int ChimeraCheckCommand::execute(){
try{
if (abort == true) { if (calledHelp) { return 0; } return 2; }
for (int i = 0; i < fastaFileNames.size(); i++) {
m->mothurOut("Checking sequences from " + fastaFileNames[i] + " ..." ); m->mothurOutEndLine();
int start = time(NULL);
string thisNameFile = "";
if (nameFileNames.size() != 0) { thisNameFile = nameFileNames[i]; }
chimera = new ChimeraCheckRDP(fastaFileNames[i], templatefile, thisNameFile, svg, increment, ksize, outputDir);
if (m->control_pressed) { delete chimera; return 0; }
if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]); }//if user entered a file with a path then preserve it
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i]));
string outputFileName = getOutputFileName("chimera", variables);
outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
#ifdef USE_MPI
int pid, numSeqsPerProcessor;
int tag = 2001;
vector<unsigned long long> MPIPos;
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;
int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
int inMode=MPI_MODE_RDONLY;
char outFilename[1024];
strcpy(outFilename, outputFileName.c_str());
char inFileName[1024];
strcpy(inFileName, fastaFileNames[i].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); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); delete chimera; return 0; }
if (pid == 0) { //you are the root process
MPIPos = m->setFilePosFasta(fastaFileNames[i], numSeqs); //fills MPIPos, returns numSeqs
//send file positions to all processes
for(int j = 1; j < processors; j++) {
MPI_Send(&numSeqs, 1, MPI_INT, j, tag, MPI_COMM_WORLD);
MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, j, 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; }
//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++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); delete chimera; return 0; }
//wait on chidren
for(int j = 1; j < processors; j++) {
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);
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, MPIPos);
if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); delete chimera; return 0; }
//tell parent you are done.
char buf[5];
strcpy(buf, "done");
MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
}
//close files
MPI_File_close(&inMPI);
MPI_File_close(&outMPI);
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
//break up file
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
vector<unsigned long long> 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)]));
}
if(processors == 1){
numSeqs = driver(lines[0], outputFileName, fastaFileNames[i]);
if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } for (int j = 0; j < lines.size(); j++) { delete lines[j]; } outputTypes.clear(); lines.clear(); delete chimera; return 0; }
}else{
processIDS.resize(0);
numSeqs = createProcesses(outputFileName, fastaFileNames[i]);
rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
//append output files
for(int j=1;j<processors;j++){
m->appendFiles((outputFileName + toString(processIDS[j]) + ".temp"), outputFileName);
m->mothurRemove((outputFileName + toString(processIDS[j]) + ".temp"));
}
if (m->control_pressed) {
for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear();
for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear();
delete chimera;
return 0;
}
}
#else
lines.push_back(new linePair(0, 1000));
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++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); delete chimera; return 0; }
#endif
#endif
delete chimera;
for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear();
m->mothurOutEndLine(); m->mothurOut("This method does not determine if a sequence is chimeric, but allows you to make that determination based on the IS values."); m->mothurOutEndLine();
m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
}
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "ChimeraCheckCommand", "execute");
exit(1);
}
}
int ChimeraPintailCommand::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);
//set user options
if (maskfile == "default") { m->mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); m->mothurOutEndLine(); }
//check for quantile to save the time
string baseName = templatefile;
if (templatefile == "saved") { baseName = rdb->getSavedReference(); }
string tempQuan = "";
if ((!filter) && (maskfile == "")) {
tempQuan = inputDir + m->getRootName(m->getSimpleName(baseName)) + "pintail.quan";
}else if ((!filter) && (maskfile != "")) {
tempQuan = inputDir + m->getRootName(m->getSimpleName(baseName)) + "pintail.masked.quan";
}else if ((filter) && (maskfile != "")) {
tempQuan = inputDir + m->getRootName(m->getSimpleName(baseName)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "masked.quan";
}else if ((filter) && (maskfile == "")) {
tempQuan = inputDir + m->getRootName(m->getSimpleName(baseName)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "quan";
}
ifstream FileTest(tempQuan.c_str());
if(FileTest){
bool GoodFile = m->checkReleaseVersion(FileTest, m->getVersion());
if (GoodFile) {
m->mothurOut("I found " + tempQuan + " in your input file directory. I will use it to save time."); m->mothurOutEndLine(); quanfile = tempQuan; FileTest.close();
}
}else {
string tryPath = m->getDefaultPath();
string tempQuan = "";
if ((!filter) && (maskfile == "")) {
tempQuan = tryPath + m->getRootName(m->getSimpleName(baseName)) + "pintail.quan";
}else if ((!filter) && (maskfile != "")) {
tempQuan = tryPath + m->getRootName(m->getSimpleName(baseName)) + "pintail.masked.quan";
}else if ((filter) && (maskfile != "")) {
tempQuan = tryPath + m->getRootName(m->getSimpleName(baseName)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "masked.quan";
}else if ((filter) && (maskfile == "")) {
tempQuan = tryPath + m->getRootName(m->getSimpleName(baseName)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "quan";
}
ifstream FileTest2(tempQuan.c_str());
if(FileTest2){
bool GoodFile = m->checkReleaseVersion(FileTest2, m->getVersion());
if (GoodFile) {
m->mothurOut("I found " + tempQuan + " in your input file directory. I will use it to save time."); m->mothurOutEndLine(); quanfile = tempQuan; FileTest2.close();
