countends = globaldata->getCountEnds();
convert(globaldata->getProcessors(), processors);
convert(globaldata->getCutOff(), cutoff);
+ phylip = globaldata->getPhylipFile();
//open file
string filename = globaldata->getFastaFile();
openInputFile(filename, in);
+
int i;
int numSeqs = seqDB->getNumSeqs();
cutoff += 0.005;
+ string phylipFile = "";
string distFile = getRootName(globaldata->getFastaFile()) + "dist";
- string phylipFile = getRootName(globaldata->getFastaFile()) + "phylip.dist";
-
- remove(phylipFile.c_str());
remove(distFile.c_str());
- //output numSeqs to phylip formatted dist file
- openOutputFile(phylipFile, phylipOut);
- phylipOut << numSeqs << endl;
- phylipOut.close();
+ //doses the user want the phylip formatted file as well
+ if (isTrue(phylip) == true) {
+ phylipFile = getRootName(globaldata->getFastaFile()) + "phylip.dist";
+ remove(phylipFile.c_str());
+
+ //output numSeqs to phylip formatted dist file
+ openOutputFile(phylipFile, phylipOut);
+ phylipOut << numSeqs << endl;
+ phylipOut.close();
+ }
+
//# if defined (_WIN32)
//figure out how to implement the fork and wait commands in windows
// driver(distCalculator, seqDB, 0, numSeqs, distFile, phylipFile, cutoff);
//# endif
-#if defined (__APPLE__) || (__MACH__)
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ //if you don't need to fork anything
if(processors == 1){
driver(distCalculator, seqDB, 0, numSeqs, distFile, phylipFile + "tempPhylipA", cutoff);
- appendFiles((phylipFile + "tempPhylipA"), phylipFile);
- remove((phylipFile + "tempPhylipA").c_str());
- }
- else if(processors == 2){
- int pid = fork();
- if(pid > 0){
- driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", phylipFile + "tempPhylipA", cutoff);
- appendFiles((distFile+"tempa"), distFile);
- remove((distFile + "tempa").c_str());
+ if (isTrue(phylip) == true) {
appendFiles((phylipFile + "tempPhylipA"), phylipFile);
remove((phylipFile + "tempPhylipA").c_str());
}
- else{
- driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", phylipFile + "tempPhylipB", cutoff);
- appendFiles((distFile+"tempb"), distFile);
- remove((distFile + "tempb").c_str());
- appendFiles((phylipFile + "tempPhylipB"), phylipFile);
- remove((phylipFile + "tempPhylipB").c_str());
- }
- wait(NULL);
+ }else{ //you have multiple processors
- }
- else if(processors == 3){
- int pid1 = fork();
- if(pid1 > 0){
- int pid2 = fork();
- if(pid2 > 0){
- driver(distCalculator, seqDB, 0, sqrt(3) * numSeqs / 3, distFile + "tempa", phylipFile + "tempPhylipA", cutoff);
- appendFiles(distFile+"tempa", distFile);
- appendFiles((phylipFile + "tempPhylipA"), phylipFile);
- remove((distFile + "tempa").c_str());
- remove((phylipFile + "tempPhylipA").c_str());
- }
- else{
- driver(distCalculator, seqDB, sqrt(3) * numSeqs / 3, sqrt(6) * numSeqs / 3, distFile + "tempb", phylipFile + "tempPhylipB", cutoff);
- appendFiles(distFile+"tempb", distFile);
- appendFiles((phylipFile + "tempPhylipB"), phylipFile);
- remove((distFile + "tempb").c_str());
- remove((phylipFile + "tempPhylipB").c_str());
- }
- wait(NULL);
- }
- else{
- driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", phylipFile + "tempPhylipC", cutoff);
- appendFiles(distFile+"tempc", distFile);
- appendFiles((phylipFile + "tempPhylipC"), phylipFile);
- remove((distFile + "tempc").c_str());
- remove((phylipFile + "tempPhylipC").c_str());
- }
- wait(NULL);
- }
- else if(processors == 4){
- int pid1 = fork();
- if(pid1 > 0){
- int pid2 = fork();
- if(pid2 > 0){
- driver(distCalculator, seqDB, 0, numSeqs / 2, distFile + "tempa", phylipFile + "tempPhylipA", cutoff);
- appendFiles(distFile+"tempa", distFile);
- appendFiles((phylipFile + "tempPhylipA"), phylipFile);
- remove((distFile + "tempa").c_str());
- remove((phylipFile + "tempPhylipA").c_str());
- }
- else{
- driver(distCalculator, seqDB, numSeqs / 2, (numSeqs/sqrt(2)), distFile + "tempb", phylipFile + "tempPhylipB", cutoff);
