*/
#include "splitmatrix.h"
+#include "phylotree.h"
/***********************************************************************/
-SplitMatrix::SplitMatrix(string distfile, string name, float c){
+SplitMatrix::SplitMatrix(string distfile, string name, string tax, float c, string t, bool l){
m = MothurOut::getInstance();
distFile = distfile;
cutoff = c;
namefile = name;
+ method = t;
+ taxFile = tax;
+ large = l;
}
/***********************************************************************/
int SplitMatrix::split(){
try {
+ if (method == "distance") {
+ splitDistance();
+ }else if (method == "classify") {
+ splitClassify();
+ }else {
+ m->mothurOut("Unknown splitting method, aborting split."); m->mothurOutEndLine();
+ map<string, string> temp;
+ temp[distFile] = namefile;
+ dists.push_back(temp);
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitMatrix", "split");
+ exit(1);
+ }
+}
+/***********************************************************************/
+int SplitMatrix::splitDistance(){
+ try {
+
+ if (large) { splitDistanceLarge(); }
+ else { splitDistanceRAM(); }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitMatrix", "splitDistance");
+ 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();
+
+ ifstream in;
+ openInputFile(taxFile, in);
+
+ //read in users taxonomy file and add sequences to tree
+ string seqname, tax;
+ while(!in.eof()){
+ in >> seqname >> tax; gobble(in);
+
+ phylo->addSeqToTree(seqname, tax);
+ }
+ in.close();
+
+ 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++;
+ }
+ }
+ }
+
+ ifstream dFile;
+ openInputFile(distFile, dFile);
+ ofstream outFile;
+
+ for (int i = 0; i < numGroups; i++) { //remove old temp files, just in case
+ remove((distFile + "." + toString(i) + ".temp").c_str());
+ }
+
+
+ //for buffering the io to improve speed
+ //allow for 10 dists to be stored, then output.
+ vector<string> outputs; outputs.resize(numGroups, "");
+ vector<int> numOutputs; numOutputs.resize(numGroups, 0);
+
+ //for each distance
+ while(dFile){
+ string seqA, seqB;
+ float dist;
+
+ if (m->control_pressed) { dFile.close(); for (int i = 0; i < numGroups; i++) { remove((distFile + "." + toString(i) + ".temp").c_str()); } }
+
+ dFile >> seqA >> seqB >> dist; gobble(dFile);
+
+ //if both sequences are in the same group then they are within the cutoff
+ it = seqGroup.find(seqA);
+ it2 = seqGroup.find(seqB);
+
+ if ((it != seqGroup.end()) && (it2 != seqGroup.end())) { //they are both not singletons
+ if (it->second == it2->second) { //they are from the same group so add the distance
+ if (numOutputs[it->second] > 10) {
+ openOutputFileAppend((distFile + "." + toString(it->second) + ".temp"), outFile);
+ outFile << outputs[it->second] << seqA << '\t' << seqB << '\t' << dist << endl;
+ outFile.close();
+ outputs[it->second] = "";
+ numOutputs[it->second] = 0;
+ }else{
+ outputs[it->second] += seqA + '\t' + seqB + '\t' + toString(dist) + '\n';
+ numOutputs[it->second]++;
+ }
+ }
+ }
+ }
+ dFile.close();
+
+ for (int i = 0; i < numGroups; i++) { //remove old temp files, just in case
+ remove((namefile + "." + toString(i) + ".temp").c_str());
+
+ //write out any remaining buffers
+ if (numOutputs[it->second] > 0) {
+ openOutputFileAppend((distFile + "." + toString(i) + ".temp"), outFile);
+ outFile << outputs[i];
+ outFile.close();
+ outputs[i] = "";
+ numOutputs[i] = 0;
+ }
+ }
+
+ ifstream bigNameFile;
+ openInputFile(namefile, bigNameFile);
+
+ singleton = namefile + ".extra.temp";
+ ofstream remainingNames;
+ openOutputFile(singleton, remainingNames);
+
+ bool wroteExtra = false;
+
+ string name, nameList;
+ while(!bigNameFile.eof()){
+ bigNameFile >> name >> nameList; gobble(bigNameFile);
+
+ //did this sequence get assigned a group
+ it = seqGroup.find(name);
+
+ if (it != seqGroup.end()) {
+ openOutputFileAppend((namefile + "." + toString(it->second) + ".temp"), outFile);
+ outFile << name << '\t' << nameList << endl;
+ outFile.close();
+ }else{
+ wroteExtra = true;
+ remainingNames << name << '\t' << nameList << endl;
+ }
+ }
+ bigNameFile.close();
+ remainingNames.close();
+
+ if (!wroteExtra) {
+ remove(singleton.c_str());
+ singleton = "none";
+ }
+
+ for(int i=0;i<numGroups;i++){
+ string tempNameFile = namefile + "." + toString(i) + ".temp";
+ string tempDistFile = distFile + "." + toString(i) + ".temp";
+
+ map<string, string> temp;
+ temp[tempDistFile] = tempNameFile;
+ dists.push_back(temp);
+ }
+
+ if (m->control_pressed) {
+ for (int i = 0; i < dists.size(); i++) {
+ remove((dists[i].begin()->first).c_str());
+ remove((dists[i].begin()->second).c_str());
+ }
+ dists.clear();
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitMatrix", "splitClassify");
+ exit(1);
+ }
+}
+/***********************************************************************/
+int SplitMatrix::splitDistanceLarge(){
+ try {
vector<set<string> > groups;
+
+ //for buffering the io to improve speed
+ //allow for 30 dists to be stored, then output.
