2 * bootstrapsharedcommand.cpp
5 * Created by Sarah Westcott on 4/16/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "bootstrapsharedcommand.h"
11 #include "sharedjabund.h"
12 #include "sharedsorabund.h"
13 #include "sharedjclass.h"
14 #include "sharedsorclass.h"
15 #include "sharedjest.h"
16 #include "sharedsorest.h"
17 #include "sharedthetayc.h"
18 #include "sharedthetan.h"
19 #include "sharedmorisitahorn.h"
20 #include "sharedbraycurtis.h"
23 //**********************************************************************************************************************
25 BootSharedCommand::BootSharedCommand(string option){
27 globaldata = GlobalData::getInstance();
35 //allow user to run help
36 if(option == "help") { help(); abort = true; }
39 //valid paramters for this command
40 string Array[] = {"line","label","calc","groups","iters"};
41 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
43 parser = new OptionParser();
44 parser->parse(option, parameters); delete parser;
46 ValidParameters* validParameter = new ValidParameters();
48 //check to make sure all parameters are valid for command
49 for (it = parameters.begin(); it != parameters.end(); it++) {
50 if (validParameter->isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
53 //make sure the user has already run the read.otu command
54 if (globaldata->getSharedFile() == "") {
55 if (globaldata->getListFile() == "") { cout << "You must read a list and a group, or a shared before you can use the bootstrap.shared command." << endl; abort = true; }
56 else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group, or a shared before you can use the bootstrap.shared command." << endl; abort = true; }
59 //check for optional parameter and set defaults
60 // ...at some point should added some additional type checking...
61 line = validParameter->validFile(parameters, "line", false);
62 if (line == "not found") { line = ""; }
64 if(line != "all") { splitAtDash(line, lines); allLines = 0; }
65 else { allLines = 1; }
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 //make sure user did not use both the line and label parameters
76 if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; }
77 //if the user has not specified any line or labels use the ones from read.otu
78 else if((line == "") && (label == "")) {
79 allLines = globaldata->allLines;
80 labels = globaldata->labels;
81 lines = globaldata->lines;
84 groups = validParameter->validFile(parameters, "groups", false);
85 if (groups == "not found") { groups = ""; }
87 splitAtDash(groups, Groups);
88 globaldata->Groups = Groups;
91 calc = validParameter->validFile(parameters, "calc", false);
92 if (calc == "not found") { calc = "jclass-thetayc"; }
94 if (calc == "default") { calc = "jclass-thetayc"; }
96 splitAtDash(calc, Estimators);
99 temp = validParameter->validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
100 convert(temp, iters);
102 delete validParameter;
104 if (abort == false) {
106 validCalculator = new ValidCalculators();
109 for (i=0; i<Estimators.size(); i++) {
110 if (validCalculator->isValidCalculator("boot", Estimators[i]) == true) {
111 if (Estimators[i] == "jabund") {
112 treeCalculators.push_back(new JAbund());
113 }else if (Estimators[i] == "sorabund") {
114 treeCalculators.push_back(new SorAbund());
115 }else if (Estimators[i] == "jclass") {
116 treeCalculators.push_back(new Jclass());
117 }else if (Estimators[i] == "sorclass") {
118 treeCalculators.push_back(new SorClass());
119 }else if (Estimators[i] == "jest") {
120 treeCalculators.push_back(new Jest());
121 }else if (Estimators[i] == "sorest") {
122 treeCalculators.push_back(new SorEst());
123 }else if (Estimators[i] == "thetayc") {
124 treeCalculators.push_back(new ThetaYC());
125 }else if (Estimators[i] == "thetan") {
126 treeCalculators.push_back(new ThetaN());
127 }else if (Estimators[i] == "morisitahorn") {
128 treeCalculators.push_back(new MorHorn());
129 }else if (Estimators[i] == "braycurtis") {
130 treeCalculators.push_back(new BrayCurtis());
135 delete validCalculator;
138 for (int i=0; i < treeCalculators.size(); i++) {
139 tempo = new ofstream;
140 out.push_back(tempo);
146 catch(exception& e) {
147 cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function BootSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
151 cout << "An unknown error has occurred in the BootSharedCommand class function BootSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
156 //**********************************************************************************************************************
158 void BootSharedCommand::help(){
160 cout << "The bootstrap.shared command can only be executed after a successful read.otu command." << "\n";
161 cout << "The bootstrap.shared command parameters are groups, calc, iters, line and label. You may not use line and label at the same time." << "\n";
162 cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included used." << "\n";
163 cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like trees created for, and are also separated by dashes." << "\n";
