}
/**************************************************************************************************/
-PhyloTree::PhyloTree(ifstream& in){
+PhyloTree::PhyloTree(ifstream& in, string filename){
try {
m = MothurOut::getInstance();
calcTotals = false;
- in >> numNodes; gobble(in);
-
- tree.resize(numNodes);
-
- for (int i = 0; i < tree.size(); i++) {
- in >> tree[i].name >> tree[i].level >> tree[i].parent; gobble(in);
-
- }
-
- //read genus nodes
- int numGenus = 0;
- in >> numGenus; gobble(in);
-
- int gnode, gsize;
- totals.clear();
- for (int i = 0; i < numGenus; i++) {
- in >> gnode >> gsize; gobble(in);
+ #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);
- uniqueTaxonomies[gnode] = gnode;
- totals.push_back(gsize);
- }
+ 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;
+
+ iss >> numNodes; gobble(iss);
+
+ tree.resize(numNodes);
+
+ for (int i = 0; i < tree.size(); i++) {
+ iss >> tree[i].name >> tree[i].level >> tree[i].parent; gobble(iss);
+ }
- in.close();
+ //read genus nodes
+ int numGenus = 0;
+ iss >> numGenus; gobble(iss);
+
+ int gnode, gsize;
+ totals.clear();
+ for (int i = 0; i < numGenus; i++) {
+ iss >> gnode >> gsize; gobble(iss);
+
+ uniqueTaxonomies[gnode] = gnode;
+ totals.push_back(gsize);
+ }
+
+ MPI_File_close(&inMPI);
+
+ #else
+ in >> numNodes; gobble(in);
+
+ tree.resize(numNodes);
+
+ for (int i = 0; i < tree.size(); i++) {
+ in >> tree[i].name >> tree[i].level >> tree[i].parent; gobble(in);
+ }
+
+ //read genus nodes
+ int numGenus = 0;
+ in >> numGenus; gobble(in);
+
+ int gnode, gsize;
+ totals.clear();
+ for (int i = 0; i < numGenus; i++) {
+ in >> gnode >> gsize; gobble(in);
+
+ uniqueTaxonomies[gnode] = gnode;
+ totals.push_back(gsize);
+ }
+
+ in.close();
+
+ #endif
}
catch(exception& e) {
tree[0].heirarchyID = "0";
maxLevel = 0;
calcTotals = true;
+ string name, tax;
+
- ifstream in;
- openInputFile(tfile, in);
+ #ifdef USE_MPI
+ int pid, num;
+ vector<long> positions;
+
+ MPI_Status status;
+ MPI_File inMPI;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+
+ 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 = setFilePosEachLine(tfile, num);
+
+ //send file positions to all processes
+ MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD); //send numSeqs
+ MPI_Bcast(&positions[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos
+ }else{
+ MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
+ positions.resize(num);
+ MPI_Bcast(&positions[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
+ }
- //read in users taxonomy file and add sequences to tree
- string name, tax;
- while(!in.eof()){
- in >> name >> tax; gobble(in);
+ //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);
+ }
- addSeqToTree(name, tax);
- }
- in.close();
-
+ MPI_File_close(&inMPI);
+
+ #else
+ ifstream in;
+ openInputFile(tfile, in);
+
+ //read in users taxonomy file and add sequences to tree
+ while(!in.eof()){
+ in >> name >> tax; gobble(in);
+
+ addSeqToTree(name, tax);
+ }
+ in.close();
+ #endif
+
assignHeirarchyIDs(0);
+
+ //create file for summary if needed
+ setUp(tfile);
}
catch(exception& e) {
m->errorOut(e, "PhyloTree", "PhyloTree");
}
}
/**************************************************************************************************/
-void PhyloTree::binUnclassified(){
+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
+ //create file needed for summary if it doesn't exist
+ ifstream FileTest(taxFileNameTest.c_str());
+
+ if (!FileTest) {
+ binUnclassified(taxFileNameTest);
+ }
+ #endif
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloTree", "setUp");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+void PhyloTree::binUnclassified(string file){
try {
+
+ ofstream out;
+ openOutputFile(file, out);
+
map<string, int>::iterator itBin;
map<string, int>::iterator childPointer;
+ vector<TaxNode> copy = tree;
+ int copyNodes = numNodes;
+
//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
for (itBin = name2Taxonomy.begin(); itBin != name2Taxonomy.end(); itBin++) {
-
- int level = tree[itBin->second].level;
+
+ if (m->control_pressed) { out.close(); break; }
+
+ int level = copy[itBin->second].level;
int currentNode = itBin->second;
//this sequence is unclassified at some levels
string taxon = "unclassified";
//does the parent have a child names 'unclassified'?
