2 * summarysharedcommand.cpp
5 * Created by Sarah Westcott on 1/2/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "summarysharedcommand.h"
11 #include "sharedsobscollectsummary.h"
12 #include "sharedchao1.h"
13 #include "sharedace.h"
14 #include "sharednseqs.h"
15 #include "sharedjabund.h"
16 #include "sharedsorabund.h"
17 #include "sharedjclass.h"
18 #include "sharedsorclass.h"
19 #include "sharedjest.h"
20 #include "sharedsorest.h"
21 #include "sharedthetayc.h"
22 #include "sharedthetan.h"
23 #include "sharedkstest.h"
24 #include "whittaker.h"
25 #include "sharedochiai.h"
26 #include "sharedanderbergs.h"
27 #include "sharedkulczynski.h"
28 #include "sharedkulczynskicody.h"
29 #include "sharedlennon.h"
30 #include "sharedmorisitahorn.h"
31 #include "sharedbraycurtis.h"
32 #include "sharedjackknife.h"
33 #include "whittaker.h"
36 //**********************************************************************************************************************
38 SummarySharedCommand::SummarySharedCommand(string option){
40 globaldata = GlobalData::getInstance();
46 //allow user to run help
47 if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
50 //valid paramters for this command
51 string Array[] = {"label","calc","groups"};
52 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
54 OptionParser parser(option);
55 map<string, string> parameters = parser.getParameters();
57 ValidParameters validParameter;
59 //check to make sure all parameters are valid for command
60 for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
61 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
64 //make sure the user has already run the read.otu command
65 if (globaldata->getSharedFile() == "") {
66 mothurOut("You must read a list and a group, or a shared before you can use the summary.shared command."); mothurOutEndLine(); abort = true;
69 //check for optional parameter and set defaults
70 // ...at some point should added some additional type checking...
71 label = validParameter.validFile(parameters, "label", false);
72 if (label == "not found") { label = ""; }
74 if(label != "all") { splitAtDash(label, labels); allLines = 0; }
75 else { allLines = 1; }
78 //if the user has not specified any labels use the ones from read.otu
80 allLines = globaldata->allLines;
81 labels = globaldata->labels;
84 calc = validParameter.validFile(parameters, "calc", false);
85 if (calc == "not found") { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
87 if (calc == "default") { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
89 splitAtDash(calc, Estimators);
91 groups = validParameter.validFile(parameters, "groups", false);
92 if (groups == "not found") { groups = ""; }
94 splitAtDash(groups, Groups);
95 globaldata->Groups = Groups;
100 validCalculator = new ValidCalculators();
103 for (i=0; i<Estimators.size(); i++) {
104 if (validCalculator->isValidCalculator("sharedsummary", Estimators[i]) == true) {
105 if (Estimators[i] == "sharedsobs") {
106 sumCalculators.push_back(new SharedSobsCS());
107 }else if (Estimators[i] == "sharedchao") {
108 sumCalculators.push_back(new SharedChao1());
109 }else if (Estimators[i] == "sharedace") {
110 sumCalculators.push_back(new SharedAce());
111 }else if (Estimators[i] == "jabund") {
112 sumCalculators.push_back(new JAbund());
113 }else if (Estimators[i] == "sorabund") {
114 sumCalculators.push_back(new SorAbund());
115 }else if (Estimators[i] == "jclass") {
116 sumCalculators.push_back(new Jclass());
117 }else if (Estimators[i] == "sorclass") {
118 sumCalculators.push_back(new SorClass());
119 }else if (Estimators[i] == "jest") {
120 sumCalculators.push_back(new Jest());
121 }else if (Estimators[i] == "sorest") {
122 sumCalculators.push_back(new SorEst());
123 }else if (Estimators[i] == "thetayc") {
124 sumCalculators.push_back(new ThetaYC());
125 }else if (Estimators[i] == "thetan") {
126 sumCalculators.push_back(new ThetaN());
127 }else if (Estimators[i] == "kstest") {
128 sumCalculators.push_back(new KSTest());
129 }else if (Estimators[i] == "sharednseqs") {
130 sumCalculators.push_back(new SharedNSeqs());
