//**********************************************************************************************************************
vector<string> CatchAllCommand::getValidParameters(){
try {
- string AlignArray[] = {"sabund","label","inputdir","outputdir"};
+ string AlignArray[] = {"sabund","shared","label","inputdir","outputdir"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
return myArray;
}
//**********************************************************************************************************************
vector<string> CatchAllCommand::getRequiredParameters(){
try {
- string AlignArray[] = {"sabund"};
+ string AlignArray[] = {"sabund","shared","or"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
return myArray;
}
else {
//valid paramters for this command
- string Array[] = {"sabund","label","inputdir","outputdir"};
+ string Array[] = {"shared","sabund","label","inputdir","outputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
//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 if (sabundfile == "not found") { sabundfile = ""; }
else { globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); }
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else if (sharedfile == "not found") { sharedfile = ""; }
+
string label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
else { allLines = 1; }
}
+ if ((sharedfile == "") && (sabundfile == "")) { m->mothurOut("You must provide a sabund or shared file for 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); }
+ }
}
}
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 the same folder as your mothur executable. \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 catchall command parameters are shared, sabund and label. shared or 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");
catchAllCommandExe += "\"" + path + "CatchAllcmdW.exe\"" + " ";
#endif
- read = new ReadOTUFile(sabundfile);
- read->read(&*globaldata);
+ vector<string> inputFileNames;
+ if (sharedfile != "") { inputFileNames = parseSharedFile(sharedfile); globaldata->setFormat("sabund"); }
+ else { inputFileNames.push_back(sabundfile); }
- SAbundVector* sabund = globaldata->sabund;
- string lastLabel = sabund->getLabel();
- input = globaldata->ginput;
-
- set<string> processedLabels;
- set<string> userLabels = labels;
-
- string summaryfilename = outputDir + m->getRootName(m->getSimpleName(sabundfile)) + "catchall.summary";
- summaryfilename = m->getFullPathName(summaryfilename);
- outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);
-
- ofstream out;
- m->openOutputFile(summaryfilename, out);
-
- out << "label\tmodel\testimate\tlci\tuci" << endl;
-
- //for each label the user selected
- while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+ 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 = new InputData(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";
+ summaryfilename = m->getFullPathName(summaryfilename);
+
+ ofstream out;
+ m->openOutputFile(summaryfilename, out);
+
+ out << "label\tmodel\testimate\tlci\tuci" << endl;
+
+ //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);
- if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
- m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
+ //create system command
+ string catchAllCommand = "";
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ 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 + "\"";
+ #endif
+ //run catchall
+ system(catchAllCommand.c_str());
- //create catchall input file from mothur's inputfile
- string filename = process(sabund);
- string outputPath = m->getPathName(filename);
-
- //create system command
- string catchAllCommand = "";
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- 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 + "\"";
- #endif
- //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"); 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");
+ remove(filename.c_str());
+
+ filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+
+ 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");
+
+ createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
+
+ 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; }
+
+ processedLabels.insert(sabund->getLabel());
+ userLabels.erase(sabund->getLabel());
+ }
- createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
-
- if (m->control_pressed) { out.close(); 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();
+
- processedLabels.insert(sabund->getLabel());
- userLabels.erase(sabund->getLabel());
- }
-
- if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- string saveLabel = sabund->getLabel();
+ //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";
+ #else
+ if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
+ catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + "\" 1";
+ catchAllCommand = "\"" + catchAllCommand + "\"";
+ #endif
+
+ //run catchall
+ system(catchAllCommand.c_str());
- delete sabund;
- sabund = (input->getSAbundVector(lastLabel));
+ remove(filename.c_str());
- m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
+ filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
-
- //create catchall input file from mothur's inputfile
- string filename = process(sabund);
- string outputPath = m->getPathName(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");
- //create system command
- string catchAllCommand = "";
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
- #else
- if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
- catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + "\" 1";
- catchAllCommand = "\"" + catchAllCommand + "\"";
- #endif
+ createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
+
+ 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; }
- //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"); 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");
+ 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();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ if (sabund != NULL) { delete sabund; }
+ sabund = (input->getSAbundVector(lastLabel));
- createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
+ m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
- if (m->control_pressed) { out.close(); 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);
+ //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";
+ #else
+ if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
+ catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + "\" 1";
+ catchAllCommand = "\"" + catchAllCommand + "\"";
+ #endif
+
+ //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"); 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");
+
+ createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
+
+ delete sabund;
}
+ out.close();
+ delete input;
- lastLabel = sabund->getLabel();
-
- delete sabund;
- sabund = (input->getSAbundVector());
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } return 0; }
+
}
- //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();
+ if (sharedfile == "") {
+ string summaryfilename = outputDir + 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);
}
- //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 = "";
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
- #else
- if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
- catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + "\" 1";
- catchAllCommand = "\"" + catchAllCommand + "\"";
- #endif
-
- //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"); 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");
-
- createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
-
- delete sabund;
- }
-
- out.close();
- 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(); }
}
}
//**********************************************************************************************************************
-string CatchAllCommand::process(SAbundVector* sabund) {
+string CatchAllCommand::process(SAbundVector* sabund, string file1) {
try {
- string filename = outputDir + m->getRootName(m->getSimpleName(sabundfile)) + sabund->getLabel() + ".csv";
+ string filename = outputDir + m->getRootName(m->getSimpleName(file1)) + sabund->getLabel() + ".csv";
filename = m->getFullPathName(filename);
ofstream out;
exit(1);
}
}
+//*********************************************************************************************************************
+string CatchAllCommand::combineSummmary(vector<string>& outputNames) {
+ try {
+
+ ofstream out;
+ string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "catchall.summary";
+
+ //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();
+ remove(outputNames[i].c_str());
+ }
+
+ //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 {
exit(1);
}
}
+//**********************************************************************************************************************
+vector<string> CatchAllCommand::parseSharedFile(string filename) {
+ try {
+ vector<string> filenames;
+
+ //read first line
+ InputData* input = new InputData(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());
+ 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();
+ }
+
+ delete input;
+
+ return filenames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CatchAllCommand", "parseSharedFile");
+ exit(1);
+ }
+}
/**************************************************************************************/
projects / mothur.git / commitdiff