it = parameters.find("template");
//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["template"] = inputDir + it->second; }
}
it = parameters.find("conservation");
//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["conservation"] = inputDir + it->second; }
}
it = parameters.find("quantile");
//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["quantile"] = inputDir + it->second; }
}
fastafile = validParameter.validFile(parameters, "fasta", false);
if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.pintail command."); m->mothurOutEndLine(); abort = true; }
else {
- splitAtDash(fastafile, fastaFileNames);
+ m->splitAtDash(fastafile, fastaFileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < fastaFileNames.size(); i++) {
if (inputDir != "") {
- string path = hasPath(fastaFileNames[i]);
+ string path = m->hasPath(fastaFileNames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
}
int ableToOpen;
ifstream in;
- ableToOpen = openInputFile(fastaFileNames[i], in, "noerror");
+ ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
- string tryPath = m->getDefaultPath() + getSimpleName(fastaFileNames[i]);
+ string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
- ableToOpen = openInputFile(tryPath, in, "noerror");
+ ableToOpen = m->openInputFile(tryPath, in, "noerror");
fastaFileNames[i] = tryPath;
}
}
string temp;
temp = validParameter.validFile(parameters, "filter", false); if (temp == "not found") { temp = "F"; }
- filter = isTrue(temp);
+ filter = m->isTrue(temp);
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; }
convert(temp, processors);
if (maskfile == "not found") { maskfile = ""; }
else if (maskfile != "default") {
if (inputDir != "") {
- string path = hasPath(maskfile);
+ string path = m->hasPath(maskfile);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { maskfile = inputDir + maskfile; }
}
ifstream in;
- int ableToOpen = openInputFile(maskfile, in);
- if (ableToOpen == 1) { abort = true; }
- in.close();
+ int ableToOpen = m->openInputFile(maskfile, in, "no error");
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(maskfile);
+ m->mothurOut("Unable to open " + maskfile + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ableToOpen = m->openInputFile(tryPath, in, "noerror");
+ maskfile = tryPath;
+ }
+ }
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + maskfile + "."); m->mothurOutEndLine();
+ abort = true;
+ }
}
//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
}
templatefile = validParameter.validFile(parameters, "template", true);
else if (consfile == "not found") {
consfile = "";
//check for consfile
- string tempConsFile = getRootName(inputDir + getSimpleName(templatefile)) + "freq";
+ string tempConsFile = m->getRootName(inputDir + m->getSimpleName(templatefile)) + "freq";
ifstream FileTest(tempConsFile.c_str());
if(FileTest){
- bool GoodFile = checkReleaseVersion(FileTest, m->getVersion());
+ bool GoodFile = m->checkReleaseVersion(FileTest, m->getVersion());
if (GoodFile) {
m->mothurOut("I found " + tempConsFile + " in your input file directory. I will use it to save time."); m->mothurOutEndLine(); consfile = tempConsFile; FileTest.close();
}
+ }else {
+ string tempConsFile = m->getDefaultPath() + m->getRootName(m->getSimpleName(templatefile)) + "freq";
+ ifstream FileTest2(tempConsFile.c_str());
+ if(FileTest2){
+ bool GoodFile = m->checkReleaseVersion(FileTest2, m->getVersion());
+ if (GoodFile) {
+ m->mothurOut("I found " + tempConsFile + " in your input file directory. I will use it to save time."); m->mothurOutEndLine(); consfile = tempConsFile; FileTest2.close();
+ }
+ }
}
}
//check for quantile to save the time
string tempQuan = "";
if ((!filter) && (maskfile == "")) {
- tempQuan = inputDir + getRootName(getSimpleName(templatefile)) + "pintail.quan";
+ tempQuan = inputDir + m->getRootName(m->getSimpleName(templatefile)) + "pintail.quan";
}else if ((!filter) && (maskfile != "")) {
- tempQuan = inputDir + getRootName(getSimpleName(templatefile)) + "pintail.masked.quan";
+ tempQuan = inputDir + m->getRootName(m->getSimpleName(templatefile)) + "pintail.masked.quan";
}else if ((filter) && (maskfile != "")) {
- tempQuan = inputDir + getRootName(getSimpleName(templatefile)) + "pintail.filtered." + getSimpleName(getRootName(fastaFileNames[s])) + "masked.quan";
+ tempQuan = inputDir + m->getRootName(m->getSimpleName(templatefile)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "masked.quan";
