X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=seqsummarycommand.cpp;h=27bb8d95190fb66ea03510cf266d2d53824d988c;hp=a9bb5737eac832a203969460f7f4e2759849a975;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=ea4f373c28543cd1002b0dd7dc6e55c526647d59

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index a9bb573..27bb8d9 100644
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -13,12 +13,12 @@
 //**********************************************************************************************************************
 vector<string> SeqSummaryCommand::setParameters(){	
 	try {
-		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
-		CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pname);
-        CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pcount);
-		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pfasta);
+		CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pname);
+        CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pcount);
+		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
 		
 		vector<string> myArray;
 		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
@@ -48,24 +48,19 @@ string SeqSummaryCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
-string SeqSummaryCommand::getOutputFileNameTag(string type, string inputName=""){	
-	try {
-        string outputFileName = "";
-		map<string, vector<string> >::iterator it;
+string SeqSummaryCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
         
-        //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 == "summary")            {   outputFileName =  "summary";   }
-            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, "SeqSummaryCommand", "getOutputFileNameTag");
-		exit(1);
-	}
+        if (type == "summary") {  pattern = "[filename],summary"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "SeqSummaryCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 
 //**********************************************************************************************************************
@@ -193,7 +188,9 @@ int SeqSummaryCommand::execute(){
 		//set current fasta to fastafile
 		m->setFastaFile(fastafile);
 		
-		string summaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("summary");
+        map<string, string> variables; 
+		variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+		string summaryFile = getOutputFileName("summary",variables);
 				
 		int numSeqs = 0;
 		
@@ -206,7 +203,7 @@ int SeqSummaryCommand::execute(){
 		if (namefile != "") { nameMap = m->readNames(namefile); }
         else if (countfile != "") {
             CountTable ct;
-            ct.readTable(countfile);
+            ct.readTable(countfile, false);
             nameMap = ct.getNameMap();
         }
 		
@@ -410,7 +407,7 @@ int SeqSummaryCommand::execute(){
 		if (m->control_pressed) {  m->mothurRemove(summaryFile); return 0; }
 		
 		m->mothurOutEndLine();
-		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		m->mothurOut(summaryFile); m->mothurOutEndLine();	outputNames.push_back(summaryFile); outputTypes["summary"].push_back(summaryFile);
 		m->mothurOutEndLine();
 		
@@ -418,6 +415,13 @@ int SeqSummaryCommand::execute(){
 			}
 		#endif
 
+        //set fasta file as new current fastafile
+		string current = "";
+		itTypes = outputTypes.find("summary");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSummaryFile(current); }
+		}
+        
 		return 0;
 	}
 	catch(exception& e) {
@@ -448,11 +452,15 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
 		while (!done) {
 				
 			if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
-					
+            
+            if (m->debug) { m->mothurOut("[DEBUG]: count = " + toString(count) + "\n");  }
+            
 			Sequence current(in); m->gobble(in);
-	
+           
 			if (current.getName() != "") {
 				
+                if (m->debug) { m->mothurOut("[DEBUG]: " + current.getName() + '\t' + toString(current.getNumBases()) + "\n");  }
+                
 				int num = 1;
 				if ((namefile != "") || (countfile != "")) {
 					//make sure this sequence is in the namefile, else error 
@@ -476,6 +484,8 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
 				outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
 				outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
 				outSummary << current.getLongHomoPolymer() << '\t' << num << endl;
+                
+                if (m->debug) { m->mothurOut("[DEBUG]: " + current.getName() + '\t' + toString(current.getNumBases()) + "\n");  }
 			}
 			
 			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
@@ -484,13 +494,8 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
 			#else
 				if (in.eof()) { break; }
 			#endif
-			
-			//report progress
-			//if((count) % 100 == 0){	m->mothurOut(toString(count)); m->mothurOutEndLine();		}
 		}
-		//report progress
-		//if((count) % 100 != 0){	m->mothurOut(toString(count)); m->mothurOutEndLine();		}
-		
+				
 		in.close();
 		
 		return count;
@@ -678,6 +683,9 @@ int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition,
 		//Close all thread handles and free memory allocations.
 		for(int i=0; i < pDataArray.size(); i++){
 			num += pDataArray[i]->count;
+            if (pDataArray[i]->count != pDataArray[i]->end) {
+                m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true; 
+            }
             for (int k = 0; k < pDataArray[i]->startPosition.size(); k++) {	startPosition.push_back(pDataArray[i]->startPosition[k]);       }
 			for (int k = 0; k < pDataArray[i]->endPosition.size(); k++) {	endPosition.push_back(pDataArray[i]->endPosition[k]);       }
             for (int k = 0; k < pDataArray[i]->seqLength.size(); k++) {	seqLength.push_back(pDataArray[i]->seqLength[k]);       }