164 cout << "The bootstrap.shared command should be in the following format: bootstrap.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels, iters=yourIters)." << "\n";
165 cout << "Example bootstrap.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund, iters=100)." << "\n";
166 cout << "The default value for groups is all the groups in your groupfile." << "\n";
167 cout << "The default value for calc is jclass-thetayc. The default for iters is 1000." << "\n";
169 catch(exception& e) {
170 cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
174 cout << "An unknown error has occurred in the BootSharedCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
179 //**********************************************************************************************************************
181 BootSharedCommand::~BootSharedCommand(){
182 //made new in execute
183 if (abort == false) {
190 //**********************************************************************************************************************
192 int BootSharedCommand::execute(){
195 if (abort == true) { return 0; }
198 util = new SharedUtil();
201 read = new ReadOTUFile(globaldata->inputFileName);
202 read->read(&*globaldata);
203 input = globaldata->ginput;
204 order = input->getSharedOrderVector();
205 SharedOrderVector* lastOrder = order;
207 //if the users entered no valid calculators don't execute command
208 if (treeCalculators.size() == 0) { return 0; }
210 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
211 set<string> processedLabels;
212 set<string> userLabels = labels;
213 set<int> userLines = lines;
216 util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "treegroup");
217 numGroups = globaldata->Groups.size();
219 //clear globaldatas old tree names if any
220 globaldata->Treenames.clear();
222 //fills globaldatas tree names
223 globaldata->Treenames = globaldata->Groups;
225 //create treemap class from groupmap for tree class to use
226 tmap = new TreeMap();
227 tmap->makeSim(globaldata->gGroupmap);
228 globaldata->gTreemap = tmap;
230 while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
232 if(allLines == 1 || lines.count(count) == 1 || labels.count(order->getLabel()) == 1){
234 cout << order->getLabel() << '\t' << count << endl;
237 processedLabels.insert(order->getLabel());
238 userLabels.erase(order->getLabel());
239 userLines.erase(count);
242 //you have a label the user want that is smaller than this line and the last line has not already been processed
243 if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
245 cout << lastOrder->getLabel() << '\t' << count << endl;
248 processedLabels.insert(lastOrder->getLabel());
249 userLabels.erase(lastOrder->getLabel());
252 if (count != 1) { delete lastOrder; }
255 //get next line to process
256 order = input->getSharedOrderVector();
260 //output error messages about any remaining user labels
261 set<string>::iterator it;
262 bool needToRun = false;
263 for (it = userLabels.begin(); it != userLabels.end(); it++) {
264 cout << "Your file does not include the label "<< *it;
265 if (processedLabels.count(lastOrder->getLabel()) != 1) {
266 cout << ". I will use " << lastOrder->getLabel() << "." << endl;
269 cout << ". Please refer to " << lastOrder->getLabel() << "." << endl;
273 //run last line if you need to
274 if (needToRun == true) {
276 cout << lastOrder->getLabel() << '\t' << count << endl;
281 //reset groups parameter
282 globaldata->Groups.clear();
286 catch(exception& e) {
287 cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
291 cout << "An unknown error has occurred in the BootSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
295 //**********************************************************************************************************************
297 void BootSharedCommand::createTree(ostream* out){
302 //do merges and create tree structure by setting parents and children
303 //there are numGroups - 1 merges to do
304 for (int i = 0; i < (numGroups - 1); i++) {
306 float largest = -1.0;
308 //find largest value in sims matrix by searching lower triangle
309 for (int j = 1; j < simMatrix.size(); j++) {
310 for (int k = 0; k < j; k++) {
311 if (simMatrix[j][k] > largest) { largest = simMatrix[j][k]; row = j; column = k; }
315 //set non-leaf node info and update leaves to know their parents
317 t->tree[numGroups + i].setChildren(index[row], index[column]);
320 t->tree[index[row]].setParent(numGroups + i);
321 t->tree[index[column]].setParent(numGroups + i);
323 //blength = distance / 2;
324 float blength = ((1.0 - largest) / 2);
327 t->tree[index[row]].setBranchLength(blength - t->tree[index[row]].getLengthToLeaves());
328 t->tree[index[column]].setBranchLength(blength - t->tree[index[column]].getLengthToLeaves());
330 //set your length to leaves to your childs length plus branchlength
331 t->tree[numGroups + i].setLengthToLeaves(t->tree[index[row]].getLengthToLeaves() + t->tree[index[row]].getBranchLength());
335 index[row] = numGroups+i;
336 index[column] = numGroups+i;
338 //zero out highest value that caused the merge.
