//**********************************************************************************************************************
-DistanceCommand::DistanceCommand(string option){
+DistanceCommand::DistanceCommand(string option) {
try {
abort = false;
Estimators.clear();
-
+
//allow user to run help
if(option == "help") { help(); abort = true; }
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not found") { mothurOut("fasta is a required parameter for the dist.seqs command."); mothurOutEndLine(); abort = true; }
+ if (fastafile == "not found") { m->mothurOut("fasta is a required parameter for the dist.seqs command."); m->mothurOutEndLine(); abort = true; }
else if (fastafile == "not open") { abort = true; }
else{
ifstream inFASTA;
output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "column"; }
- if ((output != "column") && (output != "lt") && (output != "square")) { mothurOut(output + " is not a valid output form. Options are column, lt and square. I will use column."); mothurOutEndLine(); output = "column"; }
+ if ((output != "column") && (output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are column, lt and square. I will use column."); m->mothurOutEndLine(); output = "column"; }
ValidCalculators validCalculator;
}
catch(exception& e) {
- errorOut(e, "DistanceCommand", "DistanceCommand");
+ m->errorOut(e, "DistanceCommand", "DistanceCommand");
exit(1);
}
}
void DistanceCommand::help(){
try {
- mothurOut("The dist.seqs command reads a file containing sequences and creates a distance file.\n");
- mothurOut("The dist.seqs command parameters are fasta, calc, countends, output, cutoff and processors. \n");
- mothurOut("The fasta parameter is required.\n");
- mothurOut("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");
- mothurOut("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");
- mothurOut("The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n");
- mothurOut("The output parameter allows you to specify format of your distance matrix. Options are column, lt, and square. The default is column.\n");
- mothurOut("The processors parameter allows you to specify number of processors to use. The default is 1.\n");
- mothurOut("The dist.seqs command should be in the following format: \n");
- mothurOut("dist.seqs(fasta=yourFastaFile, calc=yourCalc, countends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) \n");
- mothurOut("Example dist.seqs(fasta=amazon.fasta, calc=eachgap, countends=F, cutoff= 2.0, processors=3).\n");
- mothurOut("Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc).\n\n");
+ m->mothurOut("The dist.seqs command reads a file containing sequences and creates a distance file.\n");
+ m->mothurOut("The dist.seqs command parameters are fasta, calc, countends, output, cutoff and processors. \n");
+ m->mothurOut("The fasta parameter is required.\n");
+ m->mothurOut("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");
+ m->mothurOut("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");
+ m->mothurOut("The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n");
+ m->mothurOut("The output parameter allows you to specify format of your distance matrix. Options are column, lt, and square. The default is column.\n");
+ m->mothurOut("The processors parameter allows you to specify number of processors to use. The default is 1.\n");
+ m->mothurOut("The dist.seqs command should be in the following format: \n");
+ m->mothurOut("dist.seqs(fasta=yourFastaFile, calc=yourCalc, countends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) \n");
+ m->mothurOut("Example dist.seqs(fasta=amazon.fasta, calc=eachgap, countends=F, cutoff= 2.0, processors=3).\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc).\n\n");
}
catch(exception& e) {
- errorOut(e, "DistanceCommand", "help");
+ m->errorOut(e, "DistanceCommand", "help");
exit(1);
}
}
cutoff += 0.005;
string outputFile;
-
+
if (output == "lt") { //does the user want lower triangle phylip formatted file
outputFile = outputDir + getRootName(getSimpleName(fastafile)) + "phylip.dist";
remove(outputFile.c_str());
outputFile = outputDir + getRootName(getSimpleName(fastafile)) + "square.dist";
remove(outputFile.c_str());
}
+
+
+#ifdef USE_MPI
+
+ int pid, start, end;
+ int tag = 2001;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ MPI_Status status;
+ MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+
+ //each process gets where it should start and stop in the file
+ start = int (sqrt(float(pid)/float(processors)) * numSeqs);
+ end = int (sqrt(float(pid+1)/float(processors)) * numSeqs);
+
+ MPI_File outMPI;
+ int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
+
+ char filename[outputFile.length()];
+ strcpy(filename, outputFile.c_str());
+
+ MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
+
+ if (pid == 0) { //you are the root process
+
+ //do your part
+ string outputMyPart;
+ driverMPI(start, end, outMPI, cutoff);
+
+ //wait on chidren
+ for(int i = 1; i < processors; i++) {
+ char buf[4];
+ MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
+ }
+
+ if (output == "lt") {
+ convertToLowerTriangle(outputFile);
+ }
+
+ }else { //you are a child process
+ //do your part
+ driverMPI(start, end, outMPI, cutoff);
+
+ char buf[4];
+ strcpy(buf, "done");
+
+ //tell parent you are done.
+ MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
+ }
+
+ MPI_File_close(&outMPI);
+#else
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
//if you don't need to fork anything
if(processors == 1){
driver(0, numSeqs, outputFile, cutoff);
remove((outputFile + toString(it->second) + ".temp").c_str());
}
}
-#else
+ #else
ifstream inFASTA;
driver(0, numSeqs, outputFile, cutoff);
+ #endif
+
#endif
+ if (m->control_pressed) { delete distCalculator; remove(outputFile.c_str()); return 0; }
+
+ #ifdef USE_MPI
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ if (pid == 0) { //only one process should output to screen
+ #endif
if (output == "square") { convertMatrix(outputFile); }
+ #ifdef USE_MPI
+ }
+ #endif
+
+ if (m->control_pressed) { delete distCalculator; remove(outputFile.c_str()); return 0; }
+
delete distCalculator;
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut(outputFile); m->mothurOutEndLine();
+ m->mothurOutEndLine();
+
return 0;
}
catch(exception& e) {
- errorOut(e, "DistanceCommand", "execute");
+ m->errorOut(e, "DistanceCommand", "execute");
exit(1);
}
}
}else if (pid == 0){
driver(lines[process]->start, lines[process]->end, filename + toString(getpid()) + ".temp", cutoff);
exit(0);
- }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
+ }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
}
//force parent to wait until all the processes are done
#endif
}
catch(exception& e) {
- errorOut(e, "DistanceCommand", "createProcesses");
+ m->errorOut(e, "DistanceCommand", "createProcesses");
exit(1);
}
}
outFile << name << '\t';
}
for(int j=0;j<i;j++){
+
+ if (m->control_pressed) { outFile.close(); return 0; }
+
distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
double dist = distCalculator->getDist();
if (output == "lt") { outFile << endl; }
if(i % 100 == 0){
- mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); mothurOutEndLine();
+ m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
}
}
- mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); mothurOutEndLine();
+ m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
outFile.close();
return 1;
}
catch(exception& e) {
- errorOut(e, "DistanceCommand", "driver");
+ m->errorOut(e, "DistanceCommand", "driver");
exit(1);
}
}
+#ifdef USE_MPI
/**************************************************************************************************/
-void DistanceCommand::convertMatrix(string outputFile) {
+/////// need to fix to work with calcs and sequencedb
+int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
+ try {
+ MPI_Status status;
+ int startTime = time(NULL);
+
+ string outputString = "";
+
+ for(int i=startLine;i<endLine;i++){
+
+ for(int j=0;j<i;j++){
+
+ if (m->control_pressed) { return 0; }
+
+ distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
+ double dist = distCalculator->getDist();
+
+ if(dist <= cutoff){
+ if (output == "column") { outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n'); }
+ }
+
+ if ((output == "square") || (output == "lt")){ //make a square column you can convert to square phylip
+ outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
+ outputString += (alignDB.get(j).getName() + ' ' + alignDB.get(i).getName() + ' ' + toString(dist) + '\n');
+ }
+
+ }
+
+ if(i % 100 == 0){
+ m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+ }
+
+ if(i % 10 == 0){ //output to file
+ //send results to parent
+ int length = outputString.length();
+ char buf[length];
+ strcpy(buf, outputString.c_str());
+
+ MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
+ outputString = "";
+ }
+
+ }
+
+ m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+ if(outputString != ""){ //output to file
+ //send results to parent
+ int length = outputString.length();
+ char buf[length];
+ strcpy(buf, outputString.c_str());
+
+ MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
+ outputString = "";
+ }
+
+ return 1;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "driverMPI");
+ exit(1);
+ }
+}
+#endif
+/**************************************************************************************************/
+int DistanceCommand::convertMatrix(string outputFile) {
try{
//sort file by first column so the distances for each row are together
//openInputFile(outfile, in);
while(!in.eof()) {
+ if (m->control_pressed) { in.close(); remove(outfile.c_str()); out.close(); return 0; }
+
in >> first >> second >> dist; gobble(in);
if (first != currentRow) {
remove(outfile.c_str());
+ return 1;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "convertMatrix");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int DistanceCommand::convertToLowerTriangle(string outputFile) {
+ try{
+
+ //sort file by first column so the distances for each row are together
+ string outfile = getRootName(outputFile) + "sorted.dist.temp";
+
+ //use the unix sort
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ string command = "sort -n " + outputFile + " -o " + outfile;
+ system(command.c_str());
+ #else //sort using windows sort
+ string command = "sort " + outputFile + " /O " + outfile;
+ system(command.c_str());
+ #endif
+
+
+ //output to new file distance for each row and save positions in file where new row begins
+ ifstream in;
+ openInputFile(outfile, in);
+
+ ofstream out;
+ openOutputFile(outputFile, out);
+
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+
+ out << alignDB.getNumSeqs() << endl;
+
+ //get first currentRow
+ string first, currentRow, second;
+ float dist;
+ int i, j;
+ i = 0; j = 0;
+ map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
+ map<string, float>::iterator it;
+
+ in >> first;
+ currentRow = first;
+
+ rowDists[first] = 0.00; //distance to yourself is 0.0
+
+ in.seekg(0);
+ //openInputFile(outfile, in);
+
+ while(!in.eof()) {
+ if (m->control_pressed) { in.close(); remove(outfile.c_str()); out.close(); return 0; }
+
+ in >> first >> second >> dist; gobble(in);
+
+ if (first != currentRow) {
+ //print out last row
+ out << currentRow << '\t'; //print name
+
+ //print dists
+ for (it = rowDists.begin(); it != rowDists.end(); it++) {
+ if (j >= i) { break; }
+ out << it->second << '\t';
+ j++;
+ }
+ out << endl;
+
+ //start new row
+ currentRow = first;
+ rowDists.clear();
+ rowDists[first] = 0.00;
+ rowDists[second] = dist;
+ j = 0;
+ i++;
+ }else{
+ rowDists[second] = dist;
+ }
+ }
+ //print out last row
+ out << currentRow << '\t'; //print name
+
+ //print dists
+ for (it = rowDists.begin(); it != rowDists.end(); it++) {
+ out << it->second << '\t';
+ }
+ out << endl;
+
+ in.close();
+ out.close();
+
+ remove(outfile.c_str());
+
+ return 1;
+
}
catch(exception& e) {
- errorOut(e, "DistanceCommand", "convertMatrix");
+ m->errorOut(e, "DistanceCommand", "convertToLowerTriangle");
exit(1);
}
}
output.close();
}
catch(exception& e) {
- errorOut(e, "DistanceCommand", "appendFiles");
+ m->errorOut(e, "DistanceCommand", "appendFiles");
exit(1);
}
}
projects / mothur.git / blobdiff