5 * Created by Sarah Westcott on 3/9/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 /* This class is designed to implement an integral form of the Cramer-von Mises statistic.
11 you may refer to the "Integration of Microbial Ecology and Statistics: A Test To Compare Gene Libraries"
12 paper in Applied and Environmental Microbiology, Sept. 2004, p. 5485-5492 0099-2240/04/$8.00+0
13 DOI: 10.1128/AEM.70.9.5485-5492.2004 Copyright 2004 American Society for Microbiology for more information. */
16 #include "libshuffcommand.h"
18 #include "slibshuff.h"
19 #include "dlibshuff.h"
21 //**********************************************************************************************************************
22 vector<string> LibShuffCommand::getValidParameters(){
24 string Array[] = {"iters","groups","step","form","cutoff","outputdir","inputdir"};
25 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
29 m->errorOut(e, "LibShuffCommand", "getValidParameters");
33 //**********************************************************************************************************************
34 LibShuffCommand::LibShuffCommand(){
36 abort = true; calledHelp = true;
37 vector<string> tempOutNames;
38 outputTypes["coverage"] = tempOutNames;
39 outputTypes["libshuffsummary"] = tempOutNames;
42 m->errorOut(e, "LibShuffCommand", "LibShuffCommand");
46 //**********************************************************************************************************************
47 vector<string> LibShuffCommand::getRequiredParameters(){
49 vector<string> myArray;
53 m->errorOut(e, "LibShuffCommand", "getRequiredParameters");
57 //**********************************************************************************************************************
58 vector<string> LibShuffCommand::getRequiredFiles(){
60 string Array[] = {"phylip","group"};
61 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
65 m->errorOut(e, "LibShuffCommand", "getRequiredFiles");
69 //**********************************************************************************************************************
71 LibShuffCommand::LibShuffCommand(string option) {
73 globaldata = GlobalData::getInstance();
74 abort = false; calledHelp = false;
77 //allow user to run help
78 if(option == "help") { help(); abort = true; calledHelp = true; }
81 //valid paramters for this command
82 string Array[] = {"iters","groups","step","form","cutoff","outputdir","inputdir"};
83 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
85 OptionParser parser(option);
86 map<string, string> parameters = parser.getParameters();
88 ValidParameters validParameter;
90 //check to make sure all parameters are valid for command
91 for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
92 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
95 //initialize outputTypes
96 vector<string> tempOutNames;
97 outputTypes["coverage"] = tempOutNames;
98 outputTypes["libshuffsummary"] = tempOutNames;
100 //if the user changes the output directory command factory will send this info to us in the output parameter
101 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
103 outputDir += m->hasPath(globaldata->getPhylipFile()); //if user entered a file with a path then preserve it
106 //make sure the user has already run the read.dist command
107 if ((globaldata->gMatrix == NULL) || (globaldata->gGroupmap == NULL)) {
108 m->mothurOut("You must read in a matrix and groupfile using the read.dist command, before you use the libshuff command. "); m->mothurOutEndLine(); abort = true;;
111 //check for optional parameter and set defaults
112 // ...at some point should added some additional type checking...
