X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.cpp;h=1b3b3cfd415cd51605fe3c09a8b3b5a9f11b160d;hb=c6e5f84783b39a558119835963dec3c4facb0154;hp=f3b543c7636af24e333dcf301d897fa86beb9746;hpb=94ba64671398f3c9e591df90536833123de0fd34;p=mothur.git diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp index f3b543c..1b3b3cf 100644 --- a/filterseqscommand.cpp +++ b/filterseqscommand.cpp @@ -44,7 +44,7 @@ FilterSeqsCommand::FilterSeqsCommand(string option) { it = parameters.find("fasta"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + path = m->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; } } @@ -52,7 +52,7 @@ FilterSeqsCommand::FilterSeqsCommand(string option) { it = parameters.find("hard"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + path = m->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; } } @@ -62,25 +62,25 @@ FilterSeqsCommand::FilterSeqsCommand(string option) { 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); + m->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]); + string path = m->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"); + int ableToOpen = m->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]); + string tryPath = m->getDefaultPath() + m->getSimpleName(fastafileNames[i]); m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); - ableToOpen = openInputFile(tryPath, in, "noerror"); + ableToOpen = m->openInputFile(tryPath, in, "noerror"); fastafileNames[i] = tryPath; } } @@ -92,7 +92,7 @@ FilterSeqsCommand::FilterSeqsCommand(string option) { fastafileNames.erase(fastafileNames.begin()+i); i--; }else{ - string simpleName = getSimpleName(fastafileNames[i]); + string simpleName = m->getSimpleName(fastafileNames[i]); filterFileName += simpleName.substr(0, simpleName.find_first_of('.')); } in.close(); @@ -106,7 +106,7 @@ FilterSeqsCommand::FilterSeqsCommand(string option) { //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 + outputDir += m->hasPath(fastafileNames[0]); //if user entered a file with a path then preserve it } } //check for optional parameter and set defaults @@ -174,7 +174,7 @@ int FilterSeqsCommand::execute() { if (abort == true) { return 0; } ifstream inFASTA; - openInputFile(fastafileNames[0], inFASTA); + m->openInputFile(fastafileNames[0], inFASTA); Sequence testSeq(inFASTA); alignmentLength = testSeq.getAlignLength(); @@ -199,7 +199,7 @@ int FilterSeqsCommand::execute() { ofstream outFilter; string filterFile = outputDir + filterFileName + ".filter"; - openOutputFile(filterFile, outFilter); + m->openOutputFile(filterFile, outFilter); outFilter << filter << endl; outFilter.close(); outputNames.push_back(filterFile); @@ -254,7 +254,7 @@ int FilterSeqsCommand::filterSequences() { for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); - string filteredFasta = outputDir + getRootName(getSimpleName(fastafileNames[s])) + "filter.fasta"; + string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + "filter.fasta"; #ifdef USE_MPI int pid, start, end, numSeqsPerProcessor, num; int tag = 2001; @@ -283,7 +283,7 @@ int FilterSeqsCommand::filterSequences() { if (pid == 0) { //you are the root process - MPIPos = setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs + MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs numSeqs += num; //send file positions to all processes @@ -338,7 +338,7 @@ int FilterSeqsCommand::filterSequences() { MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case #else - vector positions = divideFile(fastafileNames[s], processors); + vector positions = m->divideFile(fastafileNames[s], processors); for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(new linePair(positions[i], positions[(i+1)])); @@ -355,14 +355,14 @@ int FilterSeqsCommand::filterSequences() { //append fasta files for(int i=1;iappendFiles((fastafileNames[s] + toString(processIDS[i]) + ".temp"), filteredFasta); remove((fastafileNames[s] + toString(processIDS[i]) + ".temp").c_str()); } } if (m->control_pressed) { return 1; } #else - numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]); + int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]); numSeqs += numFastaSeqs; if (m->control_pressed) { return 1; } @@ -400,7 +400,7 @@ int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_Fil istringstream iss (tempBuf,istringstream::in); delete buf4; - Sequence seq(iss); gobble(iss); + Sequence seq(iss); m->gobble(iss); if (seq.getName() != "") { string align = seq.getAligned(); @@ -456,10 +456,10 @@ int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_Fil int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* filePos) { try { ofstream out; - openOutputFile(outputFilename, out); + m->openOutputFile(outputFilename, out); ifstream in; - openInputFile(inputFilename, in); + m->openInputFile(inputFilename, in); in.seekg(filePos->start); @@ -470,7 +470,7 @@ int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string i if (m->control_pressed) { in.close(); out.close(); return 0; } - Sequence seq(in); gobble(in); + Sequence seq(in); m->gobble(in); if (seq.getName() != "") { string align = seq.getAligned(); string filterSeq = ""; @@ -527,8 +527,8 @@ int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) { //pass numSeqs to parent ofstream out; - string tempFile = toString(getpid()) + ".temp"; - openOutputFile(tempFile, out); + string tempFile = filename + toString(getpid()) + ".num.temp"; + m->openOutputFile(tempFile, out); out << num << endl; out.close(); @@ -544,8 +544,8 @@ int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) { for (int i = 0; i < processIDS.size(); i++) { ifstream in; - string tempFile = toString(processIDS[i]) + ".temp"; - openInputFile(tempFile, in); + string tempFile = filename + toString(processIDS[i]) + ".num.temp"; + m->openInputFile(tempFile, in); if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; } in.close(); remove(tempFile.c_str()); } @@ -570,7 +570,7 @@ string FilterSeqsCommand::createFilter() { F.setLength(alignmentLength); - if(trump != '*' || isTrue(vertical) || soft != 0){ + if(trump != '*' || m->isTrue(vertical) || soft != 0){ F.initialize(); } @@ -578,7 +578,7 @@ string FilterSeqsCommand::createFilter() { else { F.setFilter(string(alignmentLength, '1')); } numSeqs = 0; - if(trump != '*' || isTrue(vertical) || soft != 0){ + if(trump != '*' || m->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(); @@ -604,7 +604,7 @@ string FilterSeqsCommand::createFilter() { 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 + MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs numSeqs += num; //send file positions to all processes @@ -646,7 +646,7 @@ string FilterSeqsCommand::createFilter() { MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case #else - vector positions = divideFile(fastafileNames[s], processors); + vector positions = m->divideFile(fastafileNames[s], processors); for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(new linePair(positions[i], positions[(i+1)])); @@ -662,7 +662,7 @@ string FilterSeqsCommand::createFilter() { if (m->control_pressed) { return filterString; } #else - numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]); + int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]); numSeqs += numFastaSeqs; if (m->control_pressed) { return filterString; } #endif @@ -679,7 +679,7 @@ string FilterSeqsCommand::createFilter() { MPI_Comm_rank(MPI_COMM_WORLD, &pid); - if(trump != '*' || isTrue(vertical) || soft != 0){ + if(trump != '*' || m->isTrue(vertical) || soft != 0){ if (pid == 0) { //only one process should output the filter @@ -727,8 +727,9 @@ string FilterSeqsCommand::createFilter() { if (pid == 0) { //only one process should output the filter #endif + F.setNumSeqs(numSeqs); - if(isTrue(vertical) == 1) { F.doVertical(); } + if(m->isTrue(vertical) == 1) { F.doVertical(); } if(soft != 0) { F.doSoft(); } filterString = F.getFilter(); @@ -764,7 +765,7 @@ int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* try { ifstream in; - openInputFile(filename, in); + m->openInputFile(filename, in); in.seekg(filePos->start); @@ -775,12 +776,12 @@ int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* if (m->control_pressed) { in.close(); return 1; } - Sequence seq(in); gobble(in); + Sequence seq(in); m->gobble(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); } + if(m->isTrue(vertical) || soft != 0) { F.getFreqs(seq); } cout.flush(); count++; } @@ -831,7 +832,7 @@ int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& 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); } + if(m->isTrue(vertical) || soft != 0){ F.getFreqs(seq); } cout.flush(); //report progress @@ -866,12 +867,19 @@ int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) 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){ + //reset child's filter counts to 0; + F.a.clear(); F.a.resize(alignmentLength, 0); + F.t.clear(); F.t.resize(alignmentLength, 0); + F.g.clear(); F.g.resize(alignmentLength, 0); + F.c.clear(); F.c.resize(alignmentLength, 0); + F.gap.clear(); F.gap.resize(alignmentLength, 0); + num = driverCreateFilter(F, filename, lines[process]); //write out filter counts to file filename += toString(getpid()) + "filterValues.temp"; ofstream out; - openOutputFile(filename, out); + m->openOutputFile(filename, out); out << num << endl; out << F.getFilter() << endl; @@ -881,7 +889,7 @@ int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) for (int k = 0; k < alignmentLength; k++) { out << F.c[k] << '\t'; } out << endl; for (int k = 0; k < alignmentLength; k++) { out << F.gap[k] << '\t'; } out << endl; - cout << F.getFilter() << endl; + //cout << F.getFilter() << endl; out.close(); exit(0); @@ -898,21 +906,21 @@ int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) for (int i = 0; i < processIDS.size(); i++) { string tempFilename = filename + toString(processIDS[i]) + "filterValues.temp"; ifstream in; - openInputFile(tempFilename, in); + m->openInputFile(tempFilename, in); int temp, tempNum; string tempFilterString; - in >> tempNum; gobble(in); num += tempNum; + in >> tempNum; m->gobble(in); num += tempNum; in >> tempFilterString; F.mergeFilter(tempFilterString); - for (int k = 0; k < alignmentLength; k++) { in >> temp; F.a[k] += temp; } gobble(in); - for (int k = 0; k < alignmentLength; k++) { in >> temp; F.t[k] += temp; } gobble(in); - for (int k = 0; k < alignmentLength; k++) { in >> temp; F.g[k] += temp; } gobble(in); - for (int k = 0; k < alignmentLength; k++) { in >> temp; F.c[k] += temp; } gobble(in); - for (int k = 0; k < alignmentLength; k++) { in >> temp; F.gap[k] += temp; } gobble(in); + for (int k = 0; k < alignmentLength; k++) { in >> temp; F.a[k] += temp; } m->gobble(in); + for (int k = 0; k < alignmentLength; k++) { in >> temp; F.t[k] += temp; } m->gobble(in); + for (int k = 0; k < alignmentLength; k++) { in >> temp; F.g[k] += temp; } m->gobble(in); + for (int k = 0; k < alignmentLength; k++) { in >> temp; F.c[k] += temp; } m->gobble(in); + for (int k = 0; k < alignmentLength; k++) { in >> temp; F.gap[k] += temp; } m->gobble(in); in.close(); remove(tempFilename.c_str());