X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactcommand.cpp;h=7f2a1d2e752ce54d971845acdfa8848c4bada8a1;hb=f0a594f6676ef5a52d1f122b6de70de2fda08c81;hp=d430ffc01184cd505ca97ed7a46bb727ab1292b8;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp index d430ffc..7f2a1d2 100644 --- a/rarefactcommand.cpp +++ b/rarefactcommand.cpp @@ -24,45 +24,60 @@ #include "jackknife.h" #include "coverage.h" + //********************************************************************************************************************** -vector RareFactCommand::getValidParameters(){ - try { - string Array[] = {"iters","freq","label","calc","abund","processors","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; - } - catch(exception& e) { - m->errorOut(e, "RareFactCommand", "getValidParameters"); - exit(1); - } -} -//********************************************************************************************************************** -vector RareFactCommand::getRequiredParameters(){ +vector RareFactCommand::setParameters(){ try { + CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist); + CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund); + CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund); + CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared); + CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); + CommandParameter pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq); + CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters); + CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap", "sobs", "", "", "",true,false); parameters.push_back(pcalc); + CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund); + CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } return myArray; } catch(exception& e) { - m->errorOut(e, "RareFactCommand", "getRequiredParameters"); + m->errorOut(e, "RareFactCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -vector RareFactCommand::getRequiredFiles(){ +string RareFactCommand::getHelpString(){ try { - string AlignArray[] = {"shared","list","rabund","sabund","or"}; - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); - return myArray; + ValidCalculators validCalculator; + string helpString = ""; + helpString += "The rarefaction.single command parameters are list, sabund, rabund, shared, label, iters, freq, calc, processors and abund. list, sabund, rabund or shared is required unless you have a valid current file. \n"; + helpString += "The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n"; + helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n"; + helpString += "The rarefaction.single command should be in the following format: \n"; + helpString += "rarefaction.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n"; + helpString += "Example rarefaction.single(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n"; + helpString += "The default values for iters is 1000, freq is 100, and calc is rarefaction which calculates the rarefaction curve for the observed richness.\n"; + validCalculator.printCalc("rarefaction"); + helpString += "The label parameter is used to analyze specific labels in your input.\n"; + helpString += "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n"; + return helpString; } catch(exception& e) { - m->errorOut(e, "RareFactCommand", "getRequiredFiles"); + m->errorOut(e, "RareFactCommand", "getHelpString"); exit(1); } } + //********************************************************************************************************************** RareFactCommand::RareFactCommand(){ try { - //initialize outputTypes + abort = true; calledHelp = true; + setParameters(); vector tempOutNames; outputTypes["rarefaction"] = tempOutNames; outputTypes["r_chao"] = tempOutNames; @@ -88,27 +103,23 @@ RareFactCommand::RareFactCommand(){ //********************************************************************************************************************** RareFactCommand::RareFactCommand(string option) { try { - globaldata = GlobalData::getInstance(); - abort = false; + abort = false; calledHelp = false; allLines = 1; - labels.clear(); - Estimators.clear(); - + //allow user to run help - if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; } + if(option == "help") { abort = true; calledHelp = true; } else { - //valid paramters for this command - string Array[] = {"iters","freq","label","calc","abund","processors","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); + map::iterator it; ValidParameters validParameter; //check to make sure all parameters are valid for command - for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { + for (it = parameters.begin(); it != parameters.end(); it++) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } @@ -130,15 +141,92 @@ RareFactCommand::RareFactCommand(string option) { outputTypes["r_coverage"] = tempOutNames; outputTypes["r_nseqs"] = tempOutNames; - //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 += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it + //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("shared"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["shared"] = inputDir + it->second; } + } + + it = parameters.find("rabund"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["rabund"] = inputDir + it->second; } + } + + it = parameters.find("sabund"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["sabund"] = inputDir + it->second; } + } + + it = parameters.find("list"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["list"] = inputDir + it->second; } + } } - - //make sure the user has already run the read.otu command - if ((globaldata->getSharedFile() == "") && (globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { m->mothurOut("You must read a list, sabund, rabund or shared file before you can use the rarefact.single command."); m->mothurOutEndLine(); abort = true; } + //check for required parameters + listfile = validParameter.validFile(parameters, "list", true); + if (listfile == "not open") { listfile = ""; abort = true; } + else if (listfile == "not found") { listfile = ""; } + else { format = "list"; inputfile = listfile; } + + sabundfile = validParameter.validFile(parameters, "sabund", true); + if (sabundfile == "not open") { sabundfile = ""; abort = true; } + else if (sabundfile == "not found") { sabundfile = ""; } + else { format = "sabund"; inputfile = sabundfile; } + + rabundfile = validParameter.validFile(parameters, "rabund", true); + if (rabundfile == "not open") { rabundfile = ""; abort = true; } + else if (rabundfile == "not found") { rabundfile = ""; } + else { format = "rabund"; inputfile = rabundfile; } + + sharedfile = validParameter.validFile(parameters, "shared", true); + if (sharedfile == "not open") { sharedfile = ""; abort = true; } + else if (sharedfile == "not found") { sharedfile = ""; } + else { format = "sharedfile"; inputfile = sharedfile; } + + if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) { + //is there are current file