113 groups = validParameter.validFile(parameters, "groups", false);
114 if (groups == "not found") { groups = ""; savegroups = groups; }
117 m->splitAtDash(groups, Groups);
118 globaldata->Groups = Groups;
122 temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "10000"; }
123 convert(temp, iters);
125 temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "1.0"; }
126 convert(temp, cutOff);
128 temp = validParameter.validFile(parameters, "step", false); if (temp == "not found") { temp = "0.01"; }
131 userform = validParameter.validFile(parameters, "form", false); if (userform == "not found") { userform = "integral"; }
133 if (abort == false) {
135 matrix = globaldata->gMatrix; //get the distance matrix
136 setGroups(); //set the groups to be analyzed and sorts them
138 /********************************************************************************************/
139 //this is needed because when we read the matrix we sort it into groups in alphabetical order
140 //the rest of the command and the classes used in this command assume specific order
141 /********************************************************************************************/
142 matrix->setGroups(globaldata->gGroupmap->namesOfGroups);
144 for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) { sizes.push_back(globaldata->gGroupmap->getNumSeqs(globaldata->gGroupmap->namesOfGroups[i])); }
145 matrix->setSizes(sizes);
148 if(userform == "discrete"){
149 form = new DLibshuff(matrix, iters, step, cutOff);
152 form = new SLibshuff(matrix, iters, cutOff);
159 catch(exception& e) {
160 m->errorOut(e, "LibShuffCommand", "LibShuffCommand");
164 //**********************************************************************************************************************
166 void LibShuffCommand::help(){
168 m->mothurOut("The libshuff command can only be executed after a successful read.dist command including a groupfile.\n");
169 m->mothurOut("The libshuff command parameters are groups, iters, step, form and cutoff. No parameters are required.\n");
170 m->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");
171 m->mothurOut("The group names are separated by dashes. The iters parameter allows you to specify how many random matrices you would like compared to your matrix.\n");
172 m->mothurOut("The step parameter allows you to specify change in distance you would like between each output if you are using the discrete form.\n");
173 m->mothurOut("The form parameter allows you to specify if you would like to analyze your matrix using the discrete or integral form. Your options are integral or discrete.\n");
174 m->mothurOut("The libshuff command should be in the following format: libshuff(groups=yourGroups, iters=yourIters, cutOff=yourCutOff, form=yourForm, step=yourStep).\n");
175 m->mothurOut("Example libshuff(groups=A-B-C, iters=500, form=discrete, step=0.01, cutOff=2.0).\n");
176 m->mothurOut("The default value for groups is all the groups in your groupfile, iters is 10000, cutoff is 1.0, form is integral and step is 0.01.\n");
177 m->mothurOut("The libshuff command output two files: .coverage and .slsummary their descriptions are in the manual.\n");
178 m->mothurOut("Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e.yourIters).\n\n");
180 catch(exception& e) {
181 m->errorOut(e, "LibShuffCommand", "help");
186 //**********************************************************************************************************************
188 int LibShuffCommand::execute(){
191 if (abort == true) { if (calledHelp) { return 0; } return 2; }
193 savedDXYValues = form->evaluateAll();
194 savedMinValues = form->getSavedMins();
196 if (m->control_pressed) { delete form; globaldata->Groups.clear(); delete globaldata->gMatrix; globaldata->gMatrix = NULL; return 0; }
198 pValueCounts.resize(numGroups);
199 for(int i=0;i<numGroups;i++){
200 pValueCounts[i].assign(numGroups, 0);
203 if (m->control_pressed) { outputTypes.clear(); delete form; globaldata->Groups.clear(); delete globaldata->gMatrix; globaldata->gMatrix = NULL; return 0; }
205 Progress* reading = new Progress();
207 for(int i=0;i<numGroups-1;i++) {
208 for(int j=i+1;j<numGroups;j++) {
210 if (m->control_pressed) { outputTypes.clear(); delete form; globaldata->Groups.clear(); delete globaldata->gMatrix; globaldata->gMatrix = NULL; delete reading; return 0; }
212 reading->newLine(groupNames[i]+'-'+groupNames[j], iters);
213 int spoti = globaldata->gGroupmap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix
214 int spotj = globaldata->gGroupmap->groupIndex[groupNames[j]];
216 for(int p=0;p<iters;p++) {
