X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.cpp;h=7ab00a7822f7a7fc7ddd1ef0de00d2d24b8c51de;hb=9013e13ecfb2fda3c2664a76f76cc99b8c7fa74c;hp=326be01ff722fda90a61e0dd887f8d3e57107be4;hpb=17a6a53298a907c005fa93fb82af9e533adcda09;p=mothur.git diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp index 326be01..7ab00a7 100644 --- a/filterseqscommand.cpp +++ b/filterseqscommand.cpp @@ -28,7 +28,7 @@ FilterSeqsCommand::FilterSeqsCommand(string option) { OptionParser parser(option); map parameters = parser.getParameters(); - ValidParameters validParameter; + ValidParameters validParameter("filter.seqs"); map::iterator it; //check to make sure all parameters are valid for command @@ -72,11 +72,22 @@ FilterSeqsCommand::FilterSeqsCommand(string option) { if (path == "") { fastafileNames[i] = inputDir + fastafileNames[i]; } } - int ableToOpen; ifstream in; - ableToOpen = openInputFile(fastafileNames[i], 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(fastafileNames[i] + " will be disregarded."); m->mothurOutEndLine(); + m->mothurOut("Unable to open " + fastafileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); //erase from file list fastafileNames.erase(fastafileNames.begin()+i); i--; @@ -102,6 +113,9 @@ FilterSeqsCommand::FilterSeqsCommand(string option) { // ...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]; @@ -111,13 +125,13 @@ FilterSeqsCommand::FilterSeqsCommand(string option) { 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; } - - 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; - } } @@ -131,30 +145,20 @@ FilterSeqsCommand::FilterSeqsCommand(string option) { void FilterSeqsCommand::help(){ try { - #ifdef USE_MPI - int pid; - MPI_Comm_rank(MPI_COMM_WORLD, &pid); - - if (pid == 0) { - #endif - + 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 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, soft=yourSoft, hard=yourHard, vertical=yourVertical) \n"); - m->mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=..., soft=..., hard=..., vertical=T).\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"); - #ifdef USE_MPI - } - #endif - } catch(exception& e) { m->errorOut(e, "FilterSeqsCommand", "help"); @@ -168,7 +172,6 @@ int FilterSeqsCommand::execute() { try { if (abort == true) { return 0; } - vector outputNames; ifstream inFASTA; openInputFile(fastafileNames[0], inFASTA); @@ -178,9 +181,21 @@ int FilterSeqsCommand::execute() { 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"; @@ -189,42 +204,18 @@ int FilterSeqsCommand::execute() { outFilter.close(); outputNames.push_back(filterFile); + #ifdef USE_MPI + } + #endif ////////////run filter///////////////// - numSeqs = 0; - for (int i = 0; i < fastafileNames.size(); i++) { - ifstream in; - openInputFile(fastafileNames[i], in); - string filteredFasta = outputDir + getRootName(getSimpleName(fastafileNames[i])) + "filter.fasta"; - ofstream outFASTA; - openOutputFile(filteredFasta, outFASTA); - outputNames.push_back(filteredFasta); - - - while(!in.eof()){ - if (m->control_pressed) { in.close(); outFASTA.close(); for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } - - Sequence seq(in); - if (seq.getName() != "") { - string align = seq.getAligned(); - string filterSeq = ""; - - for(int j=0;j' << seq.getName() << endl << filterSeq << endl; - numSeqs++; - } - gobble(in); - } - outFASTA.close(); - in.close(); - } + 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; } - #ifdef USE_MPI - int pid; - MPI_Comm_rank(MPI_COMM_WORLD, &pid); - - if (pid == 0) { - #endif - + m->mothurOutEndLine(); m->mothurOut("Length of filtered alignment: " + toString(filteredLength)); m->mothurOutEndLine(); m->mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); m->mothurOutEndLine(); @@ -251,23 +236,316 @@ int FilterSeqsCommand::execute() { for(int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } m->mothurOutEndLine(); - #ifdef USE_MPI - } + 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 + cout << pid << "is in create filter " << endl; + 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); + + 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 + 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;icontrol_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& 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 = 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;jmothurOutJustToLog(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 +/**************************************************************************************/ +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", "execute"); + 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 = ""; - + string filterString = ""; Filters F; if (soft != 0) { F.setSoft(soft); } @@ -275,7 +553,7 @@ string FilterSeqsCommand::createFilter() { F.setLength(alignmentLength); - if(soft != 0 || isTrue(vertical)){ + if(trump != '*' || isTrue(vertical) || soft != 0){ F.initialize(); } @@ -283,117 +561,80 @@ string FilterSeqsCommand::createFilter() { 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, rc, ierr; - char* buf; - int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5; + int pid, numSeqsPerProcessor, num; + int tag = 2001; + vector MPIPos; MPI_Status status; - MPI_File in; - rc = MPI_Comm_size(MPI_COMM_WORLD, &processors); - rc = MPI_Comm_rank(MPI_COMM_WORLD, &pid); - + MPI_File inMPI; + MPI_Comm_size(MPI_COMM_WORLD, &processors); + MPI_Comm_rank(MPI_COMM_WORLD, &pid); - char* tempFileName = &(fastafileNames[s][0]); - MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &in); //comm, filename, mode, info, filepointer - + //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 - setLines(fastafileNames[s]); + MPIPos = setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs + numSeqs += num; - for (int j = 0; j < lines.size(); j++) { //each process - if (j != 0) { //don't send to yourself - MPI_Send(&lines[j]->start, 1, MPI_INT, j, 2001, MPI_COMM_WORLD); //start position in file - MPI_Send(&lines[j]->numSeqs, 1, MPI_INT, j, 2001, MPI_COMM_WORLD); //how many sequences we are sending - MPI_Send(&bufferSizes[j], 1, MPI_INT, j, 2001, MPI_COMM_WORLD); //how bytes for the read - } + //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); } - cout << "done sending" << endl; - cout << "parent = " << pid << " lines = " << lines[pid]->start << '\t' << lines[pid]->numSeqs << " size = " << lines.size() << endl; - - buf = new char(bufferSizes[0]); - cout << pid << '\t' << bufferSizes[0] << " line 1 start pos = " << lines[1]->start << " buffer size 0 " << bufferSizes[0] << " buffer size 1 " << bufferSizes[1] << endl; - MPI_File_read_at(in, 0, buf, bufferSizes[0], MPI_CHAR, &status); + + //figure out how many sequences you have to do + numSeqsPerProcessor = num / processors; + int startIndex = pid * numSeqsPerProcessor; + if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; } - cout << pid << " done reading " << endl; - string tempBuf = buf; - cout << pid << '\t' << (tempBuf.substr(0, 10)) << endl; + //do your part - MPICreateFilter(F, tempBuf); - - vector temp; temp.resize(numSeqs); - - //get the frequencies from the child processes - for(int i = 0; i < ((processors-1)*5); i++) { - cout << "i = " << i << endl; - int ierr = MPI_Recv(&temp, numSeqs, 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 - - int sender = status.MPI_SOURCE; - - 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]; } - } - - m->mothurOut("receive tag = " + toString(receiveTag) + " " + toString(sender) + " is complete."); m->mothurOutEndLine(); - } - + MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos); + if (m->control_pressed) { MPI_File_close(&inMPI); return 0; } + }else { //i am the child process - int startPos, numLines, bufferSize; - cout << "child = " << pid << endl; - ierr = MPI_Recv(&startPos, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); - ierr = MPI_Recv(&numLines, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); - ierr = MPI_Recv(&bufferSize, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); - cout << "child = " << pid << " done recv messages startpos = " << startPos << " numLines = " << numLines << " buffersize = " << bufferSize << endl; - - - //send freqs - char* buf2 = new char(bufferSize); - MPI_File_read_at( in, startPos, buf2, bufferSize, MPI_CHAR, &status); - cout << pid << " done reading " << endl; - - string tempBuf = buf2; - cout << pid << '\t' << (tempBuf.substr(0, 10)) << endl; - MPICreateFilter(F, tempBuf); - - //send my fequency counts - F.a.push_back(Atag); - int ierr = MPI_Send( &F.a[0], alignmentLength, MPI_INT, 0, 2001, MPI_COMM_WORLD); - F.t.push_back(Ttag); - ierr = MPI_Send( &F.t[0], alignmentLength, MPI_INT, 0, 2001, MPI_COMM_WORLD); - F.c.push_back(Ctag); - ierr = MPI_Send( &F.c[0], alignmentLength, MPI_INT, 0, 2001, MPI_COMM_WORLD); - F.g.push_back(Gtag); - ierr = MPI_Send( &F.g[0], alignmentLength, MPI_INT, 0, 2001, MPI_COMM_WORLD); - F.gap.push_back(Gaptag); - ierr = MPI_Send( &F.gap[0], alignmentLength, MPI_INT, 0, 2001, MPI_COMM_WORLD); - - cout << "child " << pid << " done sending counts" << endl; + 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_Barrier(MPI_COMM_WORLD); + 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); - int numFastaSeqs=count(istreambuf_iterator(inFASTA),istreambuf_iterator(), '>'); + getNumSeqs(inFASTA, numFastaSeqs); inFASTA.close(); numSeqs += numFastaSeqs; @@ -402,44 +643,113 @@ string FilterSeqsCommand::createFilter() { 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); - int numFastaSeqs=count(istreambuf_iterator(inFASTA),istreambuf_iterator(), '>'); + getNumSeqs(inFASTA, numFastaSeqs); inFASTA.close(); numSeqs += numFastaSeqs; lines.push_back(new linePair(0, numFastaSeqs)); - driverCreateFilter(F, lines[0], fastafileNames[s]); + driverCreateFilter(F, fastafileNames[s], lines[0]); + if (m->control_pressed) { return filterString; } #endif #endif } } -#ifdef USE_MPI -//merge all frequency data and create filter string - //int pid; - //MPI_Comm_rank(MPI_COMM_WORLD, &pid); +#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 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++) { - //if (pid == 0) { //only one process should output to screen + 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 - - cout << "made it here" << endl; F.setNumSeqs(numSeqs); if(isTrue(vertical) == 1) { F.doVertical(); } if(soft != 0) { F.doSoft(); } -//cout << "Filter String = " << F.getFilter() << endl; + 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) { @@ -456,12 +766,14 @@ int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* in.seekg(line->start); - for(int i=0;inumSeqs;i++){ + 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(); @@ -472,7 +784,7 @@ int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* } //report progress - if((line->numSeqs) % 100 != 0){ m->mothurOut(toString(line->numSeqs)); m->mothurOutEndLine(); } + if((line->num) % 100 != 0){ m->mothurOut(toString(line->num)); m->mothurOutEndLine(); } in.close(); @@ -483,29 +795,44 @@ int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* exit(1); } } +#ifdef USE_MPI /**************************************************************************************/ -int FilterSeqsCommand::MPICreateFilter(Filters& F, string temp) { +int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector& MPIPos) { try { - vector seqStrings; - parseBuffer(temp, seqStrings); + MPI_Status status; + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are - for(int i=0;icontrol_pressed) { return 1; } + for(int i=0;icontrol_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); - Sequence seq("", seqStrings[0]); + 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){ m->mothurOut(toString(i+1)); m->mothurOutEndLine(); } + if((i+1) % 100 == 0){ cout << (i+1) << endl; m->mothurOutJustToLog(toString(i+1) + "\n"); } } //report progress - if((seqStrings.size()) % 100 != 0){ m->mothurOut(toString(seqStrings.size())); m->mothurOutEndLine(); } + if((num) % 100 != 0){ cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n"); } return 0; } @@ -514,7 +841,7 @@ int FilterSeqsCommand::MPICreateFilter(Filters& F, string temp) { exit(1); } } - +#endif /**************************************************************************************************/ int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) { @@ -522,7 +849,7 @@ int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) int process = 0; int exitCommand = 1; - vector processIDS; + processIDS.clear(); //loop through and create all the processes you want while (process != processors) { @@ -555,44 +882,50 @@ int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) int FilterSeqsCommand::setLines(string filename) { try { - vector positions; - map buf; + + vector positions; bufferSizes.clear(); - int pid; - MPI_Comm_rank(MPI_COMM_WORLD, &pid); - ifstream inFASTA; openInputFile(filename, inFASTA); string input; - int numbuf = 0; while(!inFASTA.eof()){ input = getline(inFASTA); if (input.length() != 0) { - numbuf += input.length(); - if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); buf[(pos - input.length() - 1)] = numbuf; } + if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); } } } - inFASTA.close(); int numFastaSeqs = positions.size(); - + + FILE * pFile; + unsigned long int 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 ]; + unsigned long int startPos = positions[ i * numSeqsPerProcessor ]; if(i == processors - 1){ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; - bufferSizes.push_back(numbuf-buf[startPos]); + bufferSizes.push_back(size - startPos); }else{ - int myEnd = positions[ (i+1) * numSeqsPerProcessor ]; - bufferSizes.push_back(buf[myEnd]-buf[startPos]); + unsigned long int myEnd = positions[ (i+1) * numSeqsPerProcessor ]; + bufferSizes.push_back(myEnd-startPos); } lines.push_back(new linePair(startPos, numSeqsPerProcessor)); } @@ -604,31 +937,4 @@ int FilterSeqsCommand::setLines(string filename) { exit(1); } } -/**************************************************************************************************/ -int FilterSeqsCommand::parseBuffer(string file, vector& seqs) { - try { - - istringstream iss (file,istringstream::in); - string name, seqstring; - - while (iss) { - - if (m->control_pressed) { return 0; } - cout << "here" << endl; - Sequence seq(iss); - cout << "here1" << endl; - gobble(iss); - cout << seq.getName() << endl; - if (seq.getName() != "") { - seqs.push_back(seq.getAligned()); - } - } - - return 0; - } - catch(exception& e) { - m->errorOut(e, "FilterSeqsCommand", "parseBuffer"); - exit(1); - } -} /**************************************************************************************/