+ vector<string> outputs;
+ vector<int> numOutputs;
+ vector<bool> wroteOutPut;
+
int numGroups = 0;
ofstream outFile;
dFile >> seqA >> seqB >> dist;
+ if (m->control_pressed) { dFile.close(); for(int i=0;i<numGroups;i++){ if(groups[i].size() > 0){ remove((distFile + "." + toString(i) + ".temp").c_str()); } } return 0; }
+
if(dist < cutoff){
//cout << "in cutoff: " << dist << endl;
int groupIDA = -1;
int groupIDB = -1;
int groupID = -1;
- int prevGroupID = -1;
for(int i=0;i<numGroups;i++){
set<string>::iterator aIt = groups[i].find(seqA);
newGroup.insert(seqB);
groups.push_back(newGroup);
- outFile.close();
- string fileName = distFile + "." + toString(numGroups) + ".temp";
- outFile.open(fileName.c_str(), ios::ate);
-
- outFile << seqA << '\t' << seqB << '\t' << dist << endl;
+ string tempOut = seqA + '\t' + seqB + '\t' + toString(dist) + '\n';
+ outputs.push_back(tempOut);
+ numOutputs.push_back(1);
+ wroteOutPut.push_back(false);
+
numGroups++;
}
else{
string fileName = distFile + "." + toString(groupID) + ".temp";
- if(groupID != prevGroupID){
- outFile.close();
+
+ //have we reached the max buffer size
+ if (numOutputs[groupID] > 60) { //write out sequence
outFile.open(fileName.c_str(), ios::app);
- prevGroupID = groupID;
+ outFile << outputs[groupID] << seqA << '\t' << seqB << '\t' << dist << endl;
+ outFile.close();
+
+ outputs[groupID] = "";
+ numOutputs[groupID] = 0;
+ wroteOutPut[groupID] = true;
+ }else {
+ outputs[groupID] += seqA + '\t' + seqB + '\t' + toString(dist) + '\n';
+ numOutputs[groupID]++;
}
- outFile << seqA << '\t' << seqB << '\t' << dist << endl;
if(groupIDA != -1 && groupIDB != -1){ //merge distance files of two groups you merged above
string row, column, distance;
if(groupIDA<groupIDB){
- string fileName = distFile + "." + toString(groupIDB) + ".temp";
- ifstream fileB(fileName.c_str());
- while(fileB){
- fileB >> row >> column >> distance;
- outFile << row << '\t' << column << '\t' << distance << endl;
- gobble(fileB);
- }
- fileB.close();
- remove(fileName.c_str());
+
+ //merge memory
+ numOutputs[groupID] += numOutputs[groupIDB];
+ outputs[groupID] += outputs[groupIDB];
+
+ outputs[groupIDB] = "";
+ numOutputs[groupIDB] = 0;
+
+ //if groupB is written to file it is above buffer size so read and write to new merged file
+ if (wroteOutPut[groupIDB]) {
+ string fileName2 = distFile + "." + toString(groupIDB) + ".temp";
+ ifstream fileB(fileName2.c_str(), ios::ate);
+
+ outFile.open(fileName.c_str(), ios::app);
+
+ long size;
+ char* memblock;
+
+ size = fileB.tellg();
+
+ fileB.seekg (0, ios::beg);
+
+ int numRead = size / 1024;
+ int lastRead = size % 1024;
+
+ for (int i = 0; i < numRead; i++) {
+
+ memblock = new char [1024];
+
+ fileB.read (memblock, 1024);
+
+ string temp = memblock;
+ outFile << temp.substr(0, 1024);
+
+ delete memblock;
+ }
+
+ memblock = new char [lastRead];
+
+ fileB.read (memblock, lastRead);
+
+ //not sure why but it will read more than lastRead char...??
