/**************************************************************************************/
-FilterSeqsCommand::FilterSeqsCommand(string option){
+FilterSeqsCommand::FilterSeqsCommand(string option) {
try {
abort = false;
+ filterFileName = "";
//allow user to run help
if(option == "help") { help(); abort = true; }
else {
//valid paramters for this command
- string Array[] = {"fasta", "trump", "soft", "hard", "vertical"};
+ string Array[] = {"fasta", "trump", "soft", "hard", "vertical", "outputdir","inputdir", "processors"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
- ValidParameters validParameter;
+ ValidParameters validParameter("filter.seqs");
+ map<string,string>::iterator it;
//check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("fasta");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["fasta"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("hard");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["hard"] = inputDir + it->second; }
+ }
+ }
+
//check for required parameters
- fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not found") { cout << "fasta is a required parameter for the filter.seqs command." << endl; abort = true; }
- else if (fastafile == "not open") { abort = true; }
+ fasta = validParameter.validFile(parameters, "fasta", false);
+ if (fasta == "not found") { m->mothurOut("fasta is a required parameter for the filter.seqs command."); m->mothurOutEndLine(); abort = true; }
+ else {
+ splitAtDash(fasta, fastafileNames);
+
+ //go through files and make sure they are good, if not, then disregard them
+ for (int i = 0; i < fastafileNames.size(); i++) {
+ if (inputDir != "") {
+ string path = hasPath(fastafileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { fastafileNames[i] = inputDir + fastafileNames[i]; }
+ }
+ ifstream in;
+ int ableToOpen = openInputFile(fastafileNames[i], in, "noerror");
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + getSimpleName(fastafileNames[i]);
+ m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ableToOpen = openInputFile(tryPath, in, "noerror");
+ fastafileNames[i] = tryPath;
+ }
+ }
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + fastafileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ fastafileNames.erase(fastafileNames.begin()+i);
+ i--;
+ }else{
+ string simpleName = getSimpleName(fastafileNames[i]);
+ filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
+ }
+ in.close();
+ }
+
+ //make sure there is at least one valid file left
+ if (fastafileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
+ }
+
+ if (!abort) {
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
+ outputDir = "";
+ outputDir += hasPath(fastafileNames[0]); //if user entered a file with a path then preserve it
+ }
+ }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
string temp;
+ hard = validParameter.validFile(parameters, "hard", true); if (hard == "not found") { hard = ""; }
+ else if (hard == "not open") { hard = ""; abort = true; }
+
temp = validParameter.validFile(parameters, "trump", false); if (temp == "not found") { temp = "*"; }
trump = temp[0];
temp = validParameter.validFile(parameters, "soft", false); if (temp == "not found") { soft = 0; }
else { soft = (float)atoi(temp.c_str()) / 100.0; }
- hard = validParameter.validFile(parameters, "hard", true); if (hard == "not found") { hard = ""; }
- else if (hard == "not open") { abort = true; }
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
+ convert(temp, processors);
- vertical = validParameter.validFile(parameters, "vertical", false); if (vertical == "not found") { vertical = "T"; }
+ vertical = validParameter.validFile(parameters, "vertical", false);
+ if (vertical == "not found") {
+ if ((hard == "") && (trump == '*') && (soft == 0)) { vertical = "T"; } //you have not given a hard file or set the trump char.