131 }else if (Estimators[i] == "ochiai") {
132 sumCalculators.push_back(new Ochiai());
133 }else if (Estimators[i] == "anderberg") {
134 sumCalculators.push_back(new Anderberg());
135 }else if (Estimators[i] == "kulczynski") {
136 sumCalculators.push_back(new Kulczynski());
137 }else if (Estimators[i] == "kulczynskicody") {
138 sumCalculators.push_back(new KulczynskiCody());
139 }else if (Estimators[i] == "lennon") {
140 sumCalculators.push_back(new Lennon());
141 }else if (Estimators[i] == "morisitahorn") {
142 sumCalculators.push_back(new MorHorn());
143 }else if (Estimators[i] == "braycurtis") {
144 sumCalculators.push_back(new BrayCurtis());
145 }else if (Estimators[i] == "whittaker") {
146 sumCalculators.push_back(new Whittaker());
151 outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary");
152 openOutputFile(outputFileName, outputFileHandle);
157 catch(exception& e) {
158 errorOut(e, "SummarySharedCommand", "SummarySharedCommand");
163 //**********************************************************************************************************************
165 void SummarySharedCommand::help(){
167 mothurOut("The summary.shared command can only be executed after a successful read.otu command.\n");
168 mothurOut("The summary.shared command parameters are label and calc. No parameters are required.\n");
169 mothurOut("The summary.shared command should be in the following format: \n");
170 mothurOut("summary.shared(label=yourLabel, calc=yourEstimators, groups=yourGroups).\n");
171 mothurOut("Example summary.shared(label=unique-.01-.03, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n");
172 validCalculator->printCalc("sharedsummary", cout);
173 mothurOut("The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan\n");
174 mothurOut("The default value for groups is all the groups in your groupfile.\n");
175 mothurOut("The label parameter is used to analyze specific labels in your input.\n");
176 mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups.\n");
177 mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n");
179 catch(exception& e) {
180 errorOut(e, "SummarySharedCommand", "help");
185 //**********************************************************************************************************************
187 SummarySharedCommand::~SummarySharedCommand(){
188 if (abort == false) {
190 delete validCalculator;
194 //**********************************************************************************************************************
196 int SummarySharedCommand::execute(){
199 if (abort == true) { return 0; }
201 //if the users entered no valid calculators don't execute command
202 if (sumCalculators.size() == 0) { return 0; }
203 //check if any calcs can do multiples
205 for (int i = 0; i < sumCalculators.size(); i++) {
206 if (sumCalculators[i]->getMultiple() == true) { mult = true; }
211 read = new ReadOTUFile(globaldata->inputFileName);
212 read->read(&*globaldata);
214 input = globaldata->ginput;
215 lookup = input->getSharedRAbundVectors();
216 string lastLabel = lookup[0]->getLabel();
218 //output estimator names as column headers
219 outputFileHandle << "label" <<'\t' << "comparison" << '\t';
220 for(int i=0;i<sumCalculators.size();i++){
221 outputFileHandle << '\t' << sumCalculators[i]->getName();
223 outputFileHandle << endl;
225 //create file and put column headers for multiple groups file
227 outAllFileName = ((getRootName(globaldata->inputFileName)) + "sharedmultiple.summary");
228 openOutputFile(outAllFileName, outAll);
230 outAll << "label" <<'\t' << "comparison" << '\t';
231 for(int i=0;i<sumCalculators.size();i++){
232 if (sumCalculators[i]->getMultiple() == true) {
233 outAll << '\t' << sumCalculators[i]->getName();
239 if (lookup.size() < 2) {
240 mothurOut("I cannot run the command without at least 2 valid groups.");
241 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
243 //close files and clean up
244 outputFileHandle.close(); remove(outputFileName.c_str());
245 if (mult == true) { outAll.close(); remove(outAllFileName.c_str()); }
247 //if you only have 2 groups you don't need a .sharedmultiple file