+ string temp = memblock;
+ outFile << temp.substr(0, lastRead);
+ delete memblock;
+
+ fileB.close();
+ remove(fileName2.c_str());
+
+ //write out the merged memory
+ if (numOutputs[groupID] > 60) {
+ outFile << outputs[groupID];
+ outputs[groupID] = "";
+ numOutputs[groupID] = 0;
+ }
+
+ outFile.close();
+
+ wroteOutPut[groupID] = true;
+ wroteOutPut[groupIDB] = false;
+ }else{ } //just merge b's memory with a's memory
}
else{
- string fileName = distFile + "." + toString(groupIDA) + ".temp";
- ifstream fileA(fileName.c_str());
- while(fileA){
- fileA >> row >> column >> distance;
- outFile << row << '\t' << column << '\t' << distance << endl;
- gobble(fileA);
- }
- fileA.close();
- remove(fileName.c_str());
+ numOutputs[groupID] += numOutputs[groupIDA];
+ outputs[groupID] += outputs[groupIDA];
+
+ outputs[groupIDA] = "";
+ numOutputs[groupIDA] = 0;
+
+ if (wroteOutPut[groupIDA]) {
+ string fileName2 = distFile + "." + toString(groupIDA) + ".temp";
+ ifstream fileB(fileName2.c_str(), ios::ate);
+
+ outFile.open(fileName.c_str(), ios::app);
+
+ long size;
+ char* memblock;
+
+ size = fileB.tellg();
+
+ fileB.seekg (0, ios::beg);
+
+ int numRead = size / 1024;
+ int lastRead = size % 1024;
+
+ for (int i = 0; i < numRead; i++) {
+
+ memblock = new char [1024];
+
+ fileB.read (memblock, 1024);
+ string temp = memblock;
+ outFile << temp.substr(0, 1024);
+
+ delete memblock;
+ }
+
+ memblock = new char [lastRead];
+
+ fileB.read (memblock, lastRead);
+
+ //not sure why but it will read more than lastRead char...??
+ string temp = memblock;
+ outFile << temp.substr(0, lastRead);
+
+ delete memblock;
+
+ fileB.close();
+ remove(fileName2.c_str());
+
+ //write out the merged memory
+ if (numOutputs[groupID] > 60) {
+ outFile << outputs[groupID];
+ outputs[groupID] = "";
+ numOutputs[groupID] = 0;
+ }
+
+ outFile.close();
+
+ wroteOutPut[groupID] = true;
+ wroteOutPut[groupIDA] = false;
+ }else { } //just merge memory
}
}
}
}
gobble(dFile);
}
- outFile.close();
dFile.close();
+
+ for (int i = 0; i < numGroups; i++) {
+ if (numOutputs[i] > 0) {
+ string fileName = distFile + "." + toString(i) + ".temp";
+ outFile.open(fileName.c_str(), ios::app);
+ outFile << outputs[i];
+ outFile.close();
+ }
+ }
+
+ splitNames(groups);
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitMatrix", "splitDistanceLarge");
+ exit(1);
+ }
+}
+//********************************************************************************************************************
+int SplitMatrix::splitNames(vector<set<string> >& groups){
+ try {
+ int numGroups = groups.size();
ifstream bigNameFile(namefile.c_str());
if(!bigNameFile){
for(set<string>::iterator gIt=groups[i].begin();gIt!=groups[i].end();gIt++){
map<string,string>::iterator nIt = nameMap.find(*gIt);
-
if (nIt != nameMap.end()) {
smallNameFile << nIt->first << '\t' << nIt->second << endl;
nameMap.erase(nIt);
smallNameFile.close();
}
}
-
+
//names of singletons
if (nameMap.size() != 0) {
singleton = namefile + ".extra.temp";
dists.push_back(temp);
}
}
-
+
+ if (m->control_pressed) {
+ for (int i = 0; i < dists.size(); i++) {
+ remove((dists[i].begin()->first).c_str());
+ remove((dists[i].begin()->second).c_str());
+ }
+ dists.clear();
+ }
+
return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitMatrix", "splitNames");
