*/
#include "catchallcommand.h"
-#include "globaldata.hpp"
//**********************************************************************************************************************
-vector<string> CatchAllCommand::getValidParameters(){
+vector<string> CatchAllCommand::setParameters(){
try {
- string AlignArray[] = {"sabund","label","inputdir","outputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ //can choose shared or sabund not both, so put them in the same chooseOnlyOneGroup
+ CommandParameter pshared("shared", "InputTypes", "", "", "catchallInputs", "catchallInputs", "none","analysis-bestanalysis-models-bubble-summary",false,false,true); parameters.push_back(pshared);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "catchallInputs", "catchallInputs", "none","analysis-bestanalysis-models-bubble-summary",false,false,true); parameters.push_back(psabund);
+ 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); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "CatchAllCommand", "getValidParameters");
+ m->errorOut(e, "CatchAllCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-CatchAllCommand::CatchAllCommand(){
+string CatchAllCommand::getHelpString(){
try {
- //initialize outputTypes
-
- //need to determine outputFIles and types
+ string helpString = "";
+ helpString += "The catchall command interfaces mothur with the catchall program written by Linda Woodard, Sean Connolly and John Bunge.\n";
+ helpString += "For more information about catchall refer to http://www.northeastern.edu/catchall/index.html \n";
+ helpString += "The catchall executable must be in the same folder as your mothur executable. \n";
+ helpString += "If you are a MAC or Linux user you must also have installed mono, a link to mono is on the webpage. \n";
+ helpString += "The catchall command parameters are shared, sabund and label. shared or sabund is required. \n";
+ helpString += "The label parameter is used to analyze specific labels in your input.\n";
+ helpString += "The catchall command should be in the following format: \n";
+ helpString += "catchall(sabund=yourSabundFile) \n";
+ helpString += "Example: catchall(sabund=abrecovery.fn.sabund) \n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
+ m->errorOut(e, "CatchAllCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> CatchAllCommand::getRequiredParameters(){
- try {
- string AlignArray[] = {"sabund"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "CatchAllCommand", "getRequiredParameters");
- exit(1);
- }
+string CatchAllCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "analysis") { pattern = "[filename],_Analysis.csv"; }
+ else if (type == "bestanalysis") { pattern = "[filename],_BestModelsAnalysis.csv"; }
+ else if (type == "models") { pattern = "[filename],_BestModelsAnalysis.csv"; }
+ else if (type == "bubble") { pattern = "[filename],_BubblePlot.csv"; }
+ else if (type == "summary") { pattern = "[filename],catchall.summary"; }
+ else if (type == "sabund") { pattern = "[filename],[distance],csv"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CatchAllCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
-vector<string> CatchAllCommand::getRequiredFiles(){
+CatchAllCommand::CatchAllCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["analysis"] = tempOutNames;
+ outputTypes["bestanalysis"] = tempOutNames;
+ outputTypes["models"] = tempOutNames;
+ outputTypes["bubble"] = tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+ outputTypes["sabund"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "CatchAllCommand", "getRequiredFiles");
+ m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
exit(1);
}
}
/**************************************************************************************/
CatchAllCommand::CatchAllCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
- abort = false;
+
+ abort = false; calledHelp = false;
allLines = 1;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"sabund","label","inputdir","outputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
-
//initialize outputTypes
- //need to determine outputFIles and types
-
+ vector<string> tempOutNames;
+ outputTypes["analysis"] = tempOutNames;
+ outputTypes["bestanalysis"] = tempOutNames;
+ outputTypes["models"] = tempOutNames;
+ outputTypes["bubble"] = tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+ outputTypes["sabund"] = 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);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["sabund"] = inputDir + it->second; }
}
+
+ it = parameters.find("shared");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["shared"] = inputDir + it->second; }
+ }
}
//check for required parameters
sabundfile = validParameter.validFile(parameters, "sabund", true);
if (sabundfile == "not open") { sabundfile = ""; abort = true; }
- else if (sabundfile == "not found") { sabundfile = ""; m->mothurOut("You must provide a sabund file for the catchall command."); m->mothurOutEndLine(); abort=true; }
- else { globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); }
+ else if (sabundfile == "not found") { sabundfile = ""; }
+ else { m->setSabundFile(sabundfile); }
+
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else if (sharedfile == "not found") { sharedfile = ""; }
+ else { m->setSharedFile(sharedfile); }
string label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else { allLines = 1; }
}
-
+ if ((sharedfile == "") && (sabundfile == "")) {
+ //is there are current file available for either of these?
