finished wrapper for catchall

diff --git a/bayesian.cpp b/bayesian.cpp
index 80518666cfe5436280f58117fe506dc132bd2754..1eee7f22fe3d75f206eacec5169c999432336ff4 100644 (file)
--- a/bayesian.cpp
+++ b/bayesian.cpp
@@ -76,9 +76,9 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
                        
                                //initialze probabilities
                                wordGenusProb.resize(numKmers);
-                       cout << numKmers << '\t' << genusNodes.size() << endl;
+                       //cout << numKmers << '\t' << genusNodes.size() << endl;
                                for (int j = 0; j < wordGenusProb.size(); j++) {        wordGenusProb[j].resize(genusNodes.size());             }
-                       cout << numKmers << '\t' << genusNodes.size() << endl;  
+                       //cout << numKmers << '\t' << genusNodes.size() << endl;        
                                ofstream out;
                                ofstream out2;
                                

diff --git a/catchallcommand.cpp b/catchallcommand.cpp
index d6264db3309bd867696ee0b89041b9e34d3b6556..7f740bd4642f5f385562141e017a37bbe5e89042 100644 (file)
--- a/catchallcommand.cpp
+++ b/catchallcommand.cpp
@@ -62,7 +62,7 @@ CatchAllCommand::CatchAllCommand(string option)  {
        try {
                globaldata = GlobalData::getInstance();
                abort = false;
-               allLines = 0;
+               allLines = 1;
                
                //allow user to run help
                if(option == "help") { help(); abort = true; }
@@ -117,7 +117,7 @@ CatchAllCommand::CatchAllCommand(string option)  {
                
 
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
-                       outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "./";       }
+                       outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(sabundfile);     }
                }
 
        }
@@ -130,9 +130,10 @@ CatchAllCommand::CatchAllCommand(string option)  {
 
 void CatchAllCommand::help(){
        try {
-               m->mothurOut("The catchall command interfaces mothur with the catchall program written by ...citation goes here...\n");
-               m->mothurOut("For more information about clearcut refer to http://catchall.cac.cornell.edu/ \n");
+               m->mothurOut("The catchall command interfaces mothur with the catchall program written by Linda Woodard, Sean Connolly and John Bunge.\n");
+               m->mothurOut("For more information about catchall refer to http://www.northeastern.edu/catchall/index.html \n");
                m->mothurOut("The catchall executable must be in a folder called catchall in the same folder as your mothur executable, similar to mothur's requirements for using blast. \n");
+               m->mothurOut("If you are a MAC or Linux user you must also have installed mono, a link to mono is on the webpage. \n");
                m->mothurOut("The catchall command parameters are sabund and label, sabund is required. \n");
                m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
                m->mothurOut("The catchall command should be in the following format: \n");
@@ -156,7 +157,7 @@ int CatchAllCommand::execute() {
                
                //get location of catchall
                GlobalData* globaldata = GlobalData::getInstance();
-               string path = globaldata->argv;
+               path = globaldata->argv;
                path = path.substr(0, (path.find_last_of('m')));
                path = m->getFullPathName(path);
 
@@ -184,26 +185,27 @@ int CatchAllCommand::execute() {
                        if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
                                        m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
                                        
-                                       //create list of output files catchall will make
-                                       //datasetname_Analysis.csv 
-                                       //datasetname_BestModelsAnalysis.csv
-                                       //datasetname_BestModelsFits.csv 
-                                       //datasetname_BubblePlot.csv 
-                                       //datasetname_Poisson_fits.csv 
-                                       //datasetname_SingleExp_fits.csv
-                                       //datasetname_ThreeMixedExp_fits.csv
-                                       //datasetname_TwoMixedExp_fits.csv
-
                                        //create catchall input file from mothur's inputfile
                                        string filename = process(sabund);
-       sabund->print(cout);                                                    
+                                       string outputPath = m->getPathName(filename);
+                               
                                        //create system command
-                                       string catchAllCommand = catchAllCommandExe + filename + " " + path;
-cout << catchAllCommand << endl;
+                                       string catchAllCommand = catchAllCommandExe + filename + " " + outputPath + " 1";
+                               
                                        //run catchall
                                        system(catchAllCommand.c_str());
+                               
+                                       remove(filename.c_str());
+                               
+                                       filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+                               
+                                       outputNames.push_back(filename + "_Analysis.csv");
+                                       outputNames.push_back(filename + "_BestModelsAnalysis.csv");
+                                       outputNames.push_back(filename + "_BestModelsFits.csv");
+                                       outputNames.push_back(filename + "_BubblePlot.csv");
+                               
                                                                                
-                                       if (m->control_pressed) { delete read;  delete input; globaldata->ginput = NULL; delete sabund;  return 0; }
+                                       if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } delete read;  delete input; globaldata->ginput = NULL; delete sabund;  return 0; }
 
