try {
//save mothurOut's binLabels to restore for next label
- vector<string> saveBinLabels = m->currentBinLabels;
+ vector<string> saveBinLabels = m->currentSharedBinLabels;
int numBins = thislookup[0]->getNumBins();
for (int i = 0; i < thislookup.size(); i++) {
for (int j = 0; j < size; j++) {
- if (m->control_pressed) { return m->currentBinLabels; }
+ if (m->control_pressed) { return m->currentSharedBinLabels; }
int bin = order.get(j);
//subsampling may have created some otus with no sequences in them
eliminateZeroOTUS(thislookup);
- if (m->control_pressed) { return m->currentBinLabels; }
+ if (m->control_pressed) { return m->currentSharedBinLabels; }
//save mothurOut's binLabels to restore for next label
- vector<string> subsampleBinLabels = m->currentBinLabels;
- m->currentBinLabels = saveBinLabels;
+ vector<string> subsampleBinLabels = m->currentSharedBinLabels;
+ m->currentSharedBinLabels = saveBinLabels;
return subsampleBinLabels;
for (int h = 0; h < diff; h++) { binLabel += "0"; }
}
binLabel += sbinNumber;
- if (i < m->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; }
+ if (i < m->currentSharedBinLabels.size()) { binLabel = m->currentSharedBinLabels[i]; }
newBinLabels.push_back(binLabel);
}
thislookup.clear();
thislookup = newLookup;
- m->currentBinLabels = newBinLabels;
+ m->currentSharedBinLabels = newBinLabels;
return 0;
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