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added load.logfile command. changed summary.single output for subsample=t.
[mothur.git] / seqerrorcommand.cpp
diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 0dc15f59ee98d0ee2d93659c4c3ad1f033f8a193..8fd6368154773bcc38e2b950d7b170c88be2186e 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -63,20 +63,52 @@ string SeqErrorCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string SeqErrorCommand::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 == "errorsummary")            {   outputFileName =  "error.summary";   }
+            else if (type == "errorseq")            {   outputFileName =  "error.seq";   }
+            else if (type == "errorquality")            {   outputFileName =  "error.quality";   }
+            else if (type == "errorqualforward")            {   outputFileName =  "error.qual.forward";   }
+            else if (type == "errorqualreverse")            {   outputFileName =  "error.qual.reverse";   }
+            else if (type == "errorforward")            {   outputFileName =  "error.seq.forward";   }
+            else if (type == "errorreverse")            {   outputFileName =  "error.seq.reverse";   }
+            else if (type == "errorcount")            {   outputFileName =  "error.count";   }
+            else if (type == "errormatrix")            {   outputFileName =  "error.matrix";   }
+            else if (type == "errorchimera")            {   outputFileName =  "error.chimera";   }
+            else if (type == "errorref-query")            {   outputFileName =  "error.ref-query";   }
+            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, "SeqErrorCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 SeqErrorCommand::SeqErrorCommand(){    
        try {
                abort = true; calledHelp = true; 
                setParameters();
                vector<string> tempOutNames;
-               outputTypes["error.summary"] = tempOutNames;
-               outputTypes["error.seq"] = tempOutNames;
-               outputTypes["error.quality"] = tempOutNames;
-               outputTypes["error.qual.forward"] = tempOutNames;
-               outputTypes["error.qual.reverse"] = tempOutNames;
-               outputTypes["error.forward"] = tempOutNames;
-               outputTypes["error.reverse"] = tempOutNames;
-               outputTypes["error.count"] = tempOutNames;
-               outputTypes["error.matrix"] = tempOutNames;
+               outputTypes["errorsummary"] = tempOutNames;
+               outputTypes["errorseq"] = tempOutNames;
+               outputTypes["errorquality"] = tempOutNames;
+               outputTypes["errorqualforward"] = tempOutNames;
+               outputTypes["errorqualreverse"] = tempOutNames;
+               outputTypes["errorforward"] = tempOutNames;
+               outputTypes["errorreverse"] = tempOutNames;
+               outputTypes["errorcount"] = tempOutNames;
+               outputTypes["errormatrix"] = tempOutNames;
+        outputTypes["errorchimera"] = tempOutNames;
+        outputTypes["errorref-query"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "SeqErrorCommand", "SeqErrorCommand");
@@ -112,15 +144,17 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                        
                        //initialize outputTypes
                        vector<string> tempOutNames;
-                       outputTypes["error.summary"] = tempOutNames;
-                       outputTypes["error.seq"] = tempOutNames;
-                       outputTypes["error.quality"] = tempOutNames;
-                       outputTypes["error.qual.forward"] = tempOutNames;
-                       outputTypes["error.qual.reverse"] = tempOutNames;
-                       outputTypes["error.forward"] = tempOutNames;
-                       outputTypes["error.reverse"] = tempOutNames;
-                       outputTypes["error.count"] = tempOutNames;
-                       outputTypes["error.matrix"] = tempOutNames;
+                       outputTypes["errorsummary"] = tempOutNames;
+                       outputTypes["errorseq"] = tempOutNames;
+                       outputTypes["errorquality"] = tempOutNames;
+                       outputTypes["errorqualforward"] = tempOutNames;
+                       outputTypes["errorqualreverse"] = tempOutNames;
+                       outputTypes["errorforward"] = tempOutNames;
+                       outputTypes["errorreverse"] = tempOutNames;
+                       outputTypes["errorcount"] = tempOutNames;
+                       outputTypes["errormatrix"] = tempOutNames;
+            outputTypes["errorchimera"] = tempOutNames;
+            outputTypes["errorref-query"] = tempOutNames;
 
