OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
- ValidParameters validParameter;
+ ValidParameters validParameter("align.seqs");
map<string, string>::iterator it;
//check to make sure all parameters are valid for command
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["template"] = inputDir + it->second; }
}
candidateFileName = validParameter.validFile(parameters, "candidate", false);
if (candidateFileName == "not found") { m->mothurOut("candidate is a required parameter for the align.seqs command."); m->mothurOutEndLine(); abort = true; }
else {
- splitAtDash(candidateFileName, candidateFileNames);
+ m->splitAtDash(candidateFileName, candidateFileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < candidateFileNames.size(); i++) {
if (inputDir != "") {
- string path = hasPath(candidateFileNames[i]);
+ string path = m->hasPath(candidateFileNames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { candidateFileNames[i] = inputDir + candidateFileNames[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(candidateFileNames[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);
+ ableToOpen = m->openInputFile(candidateFileNames[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() + m->getSimpleName(candidateFileNames[i]);
+ m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ableToOpen = m->openInputFile(tryPath, in, "noerror");
+ candidateFileNames[i] = tryPath;
}
-
- #endif
+ }
+ in.close();
if (ableToOpen == 1) {
- m->mothurOut(candidateFileNames[i] + " will be disregarded."); m->mothurOutEndLine();
+ m->mothurOut("Unable to open " + candidateFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
//erase from file list
candidateFileNames.erase(candidateFileNames.begin()+i);
i--;
convert(temp, processors);
temp = validParameter.validFile(parameters, "flip", false); if (temp == "not found"){ temp = "f"; }
- flip = isTrue(temp);
+ flip = m->isTrue(temp);
temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found"){ temp = "0.50"; }
convert(temp, threshold);
m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
- if (outputDir == "") { outputDir += hasPath(candidateFileNames[s]); }
- string alignFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align";
- string reportFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align.report";
- string accnosFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "flip.accnos";
+ 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;
#ifdef USE_MPI
int pid, end, numSeqsPerProcessor;
int tag = 2001;
- vector<long> MPIPos;
+ vector<unsigned long int> 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);
int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
int inMode=MPI_MODE_RDONLY;
- //char* outAlignFilename = new char[alignFileName.length()];
- //memcpy(outAlignFilename, alignFileName.c_str(), alignFileName.length());
-
char outAlignFilename[1024];
strcpy(outAlignFilename, alignFileName.c_str());
-
- //char* outReportFilename = new char[reportFileName.length()];
- //memcpy(outReportFilename, reportFileName.c_str(), reportFileName.length());
char outReportFilename[1024];
strcpy(outReportFilename, reportFileName.c_str());
-
- //char* outAccnosFilename = new char[accnosFileName.length()];
- //memcpy(outAccnosFilename, accnosFileName.c_str(), accnosFileName.length());
char outAccnosFilename[1024];
strcpy(outAccnosFilename, accnosFileName.c_str());
-
- //char* inFileName = new char[candidateFileNames[s].length()];
- //memcpy(inFileName, candidateFileNames[s].c_str(), candidateFileNames[s].length());
char inFileName[1024];
strcpy(inFileName, candidateFileNames[s].c_str());
if (pid == 0) { //you are the root process
- MPIPos = setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
+ MPIPos = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
//send file positions to all processes
for(int i = 1; i < processors; i++) {
int startIndex = pid * numSeqsPerProcessor;
if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
-
//align your part
driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
}
#else
-
+
+ vector<unsigned long int> 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)]));
+ }
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if(processors == 1){
- ifstream inFASTA;
- openInputFile(candidateFileNames[s], inFASTA);
- numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
- inFASTA.close();
+ numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
- lines.push_back(new linePair(0, numFastaSeqs));
-
- driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
-
- if (m->control_pressed) {
- remove(accnosFileName.c_str());
- remove(alignFileName.c_str());
- remove(reportFileName.c_str());
- return 0;
- }
+ if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); return 0; }
//delete accnos file if its blank else report to user
- if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; }
+ if (m->isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; }
else {
m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
if (!flip) {
}else{ m->mothurOut(" If the reverse compliment proved to be better it was reported."); }
m->mothurOutEndLine();
}
- }
- else{
- vector<int> positions;
+ }else{
processIDS.resize(0);
- ifstream inFASTA;
- openInputFile(candidateFileNames[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();
-
- numFastaSeqs = positions.size();
-
- int numSeqsPerProcessor = numFastaSeqs / processors;
-
- for (int i = 0; i < processors; i++) {
- long int startPos = positions[ i * numSeqsPerProcessor ];
- if(i == processors - 1){
- numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
- }
- lines.push_back(new linePair(startPos, numSeqsPerProcessor));
- }
-
- createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
+ numFastaSeqs = createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str());
rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.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"))) {
+ if (!(m->isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");
