added count file to chimera.uchime. found issue with uchime program that indicated...

[mothur.git] / getsharedotucommand.cpp

diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index 02d8413675bade0cf79f8781987cc45078b74db2..1b69a25d4af7e638dbf48a64baec2390f37dcfec 100644 (file)
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -58,6 +58,29 @@ string GetSharedOTUCommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string GetSharedOTUCommand::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 =  "shared.fasta";   }
+            else if (type == "accnos")      {   outputFileName =  "accnos";         }
+            else if (type == "sharedseqs")  {   outputFileName =  "shared.seqs";    }
+            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, "GetSharedOTUCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+
 //**********************************************************************************************************************
 GetSharedOTUCommand::GetSharedOTUCommand(){    
        try {
@@ -372,9 +395,9 @@ int GetSharedOTUCommand::process(ListVector* shared) {
                
                if (outputDir == "") { outputDir += m->hasPath(listfile); }
                if (output != "accnos") {
-                       outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".shared.seqs";
+                       outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + "." + getOutputFileNameTag("sharedseqs");
                }else {
-                       outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".accnos";
+                       outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + "." + getOutputFileNameTag("accnos");
                }
                m->openOutputFile(outputFileNames, outNames);
                
@@ -394,10 +417,11 @@ int GetSharedOTUCommand::process(ListVector* shared) {
                        
                        vector<string> namesOfSeqsInThisBin;
                        
-                       string names = shared->get(i);  
-                       while ((names.find_first_of(',') != -1)) { 
-                               string name = names.substr(0,names.find_first_of(','));
-                               names = names.substr(names.find_first_of(',')+1, names.length());
+                       string names = shared->get(i); 
+            vector<string> binNames;
+            m->splitAtComma(names, binNames);
+                       for(int j = 0; j < binNames.size(); j++) {
+                               string name = binNames[j];
                                
                                //find group
                                string seqGroup = groupMap->getGroup(name);
@@ -413,20 +437,6 @@ int GetSharedOTUCommand::process(ListVector* shared) {
                                else {  atLeastOne[seqGroup]++;  }
                        }
                        
-                       //get last name
-                       string seqGroup = groupMap->getGroup(names);
-                       if (output != "accnos") {
-                               namesOfSeqsInThisBin.push_back((names + "|" + seqGroup + "|" + toString(i+1)));
-                       }else {  namesOfSeqsInThisBin.push_back(names); }
-                       
-                       if (seqGroup == "not found") { m->mothurOut(names + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1);  }
-                       
-                       //is this seq in one of hte groups we care about
-                       it = groupFinder.find(seqGroup);
-                       if (it == groupFinder.end()) {  uniqueOTU = false;  } //you have a sequence from a group you don't want
-                       else {  atLeastOne[seqGroup]++;  }
-                       
-                       
                        //make sure you have at least one seq from each group you want
                        bool sharedByAll = true;
                        map<string, int>::iterator it2;
@@ -481,7 +491,7 @@ int GetSharedOTUCommand::process(ListVector* shared) {
                //if fasta file provided output new fasta file
                if ((fastafile != "") && wroteSomething) {
                        if (outputDir == "") { outputDir += m->hasPath(fastafile); }
-                       string outputFileFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)) + shared->getLabel() + userGroups + ".shared.fasta";
+                       string outputFileFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)) + shared->getLabel() + userGroups + "." + getOutputFileNameTag("fasta");
                        ofstream outFasta;
                        m->openOutputFile(outputFileFasta, outFasta);
                        outputNames.push_back(outputFileFasta); outputTypes["fasta"].push_back(outputFileFasta);