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("template");
//user has given a template file
if(it != parameters.end()){
}
}
-
//check for required parameters
- fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not open") { abort = true; }
- else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.ccode command."); m->mothurOutEndLine(); abort = true; }
+ fastafile = validParameter.validFile(parameters, "fasta", false);
+ if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.ccode command."); m->mothurOutEndLine(); abort = true; }
+ else {
+ 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]);
+ //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;
+
+ #ifdef USE_MPI
+ int pid;
+ 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
+
+ if (pid == 0) {
+ #endif
+
+ ableToOpen = openInputFile(fastaFileNames[i], in);
+ in.close();
+
+ #ifdef USE_MPI
+ for (int j = 1; j < processors; j++) {
+ MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD);
+ }
+ }else{
+ MPI_Status status;
+ MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+ }
+
+ #endif
+
+ if (ableToOpen == 1) {
+ m->mothurOut(fastaFileNames[i] + " will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ fastaFileNames.erase(fastaFileNames.begin()+i);
+ i--;
+ }
+ }
+
+ //make sure there is at least one valid file left
+ if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
+ }
//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"){
m->mothurOut("This command was created using the algorythms described in the 'Evaluating putative chimeric sequences from PCR-amplified products' paper by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.\n");
m->mothurOut("The chimera.ccode command parameters are fasta, template, filter, mask, processors, window and numwanted.\n");
m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \n");
+ m->mothurOut("You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. \n");
m->mothurOut("The filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter. \n");
m->mothurOut("The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n");
m->mothurOut("The numwanted parameter allows you to specify how many sequences you would each query sequence compared with.\n");
m->mothurOut("The chimera.ccode command should be in the following format: \n");
m->mothurOut("chimera.ccode(fasta=yourFastaFile, template=yourTemplate) \n");
- m->mothurOut("Example: chimera.seqs(fasta=AD.align, template=core_set_aligned.imputed.fasta) \n");
+ m->mothurOut("Example: chimera.ccode(fasta=AD.align, template=core_set_aligned.imputed.fasta) \n");
m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
}
catch(exception& e) {
if (abort == true) { return 0; }
- int start = time(NULL);
-
- //set user options
- if (maskfile == "default") { m->mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); m->mothurOutEndLine(); }
-
- chimera = new Ccode(fastafile, templatefile, filter, maskfile, window, numwanted, outputDir);
-
- //is your template aligned?
- if (chimera->getUnaligned()) { m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine(); delete chimera; return 0; }
- templateSeqsLength = chimera->getLength();
-
- string outputFileName, accnosFileName;
- if (maskfile != "") {
- outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + maskfile + ".ccode.chimeras";
- accnosFileName = outputDir + getRootName(getSimpleName(fastafile)) + maskfile + ".ccode.accnos";
- }else {
- outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "ccode.chimeras";
- accnosFileName = outputDir + getRootName(getSimpleName(fastafile)) + "ccode.accnos";
- }
-
- string mapInfo = outputDir + getRootName(getSimpleName(fastafile)) + "mapinfo";
- bool hasAccnos = true;
-
- if (m->control_pressed) { delete chimera; return 0; }
+ for (int s = 0; s < fastaFileNames.size(); s++) {
+
+ m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
- #ifdef USE_MPI
-
- int pid, end, numSeqsPerProcessor;
- int tag = 2001;
- vector<long> MPIPos;
- MPIWroteAccnos = false;
-
- MPI_Status status;
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
- MPI_Comm_size(MPI_COMM_WORLD, &processors);
-
- MPI_File inMPI;
- MPI_File outMPI;
- MPI_File outMPIAccnos;
+ int start = time(NULL);
- int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
- int inMode=MPI_MODE_RDONLY;
+ //set user options
+ if (maskfile == "default") { m->mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); m->mothurOutEndLine(); }
- //char* outFilename = new char[outputFileName.length()];
- //memcpy(outFilename, outputFileName.c_str(), outputFileName.length());
-
- char outFilename[1024];
- strcpy(outFilename, outputFileName.c_str());
+ chimera = new Ccode(fastaFileNames[s], templatefile, filter, maskfile, window, numwanted, outputDir);
- //char* outAccnosFilename = new char[accnosFileName.length()];
- //memcpy(outAccnosFilename, accnosFileName.c_str(), accnosFileName.length());
+ //is your template aligned?