+ //give priority to shared, then sabund
+ //if there is a current shared file, use it
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else {
+ sabundfile = m->getSabundFile();
+ if (sabundfile != "") { m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. You must provide a sabund or shared file before you can use the catchall command."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
+ }
+
//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 = m->hasPath(sabundfile); }
+ outputDir = validParameter.validFile(parameters, "outputdir", false);
+ if (outputDir == "not found"){
+ if (sabundfile != "") { outputDir = m->hasPath(sabundfile); }
+ else { outputDir = m->hasPath(sharedfile); }
+ }
}
}
exit(1);
}
}
-//**********************************************************************************************************************
-
-void CatchAllCommand::help(){
- try {
- 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");
- m->mothurOut("catchall(sabund=yourSabundFile) \n");
- m->mothurOut("Example: catchall(sabund=abrecovery.fn.sabund) \n");
- }
- catch(exception& e) {
- m->errorOut(e, "CatchAllCommand", "help");
- exit(1);
- }
-}
-
/**************************************************************************************/
int CatchAllCommand::execute() {
try {
- if (abort == true) { return 0; }
-
- //prepare full output directory
- outputDir = m->getFullPathName(outputDir);
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get location of catchall
- GlobalData* globaldata = GlobalData::getInstance();
- path = globaldata->argv;
- path = path.substr(0, (path.find_last_of('m')));
+ path = m->argv;
+ path = path.substr(0, (path.find_last_of("othur")-5));
path = m->getFullPathName(path);
-
- string catchAllCommandExe = "";
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- catchAllCommandExe += "mono " + path + "catchall/CatchAllcmdL.exe ";
+
+ if (m->debug) { m->mothurOut("[DEBUG]: mothur's path = " + path + "\n"); }
+
+ savedOutputDir = outputDir;
+ string catchAllCommandExe = "";
+ string catchAllTest = "";
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ if (outputDir == "") { outputDir = "./"; } //force full pathname to be created for catchall, this is necessary because if catchall is in the path it will look for input file whereever the exe is and not the cwd.
+ catchAllTest = path + "CatchAllcmdL.exe";
#else
- catchAllCommandExe += path + "catchall/CatchAllcmdW.exe ";
+ if (outputDir == "") { outputDir = ".\\"; } //force full pathname to be created for catchall, this is necessary because if catchall is in the path it will look for input file whereever the exe is and not the cwd.
+ catchAllTest = path + "CatchAllcmdW.exe";
#endif
- read = new ReadOTUFile(sabundfile);
- read->read(&*globaldata);
+ //test to make sure formatdb exists
+ ifstream in;
+ catchAllTest = m->getFullPathName(catchAllTest);
+ int ableToOpen = m->openInputFile(catchAllTest, in, "no error"); in.close();
+ if(ableToOpen == 1) {
+ m->mothurOut(catchAllTest + " file does not exist. Checking path... \n");
+ //check to see if uchime is in the path??
+
+ string programName = "CatchAllcmdW.exe";
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ programName = "CatchAllcmdL.exe";
+#endif
+ string cLocation = m->findProgramPath(programName);
+
+ ifstream in2;
+ ableToOpen = m->openInputFile(cLocation, in2, "no error"); in2.close();
+
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + cLocation + " file does not exist. mothur requires the catchall executable."); m->mothurOutEndLine(); return 0; }
+ else { m->mothurOut("Found catchall in your path, using " + cLocation + "\n"); catchAllTest = cLocation; }
+ }
+ catchAllTest = m->getFullPathName(catchAllTest);
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ catchAllCommandExe += "mono \"" + catchAllTest + "\" ";
+#else
+ catchAllCommandExe += "\"" + catchAllTest + "\" ";
+#endif
+
+ //prepare full output directory
+ outputDir = m->getFullPathName(outputDir);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: catchall location = " + catchAllCommandExe + "\n[DEBUG]: outputDir = " + outputDir + "\n"); }
+
+ vector<string> inputFileNames;
+ if (sharedfile != "") { inputFileNames = parseSharedFile(sharedfile); }
+ else { inputFileNames.push_back(sabundfile); }
- SAbundVector* sabund = globaldata->sabund;
- string lastLabel = sabund->getLabel();
- input = globaldata->ginput;
+ for (int p = 0; p < inputFileNames.size(); p++) {
+ if (inputFileNames.size() > 1) {
