne@68: //		byte[] line=bf.nextLine();
jpayne@68: //		while(line!=null){
jpayne@68: //			count++;
jpayne@68: //			int tab=Tools.indexOf(line, (byte)'\t');
jpayne@68: //			int gi=Parse.parseInt(line, 0, tab);
jpayne@68: //			int ncbi=Parse.parseInt(line, tab+1, line.length);
jpayne@68: //			//assert(x[gi]==-1 || x[gi]==ncbi) : "Contradictory entries for gi "+gi+": "+x[gi]+" -> "+ncbi;
jpayne@68: //			if(x[gi]!=-1 && x[gi]!=ncbi){
jpayne@68: //				if(!warned){
jpayne@68: //					System.err.println("***WARNING*** For file "+fname+":\n"+
jpayne@68: //							("Contradictory entries for gi "+gi+": mapped to both taxID "+x[gi]+" and taxID "+ncbi)+
jpayne@68: //							"\nThis may be an error from NCBI and you may wish to report it, but it is\n"
jpayne@68: //							+ "being suppressed because NCBI data is known to contain multi-mapped gi numbers,\n"
jpayne@68: //							+ "at least between nucleotide and protein, and gi numbers are deprecated anyway.");
jpayne@68: //					warned=true;
jpayne@68: //				}
jpayne@68: //			}else{
jpayne@68: //				x[gi]=ncbi;
jpayne@68: //			}
jpayne@68: //			line=bf.nextLine();
jpayne@68: //		}
jpayne@68: //		if(verbose){System.err.println("Count: "+count);}
jpayne@68: //		bf.close();
jpayne@68: //		return count;
jpayne@68: //	}
jpayne@68: 	
jpayne@68: 	private static int[] array;
jpayne@68: 	private static String fileString;
jpayne@68: 	
jpayne@68: 	public static boolean verbose=false;
jpayne@68: 	private static boolean initialized=false;
jpayne@68: }