+ else { vertical = "F"; }
+ }
numSeqs = 0;
-
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function FilterSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the FilterSeqsCommand class function FilterSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
void FilterSeqsCommand::help(){
try {
- cout << "The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file." << "\n";
- cout << "The filter.seqs command parameters are fasta, trump, soft, hard and vertical. " << "\n";
- cout << "The fasta parameter is required." << "\n";
- cout << "The trump parameter .... The default is ..." << "\n";
- cout << "The soft parameter .... The default is ...." << "\n";
- cout << "The hard parameter .... The default is ...." << "\n";
- cout << "The vertical parameter .... The default is T." << "\n";
- cout << "The filter.seqs command should be in the following format: " << "\n";
- cout << "filter.seqs(fasta=yourFastaFile, trump=yourTrump, soft=yourSoft, hard=yourHard, vertical=yourVertical) " << "\n";
- cout << "Example filter.seqs(fasta=abrecovery.fasta, trump=..., soft=..., hard=..., vertical=T)." << "\n";
- cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta)." << "\n" << "\n";
+
+ m->mothurOut("The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n");
+ m->mothurOut("The filter.seqs command parameters are fasta, trump, soft, hard and vertical. \n");
+ m->mothurOut("The fasta parameter is required. You may enter several fasta files to build the filter from and filter, by separating their names with -'s.\n");
+ m->mothurOut("For example: fasta=abrecovery.fasta-amazon.fasta \n");
+ m->mothurOut("The trump parameter .... The default is ...\n");
+ m->mothurOut("The soft parameter .... The default is ....\n");
+ m->mothurOut("The hard parameter allows you to enter a file containing the filter you want to use.\n");
+ m->mothurOut("The vertical parameter removes columns where all sequences contain a gap character. The default is T.\n");
+ m->mothurOut("The filter.seqs command should be in the following format: \n");
+ m->mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump) \n");
+ m->mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=.).\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "FilterSeqsCommand", "help");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the FilterSeqsCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/**************************************************************************************/
-void FilterSeqsCommand::doHard() {
-
- ifstream fileHandle;
- openInputFile(hard, fileHandle);
+int FilterSeqsCommand::execute() {
+ try {
- fileHandle >> filter;
+ if (abort == true) { return 0; }
+
+ ifstream inFASTA;
+ openInputFile(fastafileNames[0], inFASTA);
+
+ Sequence testSeq(inFASTA);
+ alignmentLength = testSeq.getAlignLength();
+ inFASTA.close();
+
+ ////////////create filter/////////////////
+ m->mothurOut("Creating Filter... "); m->mothurOutEndLine();
+
+ filter = createFilter();
+
+ m->mothurOutEndLine(); m->mothurOutEndLine();
+
+ if (m->control_pressed) { return 0; }
+
+ #ifdef USE_MPI
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ if (pid == 0) { //only one process should output the filter
+ #endif
+
+ ofstream outFilter;
+
+ string filterFile = outputDir + filterFileName + ".filter";
+ openOutputFile(filterFile, outFilter);
+ outFilter << filter << endl;
+ outFilter.close();
+ outputNames.push_back(filterFile);
+
+ #ifdef USE_MPI
+ }
+ #endif
+
+ ////////////run filter/////////////////
+
+ m->mothurOut("Running Filter... "); m->mothurOutEndLine();
+
+ filterSequences();
+
+ m->mothurOutEndLine(); m->mothurOutEndLine();
+
+ int filteredLength = 0;
+ for(int i=0;i<alignmentLength;i++){
+ if(filter[i] == '1'){ filteredLength++; }
+ }
+
+ if (m->control_pressed) { for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Length of filtered alignment: " + toString(filteredLength)); m->mothurOutEndLine();