+ if (chimera->getUnaligned()) { m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine(); delete chimera; return 0; }
+ templateSeqsLength = chimera->getLength();
- char outAccnosFilename[1024];
- strcpy(outAccnosFilename, accnosFileName.c_str());
+ string outputFileName, accnosFileName;
+ if (maskfile != "") {
+ outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + maskfile + ".ccode.chimeras";
+ accnosFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + maskfile + ".ccode.accnos";
+ }else {
+ outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "ccode.chimeras";
+ accnosFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "ccode.accnos";
+ }
- //char* inFileName = new char[fastafile.length()];
- //memcpy(inFileName, fastafile.c_str(), fastafile.length());
+ string mapInfo = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "mapinfo";
+ bool hasAccnos = true;
- char inFileName[1024];
- strcpy(inFileName, fastafile.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);
- MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
+ if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; }
- //delete inFileName;
- //delete outFilename;
- //delete outAccnosFilename;
-
- if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); delete chimera; return 0; }
+ #ifdef USE_MPI
- if (pid == 0) { //you are the root process
- string outTemp = "For full window mapping info refer to " + mapInfo + "\n\n";
+ int pid, end, numSeqsPerProcessor;
+ int tag = 2001;
+ vector<long> MPIPos;
+ MPIWroteAccnos = false;
- //print header
- int length = outTemp.length();
- char* buf2 = new char[length];
- memcpy(buf2, outTemp.c_str(), length);
+ MPI_Status status;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+ MPI_Comm_size(MPI_COMM_WORLD, &processors);
- MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
- delete buf2;
-
- MPIPos = setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
+ MPI_File inMPI;
+ MPI_File outMPI;
+ MPI_File outMPIAccnos;
- //send file positions to all processes
- for(int i = 1; i < processors; i++) {
- MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
- MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
- }
+ int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
+ int inMode=MPI_MODE_RDONLY;
- //figure out how many sequences you have to align
- numSeqsPerProcessor = numSeqs / processors;
- int startIndex = pid * numSeqsPerProcessor;
- if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
+ char outFilename[1024];
+ strcpy(outFilename, outputFileName.c_str());
+ char outAccnosFilename[1024];
+ strcpy(outAccnosFilename, accnosFileName.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);
+ MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; }
- //align your part
- driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
+ if (pid == 0) { //you are the root process
+ string outTemp = "For full window mapping info refer to " + mapInfo + "\n\n";
+
+ //print header
+ int length = outTemp.length();
+ char* buf2 = new char[length];
+ memcpy(buf2, outTemp.c_str(), length);
+
+ MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
+ delete buf2;
+
+ MPIPos = setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs
+
+ //send file positions to all processes
+ for(int i = 1; i < processors; i++) {
+ MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+ MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+ }
+
+ //figure out how many sequences you have to align
+ numSeqsPerProcessor = numSeqs / processors;
+ int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
+
- if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); remove(outputFileName.c_str()); remove(accnosFileName.c_str()); delete chimera; return 0; }
+ //align your part
+ driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; }
- for (int i = 1; i < processors; i++) {
- bool tempResult;
- MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
- if (tempResult != 0) { MPIWroteAccnos = true; }
+ for (int i = 1; i < processors; i++) {
+ bool tempResult;
+ MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
+ if (tempResult != 0) { MPIWroteAccnos = true; }
+ }
+ }else{ //you are a child process
+ MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+ MPIPos.resize(numSeqs+1);
+ MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
+
+ //figure out how many sequences you have to align
+ numSeqsPerProcessor = numSeqs / processors;
+ int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
