MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
+ vector<unsigned long int> positions = divideFile(fastafileNames[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;
- int numFastaSeqs;
- openInputFile(fastafileNames[s], inFASTA);
- getNumSeqs(inFASTA, numFastaSeqs);
- inFASTA.close();
-
- lines.push_back(new linePair(0, numFastaSeqs));
-
+ int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
numSeqs += numFastaSeqs;
-
- driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
}else{
- setLines(fastafileNames[s]);
- createProcessesRunFilter(filter, fastafileNames[s]);
+ int numFastaSeqs = createProcessesRunFilter(filter, fastafileNames[s]);
+ numSeqs += numFastaSeqs;
rename((fastafileNames[s] + toString(processIDS[0]) + ".temp").c_str(), filteredFasta.c_str());
if (m->control_pressed) { return 1; }
#else
- ifstream inFASTA;
- int numFastaSeqs;
- openInputFile(fastafileNames[s], inFASTA);
- getNumSeqs(inFASTA, numFastaSeqs);
- inFASTA.close();
-
- lines.push_back(new linePair(0, numFastaSeqs));
-
+ numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
numSeqs += numFastaSeqs;
-
- driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
if (m->control_pressed) { return 1; }
#endif
}
#endif
/**************************************************************************************/
-int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* line) {
+int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* filePos) {
try {
ofstream out;
openOutputFile(outputFilename, out);
ifstream in;
openInputFile(inputFilename, 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(); out.close(); return 0; }
- Sequence seq(in);
+ Sequence seq(in); gobble(in);
if (seq.getName() != "") {
string align = seq.getAligned();
string filterSeq = "";
}
out << '>' << seq.getName() << endl << filterSeq << endl;
- }
- gobble(in);
-
+ count++;
+ }
+
+ unsigned long int pos = in.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->num) % 100 != 0){ m->mothurOut(toString(line->num)); m->mothurOutEndLine(); }
+ if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+
out.close();
in.close();
- return 0;
+ return count;
}
catch(exception& e) {
m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
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
process++;
}else if (pid == 0){
string filteredFasta = filename + toString(getpid()) + ".temp";
- driverRunFilter(F, filteredFasta, filename, lines[process]);
+ num = driverRunFilter(F, filteredFasta, filename, lines[process]);
+
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = toString(getpid()) + ".temp";
+ openOutputFile(tempFile, out);
+ out << num << endl;
+ out.close();
+
exit(0);
}else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
}
for (int i=0;i<processors;i++) {
int temp = processIDS[i];
wait(&temp);
+ }
+
+ for (int i = 0; i < processIDS.size(); i++) {
+ ifstream in;
+ string tempFile = toString(processIDS[i]) + ".temp";
+ openInputFile(tempFile, in);
+ if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
+ in.close(); remove(tempFile.c_str());
}
+
- return exitCommand;
+ return num;
#endif
}
catch(exception& e) {
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
+ vector<unsigned long int> positions = divideFile(fastafileNames[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;
- int numFastaSeqs;
- openInputFile(fastafileNames[s], inFASTA);
- getNumSeqs(inFASTA, numFastaSeqs);
- inFASTA.close();
-
+ int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
numSeqs += numFastaSeqs;
-
- lines.push_back(new linePair(0, numFastaSeqs));
-
- driverCreateFilter(F, fastafileNames[s], lines[0]);
}else{
- setLines(fastafileNames[s]);
- createProcessesCreateFilter(F, fastafileNames[s]);
+ int numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]);
+ numSeqs += numFastaSeqs;
}
if (m->control_pressed) { return filterString; }
#else
- ifstream inFASTA;
- int numFastaSeqs;
- openInputFile(fastafileNames[s], inFASTA);
- getNumSeqs(inFASTA, numFastaSeqs);
- inFASTA.close();
-
+ numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
numSeqs += numFastaSeqs;
-
- lines.push_back(new linePair(0, numFastaSeqs));
-
- driverCreateFilter(F, fastafileNames[s], lines[0]);
if (m->control_pressed) { return filterString; }
#endif
#endif
}
}
/**************************************************************************************/
-int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* line) {
+int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* filePos) {
try {
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(); return 1; }
- Sequence seq(in);
+ Sequence seq(in); gobble(in);
if (seq.getName() != "") {
if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
if(trump != '*'){ F.doTrump(seq); }
if(isTrue(vertical) || soft != 0){ F.getFreqs(seq); }
cout.flush();
+ count++;
}
+ unsigned long int pos = in.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->num) % 100 != 0){ m->mothurOut(toString(line->num)); m->mothurOutEndLine(); }
-
+ if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
in.close();
- return 0;
+ return count;
}
catch(exception& e) {
m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
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
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){
- driverCreateFilter(F, filename, lines[process]);
+ num = driverCreateFilter(F, filename, lines[process]);
//write out filter counts to file
filename += toString(getpid()) + "filterValues.temp";
ofstream out;
openOutputFile(filename, out);
+ out << num << endl;
for (int k = 0; k < alignmentLength; k++) { out << F.a[k] << '\t'; } out << endl;
for (int k = 0; k < alignmentLength; k++) { out << F.t[k] << '\t'; } out << endl;
for (int k = 0; k < alignmentLength; k++) { out << F.g[k] << '\t'; } out << endl;
ifstream in;
openInputFile(tempFilename, in);
- int temp;
+ int temp, tempNum;
+ in >> tempNum; gobble(in); num += tempNum;
for (int k = 0; k < alignmentLength; k++) { in >> temp; F.a[k] += temp; } gobble(in);
for (int k = 0; k < alignmentLength; k++) { in >> temp; F.t[k] += temp; } gobble(in);
for (int k = 0; k < alignmentLength; k++) { in >> temp; F.g[k] += temp; } gobble(in);
remove(tempFilename.c_str());
}
- return exitCommand;
+ return num;
#endif
}
catch(exception& e) {
exit(1);
}
}
-/**************************************************************************************************/
-
-int FilterSeqsCommand::setLines(string filename) {
- try {
-
- vector<unsigned long int> positions;
- bufferSizes.clear();
-
- ifstream inFASTA;
- openInputFile(filename, inFASTA);
-
- 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);
- }
-
- numSeqs += numFastaSeqs;
-
- 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;
- bufferSizes.push_back(size - startPos);
- }else{
- unsigned long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
- bufferSizes.push_back(myEnd-startPos);
- }
- lines.push_back(new linePair(startPos, numSeqsPerProcessor));
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "FilterSeqsCommand", "setLines");
- exit(1);
- }
-}
/**************************************************************************************/
projects / mothur.git / blobdiff