5 * Created by Sarah Westcott on 1/2/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "collectcommand.h"
15 #include "bootstrap.h"
17 #include "npshannon.h"
19 #include "jackknife.h"
23 #include "bergerparker.h"
25 #include "goodscoverage.h"
33 //**********************************************************************************************************************
34 CollectCommand::CollectCommand(string option) {
36 globaldata = GlobalData::getInstance();
42 //allow user to run help
43 if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; }
46 //valid paramters for this command
47 string Array[] = {"freq","label","calc","abund","size","outputdir","inputdir"};
48 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
50 OptionParser parser(option);
51 map<string,string> parameters = parser.getParameters();
53 ValidParameters validParameter;
55 //check to make sure all parameters are valid for command
56 for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
57 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
60 //if the user changes the output directory command factory will send this info to us in the output parameter
61 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
63 //make sure the user has already run the read.otu command
64 if ((globaldata->getSharedFile() == "") && (globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { m->mothurOut("You must read a list, sabund, rabund or shared file before you can use the collect.single command."); m->mothurOutEndLine(); abort = true; }
66 //check for optional parameter and set defaults
67 // ...at some point should added some additional type checking...
68 label = validParameter.validFile(parameters, "label", false);
69 if (label == "not found") { label = ""; }
71 if(label != "all") { splitAtDash(label, labels); allLines = 0; }
72 else { allLines = 1; }
75 //if the user has not specified any labels use the ones from read.otu
77 allLines = globaldata->allLines;
78 labels = globaldata->labels;
81 calc = validParameter.validFile(parameters, "calc", false);
82 if (calc == "not found") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
84 if (calc == "default") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
86 splitAtDash(calc, Estimators);
89 temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
92 temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
95 temp = validParameter.validFile(parameters, "size", false); if (temp == "not found") { temp = "0"; }
100 catch(exception& e) {
101 m->errorOut(e, "CollectCommand", "CollectCommand");
105 //**********************************************************************************************************************
107 void CollectCommand::help(){
109 m->mothurOut("The collect.single command can only be executed after a successful read.otu command. WITH ONE EXECEPTION. \n");
110 m->mothurOut("The collect.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster.\n");
111 m->mothurOut("The collect.single command parameters are label, freq, calc and abund. No parameters are required. \n");
112 m->mothurOut("The collect.single command should be in the following format: \n");
113 m->mothurOut("The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n");
114 m->mothurOut("collect.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
115 m->mothurOut("Example collect(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-chao-ace-jack).\n");
116 m->mothurOut("The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n");
117 validCalculator->printCalc("single", cout);
118 m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
119 m->mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n");
121 catch(exception& e) {
122 m->errorOut(e, "CollectCommand", "help");
127 //**********************************************************************************************************************
129 CollectCommand::~CollectCommand(){}
131 //**********************************************************************************************************************
133 int CollectCommand::execute(){
136 if (abort == true) { return 0; }
138 vector<string> outputNames;
140 string hadShared = "";
141 if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName); }
142 else { hadShared = globaldata->getSharedFile(); inputFileNames = parseSharedFile(globaldata->getSharedFile()); globaldata->setFormat("rabund"); }
144 for (int p = 0; p < inputFileNames.size(); p++) {
146 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } return 0; }
148 if (outputDir == "") { outputDir += hasPath(inputFileNames[p]); }
149 string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[p]));
150 globaldata->inputFileName = inputFileNames[p];
152 if (inputFileNames.size() > 1) {
153 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
156 validCalculator = new ValidCalculators();
158 for (int i=0; i<Estimators.size(); i++) {
159 if (validCalculator->isValidCalculator("single", Estimators[i]) == true) {
160 if (Estimators[i] == "sobs") {
161 cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
162 outputNames.push_back(fileNameRoot+"sobs");
163 }else if (Estimators[i] == "chao") {
164 cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
165 outputNames.push_back(fileNameRoot+"chao");
166 }else if (Estimators[i] == "nseqs") {
167 cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs")));
168 outputNames.push_back(fileNameRoot+"nseqs");
169 }else if (Estimators[i] == "coverage") {
170 cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage")));
171 outputNames.push_back(fileNameRoot+"coverage");
172 }else if (Estimators[i] == "ace") {
173 cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
174 outputNames.push_back(fileNameRoot+"ace");
175 }else if (Estimators[i] == "jack") {
176 cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
177 outputNames.push_back(fileNameRoot+"jack");
178 }else if (Estimators[i] == "shannon") {
179 cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
180 outputNames.push_back(fileNameRoot+"shannon");
181 }else if (Estimators[i] == "npshannon") {
182 cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
183 outputNames.push_back(fileNameRoot+"np_shannon");
184 }else if (Estimators[i] == "simpson") {
185 cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
186 outputNames.push_back(fileNameRoot+"simpson");
187 }else if (Estimators[i] == "bootstrap") {
188 cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
189 outputNames.push_back(fileNameRoot+"bootstrap");
190 }else if (Estimators[i] == "geometric") {
191 cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric")));
192 outputNames.push_back(fileNameRoot+"geometric");
193 }else if (Estimators[i] == "qstat") {
194 cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
195 outputNames.push_back(fileNameRoot+"qstat");
196 }else if (Estimators[i] == "logseries") {
197 cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries")));
