X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerabellerophoncommand.cpp;h=34096159b4e1379d5e7c61ea6094d8514d48267c;hb=c53ef46b40b97c00e32bfd8c3924ce8c51b5cd7b;hp=d7f60e7901322b44d3548db5200bce9d723407e9;hpb=52ea8f3a52c05331b9bd7519ae0b518bda233d05;p=mothur.git diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp index d7f60e7..3409615 100644 --- a/chimerabellerophoncommand.cpp +++ b/chimerabellerophoncommand.cpp @@ -10,8 +10,56 @@ #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; + } + catch(exception& e) { + m->errorOut(e, "ChimeraBellerophonCommand", "ChimeraBellerophonCommand"); + exit(1); + } +} //*************************************************************************************************************** - ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option) { try { abort = false; @@ -27,7 +75,7 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option) { OptionParser parser(option); map parameters = parser.getParameters(); - ValidParameters validParameter; + ValidParameters validParameter("chimera.bellerophon"); map::iterator it; //check to make sure all parameters are valid for command @@ -35,6 +83,11 @@ 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; + //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 = ""; } @@ -42,43 +95,49 @@ 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]; } } int ableToOpen; ifstream in; - - #ifdef USE_MPI - int pid; - MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running - MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are - - if (pid == 0) { - #endif - ableToOpen = openInputFile(fastaFileNames[i], in); - in.close(); + 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() + m->getSimpleName(fastaFileNames[i]); + m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + fastaFileNames[i] = tryPath; + } + } - #ifdef USE_MPI - for (int j = 1; j < processors; j++) { - MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD); - } - }else{ - MPI_Status status; - MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + //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; } - - #endif + } + + in.close(); if (ableToOpen == 1) { - m->mothurOut(fastaFileNames[i] + " will be disregarded."); m->mothurOutEndLine(); + m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); //erase from file list fastaFileNames.erase(fastaFileNames.begin()+i); i--; @@ -91,17 +150,14 @@ 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); @@ -161,14 +217,14 @@ 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"; - bool hasAccnos = true; + + 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; @@ -193,10 +249,10 @@ 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); out.close(); @@ -204,15 +260,12 @@ int ChimeraBellerophonCommand::execute(){ #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; } - - //delete accnos file if its blank - if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; } + 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); - if (hasAccnos) { outputNames.push_back(accnosFileName); } + outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName); + outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName); delete chimera; }