added classify.shared command and random forest files. added count file to pcr.seqs...

[mothur.git] / makebiomcommand.cpp

diff --git a/makebiomcommand.cpp b/makebiomcommand.cpp
index acd0500963d096acfb5d1ea453cc9186feafe783..68e70ee3e48e58a89f75ef7547d7409620947cb2 100644 (file)
--- a/makebiomcommand.cpp
+++ b/makebiomcommand.cpp
@@ -129,6 +129,27 @@ string MakeBiomCommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string MakeBiomCommand::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 == "biom")             {   outputFileName =  "biom";       }
+            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, "MakeBiomCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+
 //**********************************************************************************************************************
 MakeBiomCommand::MakeBiomCommand(){    
        try {
@@ -165,7 +186,7 @@ MakeBiomCommand::MakeBiomCommand(string option) {
                        for (it = parameters.begin(); it != parameters.end(); it++) { 
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
-                       
+
                        //initialize outputTypes
                        vector<string> tempOutNames;
                        outputTypes["biom"] = tempOutNames;
@@ -352,7 +373,7 @@ int MakeBiomCommand::execute(){
 int MakeBiomCommand::getBiom(vector<SharedRAbundVector*>& lookup){
        try {
         
-        string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + ".biom";
+        string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + "." + getOutputFileNameTag("biom");
                ofstream out;
                m->openOutputFile(outputFileName, out);
                outputNames.push_back(outputFileName); outputTypes["biom"].push_back(outputFileName);
@@ -528,15 +549,16 @@ vector<string> MakeBiomCommand::getMetaData(vector<SharedRAbundVector*>& lookup)
                 if (m->control_pressed) { return metadata; }
                 
                 //if there is a bin label use it otherwise make one
-                string binLabel = binTag;
-                string sbinNumber = otuLabels[i];
-                if (sbinNumber.length() < snumBins.length()) { 
-                    int diff = snumBins.length() - sbinNumber.length();
-                    for (int h = 0; h < diff; h++) { binLabel += "0"; }
-                }
-                binLabel += sbinNumber;
-                
-                labelTaxMap[binLabel] = taxs[i];
+                if (m->isContainingOnlyDigits(otuLabels[i])) {
+                    string binLabel = binTag;
+                    string sbinNumber = otuLabels[i];
+                    if (sbinNumber.length() < snumBins.length()) { 
+                        int diff = snumBins.length() - sbinNumber.length();
+                        for (int h = 0; h < diff; h++) { binLabel += "0"; }
+                    }
+                    binLabel += sbinNumber;
+                    labelTaxMap[binLabel] = taxs[i];
+                }else {  labelTaxMap[otuLabels[i]] = taxs[i]; }
             }
             
             
@@ -612,7 +634,7 @@ vector<string> MakeBiomCommand::parseTax(string tax, vector<string>& scores) {
                         scores.push_back(confidenceScore);
                                        }else{ scores.push_back("null"); }
                                }
-                       }
+                       }else{ scores.push_back("null"); }
                        
             //strip "" if they are there
             pos = taxon.find("\"");