198 outputNames.push_back(fileNameRoot+"logseries");
199 }else if (Estimators[i] == "bergerparker") {
200 cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
201 outputNames.push_back(fileNameRoot+"bergerparker");
202 }else if (Estimators[i] == "bstick") {
203 cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick")));
204 outputNames.push_back(fileNameRoot+"bstick");
205 }else if (Estimators[i] == "goodscoverage") {
206 cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage")));
207 outputNames.push_back(fileNameRoot+"goodscoverage");
208 }else if (Estimators[i] == "efron") {
209 cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+"efron")));
210 outputNames.push_back(fileNameRoot+"efron");
211 }else if (Estimators[i] == "boneh") {
212 cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+"boneh")));
213 outputNames.push_back(fileNameRoot+"boneh");
214 }else if (Estimators[i] == "solow") {
215 cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+"solow")));
216 outputNames.push_back(fileNameRoot+"solow");
217 }else if (Estimators[i] == "shen") {
218 cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(fileNameRoot+"shen")));
219 outputNames.push_back(fileNameRoot+"shen");
224 //if the users entered no valid calculators don't execute command
225 if (cDisplays.size() == 0) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } return 0; }
227 read = new ReadOTUFile(inputFileNames[p]);
228 read->read(&*globaldata);
230 order = globaldata->gorder;
231 string lastLabel = order->getLabel();
232 input = globaldata->ginput;
234 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
235 set<string> processedLabels;
236 set<string> userLabels = labels;
238 if (m->control_pressed) {
239 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
240 for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
241 delete input; globaldata->ginput = NULL;
243 delete order; globaldata->gorder = NULL;
244 delete validCalculator;
245 globaldata->Groups.clear();
246 if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); }
251 while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
253 if (m->control_pressed) {
254 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
255 for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
256 delete input; globaldata->ginput = NULL;
258 delete order; globaldata->gorder = NULL;
259 delete validCalculator;
260 globaldata->Groups.clear();
261 if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); }
266 if(allLines == 1 || labels.count(order->getLabel()) == 1){
268 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
269 cCurve = new Collect(order, cDisplays);
270 cCurve->getCurve(freq);
273 processedLabels.insert(order->getLabel());
274 userLabels.erase(order->getLabel());
278 //you have a label the user want that is smaller than this label and the last label has not already been processed
279 if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
280 string saveLabel = order->getLabel();
283 order = (input->getOrderVector(lastLabel));
285 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
286 cCurve = new Collect(order, cDisplays);
287 cCurve->getCurve(freq);
291 processedLabels.insert(order->getLabel());
292 userLabels.erase(order->getLabel());
294 //restore real lastlabel to save below
295 order->setLabel(saveLabel);
298 lastLabel = order->getLabel();
301 order = (input->getOrderVector());
305 if (m->control_pressed) {
306 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
307 for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
308 delete input; globaldata->ginput = NULL;
310 delete validCalculator;
311 globaldata->Groups.clear();
312 if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); }
316 //output error messages about any remaining user labels
317 set<string>::iterator it;
318 bool needToRun = false;
319 for (it = userLabels.begin(); it != userLabels.end(); it++) {
320 m->mothurOut("Your file does not include the label " + *it);
321 if (processedLabels.count(lastLabel) != 1) {
322 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
325 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
329 //run last label if you need to
330 if (needToRun == true) {
331 if (order != NULL) { delete order; }
332 order = (input->getOrderVector(lastLabel));
334 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
336 cCurve = new Collect(order, cDisplays);
337 cCurve->getCurve(freq);
340 if (m->control_pressed) {
341 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
342 for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
343 delete input; globaldata->ginput = NULL;
345 delete order; globaldata->gorder = NULL;
346 delete validCalculator;
347 globaldata->Groups.clear();
348 if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); }
354 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
356 delete input; globaldata->ginput = NULL;
358 globaldata->gorder = NULL;
359 delete validCalculator;
362 //return to shared mode if you changed above
363 if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); }
365 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
367 m->mothurOutEndLine();
368 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
369 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
370 m->mothurOutEndLine();
375 catch(exception& e) {
376 m->errorOut(e, "CollectCommand", "execute");
381 //**********************************************************************************************************************
382 vector<string> CollectCommand::parseSharedFile(string filename) {
384 vector<string> filenames;
386 map<string, ofstream*> filehandles;
387 map<string, ofstream*>::iterator it3;
391 read = new ReadOTUFile(filename);
392 read->read(&*globaldata);
394 input = globaldata->ginput;
395 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
397 string sharedFileRoot = getRootName(filename);
399 //clears file before we start to write to it below
400 for (int i=0; i<lookup.size(); i++) {
401 remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
402 filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
406 for (int i=0; i<lookup.size(); i++) {
408 filehandles[lookup[i]->getGroup()] = temp;
409 groups.push_back(lookup[i]->getGroup());
412 while(lookup[0] != NULL) {
414 for (int i = 0; i < lookup.size(); i++) {
415 RAbundVector rav = lookup[i]->getRAbundVector();
416 openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
417 rav.print(*(filehandles[lookup[i]->getGroup()]));
418 (*(filehandles[lookup[i]->getGroup()])).close();
421 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
422 lookup = input->getSharedRAbundVectors();
426 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
431 globaldata->ginput = NULL;
435 catch(exception& e) {
436 m->errorOut(e, "CollectCommand", "parseSharedFile");
440 //**********************************************************************************************************************