Merge remote-tracking branch 'origin/master'

[mothur.git] / otuassociationcommand.cpp

diff --git a/otuassociationcommand.cpp b/otuassociationcommand.cpp
index 93f46ba1e716f80e321245832eb11eabb2bda733..968d76744be5b296a9b9f98a5294356366783bce 100644 (file)
--- a/otuassociationcommand.cpp
+++ b/otuassociationcommand.cpp
@@ -16,6 +16,7 @@ vector<string> OTUAssociationCommand::setParameters(){
                CommandParameter pshared("shared", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pshared);
                CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(prelabund);
         CommandParameter pmetadata("metadata", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pmetadata);
+        CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
                CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
                CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
                CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "",false,false); parameters.push_back(pmethod);
@@ -37,9 +38,10 @@ string OTUAssociationCommand::getHelpString(){
                string helpString = "";
                helpString += "The otu.association command reads a shared or relabund file and calculates the correlation coefficients between otus.\n";
         helpString += "If you provide a metadata file, mothur will calculate te correlation bewteen the metadata and the otus.\n";
-               helpString += "The otu.association command parameters are shared, relabund, metadata, groups, method and label.  The shared or relabund parameter is required.\n";
+               helpString += "The otu.association command parameters are shared, relabund, metadata, groups, method, cutoff and label.  The shared or relabund parameter is required.\n";
                helpString += "The groups parameter allows you to specify which of the groups you would like included. The group names are separated by dashes.\n";
                helpString += "The label parameter allows you to select what distances level you would like used, and are also separated by dashes.\n";
+        helpString += "The cutoff parameter allows you to set a pvalue at which the otu will be reported.\n";
                helpString += "The method parameter allows you to select what method you would like to use. Options are pearson, spearman and kendall. Default=pearson.\n";
                helpString += "The otu.association command should be in the following format: otu.association(shared=yourSharedFile, method=yourMethod).\n";
                helpString += "Example otu.association(shared=genus.pool.shared, method=kendall).\n";
@@ -53,12 +55,32 @@ string OTUAssociationCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string OTUAssociationCommand::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 == "otucorr") {  outputFileName =  "otu.corr"; }
+            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, "OTUAssociationCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 OTUAssociationCommand::OTUAssociationCommand(){        
        try {
                abort = true; calledHelp = true; 
                setParameters();
                vector<string> tempOutNames;
-               outputTypes["otu.corr"] = tempOutNames;
+               outputTypes["otucorr"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "OTUAssociationCommand", "OTUAssociationCommand");
@@ -90,7 +112,7 @@ OTUAssociationCommand::OTUAssociationCommand(string option)  {
                        }
                        
                        vector<string> tempOutNames;
-                       outputTypes["otu.corr"] = tempOutNames;
+                       outputTypes["otucorr"] = tempOutNames;
                        
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
@@ -175,6 +197,10 @@ OTUAssociationCommand::OTUAssociationCommand(string option)  {
                        
                        method = validParameter.validFile(parameters, "method", false);         if (method == "not found"){     method = "pearson";             }
                        
+            string temp = validParameter.validFile(parameters, "cutoff", false);
+                       if (temp == "not found") { temp = "10"; }
+                       m->mothurConvert(temp, cutoff); 
+            
                        if ((method != "pearson") && (method != "spearman") && (method != "kendall")) { m->mothurOut(method + " is not a valid method. Valid methods are pearson, spearman, and kendall."); m->mothurOutEndLine(); abort = true; }
                        
                }
@@ -306,8 +332,8 @@ int OTUAssociationCommand::processShared(){
 int OTUAssociationCommand::process(vector<SharedRAbundVector*>& lookup){
        try {
                
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + method + ".otu.corr";
-               outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName);
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + method + "." + getOutputFileNameTag("otucorr");
+               outputNames.push_back(outputFileName); outputTypes["otucorr"].push_back(outputFileName);
                
                ofstream out;
                m->openOutputFile(outputFileName, out);
@@ -336,7 +362,7 @@ int OTUAssociationCommand::process(vector<SharedRAbundVector*>& lookup){
                     else if (method == "kendall")      {       coef = linear.calcKendall(xy[i], xy[k], sig);   }                   
                     else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; }
                     
-                    out << m->binLabelsInFile[i] << '\t' << m->binLabelsInFile[k] << '\t' << coef << '\t' << sig << endl;
+                    if (sig < cutoff) { out << m->binLabelsInFile[i] << '\t' << m->binLabelsInFile[k] << '\t' << coef << '\t' << sig << endl; }
                 }
             }
                }else { //compare otus to metadata
@@ -353,7 +379,7 @@ int OTUAssociationCommand::process(vector<SharedRAbundVector*>& lookup){
                     else if (method == "kendall")      {       coef = linear.calcKendall(xy[i], metadata[k], sig);     }                   
                     else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; }
                     
-                    out << m->binLabelsInFile[i] << '\t' << metadataLabels[k] << '\t' << coef << '\t' << sig << endl;
+                    if (sig < cutoff) { out << m->binLabelsInFile[i] << '\t' << metadataLabels[k] << '\t' << coef << '\t' << sig << endl; }
                 }
             }
 
@@ -466,8 +492,8 @@ int OTUAssociationCommand::processRelabund(){
 int OTUAssociationCommand::process(vector<SharedRAbundFloatVector*>& lookup){
        try {
                
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + method + ".otu.corr";
-               outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName);
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + method + "." + getOutputFileNameTag("otucorr");
+               outputNames.push_back(outputFileName); outputTypes["otucorr"].push_back(outputFileName);
                
                ofstream out;
                m->openOutputFile(outputFileName, out);
@@ -495,7 +521,7 @@ int OTUAssociationCommand::process(vector<SharedRAbundFloatVector*>& lookup){
                     else if (method == "kendall")      {       coef = linear.calcKendall(xy[i], xy[k], sig);   }                   
                     else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; }
                     
-                    out << m->binLabelsInFile[i] << '\t' << m->binLabelsInFile[k] << '\t' << coef << '\t' << sig << endl;
+                    if (sig < cutoff) { out << m->binLabelsInFile[i] << '\t' << m->binLabelsInFile[k] << '\t' << coef << '\t' << sig << endl; }
                 }
             }
                }else { //compare otus to metadata
@@ -512,7 +538,7 @@ int OTUAssociationCommand::process(vector<SharedRAbundFloatVector*>& lookup){
                     else if (method == "kendall")      {       coef = linear.calcKendall(xy[i], metadata[k], sig);     }                   
                     else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; }
                     
-                    out << m->binLabelsInFile[i] << '\t' << metadataLabels[k] << '\t' << coef << '\t' << sig << endl;
+                    if (sig < cutoff) { out << m->binLabelsInFile[i] << '\t' << metadataLabels[k] << '\t' << coef << '\t' << sig << endl; }
                 }
             }