}
}
}
chimera = new Pintail(fastaFileNames[s], templatefile, filter, processors, maskfile, consfile, quanfile, window, increment, outputDir);
if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it
string outputFileName, accnosFileName;
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
if (maskfile != "") { variables["[tag]"] = m->getSimpleName(m->getRootName(maskfile)); }
outputFileName = getOutputFileName("chimera", variables);
accnosFileName = getOutputFileName("accnos", variables);
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();
#ifdef USE_MPI
int pid, numSeqsPerProcessor;
int tag = 2001;
vector<unsigned long long> MPIPos;
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 outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
int inMode=MPI_MODE_RDONLY;
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) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); 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
MPIPos = m->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; }
//do your part
driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); m->mothurRemove(outputFileName); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } delete chimera; return 0; }
}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; }
//do your part
driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } delete chimera; return 0; }
}
//close files
MPI_File_close(&inMPI);
MPI_File_close(&outMPI);
MPI_File_close(&outMPIAccnos);
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
//break up file
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
vector<unsigned long long> 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)]));
}
if(processors == 1){
numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
if (m->control_pressed) { outputTypes.clear(); 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);
rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
rename((accnosFileName + toString(processIDS[0]) + ".temp").c_str(), accnosFileName.c_str());
//append output files
for(int i=1;i<processors;i++){
m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
m->mothurRemove((outputFileName + toString(processIDS[i]) + ".temp"));
}
//append output files
for(int i=1;i<processors;i++){
m->appendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName);
m->mothurRemove((accnosFileName + toString(processIDS[i]) + ".temp"));
}
if (m->control_pressed) {
m->mothurRemove(outputFileName);
m->mothurRemove(accnosFileName);
for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear();
for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
delete chimera;
return 0;
}
}
#else
lines.push_back(new linePair(0, 1000));
numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
if (m->control_pressed) { outputTypes.clear(); 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
#endif
delete chimera;
for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
m->mothurOutEndLine();
m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
}
//set accnos file as new current accnosfile
string current = "";
itTypes = outputTypes.find("accnos");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
}
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "ChimeraPintailCommand", "execute");
exit(1);
}
}
int DistanceCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
int startTime = time(NULL);
//save number of new sequence
numNewFasta = alignDB.getNumSeqs();
//sanity check the oldfasta and column file as well as add oldfasta sequences to alignDB
if ((oldfastafile != "") && (column != "")) { if (!(sanityCheck())) { return 0; } }
if (m->control_pressed) { return 0; }
int numSeqs = alignDB.getNumSeqs();
cutoff += 0.005;
if (!alignDB.sameLength()) { m->mothurOut("[ERROR]: your sequences are not the same length, aborting."); m->mothurOutEndLine(); return 0; }
string outputFile;
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
if (output == "lt") { //does the user want lower triangle phylip formatted file
variables["[outputtag]"] = "phylip";
outputFile = getOutputFileName("phylip", variables);
m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
//output numSeqs to phylip formatted dist file
}else if (output == "column") { //user wants column format
outputFile = getOutputFileName("column", variables);
outputTypes["column"].push_back(outputFile);
//so we don't accidentally overwrite
if (outputFile == column) {
string tempcolumn = column + ".old";
rename(column.c_str(), tempcolumn.c_str());
}
m->mothurRemove(outputFile);
}else { //assume square
variables["[outputtag]"] = "square";
outputFile = getOutputFileName("phylip", variables);
m->mothurRemove(outputFile);
outputTypes["phylip"].push_back(outputFile);
}
#ifdef USE_MPI
int pid, start, end;
int tag = 2001;
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
//each process gets where it should start and stop in the file
if (output != "square") {
start = int (sqrt(float(pid)/float(processors)) * numSeqs);
end = int (sqrt(float(pid+1)/float(processors)) * numSeqs);
}else{
start = int ((float(pid)/float(processors)) * numSeqs);
end = int ((float(pid+1)/float(processors)) * numSeqs);
}
if (output == "column") {
MPI_File outMPI;
int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
//char* filename = new char[outputFile.length()];
//memcpy(filename, outputFile.c_str(), outputFile.length());
char filename[1024];
strcpy(filename, outputFile.c_str());
MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
//delete filename;
if (pid == 0) { //you are the root process
//do your part
string outputMyPart;
driverMPI(start, end, outMPI, cutoff);
if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); return 0; }
//wait on chidren
for(int i = 1; i < processors; i++) {
if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); return 0; }
char buf[5];
MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
}
}else { //you are a child process
//do your part
driverMPI(start, end, outMPI, cutoff);
if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); return 0; }
char buf[5];
strcpy(buf, "done");
//tell parent you are done.
MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
}
MPI_File_close(&outMPI);
}else { //lower triangle format
if (pid == 0) { //you are the root process
//do your part
string outputMyPart;
unsigned long long mySize;
if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
else { driverMPI(start, end, outputFile, mySize, output); }
if (m->control_pressed) { outputTypes.clear(); return 0; }
int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
MPI_File outMPI;
MPI_File inMPI;
//char* filename = new char[outputFile.length()];
//memcpy(filename, outputFile.c_str(), outputFile.length());
char filename[1024];
strcpy(filename, outputFile.c_str());
MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
//delete filename;
//wait on chidren
for(int b = 1; b < processors; b++) {
unsigned long long fileSize;
if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); return 0; }
MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
string outTemp = outputFile + toString(b) + ".temp";
char* buf = new char[outTemp.length()];
memcpy(buf, outTemp.c_str(), outTemp.length());
MPI_File_open(MPI_COMM_SELF, buf, MPI_MODE_DELETE_ON_CLOSE|MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
delete buf;
int count = 0;
while (count < fileSize) {
char buf2[1];
MPI_File_read(inMPI, buf2, 1, MPI_CHAR, &status);
MPI_File_write(outMPI, buf2, 1, MPI_CHAR, &status);
count += 1;
}
MPI_File_close(&inMPI); //deleted on close
}
MPI_File_close(&outMPI);
}else { //you are a child process
//do your part
unsigned long long size;
if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); }
else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); }
if (m->control_pressed) { return 0; }
//tell parent you are done.
MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
}
}
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
//#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//if you don't need to fork anything
if(processors == 1){
if (output != "square") { driver(0, numSeqs, outputFile, cutoff); }
else { driver(0, numSeqs, outputFile, "square"); }
}else{ //you have multiple processors
createProcesses(outputFile, numSeqs);
}
//#else
//ifstream inFASTA;
//if (output != "square") { driver(0, numSeqs, outputFile, cutoff); }
//else { driver(0, numSeqs, outputFile, "square"); }
//#endif
#endif
if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFile); return 0; }
#ifdef USE_MPI
MPI_Comm_rank(MPI_COMM_WORLD, &pid);
if (pid == 0) { //only one process should output to screen
#endif
//if (output == "square") { convertMatrix(outputFile); }
ifstream fileHandle;
fileHandle.open(outputFile.c_str());
if(fileHandle) {
m->gobble(fileHandle);
if (fileHandle.eof()) { m->mothurOut(outputFile + " is blank. This can result if there are no distances below your cutoff."); m->mothurOutEndLine(); }
}
//append the old column file to the new one
if ((oldfastafile != "") && (column != "")) {
//we had to rename the column file so we didnt overwrite above, but we want to keep old name
if (outputFile == column) {
string tempcolumn = column + ".old";
m->appendFiles(tempcolumn, outputFile);
m->mothurRemove(tempcolumn);
}else{
m->appendFiles(outputFile, column);
m->mothurRemove(outputFile);
outputFile = column;
}
if (outputDir != "") {
string newOutputName = outputDir + m->getSimpleName(outputFile);
rename(outputFile.c_str(), newOutputName.c_str());
m->mothurRemove(outputFile);
outputFile = newOutputName;
}
}
#ifdef USE_MPI
}
#endif
if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFile); return 0; }
//set phylip file as new current phylipfile
string current = "";
itTypes = outputTypes.find("phylip");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
}
//set column file as new current columnfile
itTypes = outputTypes.find("column");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setColumnFile(current); }
}
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(outputFile); m->mothurOutEndLine();
m->mothurOutEndLine();
m->mothurOut("It took " + toString(time(NULL) - startTime) + " seconds to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
if (m->isTrue(compress)) {
m->mothurOut("Compressing..."); m->mothurOutEndLine();
m->mothurOut("(Replacing " + outputFile + " with " + outputFile + ".gz)"); m->mothurOutEndLine();
system(("gzip -v " + outputFile).c_str());
outputNames.push_back(outputFile + ".gz");
}else { outputNames.push_back(outputFile); }
return 0;
}
catch(exception& e) {
m->errorOut(e, "DistanceCommand", "execute");
exit(1);
}
}
int AlignCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, rand());
for (int s = 0; s < candidateFileNames.size(); s++) {
if (m->control_pressed) { outputTypes.clear(); return 0; }
m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
if (outputDir == "") { outputDir += m->hasPath(candidateFileNames[s]); }
string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align";
