--- /dev/null
+/*
+ * doTaxonomy.cpp
+ *
+ *
+ * Created by Pat Schloss on 6/17/09.
+ * Copyright 2009 Patrick D. Schloss. All rights reserved.
+ *
+ */
+
+#include "phylotree.h"
+
+/**************************************************************************************************/
+
+PhyloTree::PhyloTree(){
+ try {
+ m = MothurOut::getInstance();
+ numNodes = 1;
+ numSeqs = 0;
+ tree.push_back(TaxNode("Root"));
+ tree[0].heirarchyID = "0";
+ maxLevel = 0;
+ calcTotals = true;
+ addSeqToTree("unknown", "unknown;");
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloTree", "PhyloTree");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+PhyloTree::PhyloTree(ifstream& in, string filename){
+ try {
+ m = MothurOut::getInstance();
+ calcTotals = false;
+ numNodes = 0;
+ numSeqs = 0;
+
+ #ifdef USE_MPI
+ MPI_File inMPI;
+ MPI_Offset size;
+ MPI_Status status;
+
+ char inFileName[1024];
+ strcpy(inFileName, filename.c_str());
+
+ MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
+ MPI_File_get_size(inMPI, &size);
+
+ char* buffer = new char[size];
+ MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
+
+ string tempBuf = buffer;
+ if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size); }
+ istringstream iss (tempBuf,istringstream::in);
+ delete buffer;
+
+ //read version
+ m->getline(iss); m->gobble(iss);
+
+ iss >> numNodes; m->gobble(iss);
+
+ tree.resize(numNodes);
+
+ for (int i = 0; i < tree.size(); i++) {
+ iss >> tree[i].name >> tree[i].level >> tree[i].parent; m->gobble(iss);
+ }
+
+ //read genus nodes
+ int numGenus = 0;
+ iss >> numGenus; m->gobble(iss);
+
+ int gnode, gsize;
+ totals.clear();
+ for (int i = 0; i < numGenus; i++) {
+ iss >> gnode >> gsize; m->gobble(iss);
+
+ uniqueTaxonomies[gnode] = gnode;
+ totals.push_back(gsize);
+ }
+
+ MPI_File_close(&inMPI);
+
+ #else
+ //read version
+ string line = m->getline(in); m->gobble(in);
+
+ in >> numNodes; m->gobble(in);
+
+ tree.resize(numNodes);
+
+ for (int i = 0; i < tree.size(); i++) {
+ in >> tree[i].name >> tree[i].level >> tree[i].parent; m->gobble(in);
+ }
+
+ //read genus nodes
+ int numGenus = 0;
+ in >> numGenus; m->gobble(in);
+
+ int gnode, gsize;
+ totals.clear();
+ for (int i = 0; i < numGenus; i++) {
+ in >> gnode >> gsize; m->gobble(in);
+
+ uniqueTaxonomies[gnode] = gnode;
+ totals.push_back(gsize);
+ }
+
+ in.close();
+
+ #endif
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloTree", "PhyloTree");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+PhyloTree::PhyloTree(string tfile){
+ try {
+ m = MothurOut::getInstance();
+ numNodes = 1;
+ numSeqs = 0;
+ tree.push_back(TaxNode("Root"));
+ tree[0].heirarchyID = "0";
+ maxLevel = 0;
+ calcTotals = true;
+ string name, tax;
+
+ #ifdef USE_MPI
+ int pid, num, processors;
+ vector<unsigned long long> positions;
+
+ MPI_Status status;
+ MPI_File inMPI;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+ MPI_Comm_size(MPI_COMM_WORLD, &processors);
+
+ char inFileName[1024];
+ strcpy(inFileName, tfile.c_str());
+
+ MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
+
+ if (pid == 0) {
+ positions = m->setFilePosEachLine(tfile, num);
+
+ //send file positions to all processes
+ for(int i = 1; i < processors; i++) {
+ MPI_Send(&num, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+ MPI_Send(&positions[0], (num+1), MPI_LONG, i, 2001, MPI_COMM_WORLD);
+ }
+ }else{
+ MPI_Recv(&num, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+ positions.resize(num+1);
+ MPI_Recv(&positions[0], (num+1), MPI_LONG, 0, 2001, MPI_COMM_WORLD, &status);
+ }
+
+ //read file
+ for(int i=0;i<num;i++){
+ //read next sequence
+ int length = positions[i+1] - positions[i];
+ char* buf4 = new char[length];
+
+ MPI_File_read_at(inMPI, positions[i], buf4, length, MPI_CHAR, &status);
+
+ string tempBuf = buf4;
+ if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
+ delete buf4;
+
+ istringstream iss (tempBuf,istringstream::in);
+ iss >> name >> tax;
+ addSeqToTree(name, tax);
+ }
+
+ MPI_File_close(&inMPI);
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+
