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[mothur.git] / otuassociationcommand.cpp
diff --git a/otuassociationcommand.cpp b/otuassociationcommand.cpp
index 93f46ba1e716f80e321245832eb11eabb2bda733..23cac294cad4f1b25caa0e4f4d55de40f1fb2876 100644 (file)
--- a/otuassociationcommand.cpp
+++ b/otuassociationcommand.cpp
@@ -13,14 +13,15 @@
 //**********************************************************************************************************************
 vector<string> OTUAssociationCommand::setParameters(){ 
        try {
-               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 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);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pshared("shared", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","otucorr",false,false,true); parameters.push_back(pshared);
+               CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","otucorr",false,false); parameters.push_back(prelabund);
+        CommandParameter pmetadata("metadata", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pmetadata);
+        CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false,true); 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,true); parameters.push_back(pmethod);
+               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);          }
@@ -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 +55,27 @@ string OTUAssociationCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string OTUAssociationCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "otucorr") {  pattern = "[filename],[distance],[tag],otu.corr"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "OTUAssociationCommand", "getOutputPattern");
+        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 +107,7 @@ 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 +192,10 @@ 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; }
                        
                }
@@ -305,9 +326,12 @@ 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);
+               map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
+        variables["[distance]"] = lookup[0]->getLabel();
+        variables["[tag]"] = method;
+               string outputFileName = getOutputFileName("otucorr",variables);
+               outputNames.push_back(outputFileName); outputTypes["otucorr"].push_back(outputFileName);
                
                ofstream out;
                m->openOutputFile(outputFileName, out);
@@ -336,7 +360,7 @@ 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 +377,7 @@ 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 +490,12 @@ 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);
+               map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
+        variables["[distance]"] = lookup[0]->getLabel();
+        variables["[tag]"] = method;
+        string outputFileName = getOutputFileName("otucorr",variables);
+               outputNames.push_back(outputFileName); outputTypes["otucorr"].push_back(outputFileName);
                
                ofstream out;
                m->openOutputFile(outputFileName, out);
@@ -495,7 +523,7 @@ 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 +540,7 @@ 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; }
                 }
             }
             
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