+ m->mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); m->mothurOutEndLine();
+ m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
+ m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
+
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for(int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "execute");
+ exit(1);
+ }
}
-
/**************************************************************************************/
+int FilterSeqsCommand::filterSequences() {
+ try {
+
+ numSeqs = 0;
+
+ for (int s = 0; s < fastafileNames.size(); s++) {
+
+ for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
+
+ string filteredFasta = outputDir + getRootName(getSimpleName(fastafileNames[s])) + "filter.fasta";
+#ifdef USE_MPI
+ int pid, start, end, numSeqsPerProcessor, num;
+ int tag = 2001;
+ vector<unsigned long int>MPIPos;
+
+ 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
+
+ MPI_File outMPI;
+ MPI_File tempMPI;
+ MPI_File inMPI;
+ int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
+ int inMode=MPI_MODE_RDONLY;
+
+ char outFilename[1024];
+ strcpy(outFilename, filteredFasta.c_str());
+
+ char inFileName[1024];
+ strcpy(inFileName, fastafileNames[s].c_str());
+
+ MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
+ MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
-void FilterSeqsCommand::doTrump(Sequence seq) {
-
- string curAligned = seq.getAligned();
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; }
- for(int j = 0; j < alignmentLength; j++) {
- if(curAligned[j] == trump){
- filter[j] = '0';
+ if (pid == 0) { //you are the root process
+
+ MPIPos = setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
+ numSeqs += num;
+
+ //send file positions to all processes
+ for(int i = 1; i < processors; i++) {
+ MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+ MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+ }
+
+ //figure out how many sequences you have to do
+ numSeqsPerProcessor = num / processors;
+ int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; }
+
+
+ //do your part
+ driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; }
+
+ //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);
+ }
+
+ }else { //you are a child process
+ MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+ MPIPos.resize(num+1);
+ numSeqs += num;
+ MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
+
+ //figure out how many sequences you have to align
+ numSeqsPerProcessor = num / processors;
+ int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; }
+
+
+ //align your part
+ driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; }
+
+ 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);
+ MPI_File_close(&inMPI);
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+
+#else
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if(processors == 1){
+ ifstream inFASTA;
+ int numFastaSeqs;
+ openInputFile(fastafileNames[s], inFASTA);
+ getNumSeqs(inFASTA, numFastaSeqs);
+ inFASTA.close();
+
+ lines.push_back(new linePair(0, numFastaSeqs));
+
+ numSeqs += numFastaSeqs;
+
+ driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
+ }else{
+ setLines(fastafileNames[s]);
+ createProcessesRunFilter(filter, fastafileNames[s]);
+
+ rename((fastafileNames[s] + toString(processIDS[0]) + ".temp").c_str(), filteredFasta.c_str());
+
+ //append fasta files
+ for(int i=1;i<processors;i++){
+ appendFiles((fastafileNames[s] + toString(processIDS[i]) + ".temp"), filteredFasta);
+ remove((fastafileNames[s] + toString(processIDS[i]) + ".temp").c_str());
+ }
+ }
+
+ if (m->control_pressed) { return 1; }
+ #else
+ ifstream inFASTA;
+ int numFastaSeqs;
+ openInputFile(fastafileNames[s], inFASTA);
+ getNumSeqs(inFASTA, numFastaSeqs);
+ inFASTA.close();
+
+ lines.push_back(new linePair(0, numFastaSeqs));
+
+ numSeqs += numFastaSeqs;
+
+ driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
+
+ if (m->control_pressed) { return 1; }
+ #endif
+#endif
+ outputNames.push_back(filteredFasta);
}
- }
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "filterSequences");
+ exit(1);
+ }
}
-
+#ifdef USE_MPI
/**************************************************************************************/
+int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long int>& MPIPos) {
+ try {
+ string outputString = "";
+ int count = 0;
+ MPI_Status status;
+
+ for(int i=0;i<num;i++){
+
+ if (m->control_pressed) { return 0; }
+
+ //read next sequence
+ int length = MPIPos[start+i+1] - MPIPos[start+i];
+ char* buf4 = new char[length];
+ MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
+
+ string tempBuf = buf4;
+ if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
+ istringstream iss (tempBuf,istringstream::in);
+ delete buf4;
+
+ Sequence seq(iss); gobble(iss);
+
+ if (seq.getName() != "") {
+ string align = seq.getAligned();
+ string filterSeq = "";
+
+ for(int j=0;j<alignmentLength;j++){
+ if(filter[j] == '1'){
+ filterSeq += align[j];
+ }
+ }
+
+ count++;
+ outputString += ">" + seq.getName() + "\n" + filterSeq + "\n";
+
+ if(count % 10 == 0){ //output to file
+ //send results to parent
+ int length = outputString.length();
+ char* buf = new char[length];
+ memcpy(buf, outputString.c_str(), length);
+
+ MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
+ outputString = "";
+ delete buf;
+ }
-void FilterSeqsCommand::doVertical() {
-
- for(int i=0;i<alignmentLength;i++){
- if(gap[i] == numSeqs) { filter[i] = '0'; }
+ }
+
+ if((i+1) % 100 == 0){ cout << (i+1) << endl; m->mothurOutJustToLog(toString(i+1) + "\n"); }
+ }
+
+ if(outputString != ""){ //output to file
+ //send results to parent
+ int length = outputString.length();
+ char* buf = new char[length];
+ memcpy(buf, outputString.c_str(), length);
+
+ MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
+ outputString = "";
+ delete buf;
+ }
+
+ if((num) % 100 != 0){ cout << (num) << endl; m->mothurOutJustToLog(toString(num) + "\n"); }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
+ exit(1);
}
-
}
-
+#endif
/**************************************************************************************/
-
-void FilterSeqsCommand::doSoft() {
-
- int threshold = int (soft * numSeqs);
-
- for(int i=0;i<alignmentLength;i++){
- if(a[i] < threshold && t[i] < threshold && g[i] < threshold && c[i] < threshold){ filter[i] = 0; }
+int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* line) {
+ try {
+ ofstream out;
+ openOutputFile(outputFilename, out);
+
+ ifstream in;
+ openInputFile(inputFilename, in);
+
+ in.seekg(line->start);
+
+ for(int i=0;i<line->num;i++){
+
+ if (m->control_pressed) { in.close(); out.close(); return 0; }
+
+ Sequence seq(in);
+ if (seq.getName() != "") {
+ string align = seq.getAligned();
+ string filterSeq = "";
+
+ for(int j=0;j<alignmentLength;j++){
+ if(filter[j] == '1'){
+ filterSeq += align[j];
+ }
+ }
+
+ out << '>' << seq.getName() << endl << filterSeq << endl;
+ }
+ gobble(in);
+ }
+ out.close();
+ in.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
+ exit(1);
}
}
+/**************************************************************************************************/
+int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ int process = 0;
+ int exitCommand = 1;
+ processIDS.clear();
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+
+ if (pid > 0) {
+ processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
+ process++;
+ }else if (pid == 0){
+ string filteredFasta = filename + toString(getpid()) + ".temp";
+ driverRunFilter(F, filteredFasta, filename, lines[process]);
+ 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
+ for (int i=0;i<processors;i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ return exitCommand;
+#endif
