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 if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName); }
141 else { inputFileNames = parseSharedFile(globaldata->getSharedFile()); globaldata->setFormat("rabund"); }
143 for (int p = 0; p < inputFileNames.size(); p++) {
145 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
147 if (outputDir == "") { outputDir += hasPath(inputFileNames[p]); }
148 string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[p]));
149 globaldata->inputFileName = inputFileNames[p];
151 if (inputFileNames.size() > 1) {
152 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
155 validCalculator = new ValidCalculators();
157 for (int i=0; i<Estimators.size(); i++) {
158 if (validCalculator->isValidCalculator("single", Estimators[i]) == true) {
159 if (Estimators[i] == "sobs") {
160 cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
161 outputNames.push_back(fileNameRoot+"sobs");
162 }else if (Estimators[i] == "chao") {
163 cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
164 outputNames.push_back(fileNameRoot+"chao");
165 }else if (Estimators[i] == "nseqs") {
166 cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs")));
167 outputNames.push_back(fileNameRoot+"nseqs");
168 }else if (Estimators[i] == "coverage") {
169 cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage")));
170 outputNames.push_back(fileNameRoot+"coverage");
171 }else if (Estimators[i] == "ace") {
172 cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
173 outputNames.push_back(fileNameRoot+"ace");
174 }else if (Estimators[i] == "jack") {
175 cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
176 outputNames.push_back(fileNameRoot+"jack");
177 }else if (Estimators[i] == "shannon") {
178 cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
179 outputNames.push_back(fileNameRoot+"shannon");
180 }else if (Estimators[i] == "npshannon") {
181 cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
182 outputNames.push_back(fileNameRoot+"np_shannon");
183 }else if (Estimators[i] == "simpson") {
184 cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
185 outputNames.push_back(fileNameRoot+"simpson");
186 }else if (Estimators[i] == "bootstrap") {
187 cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
188 outputNames.push_back(fileNameRoot+"bootstrap");
189 }else if (Estimators[i] == "geometric") {
190 cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric")));
191 outputNames.push_back(fileNameRoot+"geometric");
192 }else if (Estimators[i] == "qstat") {
193 cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
194 outputNames.push_back(fileNameRoot+"qstat");
195 }else if (Estimators[i] == "logseries") {
196 cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries")));
197 outputNames.push_back(fileNameRoot+"logseries");
198 }else if (Estimators[i] == "bergerparker") {
199 cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
200 outputNames.push_back(fileNameRoot+"bergerparker");
201 }else if (Estimators[i] == "bstick") {
202 cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick")));
203 outputNames.push_back(fileNameRoot+"bstick");
204 }else if (Estimators[i] == "goodscoverage") {
205 cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage")));
206 outputNames.push_back(fileNameRoot+"goodscoverage");
207 }else if (Estimators[i] == "efron") {
208 cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+"efron")));
209 outputNames.push_back(fileNameRoot+"efron");
210 }else if (Estimators[i] == "boneh") {
211 cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+"boneh")));
212 outputNames.push_back(fileNameRoot+"boneh");
213 }else if (Estimators[i] == "solow") {
214 cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+"solow")));
215 outputNames.push_back(fileNameRoot+"solow");
216 }else if (Estimators[i] == "shen") {
217 cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(fileNameRoot+"shen")));
218 outputNames.push_back(fileNameRoot+"shen");
223 //if the users entered no valid calculators don't execute command
224 if (cDisplays.size() == 0) { return 0; }
226 read = new ReadOTUFile(inputFileNames[p]);
227 read->read(&*globaldata);
229 order = globaldata->gorder;
230 string lastLabel = order->getLabel();
231 input = globaldata->ginput;
233 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
234 set<string> processedLabels;
235 set<string> userLabels = labels;
237 if (m->control_pressed) {
238 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
239 for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
240 delete input; globaldata->ginput = NULL;
242 delete order; globaldata->gorder = NULL;
243 delete validCalculator;
244 globaldata->Groups.clear();
249 while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
251 if (m->control_pressed) {
252 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
253 for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
254 delete input; globaldata->ginput = NULL;
256 delete order; globaldata->gorder = NULL;
257 delete validCalculator;
258 globaldata->Groups.clear();
263 if(allLines == 1 || labels.count(order->getLabel()) == 1){
265 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
266 cCurve = new Collect(order, cDisplays);
267 cCurve->getCurve(freq);
270 processedLabels.insert(order->getLabel());
271 userLabels.erase(order->getLabel());
275 //you have a label the user want that is smaller than this label and the last label has not already been processed
276 if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
277 string saveLabel = order->getLabel();
280 order = (input->getOrderVector(lastLabel));
282 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
283 cCurve = new Collect(order, cDisplays);
284 cCurve->getCurve(freq);
288 processedLabels.insert(order->getLabel());
289 userLabels.erase(order->getLabel());
291 //restore real lastlabel to save below
292 order->setLabel(saveLabel);
295 lastLabel = order->getLabel();
298 order = (input->getOrderVector());
302 if (m->control_pressed) {
303 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
304 for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
305 delete input; globaldata->ginput = NULL;
307 delete validCalculator;
308 globaldata->Groups.clear();
312 //output error messages about any remaining user labels
313 set<string>::iterator it;
314 bool needToRun = false;
315 for (it = userLabels.begin(); it != userLabels.end(); it++) {
316 m->mothurOut("Your file does not include the label " + *it);
317 if (processedLabels.count(lastLabel) != 1) {
318 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
321 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
325 //run last label if you need to
326 if (needToRun == true) {
327 if (order != NULL) { delete order; }
328 order = (input->getOrderVector(lastLabel));
330 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
332 cCurve = new Collect(order, cDisplays);
333 cCurve->getCurve(freq);
336 if (m->control_pressed) {
337 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
338 for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
339 delete input; globaldata->ginput = NULL;
341 delete order; globaldata->gorder = NULL;
342 delete validCalculator;
343 globaldata->Groups.clear();
349 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
351 delete input; globaldata->ginput = NULL;
353 globaldata->gorder = NULL;
354 delete validCalculator;
357 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
359 m->mothurOutEndLine();
360 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
361 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
362 m->mothurOutEndLine();
367 catch(exception& e) {
368 m->errorOut(e, "CollectCommand", "execute");
373 //**********************************************************************************************************************
374 vector<string> CollectCommand::parseSharedFile(string filename) {
376 vector<string> filenames;
378 map<string, ofstream*> filehandles;
379 map<string, ofstream*>::iterator it3;
383 read = new ReadOTUFile(filename);
384 read->read(&*globaldata);
386 input = globaldata->ginput;
387 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
389 string sharedFileRoot = getRootName(filename);
391 //clears file before we start to write to it below
392 for (int i=0; i<lookup.size(); i++) {
393 remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
394 filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
398 for (int i=0; i<lookup.size(); i++) {
400 filehandles[lookup[i]->getGroup()] = temp;
401 groups.push_back(lookup[i]->getGroup());
404 while(lookup[0] != NULL) {
406 for (int i = 0; i < lookup.size(); i++) {
407 RAbundVector rav = lookup[i]->getRAbundVector();
408 openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
409 rav.print(*(filehandles[lookup[i]->getGroup()]));
410 (*(filehandles[lookup[i]->getGroup()])).close();
413 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
414 lookup = input->getSharedRAbundVectors();
418 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
423 globaldata->ginput = NULL;
427 catch(exception& e) {
428 m->errorOut(e, "CollectCommand", "parseSharedFile");
432 //**********************************************************************************************************************