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; }
}
it = parameters.find("oligos");
//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["oligos"] = inputDir + it->second; }
}
it = parameters.find("qfile");
//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["qfile"] = 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;
temp = validParameter.validFile(parameters, "flip", false);
if (temp == "not found"){ flip = 0; }
- else if(isTrue(temp)) { flip = 1; }
+ else if(m->isTrue(temp)) { flip = 1; }
temp = validParameter.validFile(parameters, "oligos", true);
if (temp == "not found"){ oligoFile = ""; }
convert(temp, qThreshold);
temp = validParameter.validFile(parameters, "qtrim", false); if (temp == "not found") { temp = "F"; }
- qtrim = isTrue(temp);
+ qtrim = m->isTrue(temp);
temp = validParameter.validFile(parameters, "rollaverage", false); if (temp == "not found") { temp = "0"; }
convert(temp, qRollAverage);
convert(temp, qAverage);
temp = validParameter.validFile(parameters, "allfiles", false); if (temp == "not found") { temp = "F"; }
- allFiles = isTrue(temp);
+ allFiles = m->isTrue(temp);
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; }
convert(temp, processors);
numFPrimers = 0; //this needs to be initialized
numRPrimers = 0;
- string trimSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "trim.fasta";
+ string trimSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.fasta";
outputNames.push_back(trimSeqFile);
- string scrapSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "scrap.fasta";
+ string scrapSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.fasta";
outputNames.push_back(scrapSeqFile);
- string trimQualFile = outputDir + getRootName(getSimpleName(fastaFile)) + "trim.qual";
+ string trimQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.qual";
outputNames.push_back(trimQualFile);
- string scrapQualFile = outputDir + getRootName(getSimpleName(fastaFile)) + "scrap.qual";
+ string scrapQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.qual";
outputNames.push_back(scrapQualFile);
- string groupFile = outputDir + getRootName(getSimpleName(fastaFile)) + "groups";
+ string groupFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups";
vector<string> fastaFileNames;
vector<string> qualFileNames;
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());
//append files
for(int i=1;i<processors;i++){
- appendFiles((trimSeqFile + toString(processIDS[i]) + ".temp"), trimSeqFile);
+ m->appendFiles((trimSeqFile + toString(processIDS[i]) + ".temp"), trimSeqFile);
remove((trimSeqFile + toString(processIDS[i]) + ".temp").c_str());
- appendFiles((scrapSeqFile + toString(processIDS[i]) + ".temp"), scrapSeqFile);
+ m->appendFiles((scrapSeqFile + toString(processIDS[i]) + ".temp"), scrapSeqFile);
remove((scrapSeqFile + toString(processIDS[i]) + ".temp").c_str());
- appendFiles((trimQualFile + toString(processIDS[i]) + ".temp"), trimQualFile);
+ m->appendFiles((trimQualFile + toString(processIDS[i]) + ".temp"), trimQualFile);
remove((trimQualFile + toString(processIDS[i]) + ".temp").c_str());
- appendFiles((scrapQualFile + toString(processIDS[i]) + ".temp"), scrapQualFile);
+ m->appendFiles((scrapQualFile + toString(processIDS[i]) + ".temp"), scrapQualFile);
remove((scrapQualFile + toString(processIDS[i]) + ".temp").c_str());
- appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
+ m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
for (int j = 0; j < fastaFileNames.size(); j++) {
- appendFiles((fastaFileNames[j] + toString(processIDS[i]) + ".temp"), fastaFileNames[j]);
+ m->appendFiles((fastaFileNames[j] + toString(processIDS[i]) + ".temp"), fastaFileNames[j]);
remove((fastaFileNames[j] + toString(processIDS[i]) + ".temp").c_str());
}
if(qFileName != ""){
for (int j = 0; j < qualFileNames.size(); j++) {
- appendFiles((qualFileNames[j] + toString(processIDS[i]) + ".temp"), qualFileNames[j]);
+ m->appendFiles((qualFileNames[j] + toString(processIDS[i]) + ".temp"), qualFileNames[j]);
remove((qualFileNames[j] + toString(processIDS[i]) + ".temp").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());
for(int i=0;i<fastaFileNames.size();i++){
- if (isBlank(fastaFileNames[i])) { remove(fastaFileNames[i].c_str()); }
+ if (m->isBlank(fastaFileNames[i])) { remove(fastaFileNames[i].c_str()); }
else if (filesToRemove.count(fastaFileNames[i]) > 0) { remove(fastaFileNames[i].c_str()); }
else {
ifstream inFASTA;
string seqName;
- openInputFile(fastaFileNames[i], inFASTA);
+ m->openInputFile(fastaFileNames[i], inFASTA);
ofstream outGroups;
- string outGroupFilename = outputDir + getRootName(getSimpleName(fastaFileNames[i])) + "groups";
- openOutputFile(outGroupFilename, outGroups);
+ string outGroupFilename = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "groups";
+ m->openOutputFile(outGroupFilename, outGroups);
outputNames.push_back(outGroupFilename);
string thisGroup = "";
if(qFileName != ""){
for(int i=0;i<qualFileNames.size();i++){
- if (isBlank(qualFileNames[i])) { remove(qualFileNames[i].c_str()); }
+ if (m->isBlank(qualFileNames[i])) { remove(qualFileNames[i].c_str()); }
else if (filesToRemove.count(qualFileNames[i]) > 0) { remove(qualFileNames[i].c_str()); }
else {
ifstream inQual;
string seqName;