+ m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
+ }
+
+ InputData input(inputFileNames[p], "sabund");
+ SAbundVector* sabund = input.getSAbundVector();
+ string lastLabel = sabund->getLabel();
+
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
+ string summaryfilename = getOutputFileName("summary", variables);
+ summaryfilename = m->getFullPathName(summaryfilename);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: Input File = " + inputFileNames[p] + ".\n[DEBUG]: inputdata address = " + toString(&input) + ".\n[DEBUG]: sabund address = " + toString(&sabund) + ".\n"); }
+
+ ofstream out;
+ m->openOutputFile(summaryfilename, out);
+
+ out << "label\tmodel\testimate\tlci\tuci" << endl;
+
+ if (m->debug) { string open = "no"; if (out.is_open()) { open = "yes"; } m->mothurOut("[DEBUG]: output stream is open = " + open + ".\n"); }
+
+ //for each label the user selected
+ while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
- set<string> processedLabels;
- set<string> userLabels = labels;
-
- //for each label the user selected
- while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+ if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
+ m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
+
+ //create catchall input file from mothur's inputfile
+ string filename = process(sabund, inputFileNames[p]);
+ string outputPath = m->getPathName(filename);
+
+ //create system command
+ string catchAllCommand = "";
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + + "\" 1";
+ #else
+ //removes extra '\\' catchall doesnt like that
+ vector<string> tempNames;
+ string tempFilename = filename;
+ m->splitAtDash(tempFilename, tempNames);
+ tempFilename = tempNames[0];
+ tempNames.clear();
+ string tempOutputPath = outputPath;
+ m->splitAtDash(tempOutputPath, tempNames);
+ tempOutputPath = tempNames[0];
+ if (tempOutputPath.length() > 0) { tempOutputPath = tempOutputPath.substr(0, tempOutputPath.length()-1); }
+ catchAllCommand += catchAllCommandExe + "\"" + tempFilename + "\" \"" + tempOutputPath + "\" 1";
+ catchAllCommand = "\"" + catchAllCommand + "\"";
+ #endif
+
+ if (m->debug) { m->mothurOut("[DEBUG]: catchall command = " + catchAllCommand + ". About to call system.\n"); }
+
+ //run catchall
+ system(catchAllCommand.c_str());
+
+ if (m->debug) { m->mothurOut("[DEBUG]: back from system call. Keeping file: " + filename + ".\n"); }
+
+ if (!m->debug) { m->mothurRemove(filename); }
- if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
- m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
+ filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+ if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
- //create catchall input file from mothur's inputfile
- string filename = process(sabund);
- string outputPath = m->getPathName(filename);
-
- //create system command
- 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");
+ variables["[filename]"] = filename;
+ outputNames.push_back(getOutputFileName("analysis", variables)); outputTypes["analysis"].push_back(getOutputFileName("analysis", variables));
+ outputNames.push_back(getOutputFileName("bestanalysis", variables)); outputTypes["bestanalysis"].push_back(getOutputFileName("bestanalysis", variables));
+ outputNames.push_back(getOutputFileName("models", variables)); outputTypes["models"].push_back(getOutputFileName("models", variables));
+ outputNames.push_back(getOutputFileName("bubble", variables)); outputTypes["bubble"].push_back(getOutputFileName("bubble", variables));
+
+ if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); }
+
+ createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: Done creating summary file.\n"); }
+
+ if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {m->mothurRemove(outputNames[i]); } delete sabund; return 0; }
+
+ processedLabels.insert(sabund->getLabel());
+ userLabels.erase(sabund->getLabel());
+ }
-
- 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; }
+ if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = sabund->getLabel();
+
+ delete sabund;
+ sabund = (input.getSAbundVector(lastLabel));
+
+ m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
+
+
+ //create catchall input file from mothur's inputfile
+ string filename = process(sabund, inputFileNames[p]);
+ string outputPath = m->getPathName(filename);
+
+ //create system command
+ string catchAllCommand = "";
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + + "\" 1";
+ #else