available for any of these? + //give priority to shared, then list, then rabund, then sabund + //if there is a current shared file, use it + sharedfile = m->getSharedFile(); + if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); } + else { + listfile = m->getListFile(); + if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); } + else { + rabundfile = m->getRabundFile(); + if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); } + else { + sabundfile = m->getSabundFile(); + if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("No valid current files. You must provide a list, sabund, rabund or shared file before you can use the collect.single 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 = m->hasPath(inputfile); } + //check for optional parameter and set defaults // ...at some point should added some additional type checking... label = validParameter.validFile(parameters, "label", false); @@ -147,12 +235,6 @@ RareFactCommand::RareFactCommand(string option) { if(label != "all") { m->splitAtDash(label, labels); allLines = 0; } else { allLines = 1; } } - - //if the user has not specified any labels use the ones from read.otu - if(label == "") { - allLines = globaldata->allLines; - labels = globaldata->labels; - } calc = validParameter.validFile(parameters, "calc", false); if (calc == "not found") { calc = "sobs"; } @@ -171,7 +253,8 @@ RareFactCommand::RareFactCommand(string option) { temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; } convert(temp, nIters); - temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; } + temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } + m->setProcessors(temp); convert(temp, processors); } @@ -183,60 +266,31 @@ RareFactCommand::RareFactCommand(string option) { } //********************************************************************************************************************** -void RareFactCommand::help(){ - try { - m->mothurOut("The rarefaction.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n"); - m->mothurOut("The rarefaction.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster.\n"); - m->mothurOut("The rarefaction.single command parameters are label, iters, freq, calc, processors and abund. No parameters are required. \n"); - m->mothurOut("The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n"); - m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n"); - m->mothurOut("The rarefaction.single command should be in the following format: \n"); - m->mothurOut("rarefaction.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n"); - m->mothurOut("Example rarefaction.single(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n"); - m->mothurOut("The default values for iters is 1000, freq is 100, and calc is rarefaction which calculates the rarefaction curve for the observed richness.\n"); - validCalculator->printCalc("rarefaction", cout); - m->mothurOut("The label parameter is used to analyze specific labels in your input.\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "RareFactCommand", "help"); - exit(1); - } -} - -//********************************************************************************************************************** - -RareFactCommand::~RareFactCommand(){} - -//********************************************************************************************************************** - int RareFactCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } - string hadShared = ""; - if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName); } - else { hadShared = globaldata->getSharedFile(); inputFileNames = parseSharedFile(globaldata->getSharedFile()); globaldata->setFormat("rabund"); } + if ((format != "sharedfile")) { inputFileNames.push_back(inputfile); } + else { inputFileNames = parseSharedFile(sharedfile); format = "rabund"; } - if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } return 0; } + if (m->control_pressed) { return 0; } for (int p = 0; p < inputFileNames.size(); p++) { string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])); - globaldata->inputFileName = inputFileNames[p]; - - if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } return 0; } + + if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } m->Groups.clear(); return 0; } if (inputFileNames.size() > 1) { m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine(); } int i; - validCalculator = new ValidCalculators(); - + ValidCalculators validCalculator; + for (i=0; iisValidCalculator("rarefaction", Estimators[i]) == true) { + if (validCalculator.isValidCalculator("rarefaction", Estimators[i]) == true) { if (Estimators[i] == "sobs") { rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction"))); outputNames.push_back(fileNameRoot+"rarefaction"); outputTypes["rarefaction"].push_back(fileNameRoot+"rarefaction"); @@ -290,25 +344,22 @@ int RareFactCommand::execute(){ //if the users entered no valid calculators don't execute command - if (rDisplays.size() == 0) { for(int i=0;iinputFileName); - read->read(&*globaldata); + if (rDisplays.size() == 0) { for(int i=0;igorder; + input = new InputData(inputFileNames[p], format); + order = input->getOrderVector(); string lastLabel = order->getLabel(); - input = globaldata->ginput; //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. set processedLabels; set userLabels = labels; - if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } for(int i=0;iginput = NULL; delete order; globaldata->gorder = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { for(int i=0;icontrol_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } for(int i=0;iginput = NULL; delete order; globaldata->gorder = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { for(int i=0;igetLabel()) == 1){ @@ -346,7 +397,7 @@ int RareFactCommand::execute(){ order = (input->getOrderVector()); } - if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } for(int i=0;iginput = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { for(int i=0;i::iterator it; @@ -361,7 +412,7 @@ int RareFactCommand::execute(){ } } - if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } for(int i=0;iginput = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { for(int i=0;igorder = NULL; - delete input; globaldata->ginput = NULL; - delete read; - delete validCalculator; - + delete input; } - if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } @@ -410,12 +456,7 @@ vector RareFactCommand::parseSharedFile(string filename) { map filehandles; map::iterator it3; - - //read first line - read = new ReadOTUFile(filename); - read->read(&*globaldata); - - input = globaldata->ginput; + input = new InputData(filename, "sharedfile"); vector lookup = input->getSharedRAbundVectors(); string sharedFileRoot = m->getRootName(filename); @@ -450,9 +491,9 @@ vector RareFactCommand::parseSharedFile(string filename) { for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; } - delete read; + delete input; - globaldata->ginput = NULL; + m->Groups.clear(); return filenames; }