Merge remote-tracking branch 'origin/master'

[mothur.git] / subsamplecommand.cpp

diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index 717b1d3231c20368a2d23e9b86d52a6707f03b12..35441013919fbfe55452532e735b5bd1d7673f2f 100644 (file)
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -63,6 +63,33 @@ string SubSampleCommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string SubSampleCommand::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 =  "subsample" + m->getExtension(inputName);   }
+            else if (type == "sabund")    {   outputFileName =  "subsample" + m->getExtension(inputName);   }
+            else if (type == "name")        {   outputFileName =  "subsample" + m->getExtension(inputName);   }
+            else if (type == "group")       {   outputFileName =  "subsample" + m->getExtension(inputName);   }
+            else if (type == "list")        {   outputFileName =  "subsample" + m->getExtension(inputName);   }
+            else if (type == "rabund")       {   outputFileName =  "subsample" + m->getExtension(inputName);   }
+            else if (type == "shared") {   outputFileName =  "subsample" + m->getExtension(inputName);        }
+            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, "SubSampleCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+
 //**********************************************************************************************************************
 SubSampleCommand::SubSampleCommand(){  
        try {
@@ -479,8 +506,7 @@ int SubSampleCommand::getSubSampleFasta() {
                
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "subsample" + m->getExtension(fastafile);
-               
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);         
                ofstream out;
                m->openOutputFile(outputFileName, out);
                
@@ -528,6 +554,7 @@ int SubSampleCommand::getSubSampleFasta() {
                if (namefile != "") {
                        m->mothurOut("Deconvoluting subsampled fasta file... "); m->mothurOutEndLine();
                        
+            string outputNameFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
                        //use unique.seqs to create new name and fastafile
                        string inputString = "fasta=" + outputFileName;
                        m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
@@ -542,10 +569,11 @@ int SubSampleCommand::getSubSampleFasta() {
                        delete uniqueCommand;
                        m->mothurCalling = false;
             
-                       outputTypes["name"].push_back(filenames["name"][0]);  outputNames.push_back(filenames["name"][0]);
-                       m->mothurRemove(outputFileName);
-                       outputFileName = filenames["fasta"][0];
-                       
+            m->renameFile(filenames["name"][0], outputNameFileName);
+            m->renameFile(filenames["fasta"][0], outputFileName);
+            
+                       outputTypes["name"].push_back(outputNameFileName);  outputNames.push_back(outputNameFileName);
+
                        m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
                        
                        m->mothurOut("Done."); m->mothurOutEndLine();
@@ -558,7 +586,7 @@ int SubSampleCommand::getSubSampleFasta() {
                        
                        string groupOutputDir = outputDir;
                        if (outputDir == "") {  groupOutputDir += m->hasPath(groupfile);  }
-                       string groupOutputFileName = groupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "subsample" + m->getExtension(groupfile);
+                       string groupOutputFileName = groupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
                        
                        ofstream outGroup;
                        m->openOutputFile(groupOutputFileName, outGroup);
@@ -639,34 +667,13 @@ int SubSampleCommand::getNames() {
 int SubSampleCommand::readNames() {
        try {
                
-               ifstream in;
-               m->openInputFile(namefile, in);
-               
-               string thisname, repnames;
-               map<string, vector<string> >::iterator it;
-               
-               while(!in.eof()){
-                       
-                       if (m->control_pressed) { in.close(); return 0; }
-                       
-                       in >> thisname;         m->gobble(in);          //read from first column
-                       in >> repnames;                 //read from second column
-                       
-                       it = nameMap.find(thisname);
-                       if (it == nameMap.end()) {
-                               
-                               vector<string> splitRepNames;
-                               m->splitAtComma(repnames, splitRepNames);
-                               
-                               nameMap[thisname] = splitRepNames;      
-                               for (int i = 0; i < splitRepNames.size(); i++) { names.push_back(splitRepNames[i]); }
-                               
-                       }else{  m->mothurOut(thisname + " is already in namesfile. I will use first definition."); m->mothurOutEndLine();  }
-                       
-                       m->gobble(in);
-               }
-               in.close();     
-               
+        nameMap.clear();
+        m->readNames(namefile, nameMap);
+        
+        //save names of all sequences
+        map<string, vector<string> >::iterator it;
+        for (it = nameMap.begin(); it != nameMap.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { names.push_back((it->second)[i]); } }
+        
                return 0;
                
        }
@@ -801,8 +808,7 @@ int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup) {
                
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + thislookup[0]->getLabel() + ".subsample" + m->getExtension(sharedfile);
-        
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + thislookup[0]->getLabel() + getOutputFileNameTag("shared", sharedfile);        
         SubSample sample;
         vector<string> subsampledLabels = sample.getSample(thislookup, size);
         
@@ -840,8 +846,7 @@ int SubSampleCommand::getSubSampleList() {
                
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "subsample" + m->getExtension(listfile);
-               
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);            
                ofstream out;
                m->openOutputFile(outputFileName, out);
                outputTypes["list"].push_back(outputFileName);  outputNames.push_back(outputFileName);
@@ -1185,8 +1190,7 @@ int SubSampleCommand::getSubSampleRabund() {
                
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(rabundfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + "subsample" + m->getExtension(rabundfile);
-               
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + getOutputFileNameTag("rabund", rabundfile);              
                ofstream out;
                m->openOutputFile(outputFileName, out);
                outputTypes["rabund"].push_back(outputFileName);  outputNames.push_back(outputFileName);
@@ -1340,8 +1344,7 @@ int SubSampleCommand::getSubSampleSabund() {
                
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(sabundfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + "subsample" + m->getExtension(sabundfile);
-               
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + getOutputFileNameTag("sabund", sabundfile);              
                ofstream out;
                m->openOutputFile(outputFileName, out);
                outputTypes["sabund"].push_back(outputFileName);  outputNames.push_back(outputFileName);