//**********************************************************************************************************************
-DistanceCommand::DistanceCommand(){
+DistanceCommand::DistanceCommand(string option){
try {
globaldata = GlobalData::getInstance();
- validCalculator = new ValidCalculators();
- ends = globaldata->getEnds();
- convert(globaldata->getProcessors(), processors);
- convert(globaldata->getCutOff(), cutoff);
+ abort = false;
+ Estimators.clear();
- int i;
- if (ends != "T") {
- for (i=0; i<globaldata->Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("distance", globaldata->Estimators[i]) == true) {
- if (globaldata->Estimators[i] == "nogaps") {
- distCalculator = new ignoreGaps();
- }else if (globaldata->Estimators[i] == "eachgap") {
- distCalculator = new eachGapDist();
- }else if (globaldata->Estimators[i] == "onegap") {
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"fasta", "phylip", "calc", "countends", "cutoff", "processors"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ parser = new OptionParser();
+ parser->parse(option, parameters); delete parser;
+
+ ValidParameters* validParameter = new ValidParameters();
+
+ //check to make sure all parameters are valid for command
+ for (it2 = parameters.begin(); it2 != parameters.end(); it2++) {
+ if (validParameter->isValidParameter(it2->first, myArray, it2->second) != true) { abort = true; }
+ }
+
+ //check for required parameters
+ fastafile = validParameter->validFile(parameters, "fasta", true);
+ if (fastafile == "not found") { cout << "fasta is a required parameter for the dist.seqs command." << endl; abort = true; }
+ else if (fastafile == "not open") { abort = true; }
+ else {
+ globaldata->setFastaFile(fastafile);
+ openInputFile(fastafile, in);
+ }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ calc = validParameter->validFile(parameters, "calc", false);
+ if (calc == "not found") { calc = "onegap"; }
+ else {
+ if (calc == "default") { calc = "onegap"; }
+ }
+ splitAtDash(calc, Estimators);
+
+ string temp;
+ temp = validParameter->validFile(parameters, "countends", false); if (temp == "not found") { temp = "T"; }
+ convert(temp, countends);
+
+ temp = validParameter->validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "1.0"; }
+ convert(temp, cutoff);
+
+ temp = validParameter->validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; }
+ convert(temp, processors);
+
+ phylip = validParameter->validFile(parameters, "phylip", false); if (phylip == "not found") { phylip = "F"; }
+
+ delete validParameter;
+
+ validCalculator = new ValidCalculators();
+
+ int i;
+ if (isTrue(countends) == true) {
+ for (i=0; i<Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("distance", Estimators[i]) == true) {
+ if (Estimators[i] == "nogaps") {
+ distCalculator = new ignoreGaps();
+ }else if (Estimators[i] == "eachgap") {
+ distCalculator = new eachGapDist();
+ }else if (Estimators[i] == "onegap") {
distCalculator = new oneGapDist(); }
+ }
}
- }
- }else {
- for (i=0; i<globaldata->Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("distance", globaldata->Estimators[i]) == true) {
- if (globaldata->Estimators[i] == "nogaps") {
- distCalculator = new ignoreGaps();
- }else if (globaldata->Estimators[i] == "eachgap") {
- distCalculator = new eachGapIgnoreTermGapDist();
- }else if (globaldata->Estimators[i] == "onegap") {
- distCalculator = new oneGapIgnoreTermGapDist();
+ }else {
+ for (i=0; i<Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("distance", Estimators[i]) == true) {
+ if (Estimators[i] == "nogaps") {
+ distCalculator = new ignoreGaps();
+ }else if (Estimators[i] == "eachgap") {
+ distCalculator = new eachGapIgnoreTermGapDist();
+ }else if (Estimators[i] == "onegap") {
+ distCalculator = new oneGapIgnoreTermGapDist();
+ }
}
}
}
+
+ delete validCalculator;
}
- //reset calc for next command
- globaldata->setCalc("");
-
-
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the DistanceCommand class Function DistanceCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
}
//**********************************************************************************************************************
+void DistanceCommand::help(){
+ try {
