#include "chimerapintailcommand.h"
#include "pintail.h"
+//**********************************************************************************************************************
+vector<string> ChimeraPintailCommand::getValidParameters(){
+ try {
+ string AlignArray[] = {"fasta","filter","processors","window" ,"increment","template","conservation","quantile","mask","outputdir","inputdir"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraPintailCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ChimeraPintailCommand::ChimeraPintailCommand(){
+ try {
+ abort = true; calledHelp = true;
+ vector<string> tempOutNames;
+ outputTypes["chimera"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraPintailCommand", "ChimeraPintailCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ChimeraPintailCommand::getRequiredParameters(){
+ try {
+ string AlignArray[] = {"template","fasta"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraPintailCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ChimeraPintailCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraPintailCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//***************************************************************************************************************
-
ChimeraPintailCommand::ChimeraPintailCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ vector<string> tempOutNames;
+ outputTypes["chimera"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+
//if the user changes the input directory command factory will send this info to us in the output parameter
inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
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");
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ fastaFileNames[i] = tryPath;
+ }
+ }
+
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
+ m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
fastaFileNames[i] = tryPath;
}
}
+
in.close();
if (ableToOpen == 1) {
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; }
+ 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();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ maskfile = tryPath;
+ }
+ }
+
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(maskfile);
+ m->mothurOut("Unable to open " + maskfile + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ 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 = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
templatefile = validParameter.validFile(parameters, "template", true);
if (templatefile == "not open") { abort = 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();
+ }
+ }
}
}
int ChimeraPintailCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
for (int s = 0; s < fastaFileNames.size(); s++) {
//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);
+ if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it
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; }
templateSeqsLength = chimera->getLength();
#ifdef USE_MPI
- int pid, end, numSeqsPerProcessor;
+ int pid, numSeqsPerProcessor;
int tag = 2001;
vector<unsigned long int> MPIPos;
MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
- if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; 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++) {
//do your part
driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
- if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; }
}else{ //you are a child process
MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
//do your part
driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
- if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; }
}
//close files
MPI_File_close(&outMPIAccnos);
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
- vector<unsigned long int> positions = divideFile(fastaFileNames[s], processors);
+ 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)]));
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) { outputTypes.clear(); 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{
processIDS.resize(0);
//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());
}
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 j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } outputTypes.clear();
for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
delete chimera;
return 0;
#else
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) { outputTypes.clear(); 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
delete chimera;
for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
- outputNames.push_back(outputFileName);
- outputNames.push_back(accnosFileName);
+ outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
+ outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
m->mothurOutEndLine();
m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
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(filePos->start);
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
}
delete candidateSeq;
- unsigned long int pos = inFASTA.tellg();
- if ((pos == -1) || (pos >= filePos->end)) { break; }
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ unsigned long int pos = inFASTA.tellg();
+ if ((pos == -1) || (pos >= filePos->end)) { break; }
+ #else
+ if (inFASTA.eof()) { break; }
+ #endif
//report progress
if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
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
if (m->control_pressed) { delete candidateSeq; return 1; }
//print results
- bool isChimeric = chimera->print(outMPI, outAccMPI);
+ chimera->print(outMPI, outAccMPI);
}
}
delete candidateSeq;
//pass numSeqs to parent
ofstream out;
string tempFile = outputFileName + toString(getpid()) + ".num.temp";
- openOutputFile(tempFile, out);
+ m->openOutputFile(tempFile, out);
out << num << endl;
out.close();
exit(0);
- }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
}
//force parent to wait until all the processes are done
for (int i = 0; i < processIDS.size(); i++) {
ifstream in;
string tempFile = outputFileName + toString(processIDS[i]) + ".num.temp";
- openInputFile(tempFile, in);
+ m->openInputFile(tempFile, in);
if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
in.close(); remove(tempFile.c_str());
}
projects / mothur.git / blobdiff