Split data from CNVserver

src/main/java/genepi/mitolib/splitter/Pileup2Haplogrep.java

@@ -0,0 +1,228 @@
+package genepi.mitolib.splitter;
+
+import java.io.FileWriter;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.TreeMap;
+
+import javax.swing.plaf.synth.SynthSplitPaneUI;
+
+import genepi.base.Tool;
+import genepi.io.table.TableReaderFactory;
+import genepi.io.table.reader.ITableReader;
+import genepi.mitolib.objects.CheckEntry;
+import genepi.mitolib.objects.HSDEntry;
+import genepi.mitolib.objects.HeaderNames;
+
+
+public class Pileup2Haplogrep  extends Tool {
+
+	public Pileup2Haplogrep(String[] args) {
+		super(args);
+	}
+	@Override
+	public void init() {
+
+		System.out
+				.println("Split mitochondrial raw file from CNVServer into profiles for HaploGrep 2\n\n");
+
+	}
+
+	@Override
+	public void createParameters() {
+
+		addParameter("in", 	"input raw file (pileup) from CNVServer");
+		addParameter("vaf", "variant allele frequence ");
+		addParameter("out", "output file for HaploGrep 2");
+	}
+
+
+	@Override
+	public int run() {
+
+		String in = (String) getValue("in");
+		String out = (String) getValue("out");
+		double vaf = 0.01;
+
+		try {
+			return build(in, out, vaf);
+		} catch (MalformedURLException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+			return -1;
+		} catch (IOException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+			return -1;
+		}
+	}
+
+	public int build(String variantfile, String outfile, double vaf) throws MalformedURLException, IOException {
+		try {
+
+			//	input = directoryListing[0].getAbsolutePath();
+
+				ITableReader idReader = TableReaderFactory.getReader(variantfile);
+				HashMap<String, ArrayList<CheckEntry>> hm = new HashMap<String, ArrayList<CheckEntry>>();
+
+		try {
+			while (idReader.next()) {
+				CheckEntry entry = new CheckEntry();
+				String id =  idReader.getString("SAMPLE"); //SampleID
+				entry.setID(id);
+
+				entry.setPOS(idReader.getInteger("POS"));  //Pos
+				entry.setREF(idReader.getString("REF"));	//Ref
+
+				int covFWD= idReader.getInteger("COV-FWD");
+				int covREV= idReader.getInteger("COV-REV");
+				entry.setCOV(covREV+covFWD);
+
+				String topFwd=idReader.getString("TOP-FWD");
+				String topRev=idReader.getString("TOP-REV");
+
+				String minFwd=idReader.getString("MINOR-FWD");
+				String minRev=idReader.getString("MINOR-REV");
+
+				int A= (int) (idReader.getDouble("%A")*covFWD) +  (int)(idReader.getDouble("%a")*covREV);
+				int C= (int) (idReader.getDouble("%C")*covFWD) +  (int)(idReader.getDouble("%c")*covREV);
+				int G= (int) (idReader.getDouble("%G")*covFWD) +  (int)(idReader.getDouble("%g")*covREV);
+				int T= (int) (idReader.getDouble("%T")*covFWD) +  (int)(idReader.getDouble("%t")*covREV);
+
+				TreeMap<Integer, String> map = new TreeMap<Integer, String>(Collections.reverseOrder());
+
+				map.put(A, "A");
+				map.put(C, "C");
+				map.put(G, "G");
+				map.put(T, "T");
+
+				String firstBase = (String) map.values().toArray()[0]; 
+				double firstBasePerc=  Double.valueOf((map.keySet().toArray()[0])+"") / (covFWD+covREV); 
+
+				String secondBase = (String) map.values().toArray()[1]; 
+				int secondBaseCount= Integer.valueOf(map.keySet().toArray()[1]+"");
+				double secondBasePerc= Double.valueOf( map.keySet().toArray()[1] +"") / (covFWD+covREV); 
+
+					boolean isVariant = false;
+					if (topFwd.equals(entry.getREF())) 
+					{
+						if (/*(minFwd.equals(minRev) && !(minRev.equals("-"))) &&*/ (secondBasePerc >= vaf) && secondBaseCount>1) {
+							entry.setALT(secondBase);
+							entry.setVAF(secondBasePerc);
+							isVariant = true;
+						}
+
+					} else if (topFwd.equals(topRev)) {
+						entry.setALT(firstBase);
+						entry.setVAF(firstBasePerc);
