Merge branch 'master' of https://github.com/haansi/haplocheck

src/main/java/genepi/mitolib/Tools.java

@@ -9,6 +9,7 @@
 import genepi.mitolib.contChecker.HaploChecker2;
 import genepi.mitolib.contChecker.HaploChecker2Hsd;
 import genepi.mitolib.contChecker.HaploChecker3;
+import genepi.mitolib.haplogrep.VariantsToHsd;
 import genepi.mitolib.lofreq.LoFreqReader;
 import genepi.mitolib.splitter.HeteroplasmySplitter;
 import genepi.mitolib.splitter.HeteroplasmySplitterRaw;
@@ -40,6 +41,7 @@ public static void main (String[] args){
 			tools.addTool("haplochecker2",HaploChecker2.class);
 			tools.addTool("haplochecker2hsd",HaploChecker2Hsd.class);
 			tools.addTool("haplochecker3",HaploChecker3.class);
+			tools.addTool("variants2hsd",VariantsToHsd.class);
 			try {
 				tools.start();
 			} catch (InstantiationException e) {

src/main/java/genepi/mitolib/haplogrep/VariantsToHsd.java

@@ -0,0 +1,106 @@
+package genepi.mitolib.haplogrep;
+
+import java.io.IOException;
+import java.util.HashMap;
+
+import genepi.base.Tool;
+import genepi.io.table.reader.CsvTableReader;
+import genepi.io.text.LineWriter;
+
+public class VariantsToHsd extends Tool {
+
+	public VariantsToHsd(String[] args) {
+		super(args);
+	}
+
+	@Override
+	public void init() {
+		System.out.println("Create Haplogrep Input for stable variants");
+	}
+
+	@Override
+	public void createParameters() {
+
+		addParameter("in", "variants.txt");
+		addParameter("out", "output file for HaploGrep");
+	}
+
+	@Override
+	public int run() {
+
+		String in = (String) getValue("in");
+
+		String out = (String) getValue("out");
+
+		CsvTableReader reader = new CsvTableReader(in, '\t');
+
+		HashMap<String, String> profiles = new HashMap<String, String>();
+
+		while (reader.next()) {
+
+			double level = reader.getDouble("Variant-Level");
+
+			// only take stable positions!
+			if (level > 0.5) {
+
+				String id = reader.getString("SampleID");
+
+				int pos = reader.getInteger("Pos");
+
+				String variant = reader.getString("Variant");
+
+				String snp = pos + variant;
+
+				if (profiles.get(id) == null) {
+
+					profiles.put(id, snp);
+
+				} else {
+
+					String value = profiles.get(id);
+
+					profiles.put(id, value + "\t" + snp);
+
+				}
+
+			}
+		}
+
+		LineWriter writer = null;
+		try {
+			writer = new LineWriter(out);
+
+			for (String key : profiles.keySet()) {
+
+				StringBuilder hsdLine = new StringBuilder();
+
+				hsdLine.append(key + "\t" + "1-16569" + "\t" + "?" + "\t");
+
+				hsdLine.append(profiles.get(key));
+
+				writer.write(hsdLine.toString());
+			}
+
+			writer.close();
+
+		} catch (IOException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+
+		System.out.println("Done. Written to "+out);
+
+		return 0;
+
+	}
+
+	public static void main(String[] args) throws IOException {
+
+		// new AroFilter2(args).start();
+		VariantsToHsd test = new VariantsToHsd(
+				new String[] { "--in", "data/haplogrep/variants.txt", "--out", "data/haplogrep/samples.hsd" });
+		test.start();
+
+	}
+
+}