}else if ((filter) && (maskfile == "")) {
- tempQuan = inputDir + getRootName(getSimpleName(templatefile)) + "pintail.filtered." + getSimpleName(getRootName(fastaFileNames[s])) + "quan";
+ tempQuan = inputDir + m->getRootName(m->getSimpleName(templatefile)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "quan";
}
ifstream FileTest(tempQuan.c_str());
if(FileTest){
- bool GoodFile = checkReleaseVersion(FileTest, m->getVersion());
+ bool GoodFile = m->checkReleaseVersion(FileTest, m->getVersion());
if (GoodFile) {
m->mothurOut("I found " + tempQuan + " in your input file directory. I will use it to save time."); m->mothurOutEndLine(); quanfile = tempQuan; FileTest.close();
}
+ }else {
+ string tryPath = m->getDefaultPath();
+ string tempQuan = "";
+ if ((!filter) && (maskfile == "")) {
+ tempQuan = tryPath + m->getRootName(m->getSimpleName(templatefile)) + "pintail.quan";
+ }else if ((!filter) && (maskfile != "")) {
+ tempQuan = tryPath + m->getRootName(m->getSimpleName(templatefile)) + "pintail.masked.quan";
+ }else if ((filter) && (maskfile != "")) {
+ tempQuan = tryPath + m->getRootName(m->getSimpleName(templatefile)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "masked.quan";
+ }else if ((filter) && (maskfile == "")) {
+ tempQuan = tryPath + m->getRootName(m->getSimpleName(templatefile)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "quan";
+ }
+
+ ifstream FileTest2(tempQuan.c_str());
+ if(FileTest2){
+ bool GoodFile = m->checkReleaseVersion(FileTest2, m->getVersion());
+ if (GoodFile) {
+ m->mothurOut("I found " + tempQuan + " in your input file directory. I will use it to save time."); m->mothurOutEndLine(); quanfile = tempQuan; FileTest2.close();
+ }
+ }
}
chimera = new Pintail(fastaFileNames[s], templatefile, filter, processors, maskfile, consfile, quanfile, window, increment, outputDir);
string outputFileName, accnosFileName;
if (maskfile != "") {
- outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + maskfile + ".pintail.chimeras";
- accnosFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + maskfile + ".pintail.accnos";
+ outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + m->getSimpleName(m->getRootName(maskfile)) + ".pintail.chimeras";
+ accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + m->getSimpleName(m->getRootName(maskfile)) + ".pintail.accnos";
}else {
- outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "pintail.chimeras";
- accnosFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "pintail.accnos";
+ outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "pintail.chimeras";
+ accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "pintail.accnos";
}
if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; }
if (pid == 0) { //you are the root process
- MPIPos = setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs
+ MPIPos = m->setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs
//send file positions to all processes
for(int i = 1; i < processors; i++) {
MPI_File_close(&outMPIAccnos);
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
-
+ vector<unsigned long int> positions = m->divideFile(fastaFileNames[s], processors);
+
+ for (int i = 0; i < (positions.size()-1); i++) {
+ lines.push_back(new linePair(positions[i], positions[(i+1)]));
+ }
+
//break up file
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if(processors == 1){
- ifstream inFASTA;
- openInputFile(fastaFileNames[s], inFASTA);
- getNumSeqs(inFASTA, numSeqs);
- inFASTA.close();
-
- lines.push_back(new linePair(0, numSeqs));
-
- driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
+
+ numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
- if (m->control_pressed) {
- remove(outputFileName.c_str());
- remove(accnosFileName.c_str());
- for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); }
- for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
- delete chimera;
- return 0;
- }
+ if (m->control_pressed) { remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; }
}else{
- vector<unsigned long int> positions;
processIDS.resize(0);
- ifstream inFASTA;
- openInputFile(fastaFileNames[s], 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();
-
- numSeqs = positions.size();
-
- int numSeqsPerProcessor = numSeqs / processors;
-
- for (int i = 0; i < processors; i++) {