- appendFiles(distFile+"tempb", distFile);
- appendFiles((phylipFile + "tempPhylipB"), phylipFile);
- remove((distFile + "tempb").c_str());
- remove((phylipFile + "tempPhylipB").c_str());
- }
- wait(NULL);
- }
- else{
- int pid3 = fork();
- if(pid3 > 0){
- driver(distCalculator, seqDB, (numSeqs/sqrt(2)), (sqrt(3) * numSeqs / 2), distFile + "tempc", phylipFile + "tempPhylipC", cutoff);
- appendFiles(distFile+"tempc", distFile);
- appendFiles((phylipFile + "tempPhylipC"), phylipFile);
- remove((distFile + "tempc").c_str());
- remove((phylipFile + "tempPhylipC").c_str());
-
- }
- else{
- driver(distCalculator, seqDB, (sqrt(3) * numSeqs / 2), numSeqs, distFile + "tempd", phylipFile + "tempPhylipD", cutoff);
- appendFiles(distFile+"tempd", distFile);
- appendFiles((phylipFile + "tempPhylipD"), phylipFile);
- remove((distFile + "tempd").c_str());
- remove((phylipFile + "tempPhylipD").c_str());
- }
- wait(NULL);
- }
- wait(NULL);
- }
- wait(NULL);
-#elif (linux) || (__linux)
- if(processors == 1){
- driver(distCalculator, seqDB, 0, numSeqs, distFile, phylipFile + "tempPhylipA", cutoff);
- appendFiles((phylipFile + "tempPhylipA"), phylipFile);
- remove((phylipFile + "tempPhylipA").c_str());
- }
- else if(processors == 2){
+ //create line pairs
+ int numPerGroup = numSeqs / processors;
+ int remainder = numSeqs % processors;
- int pid = fork();
- if(pid > 0){
- driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", phylipFile + "tempPhylipA", cutoff);
- appendFiles((distFile+"tempa"), distFile);
- appendFiles((phylipFile + "tempPhylipA"), phylipFile);
- remove((distFile + "tempa").c_str());
- remove((phylipFile + "tempPhylipA").c_str());
-
+ for (int i = 0; i < processors; i++) {
+ lines.push_back(new linePair());
+ lines[i]->start = i*numPerGroup;
+ lines[i]->end = (i+1)*numPerGroup;
}
- else{
- driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", phylipFile + "tempPhylipB", cutoff);
- appendFiles((distFile+"tempb"), distFile);
- appendFiles((phylipFile + "tempPhylipB"), phylipFile);
- remove((distFile + "tempb").c_str());
- remove((phylipFile + "tempPhylipB").c_str());
- }
- wait();
+ //give the last one any extra line
+ lines[lines.size()-1]->end += remainder;
- }
- else if(processors == 3){
- int pid1 = fork();
- if(pid1 > 0){
- int pid2 = fork();
- if(pid2 > 0){
- driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", phylipFile + "tempPhylipA", cutoff);
- appendFiles((distFile+"tempa"), distFile);
- appendFiles((phylipFile + "tempPhylipA"), phylipFile);
- remove((distFile + "tempa").c_str());
- remove((phylipFile + "tempPhylipA").c_str());
-
- }
- else{
- driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", phylipFile + "tempPhylipB", cutoff);
- appendFiles((distFile+"tempb"), distFile);
- appendFiles((phylipFile + "tempPhylipB"), phylipFile);
- remove((distFile + "tempb").c_str());
- remove((phylipFile + "tempPhylipB").c_str());
- }
- wait();
- }
- else{
- driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", phylipFile + "tempPhylipC", cutoff);
- appendFiles(distFile+"tempc", distFile);
- appendFiles((phylipFile + "tempPhylipC"), phylipFile);
- remove((distFile + "tempc").c_str());
- remove((phylipFile + "tempPhylipC").c_str());
- }
- wait();
- }
- else if(processors == 4){
- int pid1 = fork();
- if(pid1 > 0){
- int pid2 = fork();
- if(pid2 > 0){
- driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", phylipFile + "tempPhylipA", cutoff);
- appendFiles((distFile+"tempa"), distFile);
- appendFiles((phylipFile + "tempPhylipA"), phylipFile);
- remove((distFile + "tempa").c_str());
- remove((phylipFile + "tempPhylipA").c_str());
- }
- else{
- driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", phylipFile + "tempPhylipB", cutoff);
- appendFiles((distFile+"tempb"), distFile);
- appendFiles((phylipFile + "tempPhylipB"), phylipFile);
- remove((distFile + "tempb").c_str());
- remove((phylipFile + "tempPhylipB").c_str());