+ cout << "The dist.seqs command reads a file containing sequences and creates a distance file." << "\n";
+ cout << "The dist.seqs command parameters are fasta, calc, countends, cutoff and processors. " << "\n";
+ cout << "The fasta parameter is required." << "\n";
+ cout << "The calc parameter allows you to specify the method of calculating the distances. Your options are: nogaps, onegap or eachgap. The default is onegap." << "\n";
+ cout << "The countends parameter allows you to specify whether to include terminal gaps in distance. Your options are: T or F. The default is T." << "\n";
+ cout << "The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0." << "\n";
+ cout << "The processors parameter allows you to specify number of processors to use. The default is 1." << "\n";
+ cout << "The dist.seqs command should be in the following format: " << "\n";
+ cout << "dist.seqs(fasta=yourFastaFile, calc=yourCalc, countends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) " << "\n";
+ cout << "Example dist.seqs(fasta=amazon.fasta, calc=eachgap, countends=F, cutoff= 2.0, processors=3)." << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc)." << "\n" << "\n";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the DistanceCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the DistanceCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+
+//**********************************************************************************************************************
+
int DistanceCommand::execute(){
try {
- //read file
- string filename = globaldata->inputFileName;
+ if (abort == true) { return 0; }
- if(globaldata->getFastaFile() != "") {
- readSeqs = new ReadFasta(filename); }
- else if(globaldata->getNexusFile() != "") {
- readSeqs = new ReadNexus(filename); }
- else if(globaldata->getClustalFile() != "") {
- readSeqs = new ReadClustal(filename); }
- else if(globaldata->getPhylipFile() != "") {
- readSeqs = new ReadPhylip(filename); }
-
- readSeqs->read();
- seqDB = readSeqs->getDB();
-
+ //reads fasta file and fills sequenceDB
+ seqDB = new SequenceDB(in);
+
int numSeqs = seqDB->getNumSeqs();
+ cutoff += 0.005;
- string distFile = getRootName(globaldata->getFastaFile()) + "dist";
+ string outputFile;
- remove(distFile.c_str());
+ //doses the user want the phylip formatted file as well
+ if (isTrue(phylip) == true) {
+ outputFile = getRootName(fastafile) + "phylip.dist";
+ remove(outputFile.c_str());
+
+ //output numSeqs to phylip formatted dist file
+ openOutputFile(outputFile, outFile);
+ outFile << numSeqs << endl;
+ outFile.close();
+ }else { //user wants column format
+ outputFile = getRootName(fastafile) + "dist";
+ remove(outputFile.c_str());
+ }
+
+ //# 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__) || (linux) || (__linux)
+ //if you don't need to fork anything
if(processors == 1){
- driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff);
- }
- else if(processors == 2){
-
- int pid = fork();
- if(pid > 0){
- driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", cutoff);
- appendFiles((distFile+"tempa"), distFile);
- remove((distFile + "tempa").c_str());
- }
- else{
- driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", cutoff);
- appendFiles((distFile+"tempb"), distFile);
- remove((distFile + "tempb").c_str());
+ driver(distCalculator, seqDB, 0, numSeqs, outputFile + ".temp", cutoff);
+ appendFiles((outputFile + ".temp"), outputFile);
+ remove((outputFile + ".temp").c_str());
+ }else{ //you have multiple processors
+
+ for (int i = 0; i < processors; i++) {
+ lines.push_back(new linePair());
+ lines[i]->start = int (sqrt(float(i)/float(processors)) * numSeqs);
+ lines[i]->end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
}
- wait(NULL);
- }
- 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", cutoff);
- appendFiles(distFile+"tempa", distFile);
- remove((distFile + "tempa").c_str());
- }
- else{
- driver(distCalculator, seqDB, sqrt(3) * numSeqs / 3, sqrt(6) * numSeqs / 3, distFile + "tempb", cutoff);
- appendFiles(distFile+"tempb", distFile);
- remove((distFile + "tempb").c_str());
- }
- wait(NULL);
- }
- else{
- driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", cutoff);
- appendFiles(distFile+"tempc", distFile);
- remove((distFile + "tempc").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", cutoff);
