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//
// picrust.cpp
// Mothur
//
// Created by Sarah Westcott on 11/16/20.
// Copyright © 2020 Schloss Lab. All rights reserved.
//
#include "picrust.hpp"
/**************************************************************************************************/
Picrust::Picrust(string ref, string otumapfile){
try {
m = MothurOut::getInstance();
phyloTree = nullptr;
read(ref, otumapfile);
}
catch(exception& e) {
m->errorOut(e, "Picrust", "Picrust");
exit(1);
}
}
/**************************************************************************************************/
Picrust::Picrust(){
try {
m = MothurOut::getInstance();
phyloTree = nullptr;
}
catch(exception& e) {
m->errorOut(e, "Picrust", "Picrust");
exit(1);
}
}
/**************************************************************************************************/
Picrust::~Picrust(){
try {
if (phyloTree != nullptr) { delete phyloTree; }
}
catch(exception& e) {
m->errorOut(e, "Picrust", "Picrust");
exit(1);
}
}
/**************************************************************************************************/
void Picrust::read(string ref, string otumapfile){
try {
//read reftaxonomy
phyloTree = new PhyloTree(ref);
//read otu map file
readGGOtuMap(otumapfile); //maps reference ID -> OTU ID
}
catch(exception& e) {
m->errorOut(e, "Picrust", "read");
exit(1);
}
}
//**********************************************************************************************************************
void Picrust::setGGOTUIDs(map<string, string>& labelTaxMap, SharedRAbundFloatVectors*& lookup){
try {
map<string, vector<string> > ggOTUIDs;
//loop through otu taxonomies
for (map<string, string>::iterator it = labelTaxMap.begin(); it != labelTaxMap.end(); it++) { //maps label -> consensus taxonomy
if (m->getControl_pressed()) { break; }
string OTUTaxonomy = it->second;
//remove confidences
util.removeConfidences(OTUTaxonomy);
//remove unclassifieds to match template
int thisPos = OTUTaxonomy.find("unclassified;"); //"Porphyromonadaceae"_unclassified;
if (thisPos != string::npos) {
OTUTaxonomy = OTUTaxonomy.substr(0, thisPos);
thisPos = OTUTaxonomy.find_last_of(";"); //remove rest of parent taxon
if (thisPos != string::npos) {
OTUTaxonomy = OTUTaxonomy.substr(0, thisPos+1);
}
}
//get list of reference ids that map to this taxonomy
vector<string> referenceIds = phyloTree->getSeqs(OTUTaxonomy);
if (m->getControl_pressed()) { break; }
//look for each one in otu map to find match
string otuID = "not found";
string referenceString = "";
for (int i = 0; i < referenceIds.size(); i++) {
referenceString += referenceIds[i] + " ";
map<string, string>::iterator itMap = otuMap.find(referenceIds[i]);
if (itMap != otuMap.end()) { //found it
otuID = itMap->second;
i += referenceIds.size(); //stop looking
}
}
//if found, add otu to ggOTUID list
if (otuID != "not found") {
map<string, vector<string> >::iterator itGG = ggOTUIDs.find(otuID);
if (itGG == ggOTUIDs.end()) {
vector<string> temp; temp.push_back(it->first); //save mothur OTU label
ggOTUIDs[otuID] = temp;
}else { ggOTUIDs[otuID].push_back(it->first); } //add mothur OTU label to list
}else { m->mothurOut("[ERROR]: could not find OTUId for " + it->second + ". Its reference sequences are " + referenceString + ".\n"); m->setControl_pressed(true); }
}
vector<SharedRAbundFloatVector*> newLookup;
vector<string> namesOfGroups = lookup->getNamesGroups();
for (int i = 0; i < namesOfGroups.size(); i++) {
SharedRAbundFloatVector* temp = new SharedRAbundFloatVector();
temp->setLabel(lookup->getLabel());
temp->setGroup(namesOfGroups[i]);
newLookup.push_back(temp);
}
map<string, int> labelIndex;
vector<string> currentLabels = lookup->getOTUNames();
for (int i = 0; i < currentLabels.size(); i++) { labelIndex[util.getSimpleLabel(currentLabels[i])] = i; }
vector<string> newBinLabels;
map<string, string> newLabelTaxMap;
//loop through ggOTUID list combining mothur otus and adjusting labels
//ggOTUIDs = 16097 -> <OTU01, OTU10, OTU22>
for (map<string, vector<string> >::iterator itMap = ggOTUIDs.begin(); itMap != ggOTUIDs.end(); itMap++) {