- }
- wait();
- }
- else{
- int pid3 = fork();
- if(pid3 > 0){
- driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", phylipFile + "tempPhylipC", cutoff);
- appendFiles(distFile+"tempc", distFile);
- appendFiles((phylipFile + "tempPhylipC"), phylipFile);
- remove((distFile + "tempc").c_str());
- remove((phylipFile + "tempPhylipC").c_str());
- }
- else{
- driver(distCalculator, seqDB, (sqrt(3) * numSeqs / 2), numSeqs, distFile + "tempd", phylipFile + "tempPhylipD", cutoff);
- appendFiles(distFile+"tempd", distFile);
- appendFiles((phylipFile + "tempPhylipD"), phylipFile);
- remove((distFile + "tempd").c_str());
- remove((phylipFile + "tempPhylipD").c_str());
+ createProcesses(distFile, phylipFile);
+
+ //append and remove temp files
+ for (it = processIDS.begin(); it != processIDS.end(); it++) {
+ appendFiles((distFile + toString(it->second) + ".temp"), distFile);
+ remove((distFile + toString(it->second) + ".temp").c_str());
+
+ if (isTrue(phylip) == true) {
+ appendFiles((phylipFile + toString(it->second) + ".temp"), phylipFile);
+ remove((phylipFile + toString(it->second) + ".temp").c_str());
}
- wait();
}
- wait();
}
- wait();
-
#else
driver(distCalculator, seqDB, 0, numSeqs, distFile, phylipFile + "tempPhylipA", cutoff);
- appendFiles((phylipFile + "tempPhylipA"), phylipFile);
- remove((phylipFile + "tempPhylipA").c_str());
+
+ if (isTrue(phylip) = true) {
+ appendFiles((phylipFile + "tempPhylipA"), phylipFile);
+ remove((phylipFile + "tempPhylipA").c_str());
+ }
#endif
delete distCalculator;
exit(1);
}
}
+/**************************************************************************************************/
+void DistanceCommand::createProcesses(string column, string phylip) {
+ try {
+ int process = 0;
+ processIDS.clear();
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+
+ if (pid > 0) {
+ processIDS[lines[process]->end] = pid; //create map from line number to pid so you can append files in correct order later
+ process++;
+ }else if (pid == 0){
+ driver(distCalculator, seqDB, lines[process]->start, lines[process]->end, column + toString(getpid()) + ".temp", phylip + toString(getpid()) + ".temp", cutoff);
+ exit(0);
+ }else { cout << "unable to spawn the necessary processes." << endl; exit(0); }
+ }
+
+ //force parent to wait until all the processes are done
+ for (it = processIDS.begin(); it != processIDS.end(); it++) {
+ int temp = it->second;
+ wait(&temp);
+ }
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the DistanceCommand class Function createProcesses. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the DistanceCommand class function createProcesses. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
/**************************************************************************************************/
/////// need to fix to work with calcs and sequencedb
int DistanceCommand::driver(Dist* distCalculator, SequenceDB* align, int startLine, int endLine, string dFileName, string pFilename, float cutoff){
try {
+
int startTime = time(NULL);
//column file
distFile.setf(ios::fixed, ios::showpoint);
distFile << setprecision(4);
- //column file
ofstream philFile(pFilename.c_str(), ios::trunc);
philFile.setf(ios::fixed, ios::showpoint);
philFile << setprecision(4);
if(dist <= cutoff){
distFile << align->get(i)->getName() << ' ' << align->get(j)->getName() << ' ' << dist << endl;
}
- philFile << dist << '\t';
+ if (isTrue(phylip) == true) { philFile << dist << '\t'; }
+
}
- philFile << endl;
+ if (isTrue(phylip) == true) { philFile << endl; }
if(i % 100 == 0){
cout << i << '\t' << time(NULL) - startTime << endl;
}
cout << endLine-1 << '\t' << time(NULL) - startTime << endl;
+ if (isTrue(phylip) != true) { remove(pFilename.c_str()); }
+
//philFile.close();
//distFile.close();
try{
ofstream output;
ifstream input;
-
+
//open output file in append mode
openOutputFileAppend(filename, output);
projects / mothur.git / blobdiff