+ #else
+ ifstream in;
+ m->openInputFile(tfile, in);
+
+ //read in users taxonomy file and add sequences to tree
+ while(!in.eof()){
+ in >> name >> tax; m->gobble(in);
+
+ addSeqToTree(name, tax);
+ }
+ in.close();
+ #endif
+
+ assignHeirarchyIDs(0);
+
+
+ string unknownTax = "unknown;";
+ //added last taxon until you get desired level
+ for (int i = 1; i < maxLevel; i++) {
+ unknownTax += "unclassfied;";
+ }
+
+ addSeqToTree("unknown", unknownTax);
+
+ //create file for summary if needed
+ setUp(tfile);
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloTree", "PhyloTree");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+string PhyloTree::getNextTaxon(string& heirarchy, string seqname){
+ try {
+ string currentLevel = "";
+ if(heirarchy != ""){
+ int pos = heirarchy.find_first_of(';');
+
+ if (pos == -1) { //you can't find another ;
+ currentLevel = heirarchy;
+ heirarchy = "";
+ m->mothurOut(seqname + " is missing a ;, please check for other errors."); m->mothurOutEndLine();
+ }else{
+ currentLevel=heirarchy.substr(0,pos);
+ if (pos != (heirarchy.length()-1)) { heirarchy=heirarchy.substr(pos+1); }
+ else { heirarchy = ""; }
+ }
+
+ }
+ return currentLevel;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloTree", "getNextTaxon");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
+ try {
+ numSeqs++;
+
+ map<string, int>::iterator childPointer;
+
+ int currentNode = 0;
+ int level = 1;
+
+ tree[0].accessions.push_back(seqName);
+ m->removeConfidences(seqTaxonomy);
+
+ string taxon;// = getNextTaxon(seqTaxonomy);
+
+ while(seqTaxonomy != ""){
+
+ level++;
+
+ if (m->control_pressed) { return 0; }
+
+ //somehow the parent is getting one too many accnos
+ //use print to reassign the taxa id
+ taxon = getNextTaxon(seqTaxonomy, seqName);
+
+ if (taxon == "") { m->mothurOut(seqName + " has an error in the taxonomy. This may be due to a ;;"); m->mothurOutEndLine(); if (currentNode != 0) { uniqueTaxonomies[currentNode] = currentNode; } break; }
+
+ childPointer = tree[currentNode].children.find(taxon);
+
+ if(childPointer != tree[currentNode].children.end()){ //if the node already exists, move on
+ currentNode = childPointer->second;
+ tree[currentNode].accessions.push_back(seqName);
+ name2Taxonomy[seqName] = currentNode;
+ }
+ else{ //otherwise, create it
+ tree.push_back(TaxNode(taxon));
+ numNodes++;
+ tree[currentNode].children[taxon] = numNodes-1;
+ tree[numNodes-1].parent = currentNode;
+
+ currentNode = tree[currentNode].children[taxon];
+ tree[currentNode].accessions.push_back(seqName);
+ name2Taxonomy[seqName] = currentNode;
+ }
+
+ if (seqTaxonomy == "") { uniqueTaxonomies[currentNode] = currentNode; }
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloTree", "addSeqToTree");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+vector<int> PhyloTree::getGenusNodes() {
+ try {
+ genusIndex.clear();
+ //generate genusIndexes
+ map<int, int>::iterator it2;
+ for (it2=uniqueTaxonomies.begin(); it2!=uniqueTaxonomies.end(); it2++) { genusIndex.push_back(it2->first); }
+
+ return genusIndex;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloTree", "getGenusNodes");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+vector<int> PhyloTree::getGenusTotals() {
+ try {
+
+ if (calcTotals) {
+ totals.clear();
+ //reset counts because we are on a new word
+ for (int j = 0; j < genusIndex.size(); j++) {
+ totals.push_back(tree[genusIndex[j]].accessions.size());
+ }
+ return totals;
+ }else{
+ return totals;
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloTree", "getGenusNodes");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+void PhyloTree::assignHeirarchyIDs(int index){
+ try {
+ map<string,int>::iterator it;
+ int counter = 1;
+
+ for(it=tree[index].children.begin();it!=tree[index].children.end();it++){
+ tree[it->second].heirarchyID = tree[index].heirarchyID + '.' + toString(counter);
+ counter++;
+ tree[it->second].level = tree[index].level + 1;
+
+ //save maxLevel for binning the unclassified seqs
