*/
#include "chimeraslayercommand.h"
-#include "chimeraslayer.h"
#include "deconvolutecommand.h"
+#include "referencedb.h"
//**********************************************************************************************************************
vector<string> ChimeraSlayerCommand::setParameters(){
CommandParameter pdivergence("divergence", "Number", "", "1.007", "", "", "",false,false); parameters.push_back(pdivergence);
CommandParameter pparents("parents", "Number", "", "3", "", "", "",false,false); parameters.push_back(pparents);
CommandParameter pincrement("increment", "Number", "", "5", "", "", "",false,false); parameters.push_back(pincrement);
+ CommandParameter pblastlocation("blastlocation", "String", "", "", "", "", "",false,false); parameters.push_back(pblastlocation);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
-
+ CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
+
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
string helpString = "";
helpString += "The chimera.slayer command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n";
helpString += "This command was modeled after the chimeraSlayer written by the Broad Institute.\n";
- helpString += "The chimera.slayer command parameters are fasta, name, template, processors, trim, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment, numwanted, and realign.\n";
+ helpString += "The chimera.slayer command parameters are fasta, name, template, processors, trim, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment, numwanted, blastlocation and realign.\n";
helpString += "The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required, unless you have a valid current fasta file. \n";
- helpString += "The name parameter allows you to provide a name file, if you are using template=self. \n";
+ helpString += "The name parameter allows you to provide a name file, if you are using reference=self. \n";
helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amazon.fasta \n";
helpString += "The reference parameter allows you to enter a reference file containing known non-chimeric sequences, and is required. You may also set template=self, in this case the abundant sequences will be used as potential parents. \n";
helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n";
helpString += "The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10) \n";
helpString += "The search parameter allows you to specify search method for finding the closest parent. Choices are blast, and kmer, default blast. \n";
helpString += "The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default true. \n";
+ helpString += "The blastlocation parameter allows you to specify the location of your blast executable. By default mothur will look in ./blast/bin relative to mothur's executable. \n";
+ helpString += "If the save parameter is set to true the reference sequences will be saved in memory, to clear them later you can use the clear.memory command. Default=f.";
helpString += "The chimera.slayer command should be in the following format: \n";
helpString += "chimera.slayer(fasta=yourFastaFile, reference=yourTemplate, search=yourSearch) \n";
helpString += "Example: chimera.slayer(fasta=AD.align, reference=core_set_aligned.imputed.fasta, search=kmer) \n";
ChimeraSlayerCommand::ChimeraSlayerCommand(string option) {
try {
abort = false; calledHelp = false;
+ ReferenceDB* rdb = ReferenceDB::getInstance();
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
//erase from file list
fastaFileNames.erase(fastaFileNames.begin()+i);
i--;
+ }else {
+ m->setFastaFile(fastaFileNames[i]);
}
}
}
//erase from file list
nameFileNames.erase(nameFileNames.begin()+i);
i--;
+ }else {
+ m->setNameFile(nameFileNames[i]);
}
}
}
//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 = ""; }
+ string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ convert(temp, processors);
+
+ temp = validParameter.validFile(parameters, "save", false); if (temp == "not found"){ temp = "f"; }
+ save = m->isTrue(temp);
+ rdb->save = save;
+ if (save) { //clear out old references
+ rdb->clearMemory();
+ }
string path;
it = parameters.find("reference");
//user has given a template file
if(it != parameters.end()){
- if (it->second == "self") { templatefile = "self"; }
+ if (it->second == "self") {
+ templatefile = "self";
+ if (save) {
+ m->mothurOut("[WARNING]: You can't save reference=self, ignoring save.");
+ m->mothurOutEndLine();
+ save = false;
+ }
+ }
else {
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
templatefile = validParameter.validFile(parameters, "reference", true);
if (templatefile == "not open") { abort = true; }
- else if (templatefile == "not found") { templatefile = ""; m->mothurOut("reference is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true; }