+ //removes extra '\\' catchall doesnt like that
+ vector<string> tempNames;
+ string tempFilename = filename;
+ m->splitAtDash(tempFilename, tempNames);
+ tempFilename = tempNames[0];
+ tempNames.clear();
+ string tempOutputPath = outputPath;
+ m->splitAtDash(tempOutputPath, tempNames);
+ tempOutputPath = tempNames[0];
+ if (tempOutputPath.length() > 0) { tempOutputPath = tempOutputPath.substr(0, tempOutputPath.length()-1); }
+ catchAllCommand += catchAllCommandExe + "\"" + tempFilename + "\" \"" + tempOutputPath + "\" 1";
+ catchAllCommand = "\"" + catchAllCommand + "\"";
+ #endif
+
+ if (m->debug) { m->mothurOut("[DEBUG]: catchall command = " + catchAllCommand + ". About to call system.\n"); }
+
+ //run catchall
+ system(catchAllCommand.c_str());
+
+ if (m->debug) { m->mothurOut("[DEBUG]: back from system call. Keeping file: " + filename + ".\n"); }
+
+ if (!m->debug) { m->mothurRemove(filename); }
- processedLabels.insert(sabund->getLabel());
- userLabels.erase(sabund->getLabel());
- }
-
- if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- string saveLabel = sabund->getLabel();
-
- delete sabund;
- sabund = (input->getSAbundVector(lastLabel));
- m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
+ filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+ if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
-
- //create catchall input file from mothur's inputfile
- string filename = process(sabund);
- string outputPath = m->getPathName(filename);
+ variables["[filename]"] = filename;
+ outputNames.push_back(getOutputFileName("analysis", variables)); outputTypes["analysis"].push_back(getOutputFileName("analysis", variables));
+ outputNames.push_back(getOutputFileName("bestanalysis", variables)); outputTypes["bestanalysis"].push_back(getOutputFileName("bestanalysis", variables));
+ outputNames.push_back(getOutputFileName("models", variables)); outputTypes["models"].push_back(getOutputFileName("models", variables));
+ outputNames.push_back(getOutputFileName("bubble", variables)); outputTypes["bubble"].push_back(getOutputFileName("bubble", variables));
+
+
+ if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); }
+
+ createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: Done creating summary file.\n"); }
- //create system command
- string catchAllCommand = catchAllCommandExe + filename + " " + outputPath + " 1";
+ if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {m->mothurRemove(outputNames[i]); } delete sabund; return 0; }
- //run catchall
- system(catchAllCommand.c_str());
+ processedLabels.insert(sabund->getLabel());
+ userLabels.erase(sabund->getLabel());
+
+ //restore real lastlabel to save below
+ sabund->setLabel(saveLabel);
+ }
- remove(filename.c_str());
- filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+ lastLabel = sabund->getLabel();
- 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) { 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());
-
- //restore real lastlabel to save below
- sabund->setLabel(saveLabel);
+ delete sabund;
+ sabund = (input.getSAbundVector());
}
-
- lastLabel = sabund->getLabel();
-
- delete sabund;
- sabund = (input->getSAbundVector());
- }
-
- //output error messages about any remaining user labels
- set<string>::iterator it;
- bool needToRun = false;
- for (it = userLabels.begin(); it != userLabels.end(); it++) {
- m->mothurOut("Your file does not include the label " + *it);
- if (processedLabels.count(lastLabel) != 1) {
- m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
- needToRun = true;
- }else {
- m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
}
- }
-
- //run last label if you need to
- if (needToRun == true) {
- if (sabund != NULL) { delete sabund; }
- sabund = (input->getSAbundVector(lastLabel));
-
- m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
-
- //create catchall input file from mothur's inputfile
- string filename = process(sabund);
- string outputPath = m->getPathName(filename);
-
- //create system command
- 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");
+ //run last label if you need to
+ if (needToRun == true) {
+ if (sabund != NULL) { delete sabund; }
+ sabund = (input.getSAbundVector(lastLabel));
+
+ m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
+
+ //create catchall input file from mothur's inputfile
+ string filename = process(sabund, inputFileNames[p]);
+ string outputPath = m->getPathName(filename);
+
+ //create system command
+ string catchAllCommand = "";
