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(){
37 //initialize outputTypes
38 vector<string> tempOutNames;
39 outputTypes["coverage"] = tempOutNames;
40 outputTypes["libshuffsummary"] = tempOutNames;
43 m->errorOut(e, "LibShuffCommand", "LibShuffCommand");
47 //**********************************************************************************************************************
48 vector<string> LibShuffCommand::getRequiredParameters(){
50 vector<string> myArray;
54 m->errorOut(e, "LibShuffCommand", "getRequiredParameters");
58 //**********************************************************************************************************************
59 vector<string> LibShuffCommand::getRequiredFiles(){
61 string Array[] = {"phylip","group"};
62 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
66 m->errorOut(e, "LibShuffCommand", "getRequiredFiles");
70 //**********************************************************************************************************************
72 LibShuffCommand::LibShuffCommand(string option) {
74 globaldata = GlobalData::getInstance();
78 //allow user to run help
79 if(option == "help") { help(); abort = true; }
82 //valid paramters for this command
83 string Array[] = {"iters","groups","step","form","cutoff","outputdir","inputdir"};
84 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
86 OptionParser parser(option);
87 map<string, string> parameters = parser.getParameters();
89 ValidParameters validParameter;
91 //check to make sure all parameters are valid for command
92 for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
93 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
96 //initialize outputTypes
97 vector<string> tempOutNames;
98 outputTypes["coverage"] = tempOutNames;
99 outputTypes["libshuffsummary"] = tempOutNames;
101 //if the user changes the output directory command factory will send this info to us in the output parameter
102 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
104 outputDir += m->hasPath(globaldata->getPhylipFile()); //if user entered a file with a path then preserve it
107 //make sure the user has already run the read.dist command
108 if ((globaldata->gMatrix == NULL) || (globaldata->gGroupmap == NULL)) {
109 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;;
112 //check for optional parameter and set defaults
113 // ...at some point should added some additional type checking...
114 groups = validParameter.validFile(parameters, "groups", false);
115 if (groups == "not found") { groups = ""; savegroups = groups; }
118 m->splitAtDash(groups, Groups);
119 globaldata->Groups = Groups;
123 temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "10000"; }
124 convert(temp, iters);
126 temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "1.0"; }
127 convert(temp, cutOff);
129 temp = validParameter.validFile(parameters, "step", false); if (temp == "not found") { temp = "0.01"; }
132 userform = validParameter.validFile(parameters, "form", false); if (userform == "not found") { userform = "integral"; }
134 if (abort == false) {
136 matrix = globaldata->gMatrix; //get the distance matrix
137 setGroups(); //set the groups to be analyzed and sorts them
139 /********************************************************************************************/
140 //this is needed because when we read the matrix we sort it into groups in alphabetical order
141 //the rest of the command and the classes used in this command assume specific order
142 /********************************************************************************************/
143 matrix->setGroups(globaldata->gGroupmap->namesOfGroups);
145 for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) { sizes.push_back(globaldata->gGroupmap->getNumSeqs(globaldata->gGroupmap->namesOfGroups[i])); }
146 matrix->setSizes(sizes);
149 if(userform == "discrete"){
150 form = new DLibshuff(matrix, iters, step, cutOff);
153 form = new SLibshuff(matrix, iters, cutOff);
160 catch(exception& e) {
161 m->errorOut(e, "LibShuffCommand", "LibShuffCommand");
165 //**********************************************************************************************************************
167 void LibShuffCommand::help(){
169 m->mothurOut("The libshuff command can only be executed after a successful read.dist command including a groupfile.\n");
170 m->mothurOut("The libshuff command parameters are groups, iters, step, form and cutoff. No parameters are required.\n");
171 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");
172 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");
173 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");
174 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");
175 m->mothurOut("The libshuff command should be in the following format: libshuff(groups=yourGroups, iters=yourIters, cutOff=yourCutOff, form=yourForm, step=yourStep).\n");
176 m->mothurOut("Example libshuff(groups=A-B-C, iters=500, form=discrete, step=0.01, cutOff=2.0).\n");
177 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");
178 m->mothurOut("The libshuff command output two files: .coverage and .slsummary their descriptions are in the manual.\n");
179 m->mothurOut("Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e.yourIters).\n\n");
