//**********************************************************************************************************************
vector<string> CatchAllCommand::setParameters(){
try {
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ 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",false,false); parameters.push_back(pshared);
- CommandParameter psabund("sabund", "InputTypes", "", "", "catchallInputs", "catchallInputs", "none",false,false); parameters.push_back(psabund);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ 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); }
}
}
//**********************************************************************************************************************
+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);
+ }
+}
+//**********************************************************************************************************************
CatchAllCommand::CatchAllCommand(){
try {
abort = true; calledHelp = true;
setParameters();
//initialize outputTypes
vector<string> tempOutNames;
- outputTypes["csv"] = 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", "CatchAllCommand");
//initialize outputTypes
vector<string> tempOutNames;
- outputTypes["csv"] = tempOutNames;
- outputTypes["summary"] = 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);
path = path.substr(0, (path.find_last_of("othur")-5));
path = m->getFullPathName(path);
+ if (m->debug) { m->mothurOut("[DEBUG]: mothur's path = " + path + "\n"); }
+
savedOutputDir = outputDir;
- string catchAllCommandExe = "";
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- catchAllCommandExe += "mono " + path + "CatchAllcmdL.exe ";
+ 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 + "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
+ //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); }
m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
}
- InputData* input = new InputData(inputFileNames[p], "sabund");
- SAbundVector* sabund = input->getSAbundVector();
+ InputData input(inputFileNames[p], "sabund");
+ SAbundVector* sabund = input.getSAbundVector();
string lastLabel = sabund->getLabel();
set<string> processedLabels;
set<string> userLabels = labels;
- string summaryfilename = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "catchall.summary";
+ 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))) {
-
+
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)
- catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + + "\" 1";
#else
- if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
- catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + "\" 1";
- //wrap entire string in ""
- catchAllCommand = "\"" + catchAllCommand + "\"";
+ //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());
-
- remove(filename.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); }
- outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
- outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
- outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
- outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].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++) {remove(outputNames[i].c_str()); } delete input; delete sabund; return 0; }
+ 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());
string saveLabel = sabund->getLabel();
delete sabund;
- sabund = (input->getSAbundVector(lastLabel));
+ 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)
- catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + + "\" 1";
#else
- if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
- catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + "\" 1";
+ //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());
-
- remove(filename.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); }
- outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
- outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
- outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
- outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].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++) {remove(outputNames[i].c_str()); } delete input; delete sabund; return 0; }
+ 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());
lastLabel = sabund->getLabel();
delete sabund;
- sabund = (input->getSAbundVector());
+ sabund = (input.getSAbundVector());
}
//output error messages about any remaining user labels
//run last label if you need to
if (needToRun == true) {
if (sabund != NULL) { delete sabund; }
- sabund = (input->getSAbundVector(lastLabel));
+ sabund = (input.getSAbundVector(lastLabel));
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
//create system command
string catchAllCommand = "";
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + + "\" 1";
#else
- if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
- catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + "\" 1";
- catchAllCommand = "\"" + catchAllCommand + "\"";
+ //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"); }
- remove(filename.c_str());
+ 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); }
- outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
- outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
- outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
- outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].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"); }
delete sabund;
}
out.close();
- delete input;
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {m->mothurRemove(outputNames[i]); } return 0; }
}
//**********************************************************************************************************************
string CatchAllCommand::process(SAbundVector* sabund, string file1) {
try {
- string filename = outputDir + m->getRootName(m->getSimpleName(file1)) + 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;
try {
ofstream out;
- string combineFileName = savedOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "catchall.summary";
+ map<string, string> variables;
+ variables["[filename]"] = savedOutputDir + m->getRootName(m->getSimpleName(sharedfile));
+ string combineFileName = getOutputFileName("summary", variables);
//open combined file
m->openOutputFile(combineFileName, out);
numLines = thisFilesLines.size();
temp.close();
- remove(outputNames[i].c_str());
+ m->mothurRemove(outputNames[i]);
}
//for each label
vector<string> filenames;
//read first line
- InputData* input = new InputData(filename, "sharedfile");
- vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
+ 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++) {
- remove((sharedFileRoot + lookup[i]->getGroup() + ".sabund").c_str());
+ m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".sabund"));
filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".sabund"));
groups.push_back(lookup[i]->getGroup());
}
}
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
- lookup = input->getSharedRAbundVectors();
+ lookup = input.getSharedRAbundVectors();
}
- delete input;
-
return filenames;
}
catch(exception& e) {
projects / mothur.git / blobdiff