}
}
- //zero out spot where all sequences have blanks
//zero out spot where all sequences have blanks
int numColRemoved = 0;
for(int i = 0;i < seqs[0]->getAligned().length(); i++){
//cout << "a = " << a[i] << " t = " << t[i] << " g = " << g[i] << " c = " << c[i] << endl;
}
- m->mothurOut("Filter removed " + toString(numColRemoved) + " columns."); m->mothurOutEndLine();
+ if (threshold != 0.0) { m->mothurOut("Filter removed " + toString(numColRemoved) + " columns."); m->mothurOutEndLine(); }
+
return filterString;
}
catch(exception& e) {
vector<Sequence*> Chimera::readSeqs(string file) {
try {
- m->mothurOut("Reading sequences... "); cout.flush();
- ifstream in;
- openInputFile(file, in);
-
vector<Sequence*> container;
int count = 0;
length = 0;
unaligned = false;
+
+ m->mothurOut("Reading sequences from " + file + "..."); cout.flush();
+
+ #ifdef USE_MPI
+ int pid;
+ vector<long> positions;
+ int numSeqs;
+
+ MPI_Status status;
+ MPI_File inMPI;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+
+ char inFileName[file.length()];
+ strcpy(inFileName, file.c_str());
+
+ MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
+
+ if (pid == 0) {
+ positions = setFilePosFasta(file, numSeqs); //fills MPIPos, returns numSeqs
+
+ //send file positions to all processes
+ MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //send numSeqs
+ MPI_Bcast(&positions[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos
+ }else{
+ MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
+ positions.resize(numSeqs+1);
+ MPI_Bcast(&positions[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
+ }
+
+ //read file
+ for(int i=0;i<numSeqs;i++){
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); return container; }
+
+ //read next sequence
+ int seqlength = positions[i+1] - positions[i];
+ char buf4[seqlength];
+ MPI_File_read_at(inMPI, positions[i], buf4, seqlength, MPI_CHAR, &status);
+
+ string tempBuf = buf4;
+ if (tempBuf.length() > seqlength) { tempBuf = tempBuf.substr(0, seqlength); }
+
+ istringstream iss (tempBuf,istringstream::in);
+
+ Sequence* current = new Sequence(iss);
+ if (current->getName() != "") {
+ if (count == 0) { length = current->getAligned().length(); count++; } //gets first seqs length
+ else if (length != current->getAligned().length()) { unaligned = true; }
+
+ container.push_back(current);
+ }
+ }
+
+ MPI_File_close(&inMPI);
+ #else
+
+ ifstream in;
+ openInputFile(file, in);
//read in seqs and store in vector
while(!in.eof()){
Sequence* current = new Sequence(in); gobble(in);
if (count == 0) { length = current->getAligned().length(); count++; } //gets first seqs length
- else if (length != current->getAligned().length()) { //seqs are unaligned
- unaligned = true;
- }
-
+ else if (length != current->getAligned().length()) { unaligned = true; }
+
if (current->getName() != "") { container.push_back(current); }
}
-
in.close();
+ #endif
+
m->mothurOut("Done."); m->mothurOutEndLine();
return container;
}else if (filename == "") { //do nothing
seqMask = "";
}else{
+
+ #ifdef USE_MPI
+ MPI_File inMPI;
+ MPI_Offset size;
+ MPI_Status status;
+
+ char inFileName[filename.length()];
+ strcpy(inFileName, filename.c_str());
+
+ MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
+ MPI_File_get_size(inMPI, &size);
+
+ char buffer[size];
+ MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
+
+ string tempBuf = buffer;
+ if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size); }
+ istringstream iss (tempBuf,istringstream::in);
+
+ if (!iss.eof()) {
+ Sequence temp(iss);
+ seqMask = temp.getAligned();
+ }else {
+ m->mothurOut("Problem with mask."); m->mothurOutEndLine();
+ seqMask = "";
+ }
+
+ MPI_File_close(&inMPI);
+ #else
+
ifstream infile;
openInputFile(filename, infile);
- while (!infile.eof()) {
+ if (!infile.eof()) {
Sequence temp(infile);
seqMask = temp.getAligned();
-
- gobble(infile);
+ }else {
+ m->mothurOut("Problem with mask."); m->mothurOutEndLine();
+ seqMask = "";
}
-
infile.close();
- }
- }
- catch(exception& e) {
- m->errorOut(e, "Chimera", "setMask");
- exit(1);
- }
-}
-//***************************************************************************************************************
-
-vector< vector<float> > Chimera::readQuantiles() {
- try {
-
- ifstream in;
- openInputFile(quanfile, in);
-
- vector< vector<float> > quan;
- vector <float> temp; temp.resize(6, 0);
-
- //to fill 0
- quan.push_back(temp);
-
- int num; float ten, twentyfive, fifty, seventyfive, ninetyfive, ninetynine;
-
- while(!in.eof()){
-
- in >> num >> ten >> twentyfive >> fifty >> seventyfive >> ninetyfive >> ninetynine;
-
- temp.clear();
-
- temp.push_back(ten);
- temp.push_back(twentyfive);
- temp.push_back(fifty);
- temp.push_back(seventyfive);
- temp.push_back(ninetyfive);
- temp.push_back(ninetynine);
-
- quan.push_back(temp);
+ #endif
- gobble(in);
}
-
- in.close();
- return quan;
-
}
catch(exception& e) {
- m->errorOut(e, "Chimera", "readQuantiles");
+ m->errorOut(e, "Chimera", "setMask");
exit(1);
}
}
projects / mothur.git / blobdiff