//
#include "subsample.h"
+//**********************************************************************************************************************
+Tree* SubSample::getSample(Tree* T, TreeMap* tmap, TreeMap* newTmap, int size, map<string, string> originalNameMap) {
+ try {
+ Tree* newTree = NULL;
+
+ map<string, vector<string> > newGroups;
+ vector<string> subsampledSeqs = getSample(tmap, size, newGroups);
+
+ //remove seqs not in sample from treemap
+ for (map<string, vector<string> >::iterator it = newGroups.begin(); it != newGroups.end(); it++) {
+ for (int i = 0; i < (it->second).size(); i++) {
+ newTmap->addSeq((it->second)[i], it->first);
+ }
+ }
+
+ newTree = new Tree(newTmap);
+ newTree->getCopy(T, originalNameMap);
+
+ return newTree;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SubSample", "getSample-Tree");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************
+Tree* SubSample::getSample(Tree* T, TreeMap* tmap, map<string, string> whole, int size) {
+ try {
+ Tree* newTree = NULL;
+
+ vector<string> subsampledSeqs = getSample(tmap, size);
+ map<string, string> sampledNameMap = deconvolute(whole, subsampledSeqs);
+
+ //remove seqs not in sample from treemap
+ for (int i = 0; i < tmap->namesOfSeqs.size(); i++) {
+ //is that name in the subsample?
+ int count = 0;
+ for (int j = 0; j < subsampledSeqs.size(); j++) {
+ if (tmap->namesOfSeqs[i] == subsampledSeqs[j]) { break; } //found it
+ count++;
+ }
+ if (m->control_pressed) { return newTree; }
+
+ //if you didnt find it, remove it
+ if (count == subsampledSeqs.size()) {
+ tmap->removeSeq(tmap->namesOfSeqs[i]);
+ i--; //need this because removeSeq removes name from namesOfSeqs
+ }
+ }
+
+ //create new tree
+ int numUniques = sampledNameMap.size();
+ if (sampledNameMap.size() == 0) { numUniques = subsampledSeqs.size(); }
+
+ newTree = new Tree(numUniques, tmap); //numNodes, treemap
+ newTree->getSubTree(T, subsampledSeqs, sampledNameMap);
+
+ return newTree;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SubSample", "getSample-Tree");
+ exit(1);
+ }
+}*/
+//**********************************************************************************************************************
+//assumes whole maps dupName -> uniqueName
+map<string, string> SubSample::deconvolute(map<string, string> whole, vector<string>& wanted) {
+ try {
+ map<string, string> nameMap;
+
+ //whole will be empty if user gave no name file, so we don't need to make a new one
+ if (whole.size() == 0) { return nameMap; }
+
+ vector<string> newWanted;
+ for (int i = 0; i < wanted.size(); i++) {
+
+ if (m->control_pressed) { break; }
+
+ string dupName = wanted[i];
+
+ map<string, string>::iterator itWhole = whole.find(dupName);
+ if (itWhole != whole.end()) {
+ string repName = itWhole->second;
+
+ //do we already have this rep?
+ map<string, string>::iterator itName = nameMap.find(repName);
+ if (itName != nameMap.end()) { //add this seqs to dups list
+ (itName->second) += "," + dupName;
+ }else { //first sighting of this seq
+ nameMap[repName] = dupName;
+ newWanted.push_back(repName);
+ }
+ }else { m->mothurOut("[ERROR]: "+dupName+" is not in your name file, please correct.\n"); m->control_pressed = true; }
+ }
+
+ wanted = newWanted;
+ return nameMap;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SubSample", "deconvolute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> SubSample::getSample(TreeMap* tMap, int size, map<string, vector<string> >& sample) {
+ try {
+ vector<string> temp2;
+ sample["doNotIncludeMe"] = temp2;
+
+ vector<string> namesInSample;
+
+ vector<string> Groups = tMap->getNamesOfGroups();
+ for (int i = 0; i < Groups.size(); i++) {
+
+ if (m->inUsersGroups(Groups[i], m->getGroups())) {
+ if (m->control_pressed) { break; }
+
+ vector<string> thisGroup; thisGroup.push_back(Groups[i]);
+ vector<string> thisGroupsSeqs = tMap->getNamesSeqs(thisGroup);
+ int thisSize = thisGroupsSeqs.size();
+ vector<string> temp;
+ sample[Groups[i]] = temp;
+
+ if (thisSize >= size) {