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "createProcessesRunFilter");
+ exit(1);
+ }
+}
/**************************************************************************************/
+string FilterSeqsCommand::createFilter() {
+ try {
+ string filterString = "";
+ Filters F;
+
+ if (soft != 0) { F.setSoft(soft); }
+ if (trump != '*') { F.setTrump(trump); }
+
+ F.setLength(alignmentLength);
+
+ if(trump != '*' || isTrue(vertical) || soft != 0){
+ F.initialize();
+ }
+
+ if(hard.compare("") != 0) { F.doHard(hard); }
+ else { F.setFilter(string(alignmentLength, '1')); }
+
+ numSeqs = 0;
+ if(trump != '*' || isTrue(vertical) || soft != 0){
+ for (int s = 0; s < fastafileNames.size(); s++) {
+
+ for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
+
+#ifdef USE_MPI
+ int pid, numSeqsPerProcessor, num;
+ int tag = 2001;
+ vector<unsigned long int> MPIPos;
+
+ MPI_Status status;
+ MPI_File inMPI;
+ MPI_Comm_size(MPI_COMM_WORLD, &processors);
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ //char* tempFileName = new char(fastafileNames[s].length());
+ //tempFileName = &(fastafileNames[s][0]);
+
+ char tempFileName[1024];
+ strcpy(tempFileName, fastafileNames[s].c_str());
+
+ MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); return 0; }
+
+ if (pid == 0) { //you are the root process
+ MPIPos = setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
+ numSeqs += num;
+
+ //send file positions to all processes
+ for(int i = 1; i < processors; i++) {
+ MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+ MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+ }
+
+ //figure out how many sequences you have to do
+ numSeqsPerProcessor = num / processors;
+ int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; }
+
+
+ //do your part
+ MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); return 0; }
+
+ }else { //i am the child process
+ MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+ MPIPos.resize(num+1);
+ numSeqs += num;
+ MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
+
+ //figure out how many sequences you have to align
+ numSeqsPerProcessor = num / processors;
+ int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; }
+
+
+ //do your part
+ MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); return 0; }
+ }
+
+ MPI_File_close(&inMPI);
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+
+#else
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if(processors == 1){
+ ifstream inFASTA;
+ int numFastaSeqs;
+ openInputFile(fastafileNames[s], inFASTA);
+ getNumSeqs(inFASTA, numFastaSeqs);
+ inFASTA.close();
+
+ numSeqs += numFastaSeqs;
+
+ lines.push_back(new linePair(0, numFastaSeqs));
+
+ driverCreateFilter(F, fastafileNames[s], lines[0]);
+ }else{
+ setLines(fastafileNames[s]);
+ createProcessesCreateFilter(F, fastafileNames[s]);
+ }
+
+ if (m->control_pressed) { return filterString; }
+ #else
+ ifstream inFASTA;
+ int numFastaSeqs;
+ openInputFile(fastafileNames[s], inFASTA);
+ getNumSeqs(inFASTA, numFastaSeqs);
+ inFASTA.close();
+
+ numSeqs += numFastaSeqs;
+
+ lines.push_back(new linePair(0, numFastaSeqs));
+
+ driverCreateFilter(F, fastafileNames[s], lines[0]);
+ if (m->control_pressed) { return filterString; }
+ #endif
+#endif
+
+ }
+ }
-void FilterSeqsCommand::getFreqs(Sequence seq) {
- string curAligned = seq.getAligned();;
-
- for(int j=0;j<alignmentLength;j++){
- if(toupper(curAligned[j]) == 'A') { a[j]++; }
- else if(toupper(curAligned[j]) == 'T' || toupper(curAligned[j]) == 'U') { t[j]++; }
- else if(toupper(curAligned[j]) == 'G') { g[j]++; }
- else if(toupper(curAligned[j]) == 'C') { c[j]++; }
- else if(curAligned[j] == '-' || curAligned[j] == '.') { gap[j]++; }
+#ifdef USE_MPI
+ int pid;
+ int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
+ MPI_Status status;
+
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ if(trump != '*' || isTrue(vertical) || soft != 0){
