modified bin.seqs and get.oturep commands to include use of a groupfile if provided...

[mothur.git] / getoturepcommand.cpp

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 45f34fef5a444eb66e78788b9107152cd2b20a7d..e5f87c25f014afe8be7dda943e6f0b5e3e255908 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -37,6 +37,14 @@ GetOTURepCommand::GetOTURepCommand(){
                
                fastafile = globaldata->getFastaFile();
                namesfile = globaldata->getNameFile();
+               groupfile = globaldata->getGroupFile();
+               
+               if (groupfile != "") {
+                       //read in group map info.
+                       groupMap = new GroupMap(groupfile);
+                       groupMap->readMap();
+               }
+
                openInputFile(fastafile, in);
                
                fasta = new FastaMap();
@@ -59,6 +67,9 @@ GetOTURepCommand::~GetOTURepCommand(){
        delete input;
        delete read;
        delete fasta;
+       if (groupfile != "") {
+               delete groupMap;
+       }
 }
 
 //**********************************************************************************************************************
@@ -98,15 +109,22 @@ int GetOTURepCommand::execute(){
                                
                                //for each bin in the list vector
                                for (int i = 0; i < list->size(); i++) {
-                                       nameRep = FindRep(i);
+                                       string groups;
+                                       nameRep = FindRep(i, groups);
                                        
                                        //print out name and sequence for that bin
                                        sequence = fasta->getSequence(nameRep);
 
                                        if (sequence != "not found") {
-                                               nameRep = nameRep + "|" + toString(i+1);
-                                               out << ">" << nameRep << endl;
-                                               out << sequence << endl;
+                                               if (groupfile == "") {
+                                                       nameRep = nameRep + "|" + toString(i+1);
+                                                       out << ">" << nameRep << endl;
+                                                       out << sequence << endl;
+                                               }else {
+                                                       nameRep = nameRep + "|" + groups + "|" + toString(i+1);
+                                                       out << ">" << nameRep << endl;
+                                                       out << sequence << endl;
+                                               }
                                        }else { 
                                                cout << nameRep << " is missing from your fasta or name file. Please correct. " << endl; 
                                                remove(outputFileName.c_str());
@@ -173,7 +191,7 @@ void GetOTURepCommand::readNamesFile() {
        }       
 }
 //**********************************************************************************************************************
-string GetOTURepCommand::FindRep(int bin) {
+string GetOTURepCommand::FindRep(int bin, string& group) {
        try{
                vector<string> names;
                map<string, float> sums;
@@ -182,12 +200,34 @@ string GetOTURepCommand::FindRep(int bin) {
                string binnames;
                float min = 10000;
                string minName;
+               map<string, string> groups;
+               map<string, string>::iterator groupIt;
                
                binnames = list->get(bin);
        
                //parse names into vector
                splitAtComma(binnames, names);
                
+               //if you have a groupfile
+               if(groupfile != "") {
+                       //find the groups that are in this bin
+                       for (int i = 0; i < names.size(); i++) {
+                               string groupName = groupMap->getGroup(names[i]);
+                               if (groupName == "not found") {  
+                                       cout << names[i] << " is missing from your group file. Please correct. " << endl;
+                                       groupError = true;
+                               }else{
+                                       groups[groupName] = groupName;
+                               }
+                       }
+                       
+                       //turn the groups into a string
+                       for(groupIt = groups.begin(); groupIt != groups.end(); groupIt++) { group += groupIt->first + "-"; }
+                       
+                       //rip off last dash
+                       group = group.substr(0, group.length()-1);
+               }
+               
                //if only 1 sequence in bin then that's the rep
                if (names.size() == 1) { return names[0]; }
                else {