working on pam

[mothur.git] / getgroupscommand.cpp

diff --git a/getgroupscommand.cpp b/getgroupscommand.cpp
index e4f7450b4291e1ca281ebe806dd476fac86019b9..bb15a3f5a21e3c7785283cfc5d6eade2c1bda6ed 100644 (file)
--- a/getgroupscommand.cpp
+++ b/getgroupscommand.cpp
@@ -68,7 +68,7 @@ string GetGroupsCommand::getOutputPattern(string type) {
         else if (type == "name")        {   pattern = "[filename],pick,[extension]";    }
         else if (type == "group")       {   pattern = "[filename],pick,[extension]";    }
         else if (type == "count")       {   pattern = "[filename],pick,[extension]";    }
-        else if (type == "list")        {   pattern = "[filename],pick,[extension]";    }
+        else if (type == "list")        {   pattern = "[filename],[tag],pick,[extension]";    }
         else if (type == "shared")      {   pattern = "[filename],[tag],pick,[extension]";    }
         else if (type == "design")      {   pattern = "[filename],pick,[extension]";    }
         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
@@ -370,7 +370,7 @@ int GetGroupsCommand::execute(){
                 m->mothurOut("\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n");
             }
             CountTable ct;
-            ct.readTable(countfile);
+            ct.readTable(countfile, true, false);
             if (!ct.hasGroupInfo()) { m->mothurOut("[ERROR]: your count file does not contain group info, aborting.\n"); return 0; }
                 
             vector<string> gNamesOfGroups = ct.getNamesOfGroups();
@@ -585,10 +585,6 @@ int GetGroupsCommand::readList(){
         map<string, string> variables; 
         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
         variables["[extension]"] = m->getExtension(listfile);
-               string outputFileName = getOutputFileName("list", variables);
-               
-               ofstream out;
-               m->openOutputFile(outputFileName, out);
                
                ifstream in;
                m->openInputFile(listfile, in);
@@ -599,9 +595,19 @@ int GetGroupsCommand::readList(){
                while(!in.eof()){
                        
                        selectedCount = 0;
-                       
+
                        //read in list vector
                        ListVector list(in);
+            
+            variables["[tag]"] = list.getLabel();
+            string outputFileName = getOutputFileName("list", variables);
+                       
+                       ofstream out;
+                       m->openOutputFile(outputFileName, out);
+                       outputTypes["list"].push_back(outputFileName);  outputNames.push_back(outputFileName);
+            
+            vector<string> binLabels = list.getLabels();
+            vector<string> newBinLabels;
                        
                        //make a new list vector
                        ListVector newList;
@@ -613,13 +619,14 @@ int GetGroupsCommand::readList(){
                                
                                //parse out names that are in accnos file
                                string binnames = list.get(i);
+                vector<string> thisBinNames;
+                m->splitAtComma(binnames, thisBinNames);
                                
                                string newNames = "";
-                               while (binnames.find_first_of(',') != -1) { 
-                                       string name = binnames.substr(0,binnames.find_first_of(','));
-                                       binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
-                                       
-                                       //if that name is in the .accnos file, add it
+                for (int j = 0; j < thisBinNames.size(); j++) {
+                    string name = thisBinNames[j];
+                    
+                    //if that name is in the .accnos file, add it
                                        if (names.count(name) != 0) {  newNames += name + ",";  selectedCount++;  }
                                        else{
                                                //if you are not in the accnos file check if you are a name that needs to be changed
@@ -629,39 +636,30 @@ int GetGroupsCommand::readList(){
                                                        selectedCount++;
                                                }
                                        }
-                               }
-                               
-                               //get last name
-                               if (names.count(binnames) != 0) {  newNames += binnames + ",";  selectedCount++;  }
-                               else{
-                                       //if you are not in the accnos file check if you are a name that needs to be changed
-                                       map<string, string>::iterator it = uniqueToRedundant.find(binnames);
-                                       if (it != uniqueToRedundant.end()) {
-                                               newNames += it->second + ",";
-                                               selectedCount++;
-                                       }
-                               }
-                               
+                }
+                                                               
                                //if there are names in this bin add to new list
                                if (newNames != "") {  
                                        newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
-                                       newList.push_back(newNames);    
+                                       newList.push_back(newNames);
+                    newBinLabels.push_back(binLabels[i]);
                                }
                        }
                        
                        //print new listvector
                        if (newList.getNumBins() != 0) {
                                wroteSomething = true;
+                newList.setLabels(newBinLabels);
+                newList.printHeaders(out);
                                newList.print(out);
                        }
                        
                        m->gobble(in);
+            out.close();
                }
-               in.close();     
-               out.close();
+               in.close();
                
                if (wroteSomething == false) {  m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine();  }
-               outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
                
                m->mothurOut("Selected " + toString(selectedCount) + " sequences from your list file."); m->mothurOutEndLine();