Correcting proble due to new version of cooltools. Now it should work with the most recent cooler and cooltools versions too.

Author: PouletAxel

dependency-reduced-pom.xml

@@ -3,7 +3,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>SIP</groupId>
   <artifactId>SIP</artifactId>
-  <version>1.6.4</version>
+  <version>1.6.5</version>
   <developers>
     <developer>
       <id>axpoulet</id>

pom.xml

@@ -6,7 +6,7 @@
 	<modelVersion>4.0.0</modelVersion>
   <groupId>SIP</groupId>
   <artifactId>SIP</artifactId>
-  <version>1.6.4</version>
+  <version>1.6.5</version>
 
   	<dependencies>
 

src/main/java/plop/test/TestCoolFormat.java

@@ -6,29 +6,33 @@
 import java.util.ArrayList;
 import java.util.HashMap;
 
+import plop.multiProcesing.ProcessCoolerDumpData;
+import plop.process.CoolerDumpData;
 import plop.process.MultiResProcess;
+import plop.utils.CoolerExpected;
 import plop.utils.SIPObject;
 @SuppressWarnings("unused")
 public class TestCoolFormat {
 
 	public static void main(String[] args) throws IOException, InterruptedException {
 		String chr = "chr21";
 		//String input = "/home/plop/Desktop/SIP/testCooler/GM12878_4DNFIXP4QG5B.mcool";
-		String input = "/home/plop/Desktop/CoolTest21";
-		String output = "/home/plop/Desktop/CoolTest21Bis";
-		String expectedFile = "/home/plop/Desktop/chr21Cooler/expected.txt";
-		String fileChr = "/home/plop/Desktop/w_hg19.sizes";
-		String cooler = "/home/plop/anaconda3/bin/cooler";
-		String cooltools = "/home/plop/anaconda3/bin/cooltools";
+		String input = "//home/plop/Desktop/coolTest/MCF7_863.mcool";
+		String output = "/home/plop/Desktop/coolTest/test";
+		String expectedFile = "/home/plop/Desktop/coolTest/test/expected.txt";
+		String fileChr = "/home/plop/Desktop/coolTest/chr22.txt";
+		String cooler = "/home/plop/anaconda3/envs/cooler/bin/cooler";
+		String cooltools = "/home/plop/anaconda3/envs/cooler/bin/cooltools";
 		HashMap<String,Integer> chrsize = readChrSizeFile(fileChr);
-		int resolution = 5000;
+		int resolution = 40000;
 		int matrixSize = 2000;
-		//CoolerExpected expected = new CoolerExpected(input,  resolution, matrixSize);
+		int cpu = 5;
+		//CoolerExpected expected = new CoolerExpected(cooltools, input,  resolution, matrixSize,cpu);
 		//expected.dumpExpected(expectedFile);
 		//CoolerExpected expected = new CoolerExpected(expectedFile, matrixSize);
 		//expected.parseExpectedFile();
 		//ArrayList<Double> plop = expected.getExpected(chr);
-		//CoolerDumpData cooler = new CoolerDumpData(input, resolution, plop);
+		//CoolerDumpData coolerD = new CoolerDumpData(cooler,input);
 		//run(resolution,matrixSize,matrixSize/2,chr,output, cooler, 46709983);
 
 		int diagSize = 5;
@@ -40,20 +44,21 @@ public static void main(String[] args) throws IOException, InterruptedException
 		double saturatedPixel = 0.01;
 		ArrayList<Integer> factor = new ArrayList<Integer>();
 		factor.add(1);
-		factor.add(2);
-		factor.add(5);
-		boolean keepTif = false;
-		int cpu = 1;
+		//factor.add(2);
+		//factor.add(5);
+		boolean keepTif = true;
+
 
-		SIPObject sip = new SIPObject(input,output, chrsize, gauss, min, max, resolution, saturatedPixel, thresholdMax, diagSize, matrixSize, nbZero,factor,0.03,keepTif,false);
+		SIPObject sip = new SIPObject(input,output, chrsize, gauss, min, max, resolution, saturatedPixel, thresholdMax,
+				diagSize, matrixSize, nbZero,factor,0.03,keepTif,false);
 		sip.setIsGui(false);
 		sip.setIsCooler(true);
-		sip.setIsProcessed(true);
+		sip.setIsProcessed(false);
 
 
-		//ProcessCoolerDumpData processDumpData = new ProcessCoolerDumpData();
-	//	 go(String coolTools, String cooler, SIPObject sip, String coolFile, HashMap<String,Integer> chrSize,int nbCPU)
-		//processDumpData.go(cooltools, cooler, sip, input, chrsize,2);
+		ProcessCoolerDumpData processDumpData = new ProcessCoolerDumpData();
+		//go(String coolTools, String cooler, SIPObject sip, String coolFile, HashMap<String,Integer> chrSize,int nbCPU)
+		processDumpData.go(cooltools, cooler, sip, input, chrsize,2);
 		MultiResProcess multi = new MultiResProcess(sip, cpu, keepTif,fileChr);
 		multi.run();
 

src/main/java/plop/utils/CoolerExpected.java

@@ -69,6 +69,23 @@ public boolean dumpExpected(String expected){
 				new ReturnFlux(process.getErrorStream()).start();
 				exitValue=process.waitFor();
 
+				if(_logError.contains("Error")){
+					System.out.println(_logError);
+					System.out.println("cooltools error !!!!");
+					System.exit(0);
+				}
+			}else if(_logError.contains("Error") && _logError.contains("No such command")){
+				runtime = Runtime.getRuntime();
+				_logError ="";
+				System.out.println(_logError);
+				cmd = this._coolTools+" expected-cis "+_coolFile+" -p "+_cpu+" --ignore-diags 0 -o "+expected;
+				System.out.println(cmd);
+				process = runtime.exec(cmd);
+
+				new ReturnFlux(process.getInputStream()).start();
+				new ReturnFlux(process.getErrorStream()).start();
+				exitValue=process.waitFor();
+
 				if(_logError.contains("Error")){
 					System.out.println(_logError);
 					System.out.println("cooltools error !!!!");
@@ -91,7 +108,10 @@ public void parseExpectedFile() throws IOException {
 		String line = br.readLine();
 		for (line = null; (line = br.readLine()) != null;){
 			String [] tline = line.split("\t");
-			if(Integer.parseInt(tline[1]) < this._imgSize) {
+			int a = Integer.parseInt(tline[2]);
+			if(!tline[1].equals(tline[0]))
+				a = Integer.parseInt(tline[2]);
+			if(a < this._imgSize) {
 				if(!tline[tline.length-1].equals("nan")){
 					if (_hashExpected.containsKey(tline[0])){
 						ArrayList<Double> lExpected =  _hashExpected.get(tline[0]);