--- /dev/null
+//
+// subsample.cpp
+// Mothur
+//
+// Created by Sarah Westcott on 4/2/12.
+// Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+#include "subsample.h"
+
+//**********************************************************************************************************************
+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) {
+ 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", "getSample-TreeMap");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> SubSample::getSample(vector<SharedRAbundVector*>& thislookup, int size) {
+ try {
+
+ //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());
+
+ delete thislookup[i];
+ thislookup[i] = temp;
+
+
+ for (int j = 0; j < size; j++) {
+
+ if (m->control_pressed) { return m->currentBinLabels; }
+
+ int bin = order.get(j);
+
+ int abund = thislookup[i]->getAbundance(bin);
+ thislookup[i]->set(bin, (abund+1), thisgroup);
+ }
+ }
+ }
+
+ //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
+ vector<string> subsampleBinLabels = m->currentBinLabels;
+ m->currentBinLabels = saveBinLabels;
+
+ return subsampleBinLabels;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SubSample", "getSample-shared");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SubSample::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
+ try {
+
+ vector<SharedRAbundVector*> newLookup;
+ for (int i = 0; i < thislookup.size(); i++) {
+ SharedRAbundVector* temp = new SharedRAbundVector();
+ temp->setLabel(thislookup[i]->getLabel());
+ temp->setGroup(thislookup[i]->getGroup());
+ newLookup.push_back(temp);
+ }
+
+ //for each bin
+ vector<string> newBinLabels;
+ string snumBins = toString(thislookup[0]->getNumBins());
+ for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
+ if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
+
+ //look at each sharedRabund and make sure they are not all zero
+ bool allZero = true;
+ for (int j = 0; j < thislookup.size(); j++) {
+ if (thislookup[j]->getAbundance(i) != 0) { allZero = false; break; }
+ }
+
+ //if they are not all zero add this bin
+ if (!allZero) {
+ for (int j = 0; j < thislookup.size(); j++) {
+ newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
+ }
+ //if there is a bin label use it otherwise make one
+ string binLabel = "Otu";
+ string sbinNumber = toString(i+1);
+ if (sbinNumber.length() < snumBins.length()) {
+ int diff = snumBins.length() - sbinNumber.length();
+ for (int h = 0; h < diff; h++) { binLabel += "0"; }
+ }
+ binLabel += sbinNumber;
+ if (i < m->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; }
+
+ newBinLabels.push_back(binLabel);
+ }
+ }
+
+ for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; }
+ thislookup.clear();
+
+ thislookup = newLookup;
+ m->currentBinLabels = newBinLabels;
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SubSample", "eliminateZeroOTUS");
+ exit(1);
+ }
+}
+
+
+//**********************************************************************************************************************
+
+
projects / mothur.git / blobdiff