                                        processedLabels.insert(sabund->getLabel());
                                        userLabels.erase(sabund->getLabel());
@@ -217,27 +219,27 @@ cout << catchAllCommand << endl;
                                        
                                        m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
                                        
-                                       //create list of output files catchall will make
-                                       //datasetname_Analysis.csv 
-                                       //datasetname_BestModelsAnalysis.csv
-                                       //datasetname_BestModelsFits.csv 
-                                       //datasetname_BubblePlot.csv 
-                                       //datasetname_Poisson_fits.csv 
-                                       //datasetname_SingleExp_fits.csv
-                                       //datasetname_ThreeMixedExp_fits.csv
-                                       //datasetname_TwoMixedExp_fits.csv
 
-                                       
                                        //create catchall input file from mothur's inputfile
                                        string filename = process(sabund);
-                       
+                                       string outputPath = m->getPathName(filename);
+                                       
                                        //create system command
-                                       string catchAllCommand = catchAllCommandExe + filename + " " + path;
-cout << catchAllCommand << endl;
+                                       string catchAllCommand = catchAllCommandExe + filename + " " + outputPath + " 1";
+
                                        //run catchall
                                        system(catchAllCommand.c_str());
+                               
+                                       remove(filename.c_str());
+                               
+                                       filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+                               
+                                       outputNames.push_back(filename + "_Analysis.csv");
+                                       outputNames.push_back(filename + "_BestModelsAnalysis.csv");
+                                       outputNames.push_back(filename + "_BestModelsFits.csv");
+                                       outputNames.push_back(filename + "_BubblePlot.csv");
 
-                                       if (m->control_pressed) { delete read;  delete input; globaldata->ginput = NULL; delete sabund;  return 0; }
+                                       if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } delete read;  delete input; globaldata->ginput = NULL; delete sabund;  return 0; }
 
                                        processedLabels.insert(sabund->getLabel());
                                        userLabels.erase(sabund->getLabel());
@@ -272,25 +274,26 @@ cout << catchAllCommand << endl;
                        sabund = (input->getSAbundVector(lastLabel));
                        
                        m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
-                       //create list of output files catchall will make
-                       //datasetname_Analysis.csv 
-                       //datasetname_BestModelsAnalysis.csv
-                       //datasetname_BestModelsFits.csv 
-                       //datasetname_BubblePlot.csv 
-                       //datasetname_Poisson_fits.csv 
-                       //datasetname_SingleExp_fits.csv
-                       //datasetname_ThreeMixedExp_fits.csv
-                       //datasetname_TwoMixedExp_fits.csv
-
+                       
                        //create catchall input file from mothur's inputfile
                        string filename = process(sabund);
-
+                       string outputPath = m->getPathName(filename);
+                       
                        //create system command
-                       string catchAllCommand = catchAllCommandExe + filename + " " + path;
-cout << catchAllCommand << endl;
+                       string catchAllCommand = catchAllCommandExe + filename + " " + outputPath + " 1";
+                       
                        //run catchall
                        system(catchAllCommand.c_str());
-       
+                       
+                       remove(filename.c_str());
+                       
+                       filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+                       
+                       outputNames.push_back(filename + "_Analysis.csv");
+                       outputNames.push_back(filename + "_BestModelsAnalysis.csv");
+                       outputNames.push_back(filename + "_BestModelsFits.csv");
+                       outputNames.push_back(filename + "_BubblePlot.csv");
+                       
                        
                        delete sabund;
                }
@@ -298,6 +301,8 @@ cout << catchAllCommand << endl;
                delete read;
                delete input; globaldata->ginput = NULL;
                
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } return 0; }
+               
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }       
@@ -314,7 +319,7 @@ cout << catchAllCommand << endl;
 //**********************************************************************************************************************
 string CatchAllCommand::process(SAbundVector* sabund) {
        try {
-               string filename = outputDir + m->getRootName(m->getSimpleName(sabundfile)) + sabund->getLabel() + ".catchall";
+               string filename = outputDir + m->getRootName(m->getSimpleName(sabundfile)) + sabund->getLabel() + ".csv";
                filename = m->getFullPathName(filename);
        
                ofstream out;

diff --git a/catchallcommand.h b/catchallcommand.h
index 186185d5ea68b08b969b6a99ef090ff75d5af72a..d59855b240442d541699970cd0d75a9ef5cde452 100644 (file)
--- a/catchallcommand.h
+++ b/catchallcommand.h
@@ -41,7 +41,7 @@ private:
        ReadOTUFile* read;
        InputData* input;
        
-       string outputDir, sabundfile, rabundfile, listfile, format;
+       string outputDir, sabundfile, rabundfile, listfile, format, path;
        bool abort, allLines;
        set<string> labels;
        vector<string> outputNames;

diff --git a/mothur b/mothur
index ff1c87512ae671899e4be9c14a9f8710b2061016..d83c006c43baab3204cee6b8e4054117949ba11f 100755 (executable)
Binary files a/mothur and b/mothur differ