339 simMatrix[row][column] = -1.0;
340 simMatrix[column][row] = -1.0;
342 //merge values in simsMatrix
343 for (int n = 0; n < simMatrix.size(); n++) {
344 //row becomes merge of 2 groups
345 simMatrix[row][n] = (simMatrix[row][n] + simMatrix[column][n]) / 2;
346 simMatrix[n][row] = simMatrix[row][n];
348 simMatrix[column][n] = -1.0;
349 simMatrix[n][column] = -1.0;
363 catch(exception& e) {
364 cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
368 cout << "An unknown error has occurred in the BootSharedCommand class function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
372 /***********************************************************/
373 void BootSharedCommand::printSims() {
375 cout << "simsMatrix" << endl;
376 for (int m = 0; m < simMatrix.size(); m++) {
377 for (int n = 0; n < simMatrix.size(); n++) {
378 cout << simMatrix[m][n] << '\t';
384 catch(exception& e) {
385 cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
389 cout << "An unknown error has occurred in the BootSharedCommand class function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
393 /***********************************************************/
394 void BootSharedCommand::process(SharedOrderVector* order) {
397 vector<SharedRAbundVector*> subset;
399 //open an ostream for each calc to print to
400 for (int z = 0; z < treeCalculators.size(); z++) {
401 //create a new filename
402 outputFile = getRootName(globaldata->inputFileName) + treeCalculators[z]->getName() + ".boot" + order->getLabel() + ".tre";
403 openOutputFile(outputFile, *(out[z]));
406 //create a file for each calculator with the 1000 trees in it.
407 for (int p = 0; p < iters; p++) {
409 util->getSharedVectorswithReplacement(Groups, lookup, order); //fills group vectors from order vector.
411 //for each calculator
412 for(int i = 0 ; i < treeCalculators.size(); i++) {
414 //initialize simMatrix
416 simMatrix.resize(numGroups);
417 for (int m = 0; m < simMatrix.size(); m++) {
418 for (int j = 0; j < simMatrix.size(); j++) {
419 simMatrix[m].push_back(0.0);
425 for (int g = 0; g < numGroups; g++) { index[g] = g; }
427 for (int k = 0; k < lookup.size(); k++) { // pass cdd each set of groups to commpare
428 for (int l = k; l < lookup.size(); l++) {
429 if (k != l) { //we dont need to similiarity of a groups to itself
430 subset.clear(); //clear out old pair of sharedrabunds
431 //add new pair of sharedrabunds
432 subset.push_back(lookup[k]); subset.push_back(lookup[l]);
434 //get estimated similarity between 2 groups
435 data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
436 //save values in similarity matrix
437 simMatrix[k][l] = data[0];
438 simMatrix[l][k] = data[0];
443 //creates tree from similarity matrix and write out file
447 //close ostream for each calc
448 for (int z = 0; z < treeCalculators.size(); z++) { out[z]->close(); }
451 catch(exception& e) {
452 cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
456 cout << "An unknown error has occurred in the BootSharedCommand class function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
460 /***********************************************************/