+
+ if (pid == 0) { //only one process should output the filter
+
+ vector<int> temp; temp.resize(alignmentLength+1);
+
+ //get the frequencies from the child processes
+ for(int i = 1; i < processors; i++) {
+
+ for (int j = 0; j < 5; j++) {
+
+ MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
+ int receiveTag = temp[temp.size()-1]; //child process added a int to the end to indicate what letter count this is for
+
+ if (receiveTag == Atag) { //you are recieveing the A frequencies
+ for (int k = 0; k < alignmentLength; k++) { F.a[k] += temp[k]; }
+ }else if (receiveTag == Ttag) { //you are recieveing the T frequencies
+ for (int k = 0; k < alignmentLength; k++) { F.t[k] += temp[k]; }
+ }else if (receiveTag == Ctag) { //you are recieveing the C frequencies
+ for (int k = 0; k < alignmentLength; k++) { F.c[k] += temp[k]; }
+ }else if (receiveTag == Gtag) { //you are recieveing the G frequencies
+ for (int k = 0; k < alignmentLength; k++) { F.g[k] += temp[k]; }
+ }else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
+ for (int k = 0; k < alignmentLength; k++) { F.gap[k] += temp[k]; }
+ }
+ }
+ }
+ }else{
+
+ //send my fequency counts
+ F.a.push_back(Atag);
+ int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
+ F.t.push_back(Ttag);
+ ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
+ F.c.push_back(Ctag);
+ ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
+ F.g.push_back(Gtag);
+ ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
+ F.gap.push_back(Gaptag);
+ ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
+ }
+
+ }
+
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+
+ if (pid == 0) { //only one process should output the filter
+#endif
+ F.setNumSeqs(numSeqs);
+
+ if(isTrue(vertical) == 1) { F.doVertical(); }
+ if(soft != 0) { F.doSoft(); }
+
+ filterString = F.getFilter();
+
+#ifdef USE_MPI
+ //send filter string to kids
+ //for(int i = 1; i < processors; i++) {
+ // MPI_Send(&filterString[0], alignmentLength, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
+ //}
+ MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
+ }else{
+ //recieve filterString
+ char* tempBuf = new char[alignmentLength];
+ //MPI_Recv(&tempBuf[0], alignmentLength, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
+ MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
+
+ filterString = tempBuf;
+ if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength); }
+ delete tempBuf;
}
+ MPI_Barrier(MPI_COMM_WORLD);
+#endif
+
+ return filterString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "createFilter");
+ exit(1);
+ }
}
-
/**************************************************************************************/
-
-int FilterSeqsCommand::execute() {
+int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* line) {
try {
-
- if (abort == true) { return 0; }
- ifstream inFASTA;
- openInputFile(fastafile, inFASTA);
+ ifstream in;
+ openInputFile(filename, in);
+
+ in.seekg(line->start);
- Sequence testSeq(inFASTA);
- alignmentLength = testSeq.getAlignLength();
- inFASTA.seekg(0);
-
- if(soft != 0 || isTrue(vertical)){
- a.assign(alignmentLength, 0);
- t.assign(alignmentLength, 0);
- g.assign(alignmentLength, 0);
- c.assign(alignmentLength, 0);
- gap.assign(alignmentLength, 0);
+ for(int i=0;i<line->num;i++){
+
+ if (m->control_pressed) { in.close(); return 1; }
+
+ Sequence seq(in);
+ if (seq.getName() != "") {
+ if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ if(trump != '*'){ F.doTrump(seq); }
+ if(isTrue(vertical) || soft != 0){ F.getFreqs(seq); }
+ cout.flush();
+ }
+
+ //report progress
+ if((i+1) % 100 == 0){ m->mothurOut(toString(i+1)); m->mothurOutEndLine(); }
}
- if(hard.compare("") != 0) { doHard(); }
- else { filter = string(alignmentLength, '1'); }
-
- if(trump != '*' || isTrue(vertical) || soft != 0){
- while(!inFASTA.eof()){ //read through and create the filter...
