outputNames.push_back(groupFile);
getOligos(fastaFileNames, qualFileNames);
}
-
- if(qFileName != "") { setLines(qFileName, qLines); }
+ vector<unsigned long int> fastaFilePos;
+ vector<unsigned long int> qFilePos;
+
+ setLines(fastaFile, qFileName, fastaFilePos, qFilePos);
+
+ for (int i = 0; i < (fastaFilePos.size()-1); i++) {
+ lines.push_back(new linePair(fastaFilePos[i], fastaFilePos[(i+1)]));
+ if (qFileName != "") { qLines.push_back(new linePair(qFilePos[i], qFilePos[(i+1)])); }
+ }
+ if(qFileName == "") { qLines = lines; } //files with duds
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if(processors == 1){
- ifstream inFASTA;
- int numSeqs;
- openInputFile(fastaFile, inFASTA);
- getNumSeqs(inFASTA, numSeqs);
- inFASTA.close();
-
- lines.push_back(new linePair(0, numSeqs));
-
- driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], lines[0]);
+
+ driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
for (int j = 0; j < fastaFileNames.size(); j++) {
rename((fastaFileNames[j] + toString(getpid()) + ".temp").c_str(), fastaFileNames[j].c_str());
}
}else{
- setLines(fastaFile, lines);
- if(qFileName == "") { qLines = lines; }
-
createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames);
rename((trimSeqFile + toString(processIDS[0]) + ".temp").c_str(), trimSeqFile.c_str());
if (m->control_pressed) { return 0; }
#else
- ifstream inFASTA;
- int numSeqs;
- openInputFile(fastaFile, inFASTA);
- getNumSeqs(inFASTA, numSeqs);
- inFASTA.close();
-
- lines.push_back(new linePair(0, numSeqs));
-
- driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], lines[0]);
+ driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qlines[0]);
for (int j = 0; j < fastaFileNames.size(); j++) {
rename((fastaFileNames[j] + toString(j) + ".temp").c_str(), fastaFileNames[j].c_str());
ifstream inFASTA;
openInputFile(filename, inFASTA);
+ inFASTA.seekg(line->start);
ifstream qFile;
- if(qFileName != "") { openInputFile(qFileName, qFile); }
+ if(qFileName != "") { openInputFile(qFileName, qFile); qFile.seekg(qline->start); }
- qFile.seekg(qline->start);
- inFASTA.seekg(line->start);
-
- for(int i=0;i<line->num;i++){
+ bool done = false;
+ int count = 0;
+
+ while (!done) {
if (m->control_pressed) {
inFASTA.close(); outFASTA.close(); scrapFASTA.close();
int success = 1;
- Sequence currSeq(inFASTA);
+ Sequence currSeq(inFASTA); gobble(inFASTA);
QualityScores currQual;
if(qFileName != ""){
- currQual = QualityScores(qFile, currSeq.getNumBases());
+ currQual = QualityScores(qFile, currSeq.getNumBases()); gobble(qFile);
}
string origSeq = currSeq.getUnaligned();
currSeq.printSequence(scrapFASTA);
currQual.printQScores(scrapQual);
}
+ count++;
}
- gobble(inFASTA);
- gobble(qFile);
+
+ unsigned long int pos = inFASTA.tellg();
+ if ((pos == -1) || (pos >= line->end)) { break; }
+
+ //report progress
+ if((count) % 1000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+
}
+ //report progress
+ if((count) % 1000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+
inFASTA.close();
outFASTA.close();
}
}
- return 0;
+ return count;
}
catch(exception& e) {
m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
/**************************************************************************************************/
-int TrimSeqsCommand::setLines(string filename, vector<linePair*>& lines) {
+int TrimSeqsCommand::setLines(string filename, string qfilename, vector<unsigned long int>& fastaFilePos, vector<unsigned long int>& qfileFilePos) {
try {
- lines.clear();
+ //set file positions for fasta file
+ fastaFilePos = divideFile(filename, processors);
- vector<unsigned long int> positions;
+ if (qfilename == "") { return processors; }
- ifstream inFASTA;
- openInputFile(filename, inFASTA);
+ //get name of first sequence in each chunk
+ map<string, int> firstSeqNames;
+ for (int i = 0; i < (fastaFilePos.size()-1); i++) {
+ ifstream in;
+ openInputFile(filename, in);
+ in.seekg(fastaFilePos[i]);
+
+ Sequence temp(in);
+ firstSeqNames[temp.getName()] = i;
+
+ in.close();
+ }
+
+ //seach for filePos of each first name in the qfile and save in qfileFilePos
+ ifstream inQual;
+ openInputFile(qfilename, inQual);
string input;
- while(!inFASTA.eof()){
- input = getline(inFASTA);
+ while(!inQual.eof()){
+ input = getline(inQual);
if (input.length() != 0) {
- if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
+ if(input[0] == '>'){ //this is a sequence name line
+ istringstream nameStream(input);
+
+ string sname = ""; nameStream >> sname;
+ sname = sname.substr(1);
+
+ map<string, int>::iterator it = firstSeqNames.find(sname);
+
+ if(it != firstSeqNames.end()) { //this is the start of a new chunk
+ unsigned long int pos = inQual.tellg();
+ qfileFilePos.push_back(pos - input.length() - 1);
+ firstSeqNames.erase(it);
+ }
+ }
}
+
+ if (firstSeqNames.size() == 0) { break; }
}
- inFASTA.close();
+ inQual.close();
- int numFastaSeqs = positions.size();
-
+ if (firstSeqNames.size() != 0) {
+ for (map<string, int>::iterator it = firstSeqNames.begin(); it != firstSeqNames.end(); it++) {
+ m->mothurOut(it->first + " is in your fasta file and not in your quality file, not using quality file."); m->mothurOutEndLine();
+ }
+ qFileName = "";
+ return processors;
+ }
+
+ //get last file position of qfile
FILE * pFile;
unsigned long int size;
//get num bytes in file
- pFile = fopen (filename.c_str(),"rb");
+ pFile = fopen (qfilename.c_str(),"rb");
if (pFile==NULL) perror ("Error opening file");
else{
fseek (pFile, 0, SEEK_END);
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));
- }
+ qfileFilePos.push_back(size);
- return numFastaSeqs;
+ return processors;
}
catch(exception& e) {
m->errorOut(e, "TrimSeqsCommand", "setLines");
projects / mothur.git / blobdiff