5 * Created by westcott on 5/11/10.
6 * Copyright 2010 Schloss Lab. All rights reserved.
10 #include "catchallcommand.h"
11 #include "globaldata.hpp"
13 //**********************************************************************************************************************
14 vector<string> CatchAllCommand::getValidParameters(){
16 string AlignArray[] = {"sabund","label","inputdir","outputdir"};
17 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
21 m->errorOut(e, "CatchAllCommand", "getValidParameters");
25 //**********************************************************************************************************************
26 CatchAllCommand::CatchAllCommand(){
28 //initialize outputTypes
29 vector<string> tempOutNames;
30 outputTypes["csv"] = tempOutNames;
33 m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
37 //**********************************************************************************************************************
38 vector<string> CatchAllCommand::getRequiredParameters(){
40 string AlignArray[] = {"sabund"};
41 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
45 m->errorOut(e, "CatchAllCommand", "getRequiredParameters");
49 //**********************************************************************************************************************
50 vector<string> CatchAllCommand::getRequiredFiles(){
52 vector<string> myArray;
56 m->errorOut(e, "CatchAllCommand", "getRequiredFiles");
60 /**************************************************************************************/
61 CatchAllCommand::CatchAllCommand(string option) {
63 globaldata = GlobalData::getInstance();
67 //allow user to run help
68 if(option == "help") { help(); abort = true; }
71 //valid paramters for this command
72 string Array[] = {"sabund","label","inputdir","outputdir"};
73 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
75 OptionParser parser(option);
76 map<string,string> parameters = parser.getParameters();
78 ValidParameters validParameter;
79 map<string, string>::iterator it;
81 //check to make sure all parameters are valid for command
82 for (it = parameters.begin(); it != parameters.end(); it++) {
83 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
86 //initialize outputTypes
87 vector<string> tempOutNames;
88 outputTypes["csv"] = tempOutNames;
90 //if the user changes the input directory command factory will send this info to us in the output parameter
91 string inputDir = validParameter.validFile(parameters, "inputdir", false);
92 if (inputDir == "not found"){ inputDir = ""; }
95 it = parameters.find("sabund");
96 //user has given a template file
97 if(it != parameters.end()){
98 path = m->hasPath(it->second);
99 //if the user has not given a path then, add inputdir. else leave path alone.
100 if (path == "") { parameters["sabund"] = inputDir + it->second; }
104 //check for required parameters
105 sabundfile = validParameter.validFile(parameters, "sabund", true);
106 if (sabundfile == "not open") { sabundfile = ""; abort = true; }
107 else if (sabundfile == "not found") { sabundfile = ""; m->mothurOut("You must provide a sabund file for the catchall command."); m->mothurOutEndLine(); abort=true; }
108 else { globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); }
110 string label = validParameter.validFile(parameters, "label", false);
111 if (label == "not found") { label = ""; }
113 if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
114 else { allLines = 1; }
118 //if the user changes the output directory command factory will send this info to us in the output parameter
119 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(sabundfile); }
123 catch(exception& e) {
124 m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
128 //**********************************************************************************************************************
130 void CatchAllCommand::help(){
132 m->mothurOut("The catchall command interfaces mothur with the catchall program written by Linda Woodard, Sean Connolly and John Bunge.\n");
133 m->mothurOut("For more information about catchall refer to http://www.northeastern.edu/catchall/index.html \n");
134 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");
135 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");
136 m->mothurOut("The catchall command parameters are sabund and label, sabund is required. \n");
137 m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
138 m->mothurOut("The catchall command should be in the following format: \n");
139 m->mothurOut("catchall(sabund=yourSabundFile) \n");
140 m->mothurOut("Example: catchall(sabund=abrecovery.fn.sabund) \n");
142 catch(exception& e) {
143 m->errorOut(e, "CatchAllCommand", "help");
148 /**************************************************************************************/
149 int CatchAllCommand::execute() {
152 if (abort == true) { return 0; }
154 //prepare full output directory
155 outputDir = m->getFullPathName(outputDir);
157 //get location of catchall
158 GlobalData* globaldata = GlobalData::getInstance();