181 catch(exception& e) {
182 m->errorOut(e, "LibShuffCommand", "help");
187 //**********************************************************************************************************************
189 int LibShuffCommand::execute(){
192 if (abort == true) { return 0; }
194 savedDXYValues = form->evaluateAll();
195 savedMinValues = form->getSavedMins();
197 if (m->control_pressed) { delete form; globaldata->Groups.clear(); delete globaldata->gMatrix; globaldata->gMatrix = NULL; return 0; }
199 pValueCounts.resize(numGroups);
200 for(int i=0;i<numGroups;i++){
201 pValueCounts[i].assign(numGroups, 0);
204 if (m->control_pressed) { outputTypes.clear(); delete form; globaldata->Groups.clear(); delete globaldata->gMatrix; globaldata->gMatrix = NULL; return 0; }
206 Progress* reading = new Progress();
208 for(int i=0;i<numGroups-1;i++) {
209 for(int j=i+1;j<numGroups;j++) {
211 if (m->control_pressed) { outputTypes.clear(); delete form; globaldata->Groups.clear(); delete globaldata->gMatrix; globaldata->gMatrix = NULL; delete reading; return 0; }
213 reading->newLine(groupNames[i]+'-'+groupNames[j], iters);
214 int spoti = globaldata->gGroupmap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix
215 int spotj = globaldata->gGroupmap->groupIndex[groupNames[j]];
217 for(int p=0;p<iters;p++) {
219 if (m->control_pressed) { outputTypes.clear(); delete form; globaldata->Groups.clear(); delete globaldata->gMatrix; globaldata->gMatrix = NULL; delete reading; return 0; }
221 form->randomizeGroups(spoti,spotj);
222 if(form->evaluatePair(spoti,spotj) >= savedDXYValues[spoti][spotj]) { pValueCounts[i][j]++; }
223 if(form->evaluatePair(spotj,spoti) >= savedDXYValues[spotj][spoti]) { pValueCounts[j][i]++; }
225 if (m->control_pressed) { outputTypes.clear(); delete form; globaldata->Groups.clear(); delete globaldata->gMatrix; globaldata->gMatrix = NULL; delete reading; return 0; }
229 form->resetGroup(spoti);
230 form->resetGroup(spotj);
234 if (m->control_pressed) { outputTypes.clear(); delete form; globaldata->Groups.clear(); delete globaldata->gMatrix; globaldata->gMatrix = NULL; delete reading; return 0; }
239 m->mothurOutEndLine();
243 //clear out users groups
244 globaldata->Groups.clear();
247 //delete globaldata's copy of the gmatrix to free up memory
248 delete globaldata->gMatrix; globaldata->gMatrix = NULL;
250 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
253 m->mothurOutEndLine();
254 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
255 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
256 m->mothurOutEndLine();
260 catch(exception& e) {
261 m->errorOut(e, "LibShuffCommand", "execute");
266 //**********************************************************************************************************************
268 int LibShuffCommand::printCoverageFile() {
272 summaryFile = outputDir + m->getRootName(m->getSimpleName(globaldata->getPhylipFile())) + "libshuff.coverage";
273 m->openOutputFile(summaryFile, outCov);
274 outputNames.push_back(summaryFile); outputTypes["coverage"].push_back(summaryFile);
275 outCov.setf(ios::fixed, ios::floatfield); outCov.setf(ios::showpoint);
276 //cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
278 map<double,vector<int> > allDistances;
279 map<double,vector<int> >::iterator it;
281 vector<vector<int> > indices(numGroups);
282 int numIndices = numGroups * numGroups;
285 for(int i=0;i<numGroups;i++){
286 indices[i].assign(numGroups,0);
287 for(int j=0;j<numGroups;j++){
288 indices[i][j] = index++;
290 int spoti = globaldata->gGroupmap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix
291 int spotj = globaldata->gGroupmap->groupIndex[groupNames[j]];
293 for(int k=0;k<savedMinValues[spoti][spotj].size();k++){
295 if(m->control_pressed) { outCov.close(); return 0; }
297 if(allDistances[savedMinValues[spoti][spotj][k]].size() != 0){
298 allDistances[savedMinValues[spoti][spotj][k]][indices[i][j]]++;
301 allDistances[savedMinValues[spoti][spotj][k]].assign(numIndices, 0);
302 allDistances[savedMinValues[spoti][spotj][k]][indices[i][j]] = 1;
307 it=allDistances.begin();
309 //cout << setprecision(8);
311 vector<int> prevRow = it->second;
314 for(;it!=allDistances.end();it++){
315 for(int i=0;i<it->second.size();i++){
316 it->second[i] += prevRow[i];
318 prevRow = it->second;
321 vector<int> lastRow = allDistances.rbegin()->second;
322 outCov << setprecision(8);
325 for (int i = 0; i < numGroups; i++){
326 outCov << '\t' << groupNames[i];
328 for (int i=0;i<numGroups;i++){
329 for(int j=i+1;j<numGroups;j++){
330 if(m->control_pressed) { outCov.close(); return 0; }
331 outCov << '\t' << groupNames[i] << '-' << groupNames[j] << '\t';
332 outCov << groupNames[j] << '-' << groupNames[i];
337 for(it=allDistances.begin();it!=allDistances.end();it++){
338 outCov << it->first << '\t';
339 for(int i=0;i<numGroups;i++){
340 outCov << it->second[indices[i][i]]/(float)lastRow[indices[i][i]] << '\t';
342 for(int i=0;i<numGroups;i++){
343 for(int j=i+1;j<numGroups;j++){
344 if(m->control_pressed) { outCov.close(); return 0; }
346 outCov << it->second[indices[i][j]]/(float)lastRow[indices[i][j]] << '\t';
347 outCov << it->second[indices[j][i]]/(float)lastRow[indices[j][i]] << '\t';
