OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
- ValidParameters validParameter;
+ ValidParameters validParameter("summary.seqs");
map<string,string>::iterator it;
//check to make sure all parameters are valid for command
it = parameters.find("fasta");
//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["fasta"] = inputDir + it->second; }
}
//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 = "";
- outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
}
string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
if (abort == true) { return 0; }
- string summaryFile = outputDir + getSimpleName(fastafile) + ".summary";
+ string summaryFile = outputDir + m->getSimpleName(fastafile) + ".summary";
int numSeqs = 0;
int tag = 2001;
int startTag = 1; int endTag = 2; int lengthTag = 3; int baseTag = 4; int lhomoTag = 5;
int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
- vector<long> MPIPos;
+ vector<unsigned long int> MPIPos;
MPI_Status status;
MPI_Status statusOut;
MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &statusOut);
delete buf2;
- MPIPos = setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
+ MPIPos = m->setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
+
+ 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);
+ }
- //send file positions to all processes
- MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //send numSeqs
- MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos
-
//figure out how many sequences you have to do
numSeqsPerProcessor = numSeqs / processors;
int startIndex = pid * numSeqsPerProcessor;
//do your part
MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos);
-
- if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; }
-
- //get the info from the child processes
- for(int i = 1; i < processors; i++) {
-
- int size;
- MPI_Recv(&size, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
-
- vector<int> temp; temp.resize(size+1);
-
- for(int j = 0; j < 5; j++) {
-
- MPI_Recv(&temp[0], (size+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
- int receiveTag = temp[temp.size()-1]; //child process added a int to the end to indicate what count this is for
-
- if (receiveTag == startTag) {
- for (int k = 0; k < size; k++) { startPosition.push_back(temp[k]); }
- }else if (receiveTag == endTag) {
- for (int k = 0; k < size; k++) { endPosition.push_back(temp[k]); }
- }else if (receiveTag == lengthTag) {
- for (int k = 0; k < size; k++) { seqLength.push_back(temp[k]); }
- }else if (receiveTag == baseTag) {
- for (int k = 0; k < size; k++) { ambigBases.push_back(temp[k]); }
- }else if (receiveTag == lhomoTag) {
- for (int k = 0; k < size; k++) { longHomoPolymer.push_back(temp[k]); }
- }
- }
- }
-
-
}else { //i am the child process
- MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
+ MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
MPIPos.resize(numSeqs+1);
- MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
-
+ 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
MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos);
-
- if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; }
-
+ }
+
+ MPI_File_close(&inMPI);
+ MPI_File_close(&outMPI);
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+
+ if (pid == 0) {
+ //get the info from the child processes
+ for(int i = 1; i < processors; i++) {
+ int size;
+ MPI_Recv(&size, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
+
+ vector<int> temp; temp.resize(size+1);
+
+ for(int j = 0; j < 5; j++) {
+
+ MPI_Recv(&temp[0], (size+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
+ int receiveTag = temp[temp.size()-1]; //child process added a int to the end to indicate what count this is for
+
+ if (receiveTag == startTag) {
+ for (int k = 0; k < size; k++) { startPosition.push_back(temp[k]); }
+ }else if (receiveTag == endTag) {
+ for (int k = 0; k < size; k++) { endPosition.push_back(temp[k]); }
+ }else if (receiveTag == lengthTag) {
+ for (int k = 0; k < size; k++) { seqLength.push_back(temp[k]); }
+ }else if (receiveTag == baseTag) {
+ for (int k = 0; k < size; k++) { ambigBases.push_back(temp[k]); }
+ }else if (receiveTag == lhomoTag) {
+ for (int k = 0; k < size; k++) { longHomoPolymer.push_back(temp[k]); }
+ }
+ }
+ }
+
+ }else{
+
//send my counts
int size = startPosition.size();
MPI_Send(&size, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
ierr = MPI_Send(&(ambigBases[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
longHomoPolymer.push_back(lhomoTag);
ierr = MPI_Send(&(longHomoPolymer[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
-
}
- MPI_File_close(&inMPI);
- MPI_File_close(&outMPI);
-
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
+ vector<unsigned long int> positions = m->divideFile(fastafile, 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(fastafile, inFASTA);
- numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
- inFASTA.close();
-
- lines.push_back(new linePair(0, numSeqs));
-
- driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]);
+ numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]);
}else{
- numSeqs = setLines(fastafile);
- createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile);
+ numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile);
rename((summaryFile + toString(processIDS[0]) + ".temp").c_str(), summaryFile.c_str());
//append files
for(int i=1;i<processors;i++){
- appendFiles((summaryFile + toString(processIDS[i]) + ".temp"), summaryFile);
+ m->appendFiles((summaryFile + toString(processIDS[i]) + ".temp"), summaryFile);
remove((summaryFile + toString(processIDS[i]) + ".temp").c_str());
}
}
if (m->control_pressed) { return 0; }
#else
- ifstream inFASTA;
- openInputFile(fastafile, inFASTA);
- numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
- inFASTA.close();
-
- lines.push_back(new linePair(0, numSeqs));
-
- driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]);
+ numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]);
if (m->control_pressed) { return 0; }
#endif
#endif
}
}
/**************************************************************************************/
-int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, string sumFile, linePair* line) {
+int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, string sumFile, linePair* filePos) {
try {
ofstream outSummary;
- openOutputFile(sumFile, outSummary);
+ m->openOutputFile(sumFile, outSummary);
//print header if you are process 0
- if (line->start == 0) {
+ if (filePos->start == 0) {
outSummary << "seqname\tstart\tend\tnbases\tambigs\tpolymer" << endl;
}
ifstream in;
- openInputFile(filename, in);
+ m->openInputFile(filename, in);
- in.seekg(line->start);
-
- for(int i=0;i<line->num;i++){
+ in.seekg(filePos->start);
+
+ bool done = false;
+ int count = 0;
+
+ while (!done) {
if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
- Sequence current(in);
+ Sequence current(in); m->gobble(in);
+
if (current.getName() != "") {
startPosition.push_back(current.getStartPos());
endPosition.push_back(current.getEndPos());
outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
outSummary << current.getLongHomoPolymer() << endl;
+ count++;
}
- gobble(in);
+
+ unsigned long int pos = in.tellg();
+ if ((pos == -1) || (pos >= filePos->end)) { break; }
+
+ //report progress
+ if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
}
+ //report progress
+ if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+
in.close();
- return 0;
+ return count;
}
catch(exception& e) {
m->errorOut(e, "SeqSummaryCommand", "driverCreateSummary");
}
#ifdef USE_MPI
/**************************************************************************************/
-int SeqSummaryCommand::MPICreateSummary(int start, int num, vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, MPI_File& inMPI, MPI_File& outMPI, vector<long>& MPIPos) {
+int SeqSummaryCommand::MPICreateSummary(int start, int num, vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long int>& MPIPos) {
try {
+ int pid;
MPI_Status status;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
for(int i=0;i<num;i++){
MPI_File_write_shared(outMPI, buf3, length, MPI_CHAR, &status);
delete buf3;
- }
+ }
}
return 0;
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
int process = 0;
- int exitCommand = 1;
+ int num = 0;
processIDS.clear();
//loop through and create all the processes you want
while (process != processors) {
- int pid = vfork();
+ int pid = fork();
if (pid > 0) {
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){
- driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, sumFile + toString(getpid()) + ".temp", lines[process]);
+ num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, sumFile + toString(getpid()) + ".temp", lines[process]);
+
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = fastafile + toString(getpid()) + ".num.temp";
+ m->openOutputFile(tempFile, out);
+
+ out << num << endl;
+ for (int k = 0; k < startPosition.size(); k++) { out << startPosition[k] << '\t'; } out << endl;
+ for (int k = 0; k < endPosition.size(); k++) { out << endPosition[k] << '\t'; } out << endl;
+ for (int k = 0; k < seqLength.size(); k++) { out << seqLength[k] << '\t'; } out << endl;
+ for (int k = 0; k < ambigBases.size(); k++) { out << ambigBases[k] << '\t'; } out << endl;
+ for (int k = 0; k < longHomoPolymer.size(); k++) { out << longHomoPolymer[k] << '\t'; } out << endl;
+
+ out.close();
+
exit(0);
}else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
}
wait(&temp);
}
- return exitCommand;
-#endif
- }
- catch(exception& e) {
- m->errorOut(e, "SeqSummaryCommand", "createProcessesCreateSummary");
- exit(1);
- }
-}
-/**************************************************************************************************/
-
-int SeqSummaryCommand::setLines(string filename) {
- try {
-
- vector<long int> positions;
-
- ifstream inFASTA;
- openInputFile(filename, inFASTA);
+ //parent reads in and combine Filter info
+ for (int i = 0; i < processIDS.size(); i++) {
+ string tempFilename = fastafile + toString(processIDS[i]) + ".num.temp";
+ ifstream in;
+ m->openInputFile(tempFilename, in);
- 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();
-
- int numFastaSeqs = positions.size();
-
- FILE * pFile;
- long size;
-
- //get num bytes in file
- pFile = fopen (filename.c_str(),"rb");
- if (pFile==NULL) perror ("Error opening file");
- else{
- fseek (pFile, 0, SEEK_END);
- size=ftell (pFile);
- fclose (pFile);
- }
-
- 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;
- }else{
- long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
- }
- lines.push_back(new linePair(startPos, numSeqsPerProcessor));
+ int temp, tempNum;
+ in >> tempNum; m->gobble(in); num += tempNum;
+ for (int k = 0; k < tempNum; k++) { in >> temp; startPosition.push_back(temp); } m->gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; endPosition.push_back(temp); } m->gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; seqLength.push_back(temp); } m->gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; ambigBases.push_back(temp); } m->gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; longHomoPolymer.push_back(temp); } m->gobble(in);
+
+ in.close();
+ remove(tempFilename.c_str());
}
- return numFastaSeqs;
+ return num;
+#endif
}
catch(exception& e) {
- m->errorOut(e, "SeqSummaryCommand", "setLines");
+ m->errorOut(e, "SeqSummaryCommand", "createProcessesCreateSummary");
exit(1);
}
}
projects / mothur.git / blobdiff