159 path = globaldata->argv;
160 path = path.substr(0, (path.find_last_of('m')));
161 path = m->getFullPathName(path);
163 string catchAllCommandExe = "";
164 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
165 catchAllCommandExe += "mono " + path + "catchall/CatchAllcmdL.exe ";
167 catchAllCommandExe += path + "catchall/CatchAllcmdW.exe ";
170 read = new ReadOTUFile(sabundfile);
171 read->read(&*globaldata);
173 SAbundVector* sabund = globaldata->sabund;
174 string lastLabel = sabund->getLabel();
175 input = globaldata->ginput;
177 set<string> processedLabels;
178 set<string> userLabels = labels;
180 //for each label the user selected
181 while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
184 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
185 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
187 //create catchall input file from mothur's inputfile
188 string filename = process(sabund);
189 string outputPath = m->getPathName(filename);
191 //create system command
192 string catchAllCommand = catchAllCommandExe + filename + " " + outputPath + " 1";
195 system(catchAllCommand.c_str());
197 remove(filename.c_str());
199 filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
201 outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
202 outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
203 outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
204 outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
207 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; }
209 processedLabels.insert(sabund->getLabel());
210 userLabels.erase(sabund->getLabel());
213 if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
214 string saveLabel = sabund->getLabel();
217 sabund = (input->getSAbundVector(lastLabel));
219 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
222 //create catchall input file from mothur's inputfile
223 string filename = process(sabund);
224 string outputPath = m->getPathName(filename);
226 //create system command
227 string catchAllCommand = catchAllCommandExe + filename + " " + outputPath + " 1";
230 system(catchAllCommand.c_str());
232 remove(filename.c_str());
234 filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
236 outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
237 outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
238 outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
239 outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
241 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; }
243 processedLabels.insert(sabund->getLabel());
244 userLabels.erase(sabund->getLabel());
246 //restore real lastlabel to save below
247 sabund->setLabel(saveLabel);
251 lastLabel = sabund->getLabel();
254 sabund = (input->getSAbundVector());
257 //output error messages about any remaining user labels
258 set<string>::iterator it;
259 bool needToRun = false;
260 for (it = userLabels.begin(); it != userLabels.end(); it++) {
261 m->mothurOut("Your file does not include the label " + *it);
262 if (processedLabels.count(lastLabel) != 1) {
263 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
266 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
270 //run last label if you need to
271 if (needToRun == true) {
272 if (sabund != NULL) { delete sabund; }
273 sabund = (input->getSAbundVector(lastLabel));
275 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
277 //create catchall input file from mothur's inputfile
278 string filename = process(sabund);
279 string outputPath = m->getPathName(filename);
281 //create system command
282 string catchAllCommand = catchAllCommandExe + filename + " " + outputPath + " 1";
285 system(catchAllCommand.c_str());
287 remove(filename.c_str());
289 filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
291 outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
292 outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
293 outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
294 outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
300 delete input; globaldata->ginput = NULL;
302 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } return 0; }
304 m->mothurOutEndLine();
305 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
306 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
307 m->mothurOutEndLine();
312 catch(exception& e) {
313 m->errorOut(e, "CatchAllCommand", "execute");
317 //**********************************************************************************************************************
318 string CatchAllCommand::process(SAbundVector* sabund) {
320 string filename = outputDir + m->getRootName(m->getSimpleName(sabundfile)) + sabund->getLabel() + ".csv";
321 filename = m->getFullPathName(filename);
324 m->openOutputFile(filename, out);
326 for (int i = 1; i <= sabund->getMaxRank(); i++) {
327 int temp = sabund->get(i);
330 out << i << "," << temp << endl;
338 catch(exception& e) {
339 m->errorOut(e, "CatchAllCommand", "process");
343 /**************************************************************************************/