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + + "\" 1";
+ #else
+ //removes extra '\\' catchall doesnt like that
+ vector<string> tempNames;
+ string tempFilename = filename;
+ m->splitAtDash(tempFilename, tempNames);
+ tempFilename = tempNames[0];
+ tempNames.clear();
+ string tempOutputPath = outputPath;
+ m->splitAtDash(tempOutputPath, tempNames);
+ tempOutputPath = tempNames[0];
+ if (tempOutputPath.length() > 0) { tempOutputPath = tempOutputPath.substr(0, tempOutputPath.length()-1); }
+ catchAllCommand += catchAllCommandExe + "\"" + tempFilename + "\" \"" + tempOutputPath + "\" 1";
+ catchAllCommand = "\"" + catchAllCommand + "\"";
+ #endif
+
+ if (m->debug) { m->mothurOut("[DEBUG]: catchall command = " + catchAllCommand + ". About to call system.\n"); }
+
+ //run catchall
+ system(catchAllCommand.c_str());
+
+ if (m->debug) { m->mothurOut("[DEBUG]: back from system call. Keeping file: " + filename + ".\n"); }
+
+ if (!m->debug) { m->mothurRemove(filename); }
+
+ filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+ if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
+
+ variables["[filename]"] = filename;
+ outputNames.push_back(getOutputFileName("analysis", variables)); outputTypes["analysis"].push_back(getOutputFileName("analysis", variables));
+ outputNames.push_back(getOutputFileName("bestanalysis", variables)); outputTypes["bestanalysis"].push_back(getOutputFileName("bestanalysis", variables));
+ outputNames.push_back(getOutputFileName("models", variables)); outputTypes["models"].push_back(getOutputFileName("models", variables));
+ outputNames.push_back(getOutputFileName("bubble", variables)); outputTypes["bubble"].push_back(getOutputFileName("bubble", variables));
+ if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); }
+
+ createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: Done creating summary file.\n"); }
+
+ delete sabund;
+ }
+ out.close();
- delete sabund;
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {m->mothurRemove(outputNames[i]); } return 0; }
+
}
-
- 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; }
+ if (sharedfile == "") {
+ string summaryfilename = savedOutputDir + m->getRootName(m->getSimpleName(inputFileNames[0])) + "catchall.summary";
+ summaryfilename = m->getFullPathName(summaryfilename);
+ outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);
+ }else { //combine summaries
+ vector<string> sumNames;
+ for (int i = 0; i < inputFileNames.size(); i++) {
+ sumNames.push_back(m->getFullPathName(outputDir + m->getRootName(m->getSimpleName(inputFileNames[i])) + "catchall.summary"));
+ }
+ string summaryfilename = combineSummmary(sumNames);
+ outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);
+ }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
}
}
//**********************************************************************************************************************
-string CatchAllCommand::process(SAbundVector* sabund) {
+string CatchAllCommand::process(SAbundVector* sabund, string file1) {
try {
- string filename = outputDir + m->getRootName(m->getSimpleName(sabundfile)) + sabund->getLabel() + ".csv";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(file1));
+ variables["[distance]"] = sabund->getLabel();
+ string filename = getOutputFileName("sabund", variables);
filename = m->getFullPathName(filename);
ofstream out;
m->openOutputFile(filename, out);
+ if (m->debug) { m->mothurOut("[DEBUG]: Creating " + filename + " file for catchall, shown below.\n\n"); }
+
for (int i = 1; i <= sabund->getMaxRank(); i++) {
int temp = sabund->get(i);
if (temp != 0) {
out << i << "," << temp << endl;
+ if (m->debug) { m->mothurOut(toString(i) + "," + toString(temp) + "\n"); }
}
}
out.close();
+
+ if (m->debug) { m->mothurOut("[DEBUG]: Done creating " + filename + " file for catchall, shown above.\n\n"); }
return filename;
exit(1);
}
}
+//*********************************************************************************************************************
+string CatchAllCommand::combineSummmary(vector<string>& outputNames) {
+ try {
+
+ ofstream out;
+ map<string, string> variables;
+ variables["[filename]"] = savedOutputDir + m->getRootName(m->getSimpleName(sharedfile));
+ string combineFileName = getOutputFileName("summary", variables);
+
+ //open combined file
+ m->openOutputFile(combineFileName, out);
+
+ out << "label\tgroup\tmodel\testimate\tlci\tuci" << endl;
+
+ //open each groups summary file
+ string newLabel = "";
