//**********************************************************************************************************************
vector<string> ClassifyOtuCommand::findConsensusTaxonomy(vector<string> names, int& size, string& conTax) {
try{
conTax = "";
vector<string> allNames;
map<string, string>::iterator it;
map<string, string>::iterator it2;
//create a tree containing sequences from this bin
PhyloTree* phylo = new PhyloTree();
size = 0;
for (int i = 0; i < names.size(); i++) {
//if namesfile include the names
if (namefile != "") {
//is this sequence in the name file - namemap maps seqName -> repSeqName
it2 = nameMap.find(names[i]);
if (it2 == nameMap.end()) { //this name is not in name file, skip it
m->mothurOut(names[i] + " is not in your name file. I will not include it in the consensus."); m->mothurOutEndLine();
}else{
//is this sequence in the taxonomy file - look for repSeqName since we are assuming the taxonomy file is unique
it = taxMap.find(it2->second);
if (it == taxMap.end()) { //this name is not in taxonomy file, skip it
if (names[i] != it2->second) { m->mothurOut(names[i] + " is represented by " + it2->second + " and is not in your taxonomy file. I will not include it in the consensus."); m->mothurOutEndLine(); }
else { m->mothurOut(names[i] + " is not in your taxonomy file. I will not include it in the consensus."); m->mothurOutEndLine(); }
}else{
//add seq to tree
phylo->addSeqToTree(names[i], it->second);
size++;
allNames.push_back(names[i]);
}
}
}else{
//is this sequence in the taxonomy file - look for repSeqName since we are assuming the taxonomy file is unique
it = taxMap.find(names[i]);
if (it == taxMap.end()) { //this name is not in taxonomy file, skip it
m->mothurOut(names[i] + " is not in your taxonomy file. I will not include it in the consensus."); m->mothurOutEndLine();
}else{
if (countfile != "") {
int numDups = ct->getNumSeqs(names[i]);
for (int j = 0; j < numDups; j++) { phylo->addSeqToTree(names[i], it->second); }
size += numDups;
}else{
//add seq to tree
phylo->addSeqToTree(names[i], it->second);
size++;
}
allNames.push_back(names[i]);
}
}
if (m->control_pressed) { delete phylo; return allNames; }
}
//build tree
phylo->assignHeirarchyIDs(0);
TaxNode currentNode = phylo->get(0);
int myLevel = 0;
//at each level
while (currentNode.children.size() != 0) { //you still have more to explore
TaxNode bestChild;
int bestChildSize = 0;
//go through children
for (map<string, int>::iterator itChild = currentNode.children.begin(); itChild != currentNode.children.end(); itChild++) {
TaxNode temp = phylo->get(itChild->second);
//select child with largest accesions - most seqs assigned to it
if (temp.accessions.size() > bestChildSize) {
bestChild = phylo->get(itChild->second);
bestChildSize = temp.accessions.size();
}
}
//phylotree adds an extra unknown so we want to remove that
if (bestChild.name == "unknown") { bestChildSize--; }
//is this taxonomy above cutoff
int consensusConfidence = ceil((bestChildSize / (float) size) * 100);
if (consensusConfidence >= cutoff) { //if yes, add it
if (probs) {
conTax += bestChild.name + "(" + toString(consensusConfidence) + ");";
}else{
conTax += bestChild.name + ";";
}
myLevel++;
}else{ //if no, quit
break;
}
//move down a level
currentNode = bestChild;
}
if (myLevel != phylo->getMaxLevel()) {
while (myLevel != phylo->getMaxLevel()) {
conTax += "unclassified;";
myLevel++;
}
}
if (conTax == "") { conTax = "no_consensus;"; }
delete phylo;
return allNames;
}
catch(exception& e) {
m->errorOut(e, "ClassifyOtuCommand", "findConsensusTaxonomy");
exit(1);
}
}
int SplitMatrix::splitClassify() {
try {
cutoff = int(cutoff);
map<string, int> seqGroup;
map<string, int>::iterator it;
map<string, int>::iterator it2;
int numGroups = 0;
//build tree from users taxonomy file
PhyloTree* phylo = new PhyloTree();
map<string, string> temp;
m->readTax(taxFile, temp, true);
for (map<string, string>::iterator itTemp = temp.begin(); itTemp != temp.end();) {
phylo->addSeqToTree(itTemp->first, itTemp->second);
temp.erase(itTemp++);
}
phylo->assignHeirarchyIDs(0);
//make sure the cutoff is not greater than maxlevel
if (cutoff > phylo->getMaxLevel()) {
m->mothurOut("splitcutoff is greater than the longest taxonomy, using " + toString(phylo->getMaxLevel()));
m->mothurOutEndLine();
cutoff = phylo->getMaxLevel();
}
//for each node in tree
for (int i = 0; i < phylo->getNumNodes(); i++) {
//is this node within the cutoff
TaxNode taxon = phylo->get(i);
if (taxon.level == cutoff) {//if yes, then create group containing this nodes sequences
if (taxon.accessions.size() > 1) { //if this taxon just has one seq its a singleton
for (int j = 0; j < taxon.accessions.size(); j++) {
seqGroup[taxon.accessions[j]] = numGroups;
}
numGroups++;
}
}
}
delete phylo;
if (method == "classify") {
splitDistanceFileByTax(seqGroup, numGroups);
} else {
createDistanceFilesFromTax(seqGroup, numGroups);
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "SplitMatrix", "splitClassify");
exit(1);
}
}