if (m->getControl_pressed()) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return; }
//set new gg otu id to taxonomy. OTU01 -> k__Bacteria becomes 16097 -> k__Bacteria
//find taxonomy of this otu
map<string, string>::iterator it = labelTaxMap.find(util.getSimpleLabel(itMap->second[0]));
vector<string> scores;
vector<string> taxonomies = util.parseTax(it->second, scores);
//merge/set OTU abundances
vector<float> abunds; abunds.resize(lookup->size(), 0.0);
string mergeString = "";
vector<float> boots; boots.resize(scores.size(), 0.0);
bool scoresnullptr = false;
for (int j = 0; j < itMap->second.size(); j++) { //<OTU01, OTU10, OTU22>
if (scores[0] != "null") {
//merge bootstrap scores
vector<string> scores;
vector<string> taxonomies = util.parseTax(it->second, scores);
for (int i = 0; i < boots.size(); i++) {
if (scores[i] == "null") { scoresnullptr = true; break; }
else {
float tempScore; util.mothurConvert(scores[i], tempScore);
boots[i] += tempScore;
}
}
}else { scoresnullptr = true; }
//merge abunds
mergeString += (itMap->second)[j] + " ";
for (int i = 0; i < lookup->size(); i++) { abunds[i] += lookup->get(labelIndex[util.getSimpleLabel((itMap->second)[j])], namesOfGroups[i]); }
}
if (m->getDebug()) { m->mothurOut("[DEBUG]: merging " + mergeString + " for ggOTUid = " + itMap->first + ".\n"); }
//average scores
//add merged otu to new lookup
string newTaxString = "";
if (!scoresnullptr) {
for (int j = 0; j < boots.size(); j++) { boots[j] /= (float) itMap->second.size(); }
//assemble new taxomoy
for (int j = 0; j < boots.size(); j++) {
newTaxString += taxonomies[j] + "(" + toString(boots[j]) + ");";
}
}else {
//assemble new taxomoy
for (int j = 0; j < taxonomies.size(); j++) {
newTaxString += taxonomies[j] + ";";
}
}
//set new gg otu id to taxonomy. OTU01 -> k__Bacteria becomes 16097 -> k__Bacteria
//find taxonomy of this otu
newLabelTaxMap[itMap->first] = newTaxString;
//add merged otu to new lookup
for (int j = 0; j < abunds.size(); j++) { newLookup[j]->push_back(abunds[j]); }
//saved otu label
newBinLabels.push_back(itMap->first);
}
lookup->clear();
for (int i = 0; i < newLookup.size(); i++) { lookup->push_back(newLookup[i]); }
lookup->eliminateZeroOTUS();
lookup->setOTUNames(newBinLabels);
labelTaxMap = newLabelTaxMap;
return;
}
catch(exception& e) {
m->errorOut(e, "Picrust", "setGGOTUIDs");
exit(1);
}
}
//**********************************************************************************************************************
void Picrust::setGGOTUIDs(map<string, string>& labelTaxMap, SharedRAbundVectors*& lookup){
try {
map<string, vector<string> > ggOTUIDs;
//loop through otu taxonomies
for (map<string, string>::iterator it = labelTaxMap.begin(); it != labelTaxMap.end(); it++) { //maps label -> consensus taxonomy
if (m->getControl_pressed()) { break; }
string OTUTaxonomy = it->second;
//remove confidences
util.removeConfidences(OTUTaxonomy);
//remove unclassifieds to match template
int thisPos = OTUTaxonomy.find("unclassified;"); //"Porphyromonadaceae"_unclassified;
if (thisPos != string::npos) {
OTUTaxonomy = OTUTaxonomy.substr(0, thisPos);
thisPos = OTUTaxonomy.find_last_of(";"); //remove rest of parent taxon
if (thisPos != string::npos) {
OTUTaxonomy = OTUTaxonomy.substr(0, thisPos+1);
}
}
//get list of reference ids that map to this taxonomy
vector<string> referenceIds = phyloTree->getSeqs(OTUTaxonomy);
if (m->getControl_pressed()) { break; }
//look for each one in otu map to find match
string otuID = "not found";
string referenceString = "";
for (int i = 0; i < referenceIds.size(); i++) {
referenceString += referenceIds[i] + " ";
map<string, string>::iterator itMap = otuMap.find(referenceIds[i]);
if (itMap != otuMap.end()) { //found it
otuID = itMap->second;
i += referenceIds.size(); //stop looking
}
}
//if found, add otu to ggOTUID list
if (otuID != "not found") {
map<string, vector<string> >::iterator itGG = ggOTUIDs.find(otuID);
if (itGG == ggOTUIDs.end()) {
vector<string> temp; temp.push_back(it->first); //save mothur OTU label
ggOTUIDs[otuID] = temp;
}else { ggOTUIDs[otuID].push_back(it->first); } //add mothur OTU label to list