- openInputFile(qualFileNames[i], inQual);
+ m->openInputFile(qualFileNames[i], inQual);
// ofstream outGroups;
//
// string thisGroup = "";
try {
ofstream outFASTA;
- int able = openOutputFile(trimFile, outFASTA);
+ int able = m->openOutputFile(trimFile, outFASTA);
ofstream scrapFASTA;
- openOutputFile(scrapFile, scrapFASTA);
+ m->openOutputFile(scrapFile, scrapFASTA);
ofstream outQual;
ofstream scrapQual;
if(qFileName != ""){
- openOutputFile(trimQFile, outQual);
- openOutputFile(scrapQFile, scrapQual);
+ m->openOutputFile(trimQFile, outQual);
+ m->openOutputFile(scrapQFile, scrapQual);
}
ofstream outGroups;
vector<ofstream*> fastaFileNames;
vector<ofstream*> qualFileNames;
-
+ cout << "here" << endl;
if (oligoFile != "") {
- openOutputFile(groupFile, outGroups);
+ m->openOutputFile(groupFile, outGroups);
for (int i = 0; i < fastaNames.size(); i++) {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate));
#endif
}
}
-
+cout << "here " << filename << endl;
ifstream inFASTA;
- openInputFile(filename, inFASTA);
-
- ifstream qFile;
- if(qFileName != "") { openInputFile(qFileName, qFile); }
-
- qFile.seekg(qline->start);
+ m->openInputFile(filename, inFASTA);
inFASTA.seekg(line->start);
+ cout << "here " << qFileName << endl;
+ ifstream qFile;
+ if(qFileName != "") { m->openInputFile(qFileName, qFile); qFile.seekg(qline->start); }
- for(int i=0;i<line->num;i++){
+ bool done = false;
+ int count = 0;
+ cout << "here" << endl;
+ while (!done) {
if (m->control_pressed) {
inFASTA.close(); outFASTA.close(); scrapFASTA.close();
int success = 1;
- Sequence currSeq(inFASTA);
+
+ Sequence currSeq(inFASTA); m->gobble(inFASTA);
+
QualityScores currQual;
if(qFileName != ""){
- currQual = QualityScores(qFile, currSeq.getNumBases());
+ currQual = QualityScores(qFile, currSeq.getNumBases()); m->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 = m->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;
+ m->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;
+ m->openInputFile(qfilename, inQual);
string input;
- while(!inFASTA.eof()){
- input = getline(inFASTA);
+ while(!inQual.eof()){
+ input = m->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");
void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& outQualVec){
try {
ifstream inOligos;
- openInputFile(oligoFile, inOligos);
+ m->openInputFile(oligoFile, inOligos);
ofstream test;
groupVector.push_back(group);
if(allFiles){
- outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
+ outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
if(qFileName != ""){
- outQualVec.push_back((outputDir + getRootName(getSimpleName(qFileName)) + group + ".qual"));
+ outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
}
if (group == "") { //if there is not a group for this primer, then this file will not get written to, but we add it to keep the indexes correct
- filesToRemove.insert((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
+ filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
if(qFileName != ""){
- filesToRemove.insert((outputDir + getRootName(getSimpleName(qFileName)) + group + ".qual"));
+ filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
}
}else {
- outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
+ outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
if(qFileName != ""){
- outputNames.push_back((outputDir + getRootName(getSimpleName(qFileName)) + group + ".qual"));
+ outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
}
}
}
groupVector.push_back(group);
if(allFiles){
- outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
- outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
+ outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+ outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
if(qFileName != ""){
- outQualVec.push_back((outputDir + getRootName(getSimpleName(qFileName)) + group + ".qual"));
- outputNames.push_back((outputDir + getRootName(getSimpleName(qFileName)) + group + ".qual"));
+ outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+ outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
}
}
}else{ m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); }
}
- gobble(inOligos);
+ m->gobble(inOligos);
}
inOligos.close();
for (map<string, int>::iterator itBar = barcodes.begin(); itBar != barcodes.end(); itBar++) {
for (map<string, int>::iterator itPrime = primers.begin(); itPrime != primers.end(); itPrime++) {
if (groupVector[itPrime->second] != "") { //there is a group for this primer
- outputNames.push_back((outputDir + getRootName(getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
- outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
+ outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
+ outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
combos[(groupVector[itBar->second] + "." + groupVector[itPrime->second])] = outFASTAVec.size()-1;
if(qFileName != ""){
- outQualVec.push_back((outputDir + getRootName(getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
- outputNames.push_back((outputDir + getRootName(getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
+ outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
+ outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
}
}
}