+
+
+ //align your part
+ driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; }
+
+ MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
}
- }else{ //you are a child process
- MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
- MPIPos.resize(numSeqs+1);
- MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
-
- //figure out how many sequences you have to align
- numSeqsPerProcessor = numSeqs / processors;
- int startIndex = pid * numSeqsPerProcessor;
- if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
+ //close files
+ MPI_File_close(&inMPI);
+ MPI_File_close(&outMPI);
+ MPI_File_close(&outMPIAccnos);
- //align your part
- driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
- if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); delete chimera; return 0; }
-
- MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
- }
-
- //close files
- MPI_File_close(&inMPI);
- MPI_File_close(&outMPI);
- MPI_File_close(&outMPIAccnos);
+ //delete accnos file if blank
+ if (pid == 0) {
+ if (!MPIWroteAccnos) {
+ hasAccnos = false;
+ remove(accnosFileName.c_str());
+ }
+ }
+
+ #else
+ ofstream outHeader;
+ string tempHeader = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + maskfile + "ccode.chimeras.tempHeader";
+ openOutputFile(tempHeader, outHeader);
- MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+ outHeader << "For full window mapping info refer to " << mapInfo << endl << endl;
+
+ outHeader.close();
- //delete accnos file if blank
- if (pid == 0) {
- if (!MPIWroteAccnos) {
- //MPI_Info info;
- //MPI_File_delete(outAccnosFilename, info);
- hasAccnos = false;
- remove(accnosFileName.c_str());
+ //break up file
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if(processors == 1){
+ ifstream inFASTA;
+ openInputFile(fastaFileNames[s], inFASTA);
+ getNumSeqs(inFASTA, numSeqs);
+ inFASTA.close();
+
+ lines.push_back(new linePair(0, numSeqs));
+
+ driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
+
+ if (m->control_pressed) {
+ remove(outputFileName.c_str());
+ remove(tempHeader.c_str());
+ remove(accnosFileName.c_str());
+ for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); }
+ for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
+ delete chimera;
+ return 0;
+ }
+
+ //delete accnos file if its blank
+ if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; }
+
+ }else{
+ vector<int> positions;
+ processIDS.resize(0);
+
+ ifstream inFASTA;
+ openInputFile(fastaFileNames[s], 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();
+
+ numSeqs = positions.size();
+
+ int numSeqsPerProcessor = numSeqs / processors;
+
+ for (int i = 0; i < processors; i++) {
+ long int startPos = positions[ i * numSeqsPerProcessor ];
+ if(i == processors - 1){
+ numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;
+ }
+ lines.push_back(new linePair(startPos, numSeqsPerProcessor));
+ }
+
+
+ createProcesses(outputFileName, fastaFileNames[s], accnosFileName);
+
+ rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
+
+ //append output files
+ for(int i=1;i<processors;i++){
+ appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
+ remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
+ }
+
+ vector<string> nonBlankAccnosFiles;
+ //delete blank accnos files generated with multiple processes
+ for(int i=0;i<processors;i++){
+ if (!(isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
+ nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");
+ }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str()); }
+ }
+
+ //append accnos files
+ if (nonBlankAccnosFiles.size() != 0) {
+ rename(nonBlankAccnosFiles[0].c_str(), accnosFileName.c_str());
+
+ for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
+ appendFiles(nonBlankAccnosFiles[h], accnosFileName);
+ remove(nonBlankAccnosFiles[h].c_str());
+ }
+ }else{ hasAccnos = false; }
+
+ if (m->control_pressed) {
+ remove(outputFileName.c_str());
+ remove(accnosFileName.c_str());
+ for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); }
+ for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
+ delete chimera;
+ return 0;
+ }
+
}
- }
-
- #else
- ofstream outHeader;
- string tempHeader = outputDir + getRootName(getSimpleName(fastafile)) + maskfile + "ccode.chimeras.tempHeader";
- openOutputFile(tempHeader, outHeader);
-
- outHeader << "For full window mapping info refer to " << mapInfo << endl << endl;
- outHeader.close();
-
- //break up file