356 catch(exception& e) {
357 m->errorOut(e, "LibShuffCommand", "printCoverageFile");
362 //**********************************************************************************************************************
364 int LibShuffCommand::printSummaryFile() {
368 summaryFile = outputDir + m->getRootName(m->getSimpleName(globaldata->getPhylipFile())) + "libshuff.summary";
369 m->openOutputFile(summaryFile, outSum);
370 outputNames.push_back(summaryFile); outputTypes["libshuffsummary"].push_back(summaryFile);
372 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
373 cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
375 cout << setw(20) << left << "Comparison" << '\t' << setprecision(8) << "dCXYScore" << '\t' << "Significance" << endl;
376 m->mothurOutJustToLog("Comparison\tdCXYScore\tSignificance"); m->mothurOutEndLine();
377 outSum << setw(20) << left << "Comparison" << '\t' << setprecision(8) << "dCXYScore" << '\t' << "Significance" << endl;
379 int precision = (int)log10(iters);
380 for(int i=0;i<numGroups;i++){
381 for(int j=i+1;j<numGroups;j++){
382 if(m->control_pressed) { outSum.close(); return 0; }
384 int spoti = globaldata->gGroupmap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix
385 int spotj = globaldata->gGroupmap->groupIndex[groupNames[j]];
387 if(pValueCounts[i][j]){
388 cout << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << setprecision(precision) << pValueCounts[i][j]/(float)iters << endl;
389 m->mothurOutJustToLog(groupNames[i]+"-"+groupNames[j] + "\t" + toString(savedDXYValues[spoti][spotj]) + "\t" + toString((pValueCounts[i][j]/(float)iters))); m->mothurOutEndLine();
390 outSum << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << setprecision(precision) << pValueCounts[i][j]/(float)iters << endl;
393 cout << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << '<' <<setprecision(precision) << 1/(float)iters << endl;
394 m->mothurOutJustToLog(groupNames[i]+"-"+groupNames[j] + "\t" + toString(savedDXYValues[spoti][spotj]) + "\t" + toString((1/(float)iters))); m->mothurOutEndLine();
395 outSum << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << '<' <<setprecision(precision) << 1/(float)iters << endl;
397 if(pValueCounts[j][i]){
398 cout << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[spotj][spoti] << '\t' << setprecision (precision) << pValueCounts[j][i]/(float)iters << endl;
399 m->mothurOutJustToLog(groupNames[j]+"-"+groupNames[i] + "\t" + toString(savedDXYValues[spotj][spoti]) + "\t" + toString((pValueCounts[j][i]/(float)iters))); m->mothurOutEndLine();
400 outSum << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[spotj][spoti] << '\t' << setprecision (precision) << pValueCounts[j][i]/(float)iters << endl;
403 cout << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[spotj][spoti] << '\t' << '<' <<setprecision (precision) << 1/(float)iters << endl;
404 m->mothurOutJustToLog(groupNames[j]+"-"+groupNames[i] + "\t" + toString(savedDXYValues[spotj][spoti]) + "\t" + toString((1/(float)iters))); m->mothurOutEndLine();
405 outSum << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[spotj][spoti] << '\t' << '<' <<setprecision (precision) << 1/(float)iters << endl;
413 catch(exception& e) {
414 m->errorOut(e, "LibShuffCommand", "printSummaryFile");
419 //**********************************************************************************************************************
421 void LibShuffCommand::setGroups() {
423 //if the user has not entered specific groups to analyze then do them all
424 if (globaldata->Groups.size() == 0) {
425 numGroups = globaldata->gGroupmap->getNumGroups();
426 for (int i=0; i < numGroups; i++) {
427 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
430 if (savegroups != "all") {
431 //check that groups are valid
432 for (int i = 0; i < globaldata->Groups.size(); i++) {
433 if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
434 m->mothurOut(globaldata->Groups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
435 // erase the invalid group from globaldata->Groups
436 globaldata->Groups.erase(globaldata->Groups.begin()+i);
440 //if the user only entered invalid groups
441 if ((globaldata->Groups.size() == 0) || (globaldata->Groups.size() == 1)) {
442 numGroups = globaldata->gGroupmap->getNumGroups();
443 for (int i=0; i < numGroups; i++) {
444 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
446 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();
447 } else { numGroups = globaldata->Groups.size(); }
448 } else { //users wants all groups
449 numGroups = globaldata->gGroupmap->getNumGroups();
450 globaldata->Groups.clear();
451 for (int i=0; i < numGroups; i++) {
452 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
457 //sort so labels match
458 sort(globaldata->Groups.begin(), globaldata->Groups.end());
461 sort(globaldata->gGroupmap->namesOfGroups.begin(), globaldata->gGroupmap->namesOfGroups.end());
463 for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) { globaldata->gGroupmap->groupIndex[globaldata->gGroupmap->namesOfGroups[i]] = i; }
465 groupNames = globaldata->Groups;
468 catch(exception& e) {
469 m->errorOut(e, "LibShuffCommand", "setGroups");
474 /***********************************************************/