- unsigned long int startPos = positions[ i * numSeqsPerProcessor ];
- if(i == processors - 1){
- numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;
- }
- lines.push_back(new linePair(startPos, numSeqsPerProcessor));
- }
-
- createProcesses(outputFileName, fastaFileNames[s], accnosFileName);
+ numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName);
rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
rename((accnosFileName + toString(processIDS[0]) + ".temp").c_str(), accnosFileName.c_str());
//append output files
for(int i=1;i<processors;i++){
- appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
+ m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
}
//append output files
for(int i=1;i<processors;i++){
- appendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName);
+ m->appendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName);
remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());
}
}
#else
- ifstream inFASTA;
- openInputFile(fastaFileNames[s], inFASTA);
- getNumSeqs(inFASTA, numSeqs);
- inFASTA.close();
- lines.push_back(new linePair(0, numSeqs));
-
- driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
+ numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
- if (m->control_pressed) {
- remove(outputFileName.c_str());
- remove(accnosFileName.c_str());
- for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); }
- for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
- delete chimera;
- return 0;
- }
+ if (m->control_pressed) { remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; }
#endif
#endif
}
//**********************************************************************************************************************
-int ChimeraPintailCommand::driver(linePair* line, string outputFName, string filename, string accnos){
+int ChimeraPintailCommand::driver(linePair* filePos, string outputFName, string filename, string accnos){
try {
ofstream out;
- openOutputFile(outputFName, out);
+ m->openOutputFile(outputFName, out);
ofstream out2;
- openOutputFile(accnos, out2);
+ m->openOutputFile(accnos, out2);
ifstream inFASTA;
- openInputFile(filename, inFASTA);
+ m->openInputFile(filename, inFASTA);
- inFASTA.seekg(line->start);
-
- for(int i=0;i<line->numSeqs;i++){
-
+ inFASTA.seekg(filePos->start);
+
+ bool done = false;
+ int count = 0;
+
+ while (!done) {
+
if (m->control_pressed) { return 1; }
- Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA);
+ Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
//print results
chimera->print(out, out2);
}
+ count++;
}
delete candidateSeq;
+ unsigned long int pos = inFASTA.tellg();
+ if ((pos == -1) || (pos >= filePos->end)) { break; }
+
//report progress
- if((i+1) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(i+1)); m->mothurOutEndLine(); }
+ if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
}
//report progress
- if((line->numSeqs) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(line->numSeqs)); m->mothurOutEndLine(); }
+ if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
out.close();
out2.close();
inFASTA.close();
- return 0;
+ return count;
}
catch(exception& e) {
m->errorOut(e, "ChimeraPintailCommand", "driver");
istringstream iss (tempBuf,istringstream::in);
delete buf4;
- Sequence* candidateSeq = new Sequence(iss); gobble(iss);
+ Sequence* candidateSeq = new Sequence(iss); m->gobble(iss);
if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
int process = 0;
- // processIDS.resize(0);
+ int num = 0;
//loop through and create all the processes you want
while (process != processors) {
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){
- driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp");
+ num = driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp");
+
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = outputFileName + toString(getpid()) + ".num.temp";
+ m->openOutputFile(tempFile, out);
+ out << num << endl;
+ out.close();
+
exit(0);
}else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
}
wait(&temp);
}
- return 0;
+ for (int i = 0; i < processIDS.size(); i++) {
+ ifstream in;
+ string tempFile = outputFileName + toString(processIDS[i]) + ".num.temp";
+ m->openInputFile(tempFile, in);
+ if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
+ in.close(); remove(tempFile.c_str());
+ }
+
+ return num;
#endif
}
catch(exception& e) {
projects / mothur.git / blobdiff