+ if (tree[it->second].level > maxLevel) { maxLevel = tree[it->second].level; }
+
+ assignHeirarchyIDs(it->second);
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloTree", "assignHeirarchyIDs");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+void PhyloTree::setUp(string tfile){
+ try{
+ string taxFileNameTest = tfile.substr(0,tfile.find_last_of(".")+1) + "tree.sum";
+
+ #ifdef USE_MPI
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+
+ if (pid == 0) { binUnclassified(taxFileNameTest); }
+
+ #else
+ binUnclassified(taxFileNameTest);
+ #endif
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloTree", "setUp");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+void PhyloTree::binUnclassified(string file){
+ try {
+
+ ofstream out;
+ m->openOutputFile(file, out);
+
+ map<string, int>::iterator itBin;
+ map<string, int>::iterator childPointer;
+
+ vector<TaxNode> copy = tree;
+
+ //fill out tree
+ fillOutTree(0, copy);
+
+ //get leaf nodes that may need extension
+ for (int i = 0; i < copy.size(); i++) {
+
+ if (copy[i].children.size() == 0) {
+ leafNodes[i] = i;
+ }
+ }
+
+ int copyNodes = copy.size();
+
+ //go through the seqs and if a sequence finest taxon is not the same level as the most finely defined taxon then classify it as unclassified where necessary
+ map<int, int>::iterator itLeaf;
+ for (itLeaf = leafNodes.begin(); itLeaf != leafNodes.end(); itLeaf++) {
+
+ if (m->control_pressed) { out.close(); break; }
+
+ int level = copy[itLeaf->second].level;
+ int currentNode = itLeaf->second;
+
+ //this sequence is unclassified at some levels
+ while(level < maxLevel){
+
+ level++;
+
+ string taxon = "unclassified";
+
+ //does the parent have a child names 'unclassified'?
+ childPointer = copy[currentNode].children.find(taxon);
+
+ if(childPointer != copy[currentNode].children.end()){ //if the node already exists, move on
+ currentNode = childPointer->second; //currentNode becomes 'unclassified'
+ }
+ else{ //otherwise, create it
+ copy.push_back(TaxNode(taxon));
+ copyNodes++;
+ copy[currentNode].children[taxon] = copyNodes-1;
+ copy[copyNodes-1].parent = currentNode;
+ copy[copyNodes-1].level = copy[currentNode].level + 1;
+
+ currentNode = copy[currentNode].children[taxon];
+ }
+ }
+ }
+
+ if (!m->control_pressed) {
+ //print copy tree
+ print(out, copy);
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloTree", "binUnclassified");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+void PhyloTree::fillOutTree(int index, vector<TaxNode>& copy) {
+ try {
+
+ map<string,int>::iterator it;
+
+ it = copy[index].children.find("unclassified");
+ if (it == copy[index].children.end()) { //no unclassified at this level
+ string taxon = "unclassified";
+ copy.push_back(TaxNode(taxon));
+ copy[index].children[taxon] = copy.size()-1;
+ copy[copy.size()-1].parent = index;
+ copy[copy.size()-1].level = copy[index].level + 1;
+ }
+
+ if (tree[index].level < maxLevel) {
+ for(it=tree[index].children.begin();it!=tree[index].children.end();it++){ //check your children
+ fillOutTree(it->second, copy);
+ }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloTree", "fillOutTree");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+string PhyloTree::getFullTaxonomy(string seqName) {
+ try {
+ string tax = "";
+
+ int currentNode = name2Taxonomy[seqName];
+
+ while (tree[currentNode].parent != -1) {
+ tax = tree[currentNode].name + ";" + tax;
+ currentNode = tree[currentNode].parent;
+ }
+
+ return tax;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloTree", "getFullTaxonomy");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+void PhyloTree::print(ofstream& out, vector<TaxNode>& copy){
+ try {
+
+ //output mothur version
+ out << "#" << m->getVersion() << endl;
+
+ out << copy.size() << endl;
+
+ out << maxLevel << endl;
+
+ for (int i = 0; i < copy.size(); i++) {
+
+ out << copy[i].level << '\t'<< copy[i].name << '\t' << copy[i].children.size() << '\t';
+
+ map<string,int>::iterator it;
+ for(it=copy[i].children.begin();it!=copy[i].children.end();it++){