}else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str()); }
}
m->mothurOutEndLine();
}else{ hasAccnos = false; }
- if (m->control_pressed) {
- remove(accnosFileName.c_str());
- remove(alignFileName.c_str());
- remove(reportFileName.c_str());
- return 0;
- }
+ if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); return 0; }
}
#else
- ifstream inFASTA;
- openInputFile(candidateFileNames[s], inFASTA);
- numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
- inFASTA.close();
-
- lines.push_back(new linePair(0, numFastaSeqs));
+ numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
- driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
-
- if (m->control_pressed) {
- remove(accnosFileName.c_str());
- remove(alignFileName.c_str());
- remove(reportFileName.c_str());
- return 0;
- }
+ if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); return 0; }
//delete accnos file if its blank else report to user
- if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; }
+ if (m->isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; }
else {
m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
if (!flip) {
//**********************************************************************************************************************
-int AlignCommand::driver(linePair* line, string alignFName, string reportFName, string accnosFName, string filename){
+int AlignCommand::driver(linePair* filePos, string alignFName, string reportFName, string accnosFName, string filename){
try {
ofstream alignmentFile;
- openOutputFile(alignFName, alignmentFile);
+ m->openOutputFile(alignFName, alignmentFile);
ofstream accnosFile;
- openOutputFile(accnosFName, accnosFile);
+ m->openOutputFile(accnosFName, accnosFile);
NastReport report(reportFName);
ifstream inFASTA;
- openInputFile(filename, inFASTA);
+ m->openInputFile(filename, inFASTA);
+
+ inFASTA.seekg(filePos->start);
- inFASTA.seekg(line->start);
+ bool done = false;
+ int count = 0;
- for(int i=0;i<line->numSeqs;i++){
+ while (!done) {
if (m->control_pressed) { return 0; }
- Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA);
+ Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
int origNumBases = candidateSeq->getNumBases();
string originalUnaligned = candidateSeq->getUnaligned();
//if there is a possibility that this sequence should be reversed
if (candidateSeq->getNumBases() < numBasesNeeded) {
- string wasBetter = "";
+ string wasBetter = "";
//if the user wants you to try the reverse
if (flip) {
//get reverse compliment
delete nast;
nast = nast2;
needToDeleteCopy = true;
+ wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
}else{
- wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
+ wasBetter = "\treverse complement did NOT produce a better alignment so it was not used, please check sequence.";
delete nast2;
delete copy;
}
report.print();
delete nast;
if (needToDeleteCopy) { delete copy; }
+
+ count++;
}
delete candidateSeq;
+ unsigned long int pos = inFASTA.tellg();
+ if ((pos == -1) || (pos >= filePos->end)) { break; }
+
//report progress
- if((i+1) % 100 == 0){ m->mothurOut(toString(i+1)); m->mothurOutEndLine(); }
+ if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+
}
//report progress
- if((line->numSeqs) % 100 != 0){ m->mothurOut(toString(line->numSeqs)); m->mothurOutEndLine(); }
+ if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
alignmentFile.close();
inFASTA.close();
accnosFile.close();
- return 1;
+ return count;
}
catch(exception& e) {
m->errorOut(e, "AlignCommand", "driver");
}
//**********************************************************************************************************************
#ifdef USE_MPI
-int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<long>& MPIPos){
+int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<unsigned long int>& MPIPos){
try {
string outputString = "";
MPI_Status statusReport;
int length = MPIPos[start+i+1] - MPIPos[start+i];
char* buf4 = new char[length];
- memcpy(buf4, outputString.c_str(), length);
+ //memcpy(buf4, outputString.c_str(), length);
MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
delete buf4;
if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
- istringstream iss (tempBuf,istringstream::in);
+ istringstream iss (tempBuf,istringstream::in);
+
Sequence* candidateSeq = new Sequence(iss);
+
int origNumBases = candidateSeq->getNumBases();
string originalUnaligned = candidateSeq->getUnaligned();
int numBasesNeeded = origNumBases * threshold;
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
int process = 0;
- int exitCommand = 1;
+ int num = 0;
// processIDS.resize(0);
//loop through and create all the processes you want
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
- exitCommand = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
+ num = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
+
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = alignFileName + 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); }
}
wait(&temp);
}
- return exitCommand;
+ for (int i = 0; i < processIDS.size(); i++) {
+ ifstream in;
+ string tempFile = alignFileName + 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());
+ }
+
+ return num;
#endif
}
catch(exception& e) {
exit(1);
}
}
-
/**************************************************************************************************/
void AlignCommand::appendAlignFiles(string temp, string filename) {
ofstream output;
ifstream input;
- openOutputFileAppend(filename, output);
- openInputFile(temp, input);
+ m->openOutputFileAppend(filename, output);
+ m->openInputFile(temp, input);
while(char c = input.get()){
if(input.eof()) { break; }
ofstream output;
ifstream input;
- openOutputFileAppend(filename, output);
- openInputFile(temp, input);
+ m->openOutputFileAppend(filename, output);
+ m->openInputFile(temp, input);
while (!input.eof()) { char c = input.get(); if (c == 10 || c == 13){ break; } } // get header line
projects / mothur.git / blobdiff