                        
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
@@ -269,14 +303,15 @@ int SeqErrorCommand::execute(){
                totalBases = 0;
                totalMatches = 0;
                
-               string errorSummaryFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.summary";
-               outputNames.push_back(errorSummaryFileName); outputTypes["error.summary"].push_back(errorSummaryFileName);
+        string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(queryFileName));
+               string errorSummaryFileName = fileNameRoot + getOutputFileNameTag("errorsummary");
+               outputNames.push_back(errorSummaryFileName); outputTypes["errorsummary"].push_back(errorSummaryFileName);
                        
-               string errorSeqFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.seq";
-               outputNames.push_back(errorSeqFileName); outputTypes["error.seq"].push_back(errorSeqFileName);
+               string errorSeqFileName = fileNameRoot + getOutputFileNameTag("errorseq");
+               outputNames.push_back(errorSeqFileName); outputTypes["errorseq"].push_back(errorSeqFileName);
                
-               string errorChimeraFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.chimera";
-               outputNames.push_back(errorChimeraFileName); outputTypes["error.chimera"].push_back(errorChimeraFileName);
+               string errorChimeraFileName = fileNameRoot + getOutputFileNameTag("errorchimera");
+               outputNames.push_back(errorChimeraFileName); outputTypes["errorchimera"].push_back(errorChimeraFileName);
                
                getReferences();        //read in reference sequences - make sure there's no ambiguous bases
 
@@ -317,10 +352,10 @@ int SeqErrorCommand::execute(){
                
                if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
 
-               string errorCountFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.count";
+               string errorCountFileName = fileNameRoot + getOutputFileNameTag("errorcount");
                ofstream errorCountFile;
                m->openOutputFile(errorCountFileName, errorCountFile);
-               outputNames.push_back(errorCountFileName);  outputTypes["error.count"].push_back(errorCountFileName);
+               outputNames.push_back(errorCountFileName);  outputTypes["errorcount"].push_back(errorCountFileName);
                m->mothurOut("Overall error rate:\t" + toString((double)(totalBases - totalMatches) / (double)totalBases) + "\n");
                m->mothurOut("Errors\tSequences\n");
                errorCountFile << "Errors\tSequences\n";                
@@ -334,10 +369,10 @@ int SeqErrorCommand::execute(){
 
                printSubMatrix();
                                
-               string megAlignmentFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.ref-query";
+               string megAlignmentFileName = fileNameRoot + getOutputFileNameTag("errorref-query");
                ofstream megAlignmentFile;
                m->openOutputFile(megAlignmentFileName, megAlignmentFile);
-               outputNames.push_back(megAlignmentFileName);  outputTypes["error.ref-query"].push_back(megAlignmentFileName);
+               outputNames.push_back(megAlignmentFileName);  outputTypes["errorref-query"].push_back(megAlignmentFileName);
                
                for(int i=0;i<numRefs;i++){
                        megAlignmentFile << referenceSeqs[i].getInlineSeq() << endl;
@@ -1046,10 +1081,11 @@ void SeqErrorCommand::printErrorData(Compare error, int numParentSeqs, ofstream&
 
 void SeqErrorCommand::printSubMatrix(){
        try {
-               string subMatrixFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.matrix";
+        string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(queryFileName));
+               string subMatrixFileName = fileNameRoot + getOutputFileNameTag("errormatrix");
                ofstream subMatrixFile;
                m->openOutputFile(subMatrixFileName, subMatrixFile);
-               outputNames.push_back(subMatrixFileName);  outputTypes["error.matrix"].push_back(subMatrixFileName);
+               outputNames.push_back(subMatrixFileName);  outputTypes["errormatrix"].push_back(subMatrixFileName);
                vector<string> bases(6);
                bases[0] = "A";
                bases[1] = "T";
@@ -1092,10 +1128,11 @@ void SeqErrorCommand::printSubMatrix(){
 