248 }else if ((lookup.size() == 2) && (mult == true)) {
251 remove(outAllFileName.c_str());
254 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
255 set<string> processedLabels;
256 set<string> userLabels = labels;
258 //as long as you are not at the end of the file or done wih the lines you want
259 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
261 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
262 mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
265 processedLabels.insert(lookup[0]->getLabel());
266 userLabels.erase(lookup[0]->getLabel());
269 if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
270 string saveLabel = lookup[0]->getLabel();
272 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
273 lookup = input->getSharedRAbundVectors(lastLabel);
275 mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
278 processedLabels.insert(lookup[0]->getLabel());
279 userLabels.erase(lookup[0]->getLabel());
281 //restore real lastlabel to save below
282 lookup[0]->setLabel(saveLabel);
285 lastLabel = lookup[0]->getLabel();
287 //get next line to process
288 //prevent memory leak
289 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
290 lookup = input->getSharedRAbundVectors();
293 //output error messages about any remaining user labels
294 set<string>::iterator it;
295 bool needToRun = false;
296 for (it = userLabels.begin(); it != userLabels.end(); it++) {
297 mothurOut("Your file does not include the label " + *it);
298 if (processedLabels.count(lastLabel) != 1) {
299 mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
302 mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
306 //run last label if you need to
307 if (needToRun == true) {
308 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
309 lookup = input->getSharedRAbundVectors(lastLabel);
311 mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
313 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
317 //reset groups parameter
318 globaldata->Groups.clear();
321 outputFileHandle.close();
322 if (mult == true) { outAll.close(); }
324 for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
326 delete input; globaldata->ginput = NULL;
330 catch(exception& e) {
331 errorOut(e, "SummarySharedCommand", "execute");
336 /***********************************************************/
337 void SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup) {
339 //loop through calculators and add to file all for all calcs that can do mutiple groups
342 outAll << thisLookup[0]->getLabel() << '\t';
344 //output groups names
345 string outNames = "";
346 for (int j = 0; j < thisLookup.size(); j++) {
347 outNames += thisLookup[j]->getGroup() + "-";
349 outNames = outNames.substr(0, outNames.length()-1); //rip off extra '-';
350 outAll << outNames << '\t';
352 for(int i=0;i<sumCalculators.size();i++){
353 if (sumCalculators[i]->getMultiple() == true) {
354 sumCalculators[i]->getValues(thisLookup);
356 sumCalculators[i]->print(outAll);
363 vector<SharedRAbundVector*> subset;
364 for (int k = 0; k < (thisLookup.size() - 1); k++) { // pass cdd each set of groups to commpare
365 for (int l = n; l < thisLookup.size(); l++) {
367 outputFileHandle << thisLookup[0]->getLabel() << '\t';
369 subset.clear(); //clear out old pair of sharedrabunds
370 //add new pair of sharedrabunds
371 subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
373 //sort groups to be alphanumeric
374 if (thisLookup[k]->getGroup() > thisLookup[l]->getGroup()) {
375 outputFileHandle << (thisLookup[l]->getGroup() +'\t' + thisLookup[k]->getGroup()) << '\t'; //print out groups
377 outputFileHandle << (thisLookup[k]->getGroup() +'\t' + thisLookup[l]->getGroup()) << '\t'; //print out groups
380 for(int i=0;i<sumCalculators.size();i++) {
382 sumCalculators[i]->getValues(subset); //saves the calculator outputs
383 outputFileHandle << '\t';
384 sumCalculators[i]->print(outputFileHandle);
386 outputFileHandle << endl;
392 catch(exception& e) {
393 errorOut(e, "SummarySharedCommand", "process");
398 /***********************************************************/