X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.cpp;h=3d3062b4cc371848fdbd222b7985415a41e62e57;hb=fdc1f6eaf544f695fc1511f24bddd7e6069c33ba;hp=68450fb15a7b140803aab2d54d8c5bc84e7ce688;hpb=7e354c9abb09ea3cf5b500a16cc7f6dd79ccb6f5;p=mothur.git diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp index 68450fb..3d3062b 100644 --- a/filterseqscommand.cpp +++ b/filterseqscommand.cpp @@ -12,33 +12,92 @@ /**************************************************************************************/ -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 myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); map parameters = parser.getParameters(); ValidParameters validParameter; + map::iterator it; //check to make sure all parameters are valid for command - for (map::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") { mothurOut("fasta is a required parameter for the filter.seqs command."); mothurOutEndLine(); 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]; } + } + int ableToOpen; + ifstream in; + ableToOpen = openInputFile(fastafileNames[i], in); + if (ableToOpen == 1) { + m->mothurOut(fastafileNames[i] + " 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... @@ -49,6 +108,9 @@ FilterSeqsCommand::FilterSeqsCommand(string option){ temp = validParameter.validFile(parameters, "soft", false); if (temp == "not found") { soft = 0; } else { soft = (float)atoi(temp.c_str()) / 100.0; } + temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; } + convert(temp, processors); + hard = validParameter.validFile(parameters, "hard", true); if (hard == "not found") { hard = ""; } else if (hard == "not open") { abort = true; } @@ -56,18 +118,11 @@ FilterSeqsCommand::FilterSeqsCommand(string option){ numSeqs = 0; - if (abort == false) { - - if (soft != 0) { F.setSoft(soft); } - if (trump != '*') { F.setTrump(trump); } - - } - } } catch(exception& e) { - errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand"); + m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand"); exit(1); } } @@ -76,21 +131,23 @@ FilterSeqsCommand::FilterSeqsCommand(string option){ void FilterSeqsCommand::help(){ try { - mothurOut("The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n"); - mothurOut("The filter.seqs command parameters are fasta, trump, soft, hard and vertical. \n"); - mothurOut("The fasta parameter is required.\n"); - mothurOut("The trump parameter .... The default is ...\n"); - mothurOut("The soft parameter .... The default is ....\n"); - mothurOut("The hard parameter .... The default is ....\n"); - mothurOut("The vertical parameter .... The default is T.\n"); - mothurOut("The filter.seqs command should be in the following format: \n"); - mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump, soft=yourSoft, hard=yourHard, vertical=yourVertical) \n"); - mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=..., soft=..., hard=..., vertical=T).\n"); - mothurOut("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 .... The default is ....\n"); + m->mothurOut("The vertical parameter .... 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, soft=yourSoft, hard=yourHard, vertical=yourVertical) \n"); + m->mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=..., soft=..., hard=..., vertical=T).\n"); + m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n"); } catch(exception& e) { - errorOut(e, "FilterSeqsCommand", "help"); + m->errorOut(e, "FilterSeqsCommand", "help"); exit(1); } } @@ -103,11 +160,368 @@ int FilterSeqsCommand::execute() { if (abort == true) { return 0; } ifstream inFASTA; - openInputFile(fastafile, inFASTA); + openInputFile(fastafileNames[0], inFASTA); Sequence testSeq(inFASTA); alignmentLength = testSeq.getAlignLength(); - inFASTA.seekg(0); + 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;icontrol_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; + vectorMPIPos; + + 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[filteredFasta.length()]; + strcpy(outFilename, filteredFasta.c_str()); + + char inFileName[fastafileNames[s].length()]; + 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); + + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); 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 + MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD); //send numSeqs + MPI_Bcast(&MPIPos[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos + + //figure out how many sequences you have to do + numSeqsPerProcessor = num / processors; + if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; } + int startIndex = 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_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs + numSeqs += num; + MPIPos.resize(num+1); + MPI_Bcast(&MPIPos[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions + + //figure out how many sequences you have to align + numSeqsPerProcessor = num / processors; + if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; } + int startIndex = 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); + +#else + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + if(processors == 1){ + ifstream inFASTA; + openInputFile(fastafileNames[s], inFASTA); + int numFastaSeqs=count(istreambuf_iterator(inFASTA),istreambuf_iterator(), '>'); + inFASTA.close(); + + lines.push_back(new linePair(0, 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;icontrol_pressed) { return 1; } + #else + ifstream inFASTA; + openInputFile(fastafileNames[s], inFASTA); + int numFastaSeqs=count(istreambuf_iterator(inFASTA),istreambuf_iterator(), '>'); + inFASTA.close(); + + lines.push_back(new linePair(0, 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& MPIPos) { + try { + string outputString = ""; + int count = 0; + MPI_Status status; + + for(int i=0;icontrol_pressed) { return 0; } + + //read next sequence + int length = MPIPos[start+i+1] - MPIPos[start+i]; + char buf4[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); + + Sequence seq(iss); gobble(iss); + + if (seq.getName() != "") { + string align = seq.getAligned(); + string filterSeq = ""; + + for(int j=0;jmothurOutJustToLog(toString(i+1) + "\n"); } + } + + 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 = ""; + } + + 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 +/**************************************************************************************/ +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;inum;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' << 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;ierrorOut(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); @@ -117,76 +531,357 @@ int FilterSeqsCommand::execute() { if(hard.compare("") != 0) { F.doHard(hard); } else { F.setFilter(string(alignmentLength, '1')); } - + + numSeqs = 0; if(trump != '*' || isTrue(vertical) || soft != 0){ - while(!inFASTA.eof()){ //read through and create the filter... - Sequence seq(inFASTA); - if(trump != '*'){ F.doTrump(seq); } - if(isTrue(vertical) || soft != 0){ F.getFreqs(seq); } - numSeqs++; - cout.flush(); - } + 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 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]); + 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 + MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD); //send numSeqs + MPI_Bcast(&MPIPos[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos + + //figure out how many sequences you have to do + numSeqsPerProcessor = num / processors; + if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; } + int startIndex = 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_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs + MPIPos.resize(num+1); + numSeqs += num; + MPI_Bcast(&MPIPos[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions + + //figure out how many sequences you have to align + numSeqsPerProcessor = num / processors; + if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; } + int startIndex = 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); + +#else + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + if(processors == 1){ + ifstream inFASTA; + openInputFile(fastafileNames[s], inFASTA); + int numFastaSeqs=count(istreambuf_iterator(inFASTA),istreambuf_iterator(), '>'); + 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; + openInputFile(fastafileNames[s], inFASTA); + int numFastaSeqs=count(istreambuf_iterator(inFASTA),istreambuf_iterator(), '>'); + 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 + + } } - inFASTA.close(); - F.setNumSeqs(numSeqs); + + +#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 (pid == 0) { //only one process should output the filter + vector temp; temp.resize(alignmentLength+1); + + //get the frequencies from the child processes + for(int i = 0; i < ((processors-1)*5); i++) { + MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, MPI_ANY_SOURCE, 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); + } + 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(); - filter = F.getFilter(); - - ofstream outFilter; - string filterFile = getRootName(fastafile) + "filter"; - openOutputFile(filterFile, outFilter); - outFilter << filter << endl; - outFilter.close(); +#ifdef USE_MPI + //send filter string to kids + MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD); + }else{ + //recieve filterString + char tempBuf[alignmentLength]; + MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD); - ifstream inFasta2; - openInputFile(fastafile, inFasta2); - string filteredFasta = getRootName(fastafile) + "filter.fasta"; - ofstream outFASTA; - openOutputFile(filteredFasta, outFASTA); - - numSeqs = 0; - while(!inFasta2.eof()){ - Sequence seq(inFasta2); - string align = seq.getAligned(); - string filterSeq = ""; + filterString = tempBuf; + if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength); } + } - for(int j=0;jerrorOut(e, "FilterSeqsCommand", "createFilter"); + exit(1); + } +} +/**************************************************************************************/ +int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* line) { + try { + + ifstream in; + openInputFile(filename, in); + + in.seekg(line->start); + + for(int i=0;inum;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(); } - - outFASTA << '>' << seq.getName() << endl << filterSeq << endl; - numSeqs++; - gobble(inFasta2); + + //report progress + if((i+1) % 100 == 0){ m->mothurOut(toString(i+1)); m->mothurOutEndLine(); } } - outFASTA.close(); - inFasta2.close(); + //report progress + if((line->num) % 100 != 0){ m->mothurOut(toString(line->num)); m->mothurOutEndLine(); } - int filteredLength = 0; - for(int i=0;ierrorOut(e, "FilterSeqsCommand", "driverCreateFilter"); + exit(1); + } +} +#ifdef USE_MPI +/**************************************************************************************/ +int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector& MPIPos) { + try { + + MPI_Status status; + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are + + for(int i=0;icontrol_pressed) { return 0; } + + //read next sequence + int length = MPIPos[start+i+1] - MPIPos[start+i]; + + char buf4[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); + + 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"); } } - mothurOutEndLine(); - mothurOut("Length of filtered alignment: " + toString(filteredLength)); mothurOutEndLine(); - mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); mothurOutEndLine(); - mothurOut("Length of the original alignment: " + toString(alignmentLength)); mothurOutEndLine(); - mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); mothurOutEndLine(); + //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 +/**************************************************************************************************/ + +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;ierrorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter"); exit(1); } } +/**************************************************************************************************/ + +int FilterSeqsCommand::setLines(string filename) { + try { + + vector positions; + bufferSizes.clear(); + + ifstream inFASTA; + openInputFile(filename, inFASTA); + + string input; + while(!inFASTA.eof()){ + input = getline(inFASTA); + + if (input.length() != 0) { + if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); } + } + } + inFASTA.close(); + + int numFastaSeqs = positions.size(); + + FILE * pFile; + long size; + + //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; + + int numSeqsPerProcessor = numFastaSeqs / processors; + + for (int i = 0; i < processors; i++) { + long int startPos = positions[ i * numSeqsPerProcessor ]; + if(i == processors - 1){ + numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; + bufferSizes.push_back(size - startPos); + }else{ + long int myEnd = positions[ (i+1) * numSeqsPerProcessor ]; + bufferSizes.push_back(myEnd-startPos); + } + lines.push_back(new linePair(startPos, numSeqsPerProcessor)); + } + + return 0; + } + catch(exception& e) { + m->errorOut(e, "FilterSeqsCommand", "setLines"); + exit(1); + } +} /**************************************************************************************/