//
#include "subsample.h"
+//**********************************************************************************************************************
+Tree* SubSample::getSample(Tree* T, CountTable* ct, CountTable* newCt, int size) {
+ try {
+ Tree* newTree = NULL;
+
+ //remove seqs not in sample from counttable
+ vector<string> Groups = ct->getNamesOfGroups();
+ newCt->copy(ct);
+ newCt->addGroup("doNotIncludeMe");
+
+ map<string, int> doNotIncludeTotals;
+ vector<string> namesSeqs = ct->getNamesOfSeqs();
+ for (int i = 0; i < namesSeqs.size(); i++) { doNotIncludeTotals[namesSeqs[i]] = 0; }
+
+ for (int i = 0; i < Groups.size(); i++) {
+ if (m->inUsersGroups(Groups[i], m->getGroups())) {
+ if (m->control_pressed) { break; }
+
+ int thisSize = ct->getGroupCount(Groups[i]);
+
+ if (thisSize >= size) {
+
+ vector<string> names = ct->getNamesOfSeqs(Groups[i]);
+ vector<int> random;
+ for (int j = 0; j < names.size(); j++) {
+ int num = ct->getGroupCount(names[j], Groups[i]);
+ for (int k = 0; k < num; k++) { random.push_back(j); }
+ }
+ random_shuffle(random.begin(), random.end());
+
+ vector<int> sampleRandoms; sampleRandoms.resize(names.size(), 0);
+ for (int j = 0; j < size; j++) { sampleRandoms[random[j]]++; }
+ for (int j = 0; j < sampleRandoms.size(); j++) {
+ newCt->setAbund(names[j], Groups[i], sampleRandoms[j]);
+ }
+ sampleRandoms.clear(); sampleRandoms.resize(names.size(), 0);
+ for (int j = size; j < thisSize; j++) { sampleRandoms[random[j]]++; }
+ for (int j = 0; j < sampleRandoms.size(); j++) { doNotIncludeTotals[names[j]] += sampleRandoms[j]; }
+ }else { m->mothurOut("[ERROR]: You have selected a size that is larger than "+Groups[i]+" number of sequences.\n"); m->control_pressed = true; }
+ }
+ }
+
+ for (map<string, int>::iterator it = doNotIncludeTotals.begin(); it != doNotIncludeTotals.end(); it++) {
+ newCt->setAbund(it->first, "doNotIncludeMe", it->second);
+ }
+
+ newTree = new Tree(newCt);
+ newTree->getCopy(T, true);
+
+ return newTree;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SubSample", "getSample-Tree");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
-vector<SharedRAbundVector*> SubSample::getSamplePreserve(vector<SharedRAbundVector*>& thislookup, vector<string>& newLabels, int size) {
- try {
-
- vector<SharedRAbundVector*> newlookup; newlookup.resize(thislookup.size(), NULL);
+//assumes whole maps dupName -> uniqueName
+map<string, string> SubSample::deconvolute(map<string, string> whole, vector<string>& wanted) {
+ try {
+ map<string, string> nameMap;
- //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;
-
- }
+ //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", "getSamplePreserve");
+ m->errorOut(e, "SubSample", "deconvolute");
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);
+ }
+}
+//**********************************************************************************************************************
+CountTable SubSample::getSample(CountTable& ct, int size, vector<string> Groups) {
+ try {
+ if (!ct.hasGroupInfo()) { m->mothurOut("[ERROR]: Cannot subsample by group because your count table doesn't have group information.\n"); m->control_pressed = true; }
+
+ CountTable sampledCt;
+ map<string, vector<int> > tempCount;
+ for (int i = 0; i < Groups.size(); i++) {
+ sampledCt.addGroup(Groups[i]);
+
+ vector<string> names = ct.getNamesOfSeqs(Groups[i]);
+ vector<string> allNames;
+ for (int j = 0; j < names.size(); j++) {
+
+ if (m->control_pressed) { return sampledCt; }
+
+ int num = ct. getGroupCount(names[j], Groups[i]);
+ for (int k = 0; k < num; k++) { allNames.push_back(names[j]); }
+ }
+
+ random_shuffle(allNames.begin(), allNames.end());
+
+ if (allNames.size() < size) { m->mothurOut("[ERROR]: You have selected a size that is larger than "+Groups[i]+" number of sequences.\n"); m->control_pressed = true; }
+ else{
+ for (int j = 0; j < size; j++) {
+
+ if (m->control_pressed) { return sampledCt; }
+
+ map<string, vector<int> >::iterator it = tempCount.find(allNames[j]);
+