string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align.report";
string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "flip.accnos";
bool hasAccnos = true;
int numFastaSeqs = 0;
for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
int start = time(NULL);
#ifdef USE_MPI
int pid, numSeqsPerProcessor;
int tag = 2001;
vector<unsigned long 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 outMPIAlign;
MPI_File outMPIReport;
MPI_File outMPIAccnos;
int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
int inMode=MPI_MODE_RDONLY;
char outAlignFilename[1024];
strcpy(outAlignFilename, alignFileName.c_str());
char outReportFilename[1024];
strcpy(outReportFilename, reportFileName.c_str());
char outAccnosFilename[1024];
strcpy(outAccnosFilename, accnosFileName.c_str());
char inFileName[1024];
strcpy(inFileName, candidateFileNames[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, outAlignFilename, outMode, MPI_INFO_NULL, &outMPIAlign);
MPI_File_open(MPI_COMM_WORLD, outReportFilename, outMode, MPI_INFO_NULL, &outMPIReport);
MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
if (pid == 0) { //you are the root process
MPIPos = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
//send file positions to all processes
for(int i = 1; i < processors; i++) {
MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
}
//figure out how many sequences you have to align
numSeqsPerProcessor = numFastaSeqs / processors;
int startIndex = pid * numSeqsPerProcessor;
if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
//align your part
driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); outputTypes.clear(); 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; }
}
}else{ //you are a child process
MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
MPIPos.resize(numFastaSeqs+1);
MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
//figure out how many sequences you have to align
numSeqsPerProcessor = numFastaSeqs / processors;
int startIndex = pid * numSeqsPerProcessor;
if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
//align your part
driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
}
//close files
MPI_File_close(&inMPI);
MPI_File_close(&outMPIAlign);
MPI_File_close(&outMPIReport);
MPI_File_close(&outMPIAccnos);
//delete accnos file if blank
if (pid == 0) {
//delete accnos file if its blank else report to user
if (MPIWroteAccnos) {
m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
if (!flip) {
m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
}else{ m->mothurOut(" If the reverse compliment proved to be better it was reported."); }
m->mothurOutEndLine();
}else {
//MPI_Info info;
//MPI_File_delete(outAccnosFilename, info);
hasAccnos = false;
m->mothurRemove(accnosFileName);
}
}
#else
vector<unsigned long long> positions;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
positions = m->divideFile(candidateFileNames[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(candidateFileNames[s], numFastaSeqs);
//figure out how many sequences you have to process
int numSeqsPerProcessor = numFastaSeqs / processors;
for (int i = 0; i < processors; i++) {
int startIndex = i * numSeqsPerProcessor;
if(i == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; }
lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
}
}
#endif
if(processors == 1){
numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
}else{
numFastaSeqs = createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
}
if (m->control_pressed) { m->mothurRemove(accnosFileName); m->mothurRemove(alignFileName); m->mothurRemove(reportFileName); outputTypes.clear(); return 0; }
//delete accnos file if its blank else report to user
if (m->isBlank(accnosFileName)) { m->mothurRemove(accnosFileName); hasAccnos = false; }
else {
m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
if (!flip) {
m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
}else{ m->mothurOut(" If the reverse compliment proved to be better it was reported."); }
m->mothurOutEndLine();
}
#endif
#ifdef USE_MPI
MPI_Comm_rank(MPI_COMM_WORLD, &pid);
if (pid == 0) { //only one process should output to screen
#endif
outputNames.push_back(alignFileName); outputTypes["fasta"].push_back(alignFileName);
outputNames.push_back(reportFileName); outputTypes["alignreport"].push_back(reportFileName);
if (hasAccnos) { outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName); }
#ifdef USE_MPI
}
#endif
m->mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
m->mothurOutEndLine();
m->mothurOutEndLine();
}
//set align file as new current fastafile
string currentFasta = "";
itTypes = outputTypes.find("fasta");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
}
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "AlignCommand", "execute");
exit(1);
}
}