+ exit(1);
+ }
+}
+//********************************************************************************************************************
+int SplitMatrix::splitDistanceRAM(){
+ try {
+ vector<set<string> > groups;
+ vector<string> outputs;
+
+ int numGroups = 0;
+
+ ifstream dFile;
+ openInputFile(distFile, dFile);
+
+ while(dFile){
+ string seqA, seqB;
+ float dist;
+
+ dFile >> seqA >> seqB >> dist;
+ if (m->control_pressed) { dFile.close(); for(int i=0;i<numGroups;i++){ if(groups[i].size() > 0){ remove((distFile + "." + toString(i) + ".temp").c_str()); } } return 0; }
+
+ if(dist < cutoff){
+ //cout << "in cutoff: " << dist << endl;
+ int groupIDA = -1;
+ int groupIDB = -1;
+ int groupID = -1;
+
+ for(int i=0;i<numGroups;i++){
+ set<string>::iterator aIt = groups[i].find(seqA);
+ set<string>::iterator bIt = groups[i].find(seqB);
+
+ if(groupIDA == -1 && aIt != groups[i].end()){//seqA is not already assigned to a group and is in group[i], so assign seqB to group[i]
+ groups[i].insert(seqB);
+ groupIDA = i;
+ groupID = groupIDA;
+
+ //cout << "in aIt: " << groupID << endl;
+ // break;
+ }
+ else if(groupIDB == -1 && bIt != groups[i].end()){//seqB is not already assigned to a group and is in group[i], so assign seqA to group[i]
+ groups[i].insert(seqA);
+ groupIDB = i;
+ groupID = groupIDB;
+
+ // cout << "in bIt: " << groupID << endl;
+ // break;
+ }
+
+ if(groupIDA != -1 && groupIDB != -1){//both ifs above have been executed, so we need to decide who to assign them to
+ if(groupIDA < groupIDB){
+ // cout << "A: " << groupIDA << "\t" << groupIDB << endl;
+ groups[groupIDA].insert(groups[groupIDB].begin(), groups[groupIDB].end()); //merge two groups into groupIDA
+ groups[groupIDB].clear();
+ groupID = groupIDA;
+ }
+ else{
+ // cout << "B: " << groupIDA << "\t" << groupIDB << endl;
+ groups[groupIDB].insert(groups[groupIDA].begin(), groups[groupIDA].end()); //merge two groups into groupIDB
+ groups[groupIDA].clear();
+ groupID = groupIDB;
+ }
+ break;
+ }
+ }
+
+ //windows is gonna gag on the reuse of outFile, will need to make it local...
+
+ if(groupIDA == -1 && groupIDB == -1){ //we need a new group
+ set<string> newGroup;
+ newGroup.insert(seqA);
+ newGroup.insert(seqB);
+ groups.push_back(newGroup);
+
+ string tempOut = seqA + '\t' + seqB + '\t' + toString(dist) + '\n';
+ outputs.push_back(tempOut);
+ numGroups++;
+ }
+ else{
+
+ outputs[groupID] += seqA + '\t' + seqB + '\t' + toString(dist) + '\n';
+
+ if(groupIDA != -1 && groupIDB != -1){ //merge distance files of two groups you merged above
+ string row, column, distance;
+ if(groupIDA<groupIDB){
+ //merge memory
+ outputs[groupID] += outputs[groupIDB];
+ outputs[groupIDB] = "";
+ }else{
+ outputs[groupID] += outputs[groupIDA];
+ outputs[groupIDA] = "";
+ }
+ }
+ }
+ }
+ gobble(dFile);
+ }
+ dFile.close();
+
+ for (int i = 0; i < numGroups; i++) {
+ if (outputs[i] != "") {
+ ofstream outFile;
+ string fileName = distFile + "." + toString(i) + ".temp";
+ outFile.open(fileName.c_str(), ios::ate);
+ outFile << outputs[i];
+ outFile.close();
+ }
+ }
+
+ splitNames(groups);
+
+ return 0;
}
catch(exception& e) {
- m->errorOut(e, "SplitMatrix", "split");
+ m->errorOut(e, "SplitMatrix", "splitDistanceRAM");
exit(1);
}
}
projects / mothur.git / blobdiff