X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerapintailcommand.cpp;h=7c3b24b8c4595079a053eab7ecd9179a1ac72d69;hb=8c616f2509abd2fb9485a38607c1b439d243b85c;hp=9e1bfe19e0fd82e82425f7d76e529238a10e28b6;hpb=b45e6f3d505a212cebad5ca22e2611b1466bca48;p=mothur.git diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp index 9e1bfe1..7c3b24b 100644 --- a/chimerapintailcommand.cpp +++ b/chimerapintailcommand.cpp @@ -43,7 +43,7 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option) { 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; } } @@ -51,7 +51,7 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option) { 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; } } @@ -59,7 +59,7 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option) { 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; } } @@ -70,12 +70,12 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option) { 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]; } } @@ -83,14 +83,14 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option) { 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; } } @@ -110,7 +110,7 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option) { 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); @@ -125,22 +125,34 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option) { 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); @@ -152,13 +164,22 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option) { 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(); + } + } } } @@ -227,32 +248,52 @@ int ChimeraPintailCommand::execute(){ //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; } @@ -297,7 +338,7 @@ int ChimeraPintailCommand::execute(){ 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++) { @@ -337,7 +378,7 @@ int ChimeraPintailCommand::execute(){ MPI_File_close(&outMPIAccnos); MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case #else - vector positions = divideFile(fastaFileNames[s], processors); + vector 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)])); @@ -361,13 +402,13 @@ int ChimeraPintailCommand::execute(){ //append output files for(int i=1;iappendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName); remove((outputFileName + toString(processIDS[i]) + ".temp").c_str()); } //append output files for(int i=1;iappendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName); remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str()); } @@ -417,13 +458,13 @@ int ChimeraPintailCommand::execute(){ 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); @@ -434,7 +475,7 @@ int ChimeraPintailCommand::driver(linePair* filePos, string outputFName, string 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 @@ -453,8 +494,12 @@ int ChimeraPintailCommand::driver(linePair* filePos, string outputFName, string } 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(); } @@ -497,7 +542,7 @@ int ChimeraPintailCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fi 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 @@ -552,7 +597,7 @@ int ChimeraPintailCommand::createProcesses(string outputFileName, string filenam //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(); @@ -569,7 +614,7 @@ int ChimeraPintailCommand::createProcesses(string outputFileName, string filenam 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()); }