+ else if (templatefile == "not found") { //check for saved reference sequences
+ if (rdb->referenceSeqs.size() != 0) {
+ templatefile = "saved";
+ }else {
+ m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required.");
+ m->mothurOutEndLine();
+ abort = true;
+ }
+ }else { if (save) { rdb->setSavedReference(templatefile); } }
}
+ }else if (hasName) { templatefile = "self";
+ if (save) {
+ m->mothurOut("[WARNING]: You can't save reference=self, ignoring save.");
+ m->mothurOutEndLine();
+ save = false;
+ }
+ }
+ else {
+ if (rdb->referenceSeqs.size() != 0) {
+ templatefile = "saved";
+ }else {
+ m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required.");
+ m->mothurOutEndLine();
+ templatefile = ""; abort = true;
+ }
}
- string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
- m->setProcessors(temp);
- convert(temp, processors);
+
temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found") { temp = "7"; }
convert(temp, ksize);
temp = validParameter.validFile(parameters, "numwanted", false); if (temp == "not found") { temp = "15"; }
convert(temp, numwanted);
+
+ blastlocation = validParameter.validFile(parameters, "blastlocation", false);
+ if (blastlocation == "not found") { blastlocation = ""; }
+ else {
+ //add / to name if needed
+ string lastChar = blastlocation.substr(blastlocation.length()-1);
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if (lastChar != "/") { blastlocation += "/"; }
+#else
+ if (lastChar != "\\") { blastlocation += "\\"; }
+#endif
+ blastlocation = m->getFullPathName(blastlocation);
+ string formatdbCommand = "";
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ formatdbCommand = blastlocation + "formatdb";
+#else
+ formatdbCommand = blastlocation + "formatdb.exe";
+#endif
+
+ //test to make sure formatdb exists
+ ifstream in;
+ formatdbCommand = m->getFullPathName(formatdbCommand);
+ int ableToOpen = m->openInputFile(formatdbCommand, in, "no error"); in.close();
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requires formatdb.exe to run chimera.slayer."); m->mothurOutEndLine(); abort = true; }
+
+ string blastCommand = "";
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ blastCommand = blastlocation + "megablast";
+#else
+ blastCommand = blastlocation + "megablast.exe";
+#endif
+ //test to make sure formatdb exists
+ ifstream in2;
+ blastCommand = m->getFullPathName(blastCommand);
+ ableToOpen = m->openInputFile(blastCommand, in2, "no error"); in2.close();
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + blastCommand + " file does not exist. mothur requires blastall.exe to run chimera.slayer."); m->mothurOutEndLine(); abort = true; }
+ }
if ((search != "blast") && (search != "kmer")) { m->mothurOut(search + " is not a valid search."); m->mothurOutEndLine(); abort = true; }
+
+ if (hasName && (templatefile != "self")) { m->mothurOut("You have provided a namefile and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
}
}
catch(exception& e) {
int ChimeraSlayerCommand::execute(){
try{
if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
+
for (int s = 0; s < fastaFileNames.size(); s++) {
m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
int start = time(NULL);
- if (templatefile != "self") { //you want to run slayer with a refernce template
- chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);
- }else {
+ if (templatefile == "self") {
if (processors != 1) { m->mothurOut("When using template=self, mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; }
string nameFile = "";
if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one
string inputString = "fasta=" + fastaFileNames[s];
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
-
+
Command* uniqueCommand = new DeconvoluteCommand(inputString);
uniqueCommand->execute();
//sort fastafile by abundance, returns new sorted fastafile name
m->mothurOut("Sorting fastafile according to abundance..."); cout.flush();
- map<string, int> priority = sortFastaFile(fastaFileNames[s], nameFile);
+ priority = sortFastaFile(fastaFileNames[s], nameFile);
m->mothurOut("Done."); m->mothurOutEndLine();
- if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; }
-
- chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, priority, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);
+ if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
}
-
+
if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it
string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimera";
string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.accnos";
string trimFastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.fasta";
- if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; }
+ //create chimera here if you are mac or linux because fork will copy for you. Create in create processes instead if you are windows.