 void SeqErrorCommand::printErrorFRFile(map<char, vector<int> > errorForward, map<char, vector<int> > errorReverse){
        try{
-               string errorForwardFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.seq.forward";
+        string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(queryFileName));
+               string errorForwardFileName = fileNameRoot + getOutputFileNameTag("errorforward");
                ofstream errorForwardFile;
                m->openOutputFile(errorForwardFileName, errorForwardFile);
-               outputNames.push_back(errorForwardFileName);  outputTypes["error.forward"].push_back(errorForwardFileName);
+               outputNames.push_back(errorForwardFileName);  outputTypes["errorforward"].push_back(errorForwardFileName);
 
                errorForwardFile << "position\ttotalseqs\tmatch\tsubstitution\tinsertion\tdeletion\tambiguous" << endl;
                for(int i=0;i<maxLength;i++){
@@ -1110,10 +1147,10 @@ void SeqErrorCommand::printErrorFRFile(map<char, vector<int> > errorForward, map
                }
                errorForwardFile.close();
 
-               string errorReverseFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.seq.reverse";
+               string errorReverseFileName = fileNameRoot + getOutputFileNameTag("errorreverse");
                ofstream errorReverseFile;
                m->openOutputFile(errorReverseFileName, errorReverseFile);
-               outputNames.push_back(errorReverseFileName);  outputTypes["error.reverse"].push_back(errorReverseFileName);
+               outputNames.push_back(errorReverseFileName);  outputTypes["errorreverse"].push_back(errorReverseFileName);
 
                errorReverseFile << "position\ttotalseqs\tmatch\tsubstitution\tinsertion\tdeletion\tambiguous" << endl;
                for(int i=0;i<maxLength;i++){
@@ -1138,11 +1175,11 @@ void SeqErrorCommand::printErrorFRFile(map<char, vector<int> > errorForward, map
 
 void SeqErrorCommand::printErrorQuality(map<char, vector<int> > qScoreErrorMap){
        try{
-
-               string errorQualityFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.quality";
+        string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(queryFileName));
+               string errorQualityFileName = fileNameRoot + getOutputFileNameTag("errorquality");
                ofstream errorQualityFile;
                m->openOutputFile(errorQualityFileName, errorQualityFile);
-               outputNames.push_back(errorQualityFileName);  outputTypes["error.quality"].push_back(errorQualityFileName);
+               outputNames.push_back(errorQualityFileName);  outputTypes["errorquality"].push_back(errorQualityFileName);
 
                errorQualityFile << "qscore\tmatches\tsubstitutions\tinsertions\tambiguous" << endl;
                for(int i=0;i<41;i++){
@@ -1172,11 +1209,11 @@ void SeqErrorCommand::printQualityFR(vector<vector<int> > qualForwardMap, vector
                                }
                        }
                }
-
-               string qualityForwardFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.qual.forward";
+        string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(queryFileName));
+               string qualityForwardFileName = fileNameRoot + getOutputFileNameTag("errorqualforward");
                ofstream qualityForwardFile;
                m->openOutputFile(qualityForwardFileName, qualityForwardFile);
-               outputNames.push_back(qualityForwardFileName);  outputTypes["error.qual.forward"].push_back(qualityForwardFileName);
+               outputNames.push_back(qualityForwardFileName);  outputTypes["errorqualforward"].push_back(qualityForwardFileName);
 
                for(int i=0;i<numColumns;i++){  qualityForwardFile << '\t' << i;        }       qualityForwardFile << endl;
 
@@ -1191,10 +1228,10 @@ void SeqErrorCommand::printQualityFR(vector<vector<int> > qualForwardMap, vector
                qualityForwardFile.close();
 
                
-               string qualityReverseFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.qual.reverse";
+               string qualityReverseFileName = fileNameRoot + getOutputFileNameTag("errorqualreverse");
                ofstream qualityReverseFile;
                m->openOutputFile(qualityReverseFileName, qualityReverseFile);
-               outputNames.push_back(qualityReverseFileName);  outputTypes["error.qual.reverse"].push_back(qualityReverseFileName);
+               outputNames.push_back(qualityReverseFileName);  outputTypes["errorqualreverse"].push_back(qualityReverseFileName);
                
                for(int i=0;i<numColumns;i++){  qualityReverseFile << '\t' << i;        }       qualityReverseFile << endl;
                for(int i=0;i<numRows;i++){
Mothur--16S microbiota sequencing software; mirror of main repository with my branches