changed rarefaction.single output

[mothur.git] / rarefactcommand.cpp

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index bc27d6a3fe00b8dafaba29ce05844c6652459a77..8d1cfc864d35d12d2127672f68af60802cd8b02d 100644 (file)
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -287,6 +287,7 @@ int RareFactCommand::execute(){
                                
                if (m->control_pressed) { return 0; }
                
+               map<string, string> nameMap;
                for (int p = 0; p < inputFileNames.size(); p++) {
                        
                        string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
@@ -295,6 +296,7 @@ int RareFactCommand::execute(){
                        
                        if (inputFileNames.size() > 1) {
                                m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
+                               nameMap[fileNameRoot] = groups[p];
                        }
                        int i;
                        ValidCalculators validCalculator;
@@ -448,7 +450,7 @@ int RareFactCommand::execute(){
                if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); } return 0; }
 
                //create summary file containing all the groups data for each label - this function just combines the info from the files already created.
-               if ((sharedfile != "") && (groupMode)) {   outputNames = createGroupFile(outputNames);  }
+               if ((sharedfile != "") && (groupMode)) {   outputNames = createGroupFile(outputNames, nameMap);  }
 
                if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); } return 0; }
 
@@ -465,7 +467,7 @@ int RareFactCommand::execute(){
        }
 }
 //**********************************************************************************************************************
-vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames) {
+vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map<string, string> nameMap) {
        try {
                
                vector<string> newFileNames;
@@ -496,6 +498,7 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames) {
                }
                
                //for each type create a combo file
+               map<int, int> lineToNumber; 
                for (map<string, vector<string> >::iterator it = typesFiles.begin(); it != typesFiles.end(); it++) {
                        
                        ofstream out;
@@ -508,6 +511,7 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames) {
                        //open each type summary file
                        map<string, vector<string> > files; //maps file name to lines in file
                        int maxLines = 0;
+                       int numColumns = 0;
                        for (int i=0; i<thisTypesFiles.size(); i++) {
                                                                
                                ifstream temp;
@@ -517,15 +521,29 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames) {
                                m->getline(temp);       m->gobble(temp);
                                
                                vector<string> thisFilesLines;
-                               string group = m->getRootName(thisTypesFiles[i]);
-                               group = group.substr(0, group.length()-1);
-                               group = group.substr(group.find_last_of('.')+1);
+                               string fileNameRoot = m->getRootName(thisTypesFiles[i]);
+                               map<string, string>::iterator itName = nameMap.find(fileNameRoot);
+                               string group = "";
+                               if (itName != nameMap.end()) {
+                                       group = itName->second;
+                               }else {
+                                       group = "not found" + i;
+                                       m->mothurOut("[ERROR]: can't parse filename."); m->mothurOutEndLine();
+                               }
                                
                                thisFilesLines.push_back(group);
+                               int count = 1;
                                while (!temp.eof()){
                                
                                        string thisLine = m->getline(temp);
-                                                                               
+                                       
+                                       string numSampled = thisLine.substr(0, thisLine.find_first_of('\t'));
+                                       int num = 0;
+                                       convert(numSampled, num);
+                                       numColumns = m->getNumChar(thisLine, '\t');
+                                       lineToNumber[count] = num;
+                                       count++;
+                                                                       
                                        thisFilesLines.push_back(thisLine);
                                        
                                        m->gobble(temp);
@@ -547,15 +565,21 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames) {
                                //grab data for each group
                                for (int i=0; i<thisTypesFiles.size(); i++) {
                                        
-                                       string output = "NA\t";
-                                       if (k < files[thisTypesFiles[i]].size()) {
-                                               string line = files[thisTypesFiles[i]][k];
-                                               output = line.substr(0, line.find_first_of('\t'));
-                                               output += '\t' + files[thisTypesFiles[i]][0] + '\t' + line.substr(line.find_first_of('\t'));
-                                       }else{
-                                               output += '\t' + files[thisTypesFiles[i]][0] + '\t';
-                                       }
-                                       out << output << endl;
+                                       map<int, int>::iterator itLine = lineToNumber.find(k);
+                                       if (itLine != lineToNumber.end()) {
+                                               string output = toString(itLine->second);
+                                               if (k < files[thisTypesFiles[i]].size()) {
+                                                       string line = files[thisTypesFiles[i]][k];
+                                                       output = line.substr(0, line.find_first_of('\t'));
+                                                       output += '\t' + files[thisTypesFiles[i]][0] + '\t' + line.substr(line.find_first_of('\t'));
+                                               }else{
+                                                       output += '\t' + files[thisTypesFiles[i]][0] + '\t';
+                                                       for (int h = 0; h < numColumns; h++) {
+                                                               output += "NA\t";
+                                                       }
+                                               }
+                                               out << output << endl;
+                                       }else { m->mothurOut("[ERROR]: parsing results, cant find " + toString(k)); m->mothurOutEndLine(); }
                                }
                        }