X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=shhhseqscommand.cpp;h=63de2bb5541ddbd653b90eced12b4d59a9084629;hb=6c2b1e530a5c0bb87040e58a3e410097acdfcc3d;hp=8ef4c8c24f6d7a6398631591f0e7a2a34d7965c1;hpb=3094cb29c613d9687e861e1d0cf9104b7141d24e;p=mothur.git

diff --git a/shhhseqscommand.cpp b/shhhseqscommand.cpp
index 8ef4c8c..63de2bb 100644
--- a/shhhseqscommand.cpp
+++ b/shhhseqscommand.cpp
@@ -37,7 +37,7 @@ string ShhhSeqsCommand::getHelpString(){
 		string helpString = "";
 		helpString += "The shhh.seqs command reads a fasta and name file and ....\n";
 		helpString += "The shhh.seqs command parameters are fasta, name, group, sigma and processors.\n";
-		helpString += "The fasta parameter allows you to enter the fasta file containing your potentially sequences, and is required, unless you have a valid current fasta file. \n";
+		helpString += "The fasta parameter allows you to enter the fasta file containing your sequences, and is required, unless you have a valid current fasta file. \n";
 		helpString += "The name parameter allows you to provide a name file associated with your fasta file. It is required. \n";
 		helpString += "The group parameter allows you to provide a group file.  When checking sequences, only sequences from the same group as the query sequence will be used as the reference. \n";
 		helpString += "The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n";
@@ -54,6 +54,29 @@ string ShhhSeqsCommand::getHelpString(){
 		exit(1);
 	}
 }
+//**********************************************************************************************************************
+string ShhhSeqsCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "fasta")            {   outputFileName =  "shhh_seqs.fasta";   }
+            else if (type == "name")    {   outputFileName =  "shhh_seqs.names";   }
+            else if (type == "map")        {   outputFileName =  "shhh_seqs.map";   }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ShhhSeqsCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+
 //**********************************************************************************************************************
 
 ShhhSeqsCommand::ShhhSeqsCommand(){	
@@ -160,11 +183,17 @@ ShhhSeqsCommand::ShhhSeqsCommand(string option) {
 			else {   m->setGroupFile(groupfile);  }
 			
 			string temp	= validParameter.validFile(parameters, "sigma", false);		if(temp == "not found"){	temp = "0.01"; }
-			convert(temp, sigma); 
-			
+			m->mothurConvert(temp, sigma); 
+			sigma = 1/sigma;
+            
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors);
+			m->mothurConvert(temp, processors);
+			
+			if (namefile == "") {
+				vector<string> files; files.push_back(fastafile);
+				parser.getNameFile(files);
+			}
 		}
 	}
 	catch(exception& e) {
@@ -179,9 +208,9 @@ int ShhhSeqsCommand::execute() {
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		if (outputDir == "") { outputDir = m->hasPath(fastafile);  }//if user entered a file with a path then preserve it				
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "shhh.fasta";
-		string nameFileName = outputDir + m->getRootName(m->getSimpleName(fastafile))  + "shhh.names";
-		string mapFileName = outputDir + m->getRootName(m->getSimpleName(fastafile))  + "shhh.map";
+		string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta");
+		string nameFileName = outputDir + m->getRootName(m->getSimpleName(fastafile))  + getOutputFileNameTag("name");
+		string mapFileName = outputDir + m->getRootName(m->getSimpleName(fastafile))  + getOutputFileNameTag("map");
 		
 		if (groupfile != "") {
 			//Parse sequences by group
@@ -358,7 +387,7 @@ vector<string> ShhhSeqsCommand::createProcessesGroups(SequenceParser& parser, st
 			lines.push_back(linePair(startIndex, endIndex));
 		}
 		
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)		
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)		
 		
 		//loop through and create all the processes you want
 		while (process != processors) {
@@ -689,14 +718,15 @@ int ShhhSeqsCommand::deconvoluteResults(string fastaFile, string nameFile){
 		string inputString = "fasta=" + fastaFile + ", name=" + nameFile;
 		m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
 		m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine(); 
-		
+		m->mothurCalling = true;
+        
 		Command* uniqueCommand = new DeconvoluteCommand(inputString);
 		uniqueCommand->execute();
 		
 		map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
 		
 		delete uniqueCommand;
-		
+		m->mothurCalling = false;
 		m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
 		
 		string newnameFile = filenames["name"][0];