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || USE_MPI
+ if (templatefile != "self") { //you want to run slayer with a reference template
+ chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand());
+ }else {
+ chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, priority, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand());
+ }
+
+ if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
if (chimera->getUnaligned()) {
m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine();
return 0;
}
templateSeqsLength = chimera->getLength();
+ #else
+ if (processors == 1) {
+ if (templatefile != "self") { //you want to run slayer with a reference template
+ chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand());
+ }else {
+ chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, priority, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand());
+ }
+
+ if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
+
+ if (chimera->getUnaligned()) {
+ m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine();
+ delete chimera;
+ return 0;
+ }
+ templateSeqsLength = chimera->getLength();
+ }
+ #endif
#ifdef USE_MPI
int pid, numSeqsPerProcessor;
int tag = 2001;
- vector<unsigned long int> MPIPos;
+ vector<unsigned long long> MPIPos;
MPI_Status status;
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
if (trim) { MPI_File_open(MPI_COMM_WORLD, outFastaFilename, outMode, MPI_INFO_NULL, &outMPIFasta); }
- if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } delete chimera; return 0; }
if (pid == 0) { //you are the root process
m->mothurOutEndLine();
//do your part
driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos);
- if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } remove(outputFileName.c_str()); remove(accnosFileName.c_str()); delete chimera; return 0; }
+ int numNoParents = chimera->getNumNoParents();
+ int temp;
+ for(int i = 1; i < processors; i++) {
+ MPI_Recv(&temp, 1, MPI_INT, 1, tag, MPI_COMM_WORLD, &status);
+ numNoParents += temp;
+ }
+
+
+ if (numSeqs == numNoParents) { m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }
+
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } m->mothurRemove(outputFileName); m->mothurRemove(accnosFileName); delete chimera; return 0; }
}else{ //you are a child process
if (templatefile != "self") { //if template=self we can only use 1 processor
//do your part
driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos);
+
+ int numNoParents = chimera->getNumNoParents();
+ MPI_Send(&numNoParents, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
- if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } delete chimera; return 0; }
}
}
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
- ofstream outHeader;
- string tempHeader = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimeras.tempHeader";
- m->openOutputFile(tempHeader, outHeader);
-
- chimera->printHeader(outHeader);
- outHeader.close();
+ //break up file
+ vector<unsigned long long> positions;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ 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)])); }
+#else
+ if (processors == 1) {
+ lines.push_back(new linePair(0, 1000));
+ }else {
+ positions = m->setFilePosFasta(fastaFileNames[s], numSeqs);
+
+ //figure out how many sequences you have to process
+ int numSeqsPerProcessor = numSeqs / processors;
+ for (int i = 0; i < processors; i++) {
+ int startIndex = i * numSeqsPerProcessor;
+ if(i == (processors - 1)){ numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor; }
+ lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
+ }
+ }
+#endif
- vector<unsigned long int> positions = m->divideFile(fastaFileNames[s], processors);
+ if(processors == 1){
+ numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
- for (int i = 0; i < (positions.size()-1); i++) {
- lines.push_back(new linePair(positions[i], positions[(i+1)]));
- }
-
- //break up file
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- if(processors == 1){
- numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
-
- if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } 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; }
-
- }else{
- processIDS.resize(0);
-
- numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
+ int numNoParents = chimera->getNumNoParents();
+ if (numNoParents == numSeqs) { m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }
- rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
- rename((accnosFileName + toString(processIDS[0]) + ".temp").c_str(), accnosFileName.c_str());
- if (trim) { rename((trimFastaFileName + toString(processIDS[0]) + ".temp").c_str(), trimFastaFileName.c_str()); }
-
- //append output files
- for(int i=1;i<processors;i++){
- m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
- remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
- }
+ if (m->control_pressed) { outputTypes.clear(); if (trim) { m->mothurRemove(trimFastaFileName); } m->mothurRemove(outputFileName); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; }
+
+ }else{
+ processIDS.resize(0);
+
+ numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
+
+ rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
+ rename((accnosFileName + toString(processIDS[0]) + ".temp").c_str(), accnosFileName.c_str());
+ if (trim) { rename((trimFastaFileName + toString(processIDS[0]) + ".temp").c_str(), trimFastaFileName.c_str()); }
- //append output files
- for(int i=1;i<processors;i++){
- m->appendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName);
- remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());
- }
+ //append output files
+ for(int i=1;i<processIDS.size();i++){
+ m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
+ m->mothurRemove((outputFileName + toString(processIDS[i]) + ".temp"));
+
+ m->appendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName);
+ m->mothurRemove((accnosFileName + toString(processIDS[i]) + ".temp"));
if (trim) {
- for(int i=1;i<processors;i++){