218 if (m->control_pressed) { outputTypes.clear(); delete form; globaldata->Groups.clear(); delete globaldata->gMatrix; globaldata->gMatrix = NULL; delete reading; return 0; }
220 form->randomizeGroups(spoti,spotj);
221 if(form->evaluatePair(spoti,spotj) >= savedDXYValues[spoti][spotj]) { pValueCounts[i][j]++; }
222 if(form->evaluatePair(spotj,spoti) >= savedDXYValues[spotj][spoti]) { pValueCounts[j][i]++; }
224 if (m->control_pressed) { outputTypes.clear(); delete form; globaldata->Groups.clear(); delete globaldata->gMatrix; globaldata->gMatrix = NULL; delete reading; return 0; }
228 form->resetGroup(spoti);
229 form->resetGroup(spotj);
233 if (m->control_pressed) { outputTypes.clear(); delete form; globaldata->Groups.clear(); delete globaldata->gMatrix; globaldata->gMatrix = NULL; delete reading; return 0; }
238 m->mothurOutEndLine();
242 //clear out users groups
243 globaldata->Groups.clear();
246 //delete globaldata's copy of the gmatrix to free up memory
247 delete globaldata->gMatrix; globaldata->gMatrix = NULL;
249 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
252 m->mothurOutEndLine();
253 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
254 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
255 m->mothurOutEndLine();
259 catch(exception& e) {
260 m->errorOut(e, "LibShuffCommand", "execute");
265 //**********************************************************************************************************************
267 int LibShuffCommand::printCoverageFile() {
271 summaryFile = outputDir + m->getRootName(m->getSimpleName(globaldata->getPhylipFile())) + "libshuff.coverage";
272 m->openOutputFile(summaryFile, outCov);
273 outputNames.push_back(summaryFile); outputTypes["coverage"].push_back(summaryFile);
274 outCov.setf(ios::fixed, ios::floatfield); outCov.setf(ios::showpoint);
275 //cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
277 map<double,vector<int> > allDistances;
278 map<double,vector<int> >::iterator it;
280 vector<vector<int> > indices(numGroups);
281 int numIndices = numGroups * numGroups;
284 for(int i=0;i<numGroups;i++){
285 indices[i].assign(numGroups,0);
286 for(int j=0;j<numGroups;j++){
287 indices[i][j] = index++;
289 int spoti = globaldata->gGroupmap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix
290 int spotj = globaldata->gGroupmap->groupIndex[groupNames[j]];
292 for(int k=0;k<savedMinValues[spoti][spotj].size();k++){
294 if(m->control_pressed) { outCov.close(); return 0; }
296 if(allDistances[savedMinValues[spoti][spotj][k]].size() != 0){
297 allDistances[savedMinValues[spoti][spotj][k]][indices[i][j]]++;
300 allDistances[savedMinValues[spoti][spotj][k]].assign(numIndices, 0);
301 allDistances[savedMinValues[spoti][spotj][k]][indices[i][j]] = 1;
306 it=allDistances.begin();
308 //cout << setprecision(8);
310 vector<int> prevRow = it->second;
313 for(;it!=allDistances.end();it++){
314 for(int i=0;i<it->second.size();i++){
315 it->second[i] += prevRow[i];
317 prevRow = it->second;
320 vector<int> lastRow = allDistances.rbegin()->second;
321 outCov << setprecision(8);
324 for (int i = 0; i < numGroups; i++){
325 outCov << '\t' << groupNames[i];
327 for (int i=0;i<numGroups;i++){
328 for(int j=i+1;j<numGroups;j++){
329 if(m->control_pressed) { outCov.close(); return 0; }
330 outCov << '\t' << groupNames[i] << '-' << groupNames[j] << '\t';
331 outCov << groupNames[j] << '-' << groupNames[i];
336 for(it=allDistances.begin();it!=allDistances.end();it++){
337 outCov << it->first << '\t';
338 for(int i=0;i<numGroups;i++){
339 outCov << it->second[indices[i][i]]/(float)lastRow[indices[i][i]] << '\t';
341 for(int i=0;i<numGroups;i++){
342 for(int j=i+1;j<numGroups;j++){
343 if(m->control_pressed) { outCov.close(); return 0; }
345 outCov << it->second[indices[i][j]]/(float)lastRow[indices[i][j]] << '\t';
346 outCov << it->second[indices[j][i]]/(float)lastRow[indices[j][i]] << '\t';
355 catch(exception& e) {
356 m->errorOut(e, "LibShuffCommand", "printCoverageFile");
361 //**********************************************************************************************************************
363 int LibShuffCommand::printSummaryFile() {
367 summaryFile = outputDir + m->getRootName(m->getSimpleName(globaldata->getPhylipFile())) + "libshuff.summary";
368 m->openOutputFile(summaryFile, outSum);
369 outputNames.push_back(summaryFile); outputTypes["libshuffsummary"].push_back(summaryFile);
371 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
372 cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
