+++ /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