- //system(("cat " + distFile + "tempa" + " >> " + distFile).c_str());
- appendFiles(distFile+"tempa", distFile);
- //system(("rm " + distFile + "tempa").c_str());
- remove((distFile + "tempa").c_str());
- }
- else{
- driver(distCalculator, seqDB, numSeqs / 2, (numSeqs/sqrt(2)), distFile + "tempb", cutoff);
- //system(("cat " + distFile + "tempb" + " >> " + distFile).c_str());
- appendFiles(distFile+"tempb", distFile);
- //system(("rm " + distFile + "tempb").c_str());
- remove((distFile + "tempb").c_str());
- }
- wait(NULL);
- }
- else{
- int pid3 = fork();
- if(pid3 > 0){
- driver(distCalculator, seqDB, (numSeqs/sqrt(2)), (sqrt(3) * numSeqs / 2), distFile + "tempc", cutoff);
- //system(("cat " + distFile + "tempc" + " >> " + distFile).c_str());
- appendFiles(distFile+"tempc", distFile);
- //system(("rm " + distFile + "tempc").c_str());
- remove((distFile + "tempc").c_str());
- }
- else{
- driver(distCalculator, seqDB, (sqrt(3) * numSeqs / 2), numSeqs, distFile + "tempd", cutoff);
- //system(("cat " + distFile + "tempd" + " >> " + distFile).c_str());
- appendFiles(distFile+"tempd", distFile);
- //system(("rm " + distFile + "tempd").c_str());
- remove((distFile + "tempd").c_str());
- }
- wait(NULL);
+ cout << lines[0]->start << '\t' << lines[0]->end << endl;
+ cout << lines[1]->start << '\t' << lines[1]->end << endl;
+
+ createProcesses(outputFile);
+
+ //append and remove temp files
+ for (it = processIDS.begin(); it != processIDS.end(); it++) {
+ appendFiles((outputFile + toString(it->second) + ".temp"), outputFile);
+ remove((outputFile + toString(it->second) + ".temp").c_str());
}
- wait(NULL);
}
- wait(NULL);
-
+#else
+ driver(distCalculator, seqDB, 0, numSeqs, outputFile + ".temp", cutoff);
+ appendFiles((outputFile + ".temp"), outputFile);
+ remove((outputFile + ".temp").c_str());
+#endif
+
delete distCalculator;
-
+
return 0;
-
+
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the DistanceCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
}
+/**************************************************************************************************/
+void DistanceCommand::createProcesses(string filename) {
+ 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, filename + 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, float cutoff){
try {
+
int startTime = time(NULL);
-
- ofstream distFile(dFileName.c_str(), ios::trunc);
- distFile.setf(ios::fixed, ios::showpoint);
- distFile << setprecision(4);
-
- for(int i=startLine;i<endLine;i++){
- for(int j=0;j<i;j++){
- distCalculator->calcDist(align->get(i), align->get(j));
+ //column file
+ ofstream outFile(dFileName.c_str(), ios::trunc);
+ outFile.setf(ios::fixed, ios::showpoint);
+ outFile << setprecision(4);
+
+ for(int i=startLine;i<endLine;i++){
+
+ for(int j=0;j<i;j++){
+ distCalculator->calcDist(*(align->get(i)), *(align->get(j)));
double dist = distCalculator->getDist();
-
+
if(dist <= cutoff){
- distFile << align->get(i).getName() << ' ' << align->get(j).getName() << ' ' << dist << endl;
-//cout << align->get(i).getName() << ' ' << align->get(j).getName() << ' ' << dist << endl;
+ if (isTrue(phylip) != true) { outFile << align->get(i)->getName() << ' ' << align->get(j)->getName() << ' ' << dist << endl; }
}
-
+ if (isTrue(phylip) == true) { outFile << dist << '\t'; }
+
}
+
+ if (isTrue(phylip) == true) { outFile << endl; }
+
if(i % 100 == 0){
cout << i << '\t' << time(NULL) - startTime << endl;
}
-
+
}
cout << endLine-1 << '\t' << time(NULL) - startTime << endl;
-
+
+ //philFile.close();
+ //distFile.close();
+
return 1;
}
catch(exception& e) {
cout << "An unknown error has occurred in the DistanceCommand class function driver. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
-
+
}
/**************************************************************************************************/
try{
ofstream output;
ifstream input;
-
+
//open output file in append mode
openOutputFileAppend(filename, output);
output << line << endl; // Appending back newline char
}
}
-
+
input.close();
output.close();
}
exit(1);
}
}
+/**************************************************************************************************/
\ No newline at end of file
projects / mothur.git / blobdiff