added groups option to read.otu, added qtrim option to trim.seqs, fixed bug in get...

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 727a04b273fc3ee4b4c9c5882f55e746ad2c0d6a..0dcdfc0143b12ae0c827086465a16bfb486dc66b 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -23,20 +23,27 @@ SharedCommand::SharedCommand(){
                
                groupMap = globaldata->gGroupmap;
                
+               //if hte user has not specified any groups then use them all
+               if (globaldata->Groups.size() == 0) {
+                       groups = groupMap->namesOfGroups;
+               }else{ //they have specified groups
+                       groups = globaldata->Groups;
+               }
+               
                //fill filehandles with neccessary ofstreams
                int i;
                ofstream* temp;
-               for (i=0; i<groupMap->getNumGroups(); i++) {
+               for (i=0; i<groups.size(); i++) {
                        temp = new ofstream;
-                       filehandles[groupMap->namesOfGroups[i]] = temp;
+                       filehandles[groups[i]] = temp;
                }
                
                //set fileroot
                fileroot = getRootName(globaldata->getListFile());
                
                //clears file before we start to write to it below
-               for (int i=0; i<groupMap->getNumGroups(); i++) {
-                       remove((fileroot + groupMap->namesOfGroups[i] + ".rabund").c_str());
+               for (int i=0; i<groups.size(); i++) {
+                       remove((fileroot + groups[i] + ".rabund").c_str());
                }
 
        }
@@ -64,7 +71,7 @@ int SharedCommand::execute(){
                string lastLabel = SharedList->getLabel();
                vector<SharedRAbundVector*> lookup; 
                
-               if (SharedList->getNumSeqs() != groupMap->getNumSeqs()) {  
+               if ((globaldata->Groups.size() == 0) && (SharedList->getNumSeqs() != groupMap->getNumSeqs())) {  //if the user has not specified any groups and their files don't match exit with error
                        mothurOut("Your group file contains " + toString(groupMap->getNumSeqs()) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); mothurOutEndLine(); 
                        
                        out.close();
@@ -82,15 +89,36 @@ int SharedCommand::execute(){
                        return 1; 
                }
                
+               //if user has specified groups make new groupfile for them
+               if (globaldata->Groups.size() != 0) { //make new group file
+                       string groups = "";
+                       for (int i = 0; i < globaldata->Groups.size(); i++) {
+                               groups += globaldata->Groups[i] + ".";
+                       }
+               
+                       string newGroupFile = getRootName(globaldata->inputFileName) + groups + "groups";
+                       ofstream outGroups;
+                       openOutputFile(newGroupFile, outGroups);
+               
+                       vector<string> names = groupMap->getNamesSeqs();
+                       string groupName;
+                       for (int i = 0; i < names.size(); i++) {
+                               groupName = groupMap->getGroup(names[i]);
+                               if (isValidGroup(groupName, globaldata->Groups)) {
+                                       outGroups << names[i] << '\t' << groupName << endl;
+                               }
+                       }
+                       outGroups.close();
+               }
+               
                //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
                set<string> processedLabels;
                set<string> userLabels = globaldata->labels;    
                
                while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
                        
-
                        if(globaldata->allLines == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
-                                       
+                       
                                        lookup = SharedList->getSharedRAbundVector();
                                        mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
                                        
@@ -280,3 +308,20 @@ SharedCommand::~SharedCommand(){
 }
 
 //**********************************************************************************************************************
+
+bool SharedCommand::isValidGroup(string groupname, vector<string> groups) {
+       try {
+               for (int i = 0; i < groups.size(); i++) {
+                       if (groupname == groups[i]) { return true; }
+               }
+               
+               return false;
+       }
+       catch(exception& e) {
+               errorOut(e, "SharedCommand", "isValidGroup");
+               exit(1);
+       }
+}
+/************************************************************/
+
+