X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeracheckcommand.cpp;h=abf6b90c161671a231c370caa55c20f317319b60;hb=3a13eff5c26d6fc156a299c9fa7f5497bded94a0;hp=0ec5f4bcdba426acd22dd17f8e8e3b55f263c31a;hpb=284fd95c611ccc3b1a7875c4dacfca06d1f50ed6;p=mothur.git diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp index 0ec5f4b..abf6b90 100644 --- a/chimeracheckcommand.cpp +++ b/chimeracheckcommand.cpp @@ -9,8 +9,53 @@ #include "chimeracheckcommand.h" +//********************************************************************************************************************** +vector ChimeraCheckCommand::getValidParameters(){ + try { + string AlignArray[] = {"fasta","processors","increment","template","ksize","svg", "name","outputdir","inputdir" }; + vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ChimeraCheckCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector ChimeraCheckCommand::getRequiredParameters(){ + try { + string AlignArray[] = {"template","fasta"}; + vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ChimeraCheckCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector ChimeraCheckCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ChimeraCheckCommand", "getRequiredFiles"); + exit(1); + } +} +//********************************************************************************************************************** +ChimeraCheckCommand::ChimeraCheckCommand(){ + try { + vector tempOutNames; + outputTypes["chimera"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "ChimeraCheckCommand", "ChimeraCheckCommand"); + exit(1); + } +} //*************************************************************************************************************** - ChimeraCheckCommand::ChimeraCheckCommand(string option) { try { abort = false; @@ -34,6 +79,9 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + vector tempOutNames; + outputTypes["chimera"] = tempOutNames; + //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 = ""; } @@ -41,7 +89,7 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option) { it = parameters.find("template"); //user has given a template file if(it != parameters.end()){ - string path = hasPath(it->second); + string path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["template"] = inputDir + it->second; } } @@ -51,12 +99,12 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option) { fastafile = validParameter.validFile(parameters, "fasta", false); if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.check command."); m->mothurOutEndLine(); abort = true; } else { - splitAtDash(fastafile, fastaFileNames); + m->splitAtDash(fastafile, 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]; } } @@ -64,17 +112,32 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option) { int ableToOpen; ifstream in; - ableToOpen = openInputFile(fastaFileNames[i], in, "noerror"); + 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"); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); fastaFileNames[i] = tryPath; } } + + //if you can't open it, try default location + if (ableToOpen == 1) { + if (m->getOutputDir() != "") { //default path is set + string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]); + m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + fastaFileNames[i] = tryPath; + } + } + in.close(); if (ableToOpen == 1) { @@ -99,12 +162,12 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option) { namefile = validParameter.validFile(parameters, "name", false); if (namefile == "not found") { namefile = ""; } else { - splitAtDash(namefile, nameFileNames); + m->splitAtDash(namefile, nameFileNames); //go through files and make sure they are good, if not, then disregard them for (int i = 0; i < nameFileNames.size(); i++) { if (inputDir != "") { - string path = hasPath(nameFileNames[i]); + string path = m->hasPath(nameFileNames[i]); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { nameFileNames[i] = inputDir + nameFileNames[i]; } } @@ -112,17 +175,32 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option) { int ableToOpen; ifstream in; - ableToOpen = openInputFile(nameFileNames[i], in, "noerror"); + ableToOpen = m->openInputFile(nameFileNames[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(nameFileNames[i]); + string tryPath = m->getDefaultPath() + m->getSimpleName(nameFileNames[i]); m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); - ableToOpen = openInputFile(tryPath, in, "noerror"); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); nameFileNames[i] = tryPath; } } + + //if you can't open it, try default location + if (ableToOpen == 1) { + if (m->getOutputDir() != "") { //default path is set + string tryPath = m->getOutputDir() + m->getSimpleName(nameFileNames[i]); + m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + nameFileNames[i] = tryPath; + } + } + in.close(); if (ableToOpen == 1) { @@ -150,7 +228,7 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option) { convert(temp, ksize); temp = validParameter.validFile(parameters, "svg", false); if (temp == "not found") { temp = "F"; } - svg = isTrue(temp); + svg = m->isTrue(temp); if (nameFileNames.size() != 0) { svg = true; } temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "10"; } @@ -217,8 +295,9 @@ int ChimeraCheckCommand::execute(){ if (m->control_pressed) { delete chimera; return 0; } - string outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[i])) + "chimeracheck.chimeras"; - outputNames.push_back(outputFileName); + if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]); }//if user entered a file with a path then preserve it + string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "chimeracheck.chimeras"; + outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName); #ifdef USE_MPI @@ -245,10 +324,10 @@ int ChimeraCheckCommand::execute(){ 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); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } outputTypes.clear(); delete chimera; return 0; } if (pid == 0) { //you are the root process - MPIPos = setFilePosFasta(fastaFileNames[i], numSeqs); //fills MPIPos, returns numSeqs + MPIPos = m->setFilePosFasta(fastaFileNames[i], numSeqs); //fills MPIPos, returns numSeqs //send file positions to all processes for(int j = 1; j < processors; j++) { @@ -265,12 +344,12 @@ int ChimeraCheckCommand::execute(){ //align your part driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos); - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } outputTypes.clear(); delete chimera; return 0; } //wait on chidren for(int j = 1; j < processors; j++) { - char buf[4]; - MPI_Recv(buf, 4, MPI_CHAR, j, tag, MPI_COMM_WORLD, &status); + char buf[5]; + MPI_Recv(buf, 5, MPI_CHAR, j, tag, MPI_COMM_WORLD, &status); } }else{ //you are a child process MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); @@ -285,12 +364,12 @@ int ChimeraCheckCommand::execute(){ //align your part driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos); - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } outputTypes.clear(); delete chimera; return 0; } //tell parent you are done. - char buf[4]; + char buf[5]; strcpy(buf, "done"); - MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD); + MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD); } //close files @@ -299,7 +378,7 @@ int ChimeraCheckCommand::execute(){ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case #else - vector positions = divideFile(fastaFileNames[i], processors); + vector positions = m->divideFile(fastaFileNames[i], processors); for (int s = 0; s < (positions.size()-1); s++) { lines.push_back(new linePair(positions[s], positions[(s+1)])); @@ -310,7 +389,7 @@ int ChimeraCheckCommand::execute(){ if(processors == 1){ numSeqs = driver(lines[0], outputFileName, fastaFileNames[i]); - if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear(); delete chimera; return 0; } + if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int j = 0; j < lines.size(); j++) { delete lines[j]; } outputTypes.clear(); lines.clear(); delete chimera; return 0; } }else{ processIDS.resize(0); @@ -321,12 +400,12 @@ int ChimeraCheckCommand::execute(){ //append output files for(int j=1;jappendFiles((outputFileName + toString(processIDS[j]) + ".temp"), outputFileName); remove((outputFileName + toString(processIDS[j]) + ".temp").c_str()); } if (m->control_pressed) { - for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } + for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } outputTypes.clear(); for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear(); delete chimera; return 0; @@ -336,7 +415,7 @@ int ChimeraCheckCommand::execute(){ #else numSeqs = driver(lines[0], outputFileName, fastaFileNames[i]); - if (m->control_pressed) { for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear(); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } + if (m->control_pressed) { for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear(); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } outputTypes.clear(); delete chimera; return 0; } #endif #endif delete chimera; @@ -365,12 +444,12 @@ int ChimeraCheckCommand::execute(){ int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string filename){ try { ofstream out; - openOutputFile(outputFName, out); + m->openOutputFile(outputFName, out); ofstream out2; ifstream inFASTA; - openInputFile(filename, inFASTA); + m->openInputFile(filename, inFASTA); inFASTA.seekg(filePos->start); @@ -381,7 +460,7 @@ int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string fi if (m->control_pressed) { return 1; } - Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA); + Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA); if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file //find chimeras @@ -394,8 +473,12 @@ int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string fi } delete candidateSeq; - unsigned long int pos = inFASTA.tellg(); - if ((pos == -1) || (pos >= filePos->end)) { break; } + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + unsigned long int pos = inFASTA.tellg(); + if ((pos == -1) || (pos >= filePos->end)) { break; } + #else + if (inFASTA.eof()) { break; } + #endif //report progress if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); } @@ -437,7 +520,7 @@ int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File istringstream iss (tempBuf,istringstream::in); delete buf4; - Sequence* candidateSeq = new Sequence(iss); gobble(iss); + Sequence* candidateSeq = new Sequence(iss); m->gobble(iss); if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file //find chimeras @@ -483,13 +566,17 @@ int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) //pass numSeqs to parent ofstream out; - string tempFile = toString(getpid()) + ".temp"; - openOutputFile(tempFile, out); + string tempFile = outputFileName + toString(getpid()) + ".num.temp"; + m->openOutputFile(tempFile, out); out << num << endl; out.close(); exit(0); - }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); } + }else { + m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); + for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); } + exit(0); + } } //force parent to wait until all the processes are done @@ -500,8 +587,8 @@ int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) for (int i = 0; i < processIDS.size(); i++) { ifstream in; - string tempFile = toString(processIDS[i]) + ".temp"; - openInputFile(tempFile, in); + string tempFile = outputFileName + 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()); }