374 cout << setw(20) << left << "Comparison" << '\t' << setprecision(8) << "dCXYScore" << '\t' << "Significance" << endl;
375 m->mothurOutJustToLog("Comparison\tdCXYScore\tSignificance"); m->mothurOutEndLine();
376 outSum << setw(20) << left << "Comparison" << '\t' << setprecision(8) << "dCXYScore" << '\t' << "Significance" << endl;
378 int precision = (int)log10(iters);
379 for(int i=0;i<numGroups;i++){
380 for(int j=i+1;j<numGroups;j++){
381 if(m->control_pressed) { outSum.close(); return 0; }
383 int spoti = globaldata->gGroupmap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix
384 int spotj = globaldata->gGroupmap->groupIndex[groupNames[j]];
386 if(pValueCounts[i][j]){
387 cout << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << setprecision(precision) << pValueCounts[i][j]/(float)iters << endl;
388 m->mothurOutJustToLog(groupNames[i]+"-"+groupNames[j] + "\t" + toString(savedDXYValues[spoti][spotj]) + "\t" + toString((pValueCounts[i][j]/(float)iters))); m->mothurOutEndLine();
389 outSum << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << setprecision(precision) << pValueCounts[i][j]/(float)iters << endl;
392 cout << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << '<' <<setprecision(precision) << 1/(float)iters << endl;
393 m->mothurOutJustToLog(groupNames[i]+"-"+groupNames[j] + "\t" + toString(savedDXYValues[spoti][spotj]) + "\t" + toString((1/(float)iters))); m->mothurOutEndLine();
394 outSum << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << '<' <<setprecision(precision) << 1/(float)iters << endl;
396 if(pValueCounts[j][i]){
397 cout << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[spotj][spoti] << '\t' << setprecision (precision) << pValueCounts[j][i]/(float)iters << endl;
398 m->mothurOutJustToLog(groupNames[j]+"-"+groupNames[i] + "\t" + toString(savedDXYValues[spotj][spoti]) + "\t" + toString((pValueCounts[j][i]/(float)iters))); m->mothurOutEndLine();
399 outSum << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[spotj][spoti] << '\t' << setprecision (precision) << pValueCounts[j][i]/(float)iters << endl;
402 cout << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[spotj][spoti] << '\t' << '<' <<setprecision (precision) << 1/(float)iters << endl;
403 m->mothurOutJustToLog(groupNames[j]+"-"+groupNames[i] + "\t" + toString(savedDXYValues[spotj][spoti]) + "\t" + toString((1/(float)iters))); m->mothurOutEndLine();
404 outSum << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[spotj][spoti] << '\t' << '<' <<setprecision (precision) << 1/(float)iters << endl;
412 catch(exception& e) {
413 m->errorOut(e, "LibShuffCommand", "printSummaryFile");
418 //**********************************************************************************************************************
420 void LibShuffCommand::setGroups() {
422 //if the user has not entered specific groups to analyze then do them all
423 if (globaldata->Groups.size() == 0) {
424 numGroups = globaldata->gGroupmap->getNumGroups();
425 for (int i=0; i < numGroups; i++) {
426 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
429 if (savegroups != "all") {
430 //check that groups are valid
431 for (int i = 0; i < globaldata->Groups.size(); i++) {
432 if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
433 m->mothurOut(globaldata->Groups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
434 // erase the invalid group from globaldata->Groups
435 globaldata->Groups.erase(globaldata->Groups.begin()+i);
439 //if the user only entered invalid groups
440 if ((globaldata->Groups.size() == 0) || (globaldata->Groups.size() == 1)) {
441 numGroups = globaldata->gGroupmap->getNumGroups();
442 for (int i=0; i < numGroups; i++) {
443 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
445 m->mothurOut("When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile."); m->mothurOutEndLine();
446 } else { numGroups = globaldata->Groups.size(); }
447 } else { //users wants all groups
448 numGroups = globaldata->gGroupmap->getNumGroups();
449 globaldata->Groups.clear();
450 for (int i=0; i < numGroups; i++) {
451 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
456 //sort so labels match
457 sort(globaldata->Groups.begin(), globaldata->Groups.end());
460 sort(globaldata->gGroupmap->namesOfGroups.begin(), globaldata->gGroupmap->namesOfGroups.end());
462 for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) { globaldata->gGroupmap->groupIndex[globaldata->gGroupmap->namesOfGroups[i]] = i; }
464 groupNames = globaldata->Groups;
467 catch(exception& e) {
468 m->errorOut(e, "LibShuffCommand", "setGroups");
473 /***********************************************************/