- childPointer = tree[currentNode].children.find(taxon);
+ childPointer = copy[currentNode].children.find(taxon);
- if(childPointer != tree[currentNode].children.end()){ //if the node already exists, move on
+ if(childPointer != copy[currentNode].children.end()){ //if the node already exists, move on
currentNode = childPointer->second; //currentNode becomes 'unclassified'
- tree[currentNode].accessions.push_back(itBin->first); //add this seq
- name2Taxonomy[itBin->first] = currentNode;
+ copy[currentNode].accessions.push_back(itBin->first); //add this seq
}
else{ //otherwise, create it
- tree.push_back(TaxNode(taxon));
- numNodes++;
- tree[currentNode].children[taxon] = numNodes-1;
- tree[numNodes-1].parent = currentNode;
+ 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 = tree[currentNode].children[taxon];
- tree[currentNode].accessions.push_back(itBin->first);
- name2Taxonomy[itBin->first] = currentNode;
+ currentNode = copy[currentNode].children[taxon];
+ copy[currentNode].accessions.push_back(itBin->first);
}
-
- if (level == maxLevel) { uniqueTaxonomies[currentNode] = currentNode; }
}
}
- //clear HeirarchyIDs and reset them
- for (int i = 1; i < tree.size(); i++) {
- tree[i].heirarchyID = "";
+ if (!m->control_pressed) {
+ //print copy tree
+ print(out, copy);
}
- assignHeirarchyIDs(0);
-
+
}
catch(exception& e) {
m->errorOut(e, "PhyloTree", "binUnclassified");
}
/**************************************************************************************************/
-void PhyloTree::print(ofstream& out){
- try {
- out << tree[0].level << '\t'<< tree[0].heirarchyID << '\t' << tree[0].name << '\t' << tree[0].children.size() << '\t' << tree[0].accessions.size() << endl;
- print(0, out);
- }
- catch(exception& e) {
- m->errorOut(e, "PhyloTree", "print");
- exit(1);
- }
-}
-
-/**************************************************************************************************/
-
-void PhyloTree::print(int i, ofstream& out){
+void PhyloTree::print(ofstream& out, vector<TaxNode>& copy){
try {
- map<string,int>::iterator it;
- for(it=tree[i].children.begin();it!=tree[i].children.end();it++){
- out <<tree[it->second].level << '\t' << tree[it->second].heirarchyID << '\t' << tree[it->second].name << '\t' << tree[it->second].children.size() << '\t' << tree[it->second].accessions.size() << endl;
- print(it->second, out);
+ out << copy.size() << 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");
/**************************************************************************************************/
void PhyloTree::printTreeNodes(string treefilename) {
try {
- ofstream outTree;
- openOutputFile(treefilename, outTree);
-
- //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;
+
+ #ifdef USE_MPI
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+
+ if (pid == 0) {
+ #endif
+
+ ofstream outTree;
+ openOutputFile(treefilename, outTree);
+
+ //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();
- outTree.close();
+ #ifdef USE_MPI
+ }
+ #endif
+
}
catch(exception& e) {
projects / mothur.git / blobdiff