+++ /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