- Sequence seq(inFASTA);
- if(trump != '*'){ doTrump(seq); }
- if(isTrue(vertical) || soft != 0){ getFreqs(seq); }
- numSeqs++;
- cout.flush();
- }
+ //report progress
+ if((line->num) % 100 != 0){ m->mothurOut(toString(line->num)); m->mothurOutEndLine(); }
+
+ in.close();
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
+ exit(1);
+ }
+}
+#ifdef USE_MPI
+/**************************************************************************************/
+int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<unsigned long int>& MPIPos) {
+ try {
+
+ MPI_Status status;
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+
+ for(int i=0;i<num;i++){
+
+ if (m->control_pressed) { return 0; }
+
+ //read next sequence
+ int length = MPIPos[start+i+1] - MPIPos[start+i];
+
+ char* buf4 = new char[length];
+ MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
+
+ string tempBuf = buf4;
+ if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
+ istringstream iss (tempBuf,istringstream::in);
+ delete buf4;
+
+ Sequence seq(iss);
+
+ if (seq.getAligned().length() != alignmentLength) { cout << "Alignment length is " << alignmentLength << " and sequence " << seq.getName() << " has length " << seq.getAligned().length() << ", please correct." << endl; exit(1); }
+
+ if(trump != '*'){ F.doTrump(seq); }
+ if(isTrue(vertical) || soft != 0){ F.getFreqs(seq); }
+ cout.flush();
+
+ //report progress
+ if((i+1) % 100 == 0){ cout << (i+1) << endl; m->mothurOutJustToLog(toString(i+1) + "\n"); }
}
- inFASTA.close();
- if(isTrue(vertical) == 1) { doVertical(); }
- if(soft != 0) { doSoft(); }
+ //report progress
+ if((num) % 100 != 0){ cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n"); }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter");
+ exit(1);
+ }
+}
+#endif
+/**************************************************************************************************/
- ofstream outFilter;
- string filterFile = getRootName(fastafile) + "filter";
- openOutputFile(filterFile, outFilter);
- outFilter << filter << endl;
- outFilter.close();
+int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ int process = 0;
+ int exitCommand = 1;
+ processIDS.clear();
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = vfork();
+
+ if (pid > 0) {
+ processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
+ process++;
+ }else if (pid == 0){
+ driverCreateFilter(F, filename, lines[process]);
+ 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
+ for (int i=0;i<processors;i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ return exitCommand;
+#endif
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
- openInputFile(fastafile, inFASTA);
- string filteredFasta = getRootName(fastafile) + "filter.fasta";
- ofstream outFASTA;
- openOutputFile(filteredFasta, outFASTA);
+int FilterSeqsCommand::setLines(string filename) {
+ try {
+
+ vector<unsigned long int> positions;
+ bufferSizes.clear();
+
+ ifstream inFASTA;
+ openInputFile(filename, inFASTA);
+
+ string input;
+ while(!inFASTA.eof()){
+ input = getline(inFASTA);
- numSeqs = 0;
- while(!inFASTA.eof()){
- Sequence seq(inFASTA);
- string align = seq.getAligned();
- string filterSeq = "";
-
- for(int j=0;j<alignmentLength;j++){
- if(filter[j] == '1'){
- filterSeq += align[j];
- }
+ if (input.length() != 0) {
+ if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
}
-
- outFASTA << '>' << seq.getName() << endl << filterSeq << endl;
- numSeqs++;
- gobble(inFASTA);
}
- outFASTA.close();
inFASTA.close();
+ int numFastaSeqs = positions.size();
+
+ FILE * pFile;
+ unsigned long int size;
- int filteredLength = 0;
- for(int i=0;i<alignmentLength;i++){
- if(filter[i] == '1'){ filteredLength++; }
+ //get num bytes in file
+ pFile = fopen (filename.c_str(),"rb");
+ if (pFile==NULL) perror ("Error opening file");
+ else{
+ fseek (pFile, 0, SEEK_END);
+ size=ftell (pFile);
+ fclose (pFile);
}
+
+ numSeqs += numFastaSeqs;
- cout << endl;
- cout << "Length of filtered alignment: " << filteredLength << endl;
- cout << "Number of columns removed: " << alignmentLength-filteredLength << endl;
- cout << "Length of the original alignment: " << alignmentLength << endl;
- cout << "Number of sequences used to construct filter: " << numSeqs << endl;
+ int numSeqsPerProcessor = numFastaSeqs / processors;
- return 0;
+ for (int i = 0; i < processors; i++) {
+
+ unsigned long int startPos = positions[ i * numSeqsPerProcessor ];
+ if(i == processors - 1){
+ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
+ bufferSizes.push_back(size - startPos);
+ }else{
+ unsigned long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
+ bufferSizes.push_back(myEnd-startPos);
+ }
+ lines.push_back(new linePair(startPos, numSeqsPerProcessor));
+ }
+ return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the FilterSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "FilterSeqsCommand", "setLines");
exit(1);
}
}
-
/**************************************************************************************/
projects / mothur.git / blobdiff