test

[mothur.git] / getsharedotucommand.cpp

diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index 02d8413675bade0cf79f8781987cc45078b74db2..5ae8da588ba4a6d36b6658527d8cd12e208c50c4 100644 (file)
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -13,15 +13,15 @@
 //**********************************************************************************************************************
 vector<string> GetSharedOTUCommand::setParameters(){   
        try {
-               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
-               CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(pgroup);
-               CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(plist);
-               CommandParameter poutput("output", "Multiple", "accnos-default", "default", "", "", "",false,false); parameters.push_back(poutput);
-               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-               CommandParameter punique("unique", "String", "", "", "", "", "",false,false); parameters.push_back(punique);
-               CommandParameter pshared("shared", "String", "", "", "", "", "",false,false); parameters.push_back(pshared);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none","fasta",false,false); parameters.push_back(pfasta);
+               CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none","sharedseq",false,true,true); parameters.push_back(pgroup);
+               CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","sharedseq",false,true,true); parameters.push_back(plist);
+               CommandParameter poutput("output", "Multiple", "accnos-default", "default", "", "", "","",false,false); parameters.push_back(poutput);
+               CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+               CommandParameter punique("unique", "String", "", "", "", "", "","",false,false,true); parameters.push_back(punique);
+               CommandParameter pshared("shared", "String", "", "", "", "", "","",false,false,true); parameters.push_back(pshared);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
 
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -59,6 +59,23 @@ string GetSharedOTUCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string GetSharedOTUCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+
+        if (type == "fasta")            {   pattern =  "[filename],[distance],[group],shared.fasta";   }
+        else if (type == "accnos")      {   pattern =  "[filename],[distance],[group],accnos";         }
+        else if (type == "sharedseqs")  {   pattern =  "[filename],[distance],[group],shared.seqs";    }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "GetSharedOTUCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 GetSharedOTUCommand::GetSharedOTUCommand(){    
        try {
                abort = true; calledHelp = true;
@@ -371,11 +388,13 @@ int GetSharedOTUCommand::process(ListVector* shared) {
                string outputFileNames;
                
                if (outputDir == "") { outputDir += m->hasPath(listfile); }
-               if (output != "accnos") {
-                       outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".shared.seqs";
-               }else {
-                       outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".accnos";
-               }
+        map<string, string> variables;
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+        variables["[distance]"] = shared->getLabel();
+        variables["[group]"] = userGroups;
+               if (output != "accnos") { outputFileNames = getOutputFileName("sharedseqs", variables); }
+               else { outputFileNames = getOutputFileName("accnos", variables); }
+        
                m->openOutputFile(outputFileNames, outNames);
                
                bool wroteSomething = false;
@@ -394,10 +413,11 @@ 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 +433,6 @@ 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 +487,8 @@ 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";
+            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+                       string outputFileFasta = getOutputFileName("fasta", variables);
                        ofstream outFasta;
                        m->openOutputFile(outputFileFasta, outFasta);
                        outputNames.push_back(outputFileFasta); outputTypes["fasta"].push_back(outputFileFasta);