X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerabellerophoncommand.cpp;h=5d7d6d452b2c741ad764623557f0a0d31895ba0e;hb=4b6e3f7b5543822a2cca4fb076ab6af2ce8ca62d;hp=6d0961689d425b1ffd8ba75a86653453e3e72011;hpb=e4c80376cc4533f66c8dfc18f3e1a86a60ac17fe;p=mothur.git diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp index 6d09616..5d7d6d4 100644 --- a/chimerabellerophoncommand.cpp +++ b/chimerabellerophoncommand.cpp @@ -10,8 +10,57 @@ #include "chimerabellerophoncommand.h" #include "bellerophon.h" +//********************************************************************************************************************** +vector ChimeraBellerophonCommand::getValidParameters(){ + try { + string AlignArray[] = {"fasta","filter","correction","processors","window","increment","outputdir","inputdir"}; + vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ChimeraBellerophonCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector ChimeraBellerophonCommand::getRequiredParameters(){ + try { + string AlignArray[] = {"fasta"}; + vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ChimeraBellerophonCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector ChimeraBellerophonCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ChimeraBellerophonCommand", "getRequiredFiles"); + exit(1); + } +} +//********************************************************************************************************************** +ChimeraBellerophonCommand::ChimeraBellerophonCommand(){ + try { + abort = true; + //initialize outputTypes + vector tempOutNames; + outputTypes["chimera"] = tempOutNames; + outputTypes["accnos"] = tempOutNames; + outputTypes["fasta"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "ChimeraBellerophonCommand", "ChimeraBellerophonCommand"); + exit(1); + } +} //*************************************************************************************************************** - ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option) { try { abort = false; @@ -35,6 +84,12 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + //initialize outputTypes + vector tempOutNames; + outputTypes["chimera"] = tempOutNames; + outputTypes["accnos"] = tempOutNames; + outputTypes["fasta"] = tempOutNames; + //if the user changes the input directory command factory will send this info to us in the output parameter string inputDir = validParameter.validFile(parameters, "inputdir", false); if (inputDir == "not found"){ inputDir = ""; } @@ -42,12 +97,12 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option) { fastafile = validParameter.validFile(parameters, "fasta", false); if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.bellerophon 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]; } } @@ -55,17 +110,32 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(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"); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); fastaFileNames[i] = tryPath; } } + + //if you can't open it, try default location + 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) { @@ -82,17 +152,14 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option) { } //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 = ""; } 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, "correction", false); if (temp == "not found") { temp = "T"; } - correction = isTrue(temp); + correction = m->isTrue(temp); temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; } convert(temp, processors); @@ -152,13 +219,14 @@ int ChimeraBellerophonCommand::execute(){ int start = time(NULL); chimera = new Bellerophon(fastaFileNames[i], filter, correction, window, increment, processors, outputDir); - - string outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[i])) + "bellerophon.chimeras"; - string accnosFileName = outputDir + getRootName(getSimpleName(fastaFileNames[i])) + "bellerophon.accnos"; + + if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]); }//if user entered a file with a path then preserve it + string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "bellerophon.chimeras"; + string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "bellerophon.accnos"; chimera->getChimeras(); - if (m->control_pressed) { delete chimera; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { delete chimera; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); return 0; } #ifdef USE_MPI MPI_File outMPI; @@ -175,7 +243,7 @@ int ChimeraBellerophonCommand::execute(){ MPI_File_open(MPI_COMM_WORLD, FileName, outMode, MPI_INFO_NULL, &outMPI); //comm, filename, mode, info, filepointer MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPIAccnos); - numSeqs = chimera->print(outMPI, outMPIAccnos); + numSeqs = chimera->print(outMPI, outMPIAccnos, ""); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); @@ -183,23 +251,23 @@ int ChimeraBellerophonCommand::execute(){ #else ofstream out; - openOutputFile(outputFileName, out); + m->openOutputFile(outputFileName, out); ofstream out2; - openOutputFile(accnosFileName, out2); + m->openOutputFile(accnosFileName, out2); - numSeqs = chimera->print(out, out2); + numSeqs = chimera->print(out, out2, ""); out.close(); out2.close(); #endif - if (m->control_pressed) { remove(accnosFileName.c_str()); remove(outputFileName.c_str()); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete chimera; return 0; } + if (m->control_pressed) { remove(accnosFileName.c_str()); remove(outputFileName.c_str()); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); delete chimera; return 0; } m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine(); - 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); delete chimera; }