}else { m->mothurOut("[ERROR]: could not find OTUId for " + it->second + ". Its reference sequences are " + referenceString + ".\n"); m->setControl_pressed(true); }
}
vector<SharedRAbundVector*> newLookup;
vector<string> namesOfGroups = lookup->getNamesGroups();
for (int i = 0; i < namesOfGroups.size(); i++) {
SharedRAbundVector* temp = new SharedRAbundVector();
temp->setLabel(lookup->getLabel());
temp->setGroup(namesOfGroups[i]);
newLookup.push_back(temp);
}
map<string, int> labelIndex;
vector<string> currentLabels = lookup->getOTUNames();
for (int i = 0; i < currentLabels.size(); i++) { labelIndex[util.getSimpleLabel(currentLabels[i])] = i; }
vector<string> newBinLabels;
map<string, string> newLabelTaxMap;
//loop through ggOTUID list combining mothur otus and adjusting labels
//ggOTUIDs = 16097 -> <OTU01, OTU10, OTU22>
for (map<string, vector<string> >::iterator itMap = ggOTUIDs.begin(); itMap != ggOTUIDs.end(); itMap++) {
if (m->getControl_pressed()) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return; }
//set new gg otu id to taxonomy. OTU01 -> k__Bacteria becomes 16097 -> k__Bacteria
//find taxonomy of this otu
map<string, string>::iterator it = labelTaxMap.find(util.getSimpleLabel(itMap->second[0]));
vector<string> scores;
vector<string> taxonomies = util.parseTax(it->second, scores);
//merge/set OTU abundances
vector<float> abunds; abunds.resize(lookup->size(), 0.0);
string mergeString = "";
vector<float> boots; boots.resize(scores.size(), 0.0);
bool scoresnullptr = false;
for (int j = 0; j < itMap->second.size(); j++) { //<OTU01, OTU10, OTU22>
if (scores[0] != "null") {
//merge bootstrap scores
vector<string> scores;
vector<string> taxonomies = util.parseTax(it->second, scores);
for (int i = 0; i < boots.size(); i++) {
if (scores[i] == "null") { scoresnullptr = true; break; }
else {
float tempScore; util.mothurConvert(scores[i], tempScore);
boots[i] += tempScore;
}
}
}else { scoresnullptr = true; }
//merge abunds
mergeString += (itMap->second)[j] + " ";
for (int i = 0; i < lookup->size(); i++) { abunds[i] += lookup->get(labelIndex[util.getSimpleLabel((itMap->second)[j])], namesOfGroups[i]); }
}
if (m->getDebug()) { m->mothurOut("[DEBUG]: merging " + mergeString + " for ggOTUid = " + itMap->first + ".\n"); }
//average scores
//add merged otu to new lookup
string newTaxString = "";
if (!scoresnullptr) {
for (int j = 0; j < boots.size(); j++) { boots[j] /= (float) itMap->second.size(); }
//assemble new taxomoy
for (int j = 0; j < boots.size(); j++) {
newTaxString += taxonomies[j] + "(" + toString(boots[j]) + ");";
}
}else {
//assemble new taxomoy
for (int j = 0; j < taxonomies.size(); j++) {
newTaxString += taxonomies[j] + ";";
}
}
//set new gg otu id to taxonomy. OTU01 -> k__Bacteria becomes 16097 -> k__Bacteria
//find taxonomy of this otu
newLabelTaxMap[itMap->first] = newTaxString;
//add merged otu to new lookup
for (int j = 0; j < abunds.size(); j++) { newLookup[j]->push_back(abunds[j]); }
//saved otu label
newBinLabels.push_back(itMap->first);
}
lookup->clear();
for (int i = 0; i < newLookup.size(); i++) { lookup->push_back(newLookup[i]); }
lookup->eliminateZeroOTUS();
lookup->setOTUNames(newBinLabels);
labelTaxMap = newLabelTaxMap;
return;
}
catch(exception& e) {
m->errorOut(e, "Picrust", "setGGOTUIDs");
exit(1);
}
}
//**********************************************************************************************************************
void Picrust::readGGOtuMap(string otumapfile){
try {
ifstream in; util.openInputFile(otumapfile, in);
//map referenceIDs -> otuIDs
//lines look like:
//16097 671376 616121 533566 683683 4332909 4434717 772666 611808 695209
while(!in.eof()) {
if (m->getControl_pressed()) { break; }
string line = util.getline(in); gobble(in);
vector<string> pieces = util.splitWhiteSpace(line);
if (pieces.size() != 0) {
string otuID = pieces[1];
for (int i = 1; i < pieces.size(); i++) { otuMap[pieces[i]] = otuID; }
}
}
in.close();
}
catch(exception& e) {
m->errorOut(e, "Picrust", "readGGOtuMap");
exit(1);
}
}
/**************************************************************************************************/
|