+ if (it == tempCount.end()) { //we have not seen this sequence at all yet
+ vector<int> tempGroups; tempGroups.resize(Groups.size(), 0);
+ tempGroups[i]++;
+ tempCount[allNames[j]] = tempGroups;
+ }else{
+ tempCount[allNames[j]][i]++;
+ }
+ }
+ }
+ }
+
+ //build count table
+ for (map<string, vector<int> >::iterator it = tempCount.begin(); it != tempCount.end();) {
+ sampledCt.push_back(it->first, it->second);
+ tempCount.erase(it++);
+ }
+
+ return sampledCt;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SubSampleCommand", "getSample");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+CountTable SubSample::getSample(CountTable& ct, int size, vector<string> Groups, bool pickedGroups) {
+ try {
+ CountTable sampledCt;
+ if (!ct.hasGroupInfo() && pickedGroups) { m->mothurOut("[ERROR]: Cannot subsample with groups because your count table doesn't have group information.\n"); m->control_pressed = true; return sampledCt; }
+
+ if (ct.hasGroupInfo()) {
+ map<string, vector<int> > tempCount;
+ vector<item> allNames;
+ map<string, int> groupMap;
+
+ vector<string> myGroups;
+ if (pickedGroups) { myGroups = Groups; }
+ else { myGroups = ct.getNamesOfGroups(); }
+
+ for (int i = 0; i < myGroups.size(); i++) {
+ sampledCt.addGroup(myGroups[i]);
+ groupMap[myGroups[i]] = i;
+
+ vector<string> names = ct.getNamesOfSeqs(myGroups[i]);
+ for (int j = 0; j < names.size(); j++) {
+
+ if (m->control_pressed) { return sampledCt; }
+
+ int num = ct. getGroupCount(names[j], myGroups[i]);
+ for (int k = 0; k < num; k++) {
+ item temp(names[j], myGroups[i]);
+ allNames.push_back(temp);
+ }
+ }
+ }
+
+ random_shuffle(allNames.begin(), allNames.end());
+
+ if (allNames.size() < size) {
+ if (pickedGroups) { m->mothurOut("[ERROR]: You have selected a size that is larger than the number of sequences.\n"); }
+ else { m->mothurOut("[ERROR]: You have selected a size that is larger than the number of sequences in the groups you chose.\n"); }
+ m->control_pressed = true; return sampledCt; }
+ else{
+ for (int j = 0; j < size; j++) {
+
+ if (m->control_pressed) { return sampledCt; }
+
+ map<string, vector<int> >::iterator it = tempCount.find(allNames[j].name);
+
+ if (it == tempCount.end()) { //we have not seen this sequence at all yet
+ vector<int> tempGroups; tempGroups.resize(myGroups.size(), 0);
+ tempGroups[groupMap[allNames[j].group]]++;
+ tempCount[allNames[j].name] = tempGroups;
+ }else{
+ tempCount[allNames[j].name][groupMap[allNames[j].group]]++;
+ }
+ }
+ }
+
+ //build count table
+ for (map<string, vector<int> >::iterator it = tempCount.begin(); it != tempCount.end();) {
+ sampledCt.push_back(it->first, it->second);
+ tempCount.erase(it++);
+ }
+
+ //remove empty groups
+ for (int i = 0; i < myGroups.size(); i++) { if (sampledCt.getGroupCount(myGroups[i]) == 0) { sampledCt.removeGroup(myGroups[i]); } }
+
+ }else {
+ vector<string> names = ct.getNamesOfSeqs();
+ map<string, int> nameMap;
+ vector<string> allNames;
+
+ for (int i = 0; i < names.size(); i++) {
+ int num = ct.getNumSeqs(names[i]);
+ for (int j = 0; j < num; j++) { allNames.push_back(names[i]); }
+ }
+
+ if (allNames.size() < size) { m->mothurOut("[ERROR]: You have selected a size that is larger than the number of sequences.\n"); m->control_pressed = true; return sampledCt; }
+ else {
+ random_shuffle(allNames.begin(), allNames.end());
+
+ for (int j = 0; j < size; j++) {
+ if (m->control_pressed) { return sampledCt; }
+
+ map<string, int>::iterator it = nameMap.find(allNames[j]);
+
+ //we have not seen this sequence at all yet
+ if (it == nameMap.end()) { nameMap[allNames[j]] = 1; }
+ else{ nameMap[allNames[j]]++; }
+ }
+
+ //build count table
+ for (map<string, int>::iterator it = nameMap.begin(); it != nameMap.end();) {
+ sampledCt.push_back(it->first, it->second);
+ nameMap.erase(it++);
+ }
+ }
+ }
+
+ return sampledCt;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SubSampleCommand", "getSample");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
projects / mothur.git / blobdiff