MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
+ vector<unsigned long int> positions = 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);
- getNumSeqs(inFASTA, numSeqs);
- 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
if (m->control_pressed) { return 0; }
#else
- ifstream inFASTA;
- openInputFile(fastafile, inFASTA);
- getNumSeqs(inFASTA, numSeqs);
- 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);
//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);
- 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); gobble(in);
if (current.getName() != "") {
startPosition.push_back(current.getStartPos());
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");
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 = toString(getpid()) + ".temp";
+ 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<unsigned 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 = toString(processIDS[i]) + ".temp";
+ ifstream in;
+ openInputFile(tempFilename, in);
- string input;
- while(!inFASTA.eof()){
- input = getline(inFASTA);
-
- if (input.length() != 0) {
- if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
- }
- }
- inFASTA.close();
-
- int numFastaSeqs = positions.size();
-
- FILE * pFile;
- unsigned long int 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++) {
-
- unsigned long int startPos = positions[ i * numSeqsPerProcessor ];
- if(i == processors - 1){
- numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
- }else{
- unsigned long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
- }
- lines.push_back(new linePair(startPos, numSeqsPerProcessor));
+ int temp, tempNum;
+ in >> tempNum; gobble(in); num += tempNum;
+ for (int k = 0; k < tempNum; k++) { in >> temp; startPosition.push_back(temp); } gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; endPosition.push_back(temp); } gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; seqLength.push_back(temp); } gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; ambigBases.push_back(temp); } gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; longHomoPolymer.push_back(temp); } 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