augustus sanity check

steineggerlab · Oct 19, 2022 · a86fed8 · a86fed8
1 parent 9ebb6fa
commit a86fed8
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Showing 5 changed files with 37 additions and 1 deletion.
diff --git a/src/envs/toolkit/ExecHandler.java b/src/envs/toolkit/ExecHandler.java
@@ -25,7 +25,7 @@ protected void addArg(String val) {
 		argMap.put(val, "");
 	}
 
-	private String buildCmd() {
+	protected String buildCmd() {
 		String cmd = job;
 		for(String arg : args) {
 			cmd += " " + arg + argMap.get(arg);

diff --git a/src/module/ProfileModule.java b/src/module/ProfileModule.java
@@ -853,6 +853,7 @@ public static void run(String[] args) {
 				if(!GenericConfig.FORCE) {
 					if(query.checkResultFileExistence() > 0) {
 						Prompt.print("Result file already exists. To overwrite, use --force option.");
+						query.deactivate();
 						continue;
 					}
 				}

diff --git a/src/pipeline/ExceptionHandler.java b/src/pipeline/ExceptionHandler.java
@@ -9,6 +9,7 @@ public class ExceptionHandler {
 	public static final int EXCEPTION				= 0xF0;
 	public static final int UNEXPECTED_ERROR		= 0xF1;
 	public static final int ERROR_WITH_MESSAGE		= 0xF2;
+	public static final int FAILED_COMMAND			= 0xF3;
 
 	public static final int UNKNOWN_MODULE			= 0x00;
 	public static final int UNKNOWN_OPTION			= 0x01;
@@ -66,6 +67,8 @@ public static void handle(int exception) {
 			System.out.println("Program terminated by an unexpected error."); break;
 		case ERROR_WITH_MESSAGE:
 			System.out.println(OBJ.toString()); break;
+		case FAILED_COMMAND:
+			System.out.println("Failed subcommand : " + ANSIHandler.wrapper(OBJ.toString(), 'B')); break;
 		case UNKNOWN_OPTION:
 			System.out.println("Unrecognized option given : " + OBJ.toString()); break;
 		case MISSING_ARGUMENT:

diff --git a/src/wrapper/AugustusWrapper.java b/src/wrapper/AugustusWrapper.java
@@ -3,6 +3,7 @@
 import envs.config.PathConfig;
 import envs.toolkit.ExecHandler;
 import envs.toolkit.Shell;
+import pipeline.ExceptionHandler;
 
 public class AugustusWrapper extends ExecHandler {
 	public AugustusWrapper() {
@@ -28,6 +29,15 @@ void setOutPath(String outPath) {
 		addArg(">", outPath);
 	}
 
+	private boolean sanityCheck(String outPath) {
+		String cmd = "head -1 " + outPath;
+		String[] raw = Shell.exec(cmd);
+
+		if(raw.length < 1) return false;
+		if(raw[0].contains("gff")) return true;
+		return false;
+	}
+
 	public static void runAugustus(String ctgPath, int pst, int ped, String prfl, String outPath) {
 		AugustusWrapper aug = new AugustusWrapper();
 		aug.setCfg();
@@ -37,6 +47,12 @@ public static void runAugustus(String ctgPath, int pst, int ped, String prfl, St
 		aug.setCtgPath(ctgPath);
 		aug.setOutPath(outPath);
 		aug.exec();
+
+		// augustus failure
+		if(!aug.sanityCheck(outPath)) {
+			ExceptionHandler.pass(aug.buildCmd());
+			ExceptionHandler.handle(ExceptionHandler.FAILED_COMMAND);
+		}
 	}
 
 	// solve dependency

diff --git a/src/wrapper/FastBlockSearchWrapper.java b/src/wrapper/FastBlockSearchWrapper.java
@@ -4,6 +4,7 @@
 import envs.config.PathConfig;
 import envs.toolkit.ExecHandler;
 import envs.toolkit.Shell;
+import pipeline.ExceptionHandler;
 import envs.toolkit.Prompt;
 
 public class FastBlockSearchWrapper extends ExecHandler {
@@ -25,13 +26,28 @@ void setOutPath(String outPath) {
 		addArg("2>", "/dev/null");
 	}
 
+	private boolean sanityCheck(String outPath) {
+		String cmd = "head -1 " + outPath;
+		String[] raw = Shell.exec(cmd);
+
+		if(raw.length < 1) return false;
+		if(raw[0].contains("Hits")) return true;
+		return false;
+	}
+
 	public static void runFastBlockSearch(String seqPath, String famPath, String outPath) {
 		FastBlockSearchWrapper fbs = new FastBlockSearchWrapper();
 		fbs.setCutoff();
 		fbs.setSeqPath(seqPath);
 		fbs.setFamPath(famPath);
 		fbs.setOutPath(outPath);
 		fbs.exec();
+
+		// fastBlockSearch failure
+		if(!fbs.sanityCheck(outPath)) {
+			ExceptionHandler.pass(fbs.buildCmd());
+			ExceptionHandler.handle(ExceptionHandler.FAILED_COMMAND);
+		}
 	}
 
 	// solve dependency