fixes while testing 1.33.0

[mothur.git] / splitabundcommand.cpp

diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index 2d37e8d459857f7f0161ba87111df0403ff9c827..47372cce680a9fa907200db12926194afe8c6b00 100644 (file)
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -212,7 +212,7 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                        else if (countfile == "not found") { countfile = "";  } 
                        else {
                 m->setCountTableFile(countfile); 
-                ct.readTable(countfile);
+                ct.readTable(countfile, true, false);
             }
             
             if ((namefile != "") && (countfile != "")) {
@@ -501,17 +501,19 @@ int SplitAbundCommand::writeList(ListVector* thisList, string tag, int numRareBi
             variables["[tag]"] = tag;
             variables["[tag2]"] = "rare";
                        string rare = getOutputFileName("list",variables);
-                       m->openOutputFile(rare, rout);
+                       m->openOutputFile(rare+".temp", rout);
                        outputNames.push_back(rare); outputTypes["list"].push_back(rare);
                        
             variables["[tag2]"] = "abund";
                        string abund = getOutputFileName("list",variables);
-                       m->openOutputFile(abund, aout);
+                       m->openOutputFile(abund+".temp", aout);
                        outputNames.push_back(abund); outputTypes["list"].push_back(abund);
 
                        if (rareNames.size() != 0)      {  rout << thisList->getLabel() << '\t' << numRareBins << '\t';         }
                        if (abundNames.size() != 0) {   aout << thisList->getLabel() << '\t' << numAbundBins << '\t';   }
-
+            
+            vector<string> binLabels = thisList->getLabels();
+            string rareHeader = "label\tnumOtus\t"; string abundHeader = "label\tnumOtus\t";
                        for (int i = 0; i < thisList->getNumBins(); i++) {
                                if (m->control_pressed) { break; }
                        
@@ -525,8 +527,8 @@ int SplitAbundCommand::writeList(ListVector* thisList, string tag, int numRareBi
                     for (int j = 0; j < names.size(); j++) {  size += ct.getNumSeqs(names[j]); }
                 }
                        
-                               if (size <= cutoff) {  rout << bin << '\t';  }
-                               else                            {  aout << bin << '\t'; }
+                               if (size <= cutoff) {  rout << bin << '\t';  rareHeader += binLabels[i] + '\t'; }
+                               else                            {  aout << bin << '\t';  abundHeader += binLabels[i] + '\t'; }
                        }
                        
                        if (rareNames.size() != 0)      { rout << endl; }
@@ -534,6 +536,21 @@ int SplitAbundCommand::writeList(ListVector* thisList, string tag, int numRareBi
                        
                        rout.close();
                        aout.close();
+            
+            //add headers
+            ofstream r;
+            m->openOutputFile(rare, r);
+            r << rareHeader << endl;
+            r.close();
+            m->appendFiles(rare+".temp", rare);
+            m->mothurRemove(rare+".temp");
+            
+            ofstream a;
+            m->openOutputFile(abund, a);
+            a << abundHeader << endl;
+            a.close();
+            m->appendFiles(abund+".temp", abund);
+            m->mothurRemove(abund+".temp");
                        
                }else{ //parse names by abundance and group
                        string fileroot =  outputDir + m->getRootName(m->getSimpleName(listfile));
@@ -564,14 +581,16 @@ int SplitAbundCommand::writeList(ListVector* thisList, string tag, int numRareBi
                        }
                        
                        map<string, string> groupVector;
+            map<string, string> groupLabels;
                        map<string, string>::iterator itGroup;
                        map<string, int> groupNumBins;
                
                        for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
                                groupNumBins[it3->first] = 0;
                                groupVector[it3->first] = "";
+                groupLabels[it3->first] = "label\tnumOtus\t";
                        }
-               
+            vector<string> binLabels = thisList->getLabels();
                        for (int i = 0; i < thisList->getNumBins(); i++) {
                                if (m->control_pressed) { break; }
                        
@@ -622,12 +641,14 @@ int SplitAbundCommand::writeList(ListVector* thisList, string tag, int numRareBi
                        
                        
                                for (itGroup = groupBins.begin(); itGroup != groupBins.end(); itGroup++) {
-                                       groupVector[itGroup->first] +=  itGroup->second + '\t'; 
+                                       groupVector[itGroup->first] +=  itGroup->second + '\t';
+                    groupLabels[itGroup->first] += binLabels[i] + '\t';
                                }
                        }
                        
                        //end list vector
                        for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+                (*(filehandles[it3->first])) << groupLabels[it3->first] << endl;
                                (*(filehandles[it3->first])) << thisList->getLabel() << '\t' << groupNumBins[it3->first] << '\t' << groupVector[it3->first] << endl;  // label numBins  listvector for that group
                                (*(filehandles[it3->first])).close();
                                delete it3->second;