#include "subsample.h"
//**********************************************************************************************************************
-vector<SharedRAbundVector*> SubSample::getSamplePreserve(vector<SharedRAbundVector*>& thislookup, vector<string>& newLabels, int size) {
- try {
-
- vector<SharedRAbundVector*> newlookup; newlookup.resize(thislookup.size(), NULL);
+Tree* SubSample::getSample(Tree* T, TreeMap* tmap, map<string, string> whole, int size) {
+ try {
+ Tree* newTree = NULL;
- //save mothurOut's binLabels to restore for next label
- vector<string> saveBinLabels = m->currentBinLabels;
-
- int numBins = thislookup[0]->getNumBins();
- for (int i = 0; i < thislookup.size(); i++) {
- int thisSize = thislookup[i]->getNumSeqs();
-
- if (thisSize != size) {
-
- string thisgroup = thislookup[i]->getGroup();
-
- OrderVector order;
- for(int p=0;p<numBins;p++){
- for(int j=0;j<thislookup[i]->getAbundance(p);j++){
- order.push_back(p);
- }
- }
- random_shuffle(order.begin(), order.end());
-
- SharedRAbundVector* temp = new SharedRAbundVector(numBins);
- temp->setLabel(thislookup[i]->getLabel());
- temp->setGroup(thislookup[i]->getGroup());
-
- newlookup[i] = temp;
-
- for (int j = 0; j < size; j++) {
-
- if (m->control_pressed) { return newlookup; }
-
- int bin = order.get(j);
-
- int abund = newlookup[i]->getAbundance(bin);
- newlookup[i]->set(bin, (abund+1), thisgroup);
- }
- }
- }
-
- //subsampling may have created some otus with no sequences in them
- eliminateZeroOTUS(newlookup);
-
- if (m->control_pressed) { return newlookup; }
-
- //save mothurOut's binLabels to restore for next label
- newLabels = m->currentBinLabels;
- m->currentBinLabels = saveBinLabels;
-
- return newlookup;
-
+ 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) {
+ 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();
+
+ 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", "getSamplePreserve");
+ m->errorOut(e, "SubSample", "getSample-TreeMap");
exit(1);
}
}
}
catch(exception& e) {
- m->errorOut(e, "SubSample", "getSample");
+ m->errorOut(e, "SubSample", "getSample-shared");
exit(1);
}
}
projects / mothur.git / blobdiff