+ int numLines = 0;
+ map<string, vector<string> > files;
+ for (int i=0; i<outputNames.size(); i++) {
+ vector<string> thisFilesLines;
+
+ ifstream temp;
+ m->openInputFile(outputNames[i], temp);
+
+ //read through first line - labels
+ m->getline(temp);
+ m->gobble(temp);
+
+ //for each label
+ while (!temp.eof()) {
+
+ string thisLine = "";
+ string tempLabel;
+
+ for (int j = 0; j < 5; j++) {
+ temp >> tempLabel;
+
+ //save for later
+ if (j == 1) { thisLine += groups[i] + "\t" + tempLabel + "\t"; }
+ else{ thisLine += tempLabel + "\t"; }
+ }
+
+ thisLine += "\n";
+
+ thisFilesLines.push_back(thisLine);
+
+ m->gobble(temp);
+ }
+
+ files[outputNames[i]] = thisFilesLines;
+
+ numLines = thisFilesLines.size();
+
+ temp.close();
+ m->mothurRemove(outputNames[i]);
+ }
+
+ //for each label
+ for (int k = 0; k < numLines; k++) {
+
+ //grab summary data for each group
+ for (int i=0; i<outputNames.size(); i++) {
+ out << files[outputNames[i]][k];
+ }
+ }
+
+
+ out.close();
+
+ //return combine file name
+ return combineFileName;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CatchAllCommand", "combineSummmary");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int CatchAllCommand::createSummaryFile(string file1, string label, ofstream& out) {
+ try {
+
+ ifstream in;
+ int able = m->openInputFile(file1, in, "noerror");
+
+ if (able == 1) { m->mothurOut("[ERROR]: the catchall program did not run properly. Please check to make sure it is located in the same folder as your mothur executable.");m->mothurOutEndLine(); m->control_pressed = true; return 0; }
+
+ if (!in.eof()) {
+
+ string header = m->getline(in); m->gobble(in);
+
+ int pos = header.find("Total Number of Observed Species =");
+ string numString = "";
+
+
+ if (pos == string::npos) { m->mothurOut("[ERROR]: cannot parse " + file1); m->mothurOutEndLine(); }
+ else {
+ //pos will be the position of the T in total, so we want to count to the position of =
+ pos += 34;
+ char c=header[pos];
+ while (c != ','){
+ if (c != ' ') {
+ numString += c;
+ }
+ pos++;
+ c=header[pos];
+
+ //sanity check
+ if (pos > header.length()) { m->mothurOut("Cannot find number of OTUs in " + file1); m->mothurOutEndLine(); in.close(); return 0; }
+ }
+ }
+
+ string firstline = m->getline(in); m->gobble(in);
+ vector<string> values;
+ m->splitAtComma(firstline, values);
+
+ values.pop_back(); //last value is always a blank string since the last character in the line is always a ','
+
+ if (values.size() == 1) { //grab next line if firstline didn't have what you wanted
+ string secondline = m->getline(in); m->gobble(in);
+ values.clear();
+ m->splitAtComma(secondline, values);
+
+ values.pop_back(); //last value is always a blank string since the last character in the line is always a ','
+ }
+
+ if (values.size() == 1) { //still not what we wanted fill values with numOTUs
+ values.resize(8, "");
+ values[1] = "Sobs";
+ values[4] = numString;
+ values[6] = numString;
+ values[7] = numString;
+ }
+
+ if (values.size() < 8) { values.resize(8, ""); }
+
+ out << label << '\t' << values[1] << '\t' << values[4] << '\t' << values[6] << '\t' << values[7] << endl;
+ }
+
+ in.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CatchAllCommand", "createSummaryFile");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> CatchAllCommand::parseSharedFile(string filename) {
+ try {
+ vector<string> filenames;
+
+ //read first line
+ InputData input(filename, "sharedfile");
+ vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
+
+ string sharedFileRoot = outputDir + m->getRootName(m->getSimpleName(filename));
+
+ //clears file before we start to write to it below
+ for (int i=0; i<lookup.size(); i++) {
+ m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".sabund"));
+ filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".sabund"));
+ groups.push_back(lookup[i]->getGroup());
+ }
+
+ while(lookup[0] != NULL) {
+
+ for (int i = 0; i < lookup.size(); i++) {
+ SAbundVector sav = lookup[i]->getSAbundVector();
+ ofstream out;
+ m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".sabund", out);
+ sav.print(out);
+ out.close();
+ }
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input.getSharedRAbundVectors();
+ }
+
+ return filenames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CatchAllCommand", "parseSharedFile");
+ exit(1);
+ }
+}
/**************************************************************************************/
-
-
-
projects / mothur.git / blobdiff