#include "subsample.h"
//**********************************************************************************************************************
-Tree* SubSample::getSample(Tree* T, TreeMap* tmap, TreeMap* newTmap, int size, map<string, string> originalNameMap) {
+Tree* SubSample::getSample(Tree* T, CountTable* ct, CountTable* newCt, int size) {
try {
Tree* newTree = NULL;
- map<string, vector<string> > newGroups;
- vector<string> subsampledSeqs = getSample(tmap, size, newGroups);
+ //remove seqs not in sample from counttable
+ vector<string> Groups = ct->getNamesOfGroups();
+ newCt->copy(ct);
+ newCt->addGroup("doNotIncludeMe");
- //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);
+ 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; }
- //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++;
+ 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; }
}
- 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(); }
+ for (map<string, int>::iterator it = doNotIncludeTotals.begin(); it != doNotIncludeTotals.end(); it++) {
+ newCt->setAbund(it->first, "doNotIncludeMe", it->second);
+ }
- newTree = new Tree(numUniques, tmap); //numNodes, treemap
- newTree->getSubTree(T, subsampledSeqs, sampledNameMap);
+ newTree = new Tree(newCt);
+ newTree->getCopy(T, true);
return newTree;
}
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) {
}
}
//**********************************************************************************************************************
-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 {
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