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- if(processors == 1){
+ #else
ifstream inFASTA;
- openInputFile(fastafile, inFASTA);
+ openInputFile(fastaFileNames[s], inFASTA);
getNumSeqs(inFASTA, numSeqs);
inFASTA.close();
-
lines.push_back(new linePair(0, numSeqs));
- driver(lines[0], outputFileName, fastafile, accnosFileName);
+ driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
if (m->control_pressed) {
- remove(outputFileName.c_str());
- remove(tempHeader.c_str());
- remove(accnosFileName.c_str());
- for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
- delete chimera;
- return 0;
+ remove(outputFileName.c_str());
+ remove(tempHeader.c_str());
+ remove(accnosFileName.c_str());
+ for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); }
+ for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
+ delete chimera;
+ return 0;
}
//delete accnos file if its blank
if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; }
-
- }else{
- vector<int> positions;
- processIDS.resize(0);
-
- ifstream inFASTA;
- openInputFile(fastafile, 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();
-
- numSeqs = positions.size();
-
- int numSeqsPerProcessor = numSeqs / processors;
-
- for (int i = 0; i < processors; i++) {
- long int startPos = positions[ i * numSeqsPerProcessor ];
- if(i == processors - 1){
- numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;
- }
- lines.push_back(new linePair(startPos, numSeqsPerProcessor));
- }
-
-
- createProcesses(outputFileName, fastafile, accnosFileName);
-
- rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
-
- //append output files
- for(int i=1;i<processors;i++){
- appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
- remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
- }
-
- vector<string> nonBlankAccnosFiles;
- //delete blank accnos files generated with multiple processes
- for(int i=0;i<processors;i++){
- if (!(isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
- nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");
- }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str()); }
- }
-
- //append accnos files
- if (nonBlankAccnosFiles.size() != 0) {
- rename(nonBlankAccnosFiles[0].c_str(), accnosFileName.c_str());
-
- for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
- appendFiles(nonBlankAccnosFiles[h], accnosFileName);
- remove(nonBlankAccnosFiles[h].c_str());
- }
- }else{ hasAccnos = false; }
-
- if (m->control_pressed) {
- remove(outputFileName.c_str());
- remove(accnosFileName.c_str());
- for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
- delete chimera;
- return 0;
- }
-
- }
-
- #else
- ifstream inFASTA;
- openInputFile(fastafile, inFASTA);
- getNumSeqs(inFASTA, numSeqs);
- inFASTA.close();
- lines.push_back(new linePair(0, numSeqs));
+ #endif
+
+ appendFiles(outputFileName, tempHeader);
+
+ remove(outputFileName.c_str());
+ rename(tempHeader.c_str(), outputFileName.c_str());
+ #endif
+
+ delete chimera;
- driver(lines[0], outputFileName, fastafile, accnosFileName);
+ outputNames.push_back(outputFileName);
+ outputNames.push_back(mapInfo);
+ if (hasAccnos) { outputNames.push_back(accnosFileName); }
- if (m->control_pressed) {
- remove(outputFileName.c_str());
- remove(tempHeader.c_str());
- remove(accnosFileName.c_str());
- for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
- delete chimera;
- return 0;
- }
+ for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
- //delete accnos file if its blank
- if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; }
- #endif
-
- //m->mothurOut("Output File Names: ");
- //if ((filter) && (method == "bellerophon")) { m->mothurOut(
- //if (outputDir == "") { fastafile = getRootName(fastafile) + "filter.fasta"; }
- // else { fastafile = outputDir + getRootName(getSimpleName(fastafile)) + "filter.fasta"; }
-
- appendFiles(outputFileName, tempHeader);
-
- remove(outputFileName.c_str());
- rename(tempHeader.c_str(), outputFileName.c_str());
- #endif
-
- delete chimera;
-
+ m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
+ }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- m->mothurOut(outputFileName); m->mothurOutEndLine();
- if (hasAccnos) { m->mothurOut(accnosFileName); m->mothurOutEndLine(); }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
-
- for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
-
- m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
return 0;
projects / mothur.git / blobdiff