X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerabellerophoncommand.cpp;h=5972c62f028100b71b9007785af7c9d4600aaeb4;hb=f663afa231c9bc1b5e18e0ea3bdd2b2ee784f5b2;hp=69eb89533b4988e598c000b8bf5b8a111e07e5e1;hpb=2bbb7273d4bf5209f098c764551c6e072d60df36;p=mothur.git diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp index 69eb895..5972c62 100644 --- a/chimerabellerophoncommand.cpp +++ b/chimerabellerophoncommand.cpp @@ -27,7 +27,7 @@ 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 @@ -38,35 +38,58 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option) { //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 = ""; } - else { - string path; - it = parameters.find("fasta"); - //user has given a template file - if(it != parameters.end()){ - path = hasPath(it->second); - //if the user has not given a path then, add inputdir. else leave path alone. - if (path == "") { parameters["fasta"] = inputDir + it->second; } + + 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 { + 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 = 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 = 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(); + ableToOpen = m->openInputFile(tryPath, in, "noerror"); + fastaFileNames[i] = tryPath; + } + } + in.close(); + + if (ableToOpen == 1) { + m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); + //erase from file list + fastaFileNames.erase(fastaFileNames.begin()+i); + i--; + } + } + + //make sure there is at least one valid file left + if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; } } - - - //check for required parameters - fastafile = validParameter.validFile(parameters, "fasta", true); - if (fastafile == "not open") { abort = true; } - else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.bellerophon command."); 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 = ""; } 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); @@ -89,8 +112,9 @@ void ChimeraBellerophonCommand::help(){ try { m->mothurOut("The chimera.bellerophon command reads a fastafile and creates list of potentially chimeric sequences.\n"); m->mothurOut("The chimera.bellerophon command parameters are fasta, filter, correction, processors, window, increment. The fasta parameter is required.\n"); + m->mothurOut("The fasta parameter is required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n"); m->mothurOut("The filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter, default=false. \n"); - m->mothurOut("The correction parameter allows you to put more emphasis on the distance between highly similar sequences and less emphasis on the differences between remote homologs.\n"); + m->mothurOut("The correction parameter allows you to put more emphasis on the distance between highly similar sequences and less emphasis on the differences between remote homologs, default=true.\n"); m->mothurOut("The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n"); #ifdef USE_MPI m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n"); @@ -98,7 +122,7 @@ void ChimeraBellerophonCommand::help(){ m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras, default is 1/4 sequence length. \n"); m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default is 25.\n"); m->mothurOut("chimera.bellerophon(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors) \n"); - m->mothurOut("Example: chimera.seqs(fasta=AD.align, filter=True, correction=true, window=200) \n"); + m->mothurOut("Example: chimera.bellerophon(fasta=AD.align, filter=True, correction=true, window=200) \n"); m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n"); } catch(exception& e) { @@ -118,69 +142,70 @@ int ChimeraBellerophonCommand::execute(){ if (abort == true) { return 0; } - int start = time(NULL); - - chimera = new Bellerophon(fastafile, filter, correction, window, increment, processors, outputDir); - - string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "bellerophon.chimeras"; - string accnosFileName = outputDir + getRootName(getSimpleName(fastafile)) + "bellerophon.accnos"; - bool hasAccnos = true; - - chimera->getChimeras(); - - if (m->control_pressed) { delete chimera; return 0; } - - #ifdef USE_MPI - MPI_File outMPI; - MPI_File outMPIAccnos; - - int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; - - char* outFilename = new char[accnosFileName.length()]; - memcpy(outFilename, accnosFileName.c_str(), accnosFileName.length()); - - char* FileName = new char[outputFileName.length()]; - memcpy(FileName, outputFileName.c_str(), outputFileName.length()); - - - 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); - - delete FileName; - delete outFilename; + for (int i = 0; i < fastaFileNames.size(); i++) { + + m->mothurOut("Checking sequences from " + fastaFileNames[i] + " ..." ); m->mothurOutEndLine(); + + int start = time(NULL); + + chimera = new Bellerophon(fastaFileNames[i], filter, correction, window, increment, processors, outputDir); + + 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; } + + #ifdef USE_MPI + MPI_File outMPI; + MPI_File outMPIAccnos; + + int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; + + char outFilename[1024]; + strcpy(outFilename, accnosFileName.c_str()); - numSeqs = chimera->print(outMPI, outMPIAccnos); - - MPI_File_close(&outMPI); - MPI_File_close(&outMPIAccnos); + char FileName[1024]; + strcpy(FileName, outputFileName.c_str()); - #else + 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); - ofstream out; - openOutputFile(outputFileName, out); - - ofstream out2; - openOutputFile(accnosFileName, out2); - - numSeqs = chimera->print(out, out2); - out.close(); - out2.close(); - - #endif - - if (m->control_pressed) { remove(accnosFileName.c_str()); remove(outputFileName.c_str()); delete chimera; return 0; } + numSeqs = chimera->print(outMPI, outMPIAccnos); + + MPI_File_close(&outMPI); + MPI_File_close(&outMPIAccnos); + + #else - //delete accnos file if its blank - if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; } + ofstream out; + m->openOutputFile(outputFileName, out); + + ofstream out2; + m->openOutputFile(accnosFileName, 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; } + + 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); + + delete chimera; + } m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); - m->mothurOut(outputFileName); m->mothurOutEndLine(); - if (hasAccnos) { m->mothurOut(accnosFileName); m->mothurOutEndLine(); } + for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } m->mothurOutEndLine(); - m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); - - delete chimera; return 0;