+ out << it->first << '\t' << it->second << '\t';
+ }
+ out << endl;
+ }
+
+ out.close();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloTree", "print");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+void PhyloTree::printTreeNodes(string treefilename) {
+ try {
+
+ #ifdef USE_MPI
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+
+ if (pid == 0) {
+
+ #endif
+
+ ofstream outTree;
+ m->openOutputFile(treefilename, outTree);
+
+ //output mothur version
+ outTree << "#" << m->getVersion() << endl;
+
+ //print treenodes
+ outTree << tree.size() << endl;
+ for (int i = 0; i < tree.size(); i++) {
+ outTree << tree[i].name << '\t' << tree[i].level << '\t' << tree[i].parent << endl;
+ }
+
+ //print genus nodes
+ outTree << endl << uniqueTaxonomies.size() << endl;
+ map<int, int>::iterator it2;
+ for (it2=uniqueTaxonomies.begin(); it2!=uniqueTaxonomies.end(); it2++) { outTree << it2->first << '\t' << tree[it2->first].accessions.size() << endl; }
+ outTree << endl;
+
+ outTree.close();
+
+ #ifdef USE_MPI
+ }
+ #endif
+
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloTree", "printTreeNodes");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+TaxNode PhyloTree::get(int i ){
+ try {
+ if (i < tree.size()) { return tree[i]; }
+ else { cout << i << '\t' << tree.size() << endl ; m->mothurOut("Mismatch with taxonomy and template files. Cannot continue."); m->mothurOutEndLine(); exit(1); }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloTree", "get");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+TaxNode PhyloTree::get(string seqName){
+ try {
+ map<string, int>::iterator itFind = name2Taxonomy.find(seqName);
+
+ if (itFind != name2Taxonomy.end()) { return tree[name2Taxonomy[seqName]]; }
+ else { m->mothurOut("Cannot find " + seqName + ". Mismatch with taxonomy and template files. Cannot continue."); m->mothurOutEndLine(); exit(1);}
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloTree", "get");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+string PhyloTree::getName(int i ){
+ try {
+ if (i < tree.size()) { return tree[i].name; }
+ else { m->mothurOut("Mismatch with taxonomy and template files. Cannot continue."); m->mothurOutEndLine(); exit(1); }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloTree", "get");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int PhyloTree::getIndex(string seqName){
+ try {
+ map<string, int>::iterator itFind = name2Taxonomy.find(seqName);
+
+ if (itFind != name2Taxonomy.end()) { return name2Taxonomy[seqName]; }
+ else { m->mothurOut("Cannot find " + seqName + ". Mismatch with taxonomy and template files. Cannot continue."); m->mothurOutEndLine(); exit(1);}
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloTree", "get");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+bool PhyloTree::ErrorCheck(vector<string> templateFileNames){
+ try {
+
+ bool okay = true;
+ templateFileNames.push_back("unknown");
+
+ map<string, int>::iterator itFind;
+ map<string, int> taxonomyFileNames = name2Taxonomy;
+
+ for (int i = 0; i < templateFileNames.size(); i++) {
+ itFind = taxonomyFileNames.find(templateFileNames[i]);
+
+ if (itFind != taxonomyFileNames.end()) { //found it so erase it
+ taxonomyFileNames.erase(itFind);
+ }else {
+ m->mothurOut(templateFileNames[i] + " is in your template file and is not in your taxonomy file. Please correct."); m->mothurOutEndLine();
+ okay = false;
+ }
+
+ //templateFileNames.erase(templateFileNames.begin()+i);
+ //i--;
+ }
+ templateFileNames.clear();
+
+ if (taxonomyFileNames.size() > 0) { //there are names in tax file that are not in template
+ okay = false;
+
+ for (itFind = taxonomyFileNames.begin(); itFind != taxonomyFileNames.end(); itFind++) {
+ m->mothurOut(itFind->first + " is in your taxonomy file and is not in your template file. Please correct."); m->mothurOutEndLine();
+ }
+ }
+
+ return okay;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloTree", "ErrorCheck");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+
+
+
projects / mothur.git / blobdiff