- m->appendFiles((trimFastaFileName + toString(processIDS[i]) + ".temp"), trimFastaFileName);
- remove((trimFastaFileName + toString(processIDS[i]) + ".temp").c_str());
- }
+ m->appendFiles((trimFastaFileName + toString(processIDS[i]) + ".temp"), trimFastaFileName);
+ m->mothurRemove((trimFastaFileName + toString(processIDS[i]) + ".temp"));
}
-
- if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } 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
- numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
- if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } 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; }
-
- #endif
-
- m->appendFiles(outputFileName, tempHeader);
-
- remove(outputFileName.c_str());
- rename(tempHeader.c_str(), outputFileName.c_str());
+ if (m->control_pressed) { outputTypes.clear(); if (trim) { m->mothurRemove(trimFastaFileName); } m->mothurRemove(outputFileName); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; }
+ }
+
#endif
- delete chimera;
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || USE_MPI
+ delete chimera;
+ #endif
for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
m->openInputFile(filename, inFASTA);
inFASTA.seekg(filePos->start);
+
+ if (filePos->start == 0) { chimera->printHeader(out); }
bool done = false;
int count = 0;
string candidateAligned = candidateSeq->getAligned();
if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
-
if (candidateSeq->getAligned().length() != templateSeqsLength) {
m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
}else{
data_results rightResults = chimera->getResults();
//if either piece is chimeric then report
- Sequence* trimmed = chimera->print(out, out2, leftResults, rightResults);
- if (trim) { trimmed->printSequence(out3); delete trimmed; }
+ Sequence trimmed = chimera->print(out, out2, leftResults, rightResults);
+ if (trim) { trimmed.printSequence(out3); }
delete left; delete right;
}else { //already chimeric
//print results
- Sequence* trimmed = chimera->print(out, out2);
- if (trim) { trimmed->printSequence(out3); delete trimmed; }
+ Sequence trimmed = chimera->print(out, out2);
+ if (trim) { trimmed.printSequence(out3); }
}
}
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- unsigned long int pos = inFASTA.tellg();
+ unsigned long long pos = inFASTA.tellg();
if ((pos == -1) || (pos >= filePos->end)) { break; }
#else
if (inFASTA.eof()) { break; }
}
//**********************************************************************************************************************
#ifdef USE_MPI
-int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, MPI_File& outFastaMPI, vector<unsigned long int>& MPIPos){
+int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, MPI_File& outFastaMPI, vector<unsigned long long>& MPIPos){
try {
MPI_Status status;
int pid;
data_results rightResults = chimera->getResults();
//if either piece is chimeric then report
- Sequence* trimmed = chimera->print(outMPI, outAccMPI, leftResults, rightResults);
+ Sequence trimmed = chimera->print(outMPI, outAccMPI, leftResults, rightResults);
if (trim) {
- string outputString = ">" + trimmed->getName() + "\n" + trimmed->getAligned() + "\n";
- delete trimmed;
+ string outputString = ">" + trimmed.getName() + "\n" + trimmed.getAligned() + "\n";
//write to accnos file
int length = outputString.length();
}else {
//print results
- Sequence* trimmed = chimera->print(outMPI, outAccMPI);
+ Sequence trimmed = chimera->print(outMPI, outAccMPI);
if (trim) {
- string outputString = ">" + trimmed->getName() + "\n" + trimmed->getAligned() + "\n";
- delete trimmed;
+ string outputString = ">" + trimmed.getName() + "\n" + trimmed.getAligned() + "\n";
//write to accnos file
int length = outputString.length();
int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename, string accnos, string fasta) {
try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
int process = 0;
int num = 0;
+ int numNoParents = 0;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
//loop through and create all the processes you want
while (process != processors) {
int pid = fork();
ofstream out;
string tempFile = outputFileName + toString(getpid()) + ".num.temp";
m->openOutputFile(tempFile, out);
- out << num << endl;
+ out << num << '\t' << chimera->getNumNoParents() << endl;
out.close();
-
exit(0);
}else {
m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
ifstream 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());
+ if (!in.eof()) { int tempNum = 0; int tempNumParents = 0; in >> tempNum >> tempNumParents; num += tempNum; numNoParents += tempNumParents; }
+ in.close(); m->mothurRemove(tempFile);
+ }
+#else
+
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the slayerData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ vector<slayerData*> pDataArray;
+ DWORD dwThreadIdArray[processors];
+ HANDLE hThreadArray[processors];
+
+ //Create processor worker threads.
+ for( int i=0; i<processors; i++ ){
+ string extension = toString(i) + ".temp";
+ slayerData* tempslayer = new slayerData((outputFileName + extension), (fasta + extension), (accnos + extension), filename, templatefile, search, blastlocation, trimera, trim, realign, m, lines[i]->start, lines[i]->end, ksize, match, mismatch, window, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, divR, priority, i);
+ pDataArray.push_back(tempslayer);
+ processIDS.push_back(i);
+
+ //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
+ //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
+ hThreadArray[i] = CreateThread(NULL, 0, MySlayerThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
}
+
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors, hThreadArray, TRUE, INFINITE);
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ num += pDataArray[i]->count;
+ numNoParents += pDataArray[i]->numNoParents;
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+#endif
+ if (num == numNoParents) { m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }
return num;
-#endif
}
catch(exception& e) {
m->errorOut(e, "ChimeraSlayerCommand", "createProcesses");