X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayercommand.cpp;h=59dd0a55a27c13eb80dd521ea83516770c97ed4a;hb=d71a31a60542608595ce1278cc4a3398479cec7f;hp=2c435cadb11c1bc413b982676ac58082d4683992;hpb=91a27e0483827c06c21c4fe89558923bbfe86573;p=mothur.git diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp index 2c435ca..59dd0a5 100644 --- a/chimeraslayercommand.cpp +++ b/chimeraslayercommand.cpp @@ -98,6 +98,28 @@ string ChimeraSlayerCommand::getHelpString(){ } } //********************************************************************************************************************** +string ChimeraSlayerCommand::getOutputFileNameTag(string type, string inputName=""){ + try { + string outputFileName = ""; + map >::iterator it; + + //is this a type this command creates + it = outputTypes.find(type); + if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } + else { + if (type == "chimera") { outputFileName = "slayer.chimeras"; } + else if (type == "accnos") { outputFileName = "slayer.accnos"; } + else if (type == "fasta") { outputFileName = "slayer.fasta"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } + } + return outputFileName; + } + catch(exception& e) { + m->errorOut(e, "ChimeraSlayerCommand", "getOutputFileNameTag"); + exit(1); + } +} +//********************************************************************************************************************** ChimeraSlayerCommand::ChimeraSlayerCommand(){ try { abort = true; calledHelp = true; @@ -556,9 +578,9 @@ int ChimeraSlayerCommand::execute(){ int start = time(NULL); if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it - string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimera"; - string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.accnos"; - string trimFastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.fasta"; + string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("chimera"); + string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("accnos"); + string trimFastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("fasta"); //clears files ofstream out, out1, out2; @@ -633,6 +655,7 @@ int ChimeraSlayerCommand::execute(){ #endif totalChimeras = deconvoluteResults(parser, outputFileName, accnosFileName, trimFastaFileName); + m->mothurOutEndLine(); m->mothurOut(toString(totalChimeras) + " chimera found."); m->mothurOutEndLine(); #ifdef USE_MPI } MPI_Barrier(MPI_COMM_WORLD); //make everyone wait @@ -641,7 +664,7 @@ int ChimeraSlayerCommand::execute(){ if (parser != NULL) { delete parser; } - m->mothurOutEndLine(); m->mothurOut(toString(totalChimeras) + " chimera found."); m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); + m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); } //set accnos file as new current accnosfile