*/
#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",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);
+
+ 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");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-CatchAllCommand::CatchAllCommand(){
- try {
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["csv"] = tempOutNames;
- outputTypes["summary"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
+ m->errorOut(e, "CatchAllCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> CatchAllCommand::getRequiredParameters(){
+string CatchAllCommand::getHelpString(){
try {
- string AlignArray[] = {"sabund"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
- return myArray;
+ 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", "getRequiredParameters");
+ m->errorOut(e, "CatchAllCommand", "getHelpString");
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["csv"] = tempOutNames;
+ outputTypes["summary"] = 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 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 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 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);
-
+
+ savedOutputDir = outputDir;
string catchAllCommandExe = "";
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
catchAllCommandExe += "mono " + path + "CatchAllcmdL.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.
#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.
#endif
- read = new ReadOTUFile(sabundfile);
- read->read(&*globaldata);
-
- 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);
+ //prepare full output directory
+ outputDir = m->getFullPathName(outputDir);
- out << "label\tmodel\testimate\tlci\tuci" << endl;
+ vector<string> inputFileNames;
+ if (sharedfile != "") { inputFileNames = parseSharedFile(sharedfile); }
+ else { inputFileNames.push_back(sabundfile); }
- //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);
+
+ //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
- if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
- m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
+ //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");
+ 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");
+
+ createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
+
+ if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {m->mothurRemove(outputNames[i]); } 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));
+ m->mothurRemove(filename);
- 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);
+ 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);
- //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
+ if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {m->mothurRemove(outputNames[i]); } 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());
+
+ 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");
+
+ 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++) {m->mothurRemove(outputNames[i]); } 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 = 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);
}
- //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 = savedOutputDir + 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();
+ 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;
- m->openInputFile(file1, 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);
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++) {
+ 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();
+ }
+
+ delete input;
+
+ return filenames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CatchAllCommand", "parseSharedFile");
+ exit(1);
+ }
+}
/**************************************************************************************/
projects / mothur.git / blobdiff