+
+ random_shuffle(thisGroupsSeqs.begin(), thisGroupsSeqs.end());
+
+ for (int j = 0; j < size; j++) { sample[Groups[i]].push_back(thisGroupsSeqs[j]); namesInSample.push_back(thisGroupsSeqs[j]); }
+ for (int j = size; j < thisSize; j++) { sample["doNotIncludeMe"].push_back(thisGroupsSeqs[j]); }
+
+ }else { m->mothurOut("[ERROR]: You have selected a size that is larger than "+Groups[i]+" number of sequences.\n"); m->control_pressed = true; }
+ }
+ }
+
+ return namesInSample;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SubSample", "getSample-TreeMap");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+vector<string> SubSample::getSample(TreeMap* tMap, int size) {
+ try {
+ vector<string> sample;
+
+ vector<string> Groups = tMap->getNamesOfGroups();
+ for (int i = 0; i < Groups.size(); i++) {
+
+ if (m->inUsersGroups(Groups[i], m->getGroups())) {
+ if (m->control_pressed) { break; }
+
+ vector<string> thisGroup; thisGroup.push_back(Groups[i]);
+ vector<string> thisGroupsSeqs = tMap->getNamesSeqs(thisGroup);
+ int thisSize = thisGroupsSeqs.size();
+
+ if (thisSize >= size) {
+
+ random_shuffle(thisGroupsSeqs.begin(), thisGroupsSeqs.end());
+
+ for (int j = 0; j < size; j++) { sample.push_back(thisGroupsSeqs[j]); }
+ }else { m->mothurOut("[ERROR]: You have selected a size that is larger than "+Groups[i]+" number of sequences.\n"); m->control_pressed = true; }
+ }
+ }
+
+ return sample;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SubSample", "getSample-TreeMap");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> SubSample::getSample(TreeMap* tMap, vector<string> Groups) {
+ try {
+ vector<string> sample;
+
+ //vector<string> Groups = tMap->getNamesOfGroups();
+ for (int i = 0; i < Groups.size(); i++) {
+
+ if (m->control_pressed) { break; }
+
+ vector<string> thisGroup; thisGroup.push_back(Groups[i]);
+ vector<string> thisGroupsSeqs = tMap->getNamesSeqs(thisGroup);
+ int thisSize = thisGroupsSeqs.size();
+
+ for (int j = 0; j < thisSize; j++) { sample.push_back(thisGroupsSeqs[j]); }
+ }
+
+ return sample;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SubSample", "getSample-TreeMap");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
vector<string> SubSample::getSample(vector<SharedRAbundVector*>& thislookup, int size) {
try {
//subsampling may have created some otus with no sequences in them
eliminateZeroOTUS(thislookup);
-
+
if (m->control_pressed) { return m->currentBinLabels; }
//save mothurOut's binLabels to restore for next label
}
catch(exception& e) {
- m->errorOut(e, "SubSample", "getSample");
+ m->errorOut(e, "SubSample", "getSample-shared");
exit(1);
}
}
exit(1);
}
}
+//**********************************************************************************************************************
+int SubSample::getSample(SAbundVector*& sabund, int size) {
+ try {
+
+ OrderVector* order = new OrderVector();
+ *order = sabund->getOrderVector(NULL);
+
+ int numBins = order->getNumBins();
+ int thisSize = order->getNumSeqs();
+
+ if (thisSize > size) {
+ random_shuffle(order->begin(), order->end());
+
+ RAbundVector* rabund = new RAbundVector(numBins);
+ rabund->setLabel(order->getLabel());
-
+ for (int j = 0; j < size; j++) {
+
+ if (m->control_pressed) { delete order; delete rabund; return 0; }
+
+ int bin = order->get(j);
+
+ int abund = rabund->get(bin);
+ rabund->set(bin, (abund+1));
+ }
+
+ delete sabund;
+ sabund = new SAbundVector();
+ *sabund = rabund->getSAbundVector();
+ delete rabund;
+
+ }else if (thisSize < size) { m->mothurOut("[ERROR]: The size you requested is larger than the number of sequences in the sabund vector. You requested " + toString(size) + " and you only have " + toString(thisSize) + " seqs in your sabund vector.\n"); m->control_pressed = true; }
+
+ if (m->control_pressed) { return 0; }
+
+ delete order;
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SubSampleCommand", "getSample");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
projects / mothur.git / blobdiff