+						isVariant = true;
+					}
+
+			if (isVariant){
+				if (hm.containsKey(id)) {
+					hm.get(id).add(entry);
+				} else if (hm.get(id) == null) {
+					hm.put(id, new ArrayList<CheckEntry>());
+					hm.get(id).add(entry);
+				}
+			}
+			}
+			idReader.close();
+		} catch (Exception e) {
+			e.printStackTrace();
+		}	
+
+
+			int counter = generateHSDfile(hm, outfile, vaf);	
+
+			System.out.println(counter +" samples processed\n" +counter*2 +" profiles written");
+
+
+			} catch (Exception e) {
+				System.out.println("ERROR");
+				e.printStackTrace();
+				return -1;
+			}
+			return 0;
+		}
+
+
+
+
+
+	public static int generateHSDfile(HashMap<String, ArrayList<CheckEntry>> hm, String outfile, double vaf) throws Exception{
+		FileWriter fw, fwVariant;
+		System.out.println("outfile " + outfile);
+		fw = new FileWriter(outfile);
+		fwVariant = new FileWriter(outfile+".txt");
+
+		fw.write("SampleID\tRange\tHaplogroup\tPolymorphisms");
+		fw.write(System.lineSeparator());
+
+		fwVariant.write("SampleID\tPos\tRef\tVariant\tVariant-Level\tCoverage-Total");
+		fwVariant.write(System.lineSeparator());
+
+		int counter =0;
+		Iterator it = hm.entrySet().iterator();
+		while (it.hasNext()) {
+			counter++;
+			Map.Entry pair = (Map.Entry) it.next();
+			HSDEntry minor = new HSDEntry();
+			HSDEntry major = new HSDEntry();
+			minor.setID(pair.getKey() + "_maj");
+			minor.setRANGE("1-16569");
+			major.setID(pair.getKey() + "_min");
+			major.setRANGE("1-16569");
+			int hetcounter=0;
+			ArrayList<CheckEntry> helpArray = hm.get(pair.getKey());
+			for (int i = 0; i < helpArray.size(); i++) {
+
+
+				if (helpArray.get(i).getREF().contains("-") || helpArray.get(i).getALT().contains("-")
+						|| helpArray.get(i).getREF().equals("N") || helpArray.get(i).getALT().length() > 1
+						|| helpArray.get(i).getREF().length() > 1) {
+					// skip indel, and 3107 on rCRS;
+				} else {
+					if (helpArray.get(i).getVAF() < 0.5) {
+						fwVariant.write(pair.getKey() + "\t" + helpArray.get(i).getPOS() + "\t" + helpArray.get(i).getREF() +  "\t" + helpArray.get(i).getALT() +  "\t" + helpArray.get(i).getVAF() +  "\t" + helpArray.get(i).getCOV() );
+						fwVariant.write(System.lineSeparator());
+
+						minor.appendPROFILES(helpArray.get(i).getPOS() + helpArray.get(i).getREF());
+						major.appendPROFILES(helpArray.get(i).getPOS() + helpArray.get(i).getALT());
+						hetcounter++;
+					} else if (helpArray.get(i).getVAF() >= 0.5 && helpArray.get(i).getVAF() < 1-vaf){
+						fwVariant.write(pair.getKey() + "\t" + helpArray.get(i).getPOS() + "\t" + helpArray.get(i).getREF() +  "\t" + helpArray.get(i).getALT() +  "\t" + helpArray.get(i).getVAF() +  "\t" + helpArray.get(i).getCOV());
+						fwVariant.write(System.lineSeparator());
+
+						minor.appendPROFILES(helpArray.get(i).getPOS() + helpArray.get(i).getALT());
+						major.appendPROFILES(helpArray.get(i).getPOS() + helpArray.get(i).getREF());
+						hetcounter++;
+					}
+					else{
+						fwVariant.write(pair.getKey() + "\t" + helpArray.get(i).getPOS() + "\t" + helpArray.get(i).getREF() +  "\t" + helpArray.get(i).getALT() +  "\t"+ helpArray.get(i).getVAF() +  "\t" + helpArray.get(i).getCOV());
+						fwVariant.write(System.lineSeparator());
+						minor.appendPROFILES(helpArray.get(i).getPOS() + helpArray.get(i).getALT());
+						major.appendPROFILES(helpArray.get(i).getPOS() + helpArray.get(i).getALT());
+					}
+
+				}
+			}
+			if (hetcounter>0){
+			fw.write(minor.getString());
+			fw.write(System.lineSeparator());
+			fw.write(major.getString());
+			fw.write(System.lineSeparator());
+			}
+			it.remove(); // avoids a ConcurrentModificationException
+		}
+		fw.close();
+		fwVariant.close();
+	return counter;
+	}
+
+}