X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=rarefactcommand.cpp;h=75a87efa3a2f95259488b0abf15887fb39ee1955;hp=bb9a4fd58b7362eb1ed69216cdfa2aa16817b2c6;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=10e9f1ff74515ff887519b08e50c30c47d2472d2 diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp index bb9a4fd..75a87ef 100644 --- a/rarefactcommand.cpp +++ b/rarefactcommand.cpp @@ -24,75 +24,276 @@ #include "jackknife.h" #include "coverage.h" -//********************************************************************************************************************** - +//********************************************************************************************************************** +vector RareFactCommand::setParameters(){ + try { + CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); 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,true); 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,true); parameters.push_back(pcalc); + CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund); + CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors); + CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pgroupmode); + 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", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string RareFactCommand::getHelpString(){ + try { + ValidCalculators validCalculator; + string helpString = ""; + helpString += "The rarefaction.single command parameters are list, sabund, rabund, shared, label, iters, freq, calc, processors, groupmode 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 += "If you are running rarefaction.single with a shared file and would like your results collated in one file, set groupmode=t. (Default=true).\n"; + 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", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +string RareFactCommand::getOutputPattern(string type) { + try { + string pattern = ""; + if (type == "rarefaction") { pattern = "[filename],rarefaction"; } + else if (type == "r_chao") { pattern = "[filename],r_chao"; } + else if (type == "r_ace") { pattern = "[filename],r_ace"; } + else if (type == "r_jack") { pattern = "[filename],r_jack"; } + else if (type == "r_shannon") { pattern = "[filename],r_shannon"; } + else if (type == "r_shannoneven") { pattern = "[filename],r_shannoneven"; } + else if (type == "r_smithwilson") { pattern = "[filename],r_smithwilson"; } + else if (type == "r_npshannon") { pattern = "[filename],r_npshannon"; } + else if (type == "r_simpson") { pattern = "[filename],r_simpson"; } + else if (type == "r_simpsoneven") { pattern = "[filename],r_simpsoneven"; } + else if (type == "r_invsimpson") { pattern = "[filename],r_invsimpson"; } + else if (type == "r_bootstrap") { pattern = "[filename],r_bootstrap"; } + else if (type == "r_coverage") { pattern = "[filename],r_coverage"; } + else if (type == "r_nseqs") { pattern = "[filename],r_nseqs"; } + else if (type == "r_heip") { pattern = "[filename],r_heip"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "RareFactCommand", "getOutputPattern"); + exit(1); + } +} +//********************************************************************************************************************** +RareFactCommand::RareFactCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["rarefaction"] = tempOutNames; + outputTypes["r_chao"] = tempOutNames; + outputTypes["r_ace"] = tempOutNames; + outputTypes["r_jack"] = tempOutNames; + outputTypes["r_shannon"] = tempOutNames; + outputTypes["r_shannoneven"] = tempOutNames; + outputTypes["r_heip"] = tempOutNames; + outputTypes["r_smithwilson"] = tempOutNames; + outputTypes["r_npshannon"] = tempOutNames; + outputTypes["r_simpson"] = tempOutNames; + outputTypes["r_simpsoneven"] = tempOutNames; + outputTypes["r_invsimpson"] = tempOutNames; + outputTypes["r_bootstrap"] = tempOutNames; + outputTypes["r_coverage"] = tempOutNames; + outputTypes["r_nseqs"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "RareFactCommand", "RareFactCommand"); + exit(1); + } +} +//********************************************************************************************************************** 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") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { - //valid paramters for this command - string Array[] = {"iters","freq","label","calc","abund","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; } } - //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(globaldata->inputFileName); //if user entered a file with a path then preserve it + //initialize outputTypes + vector tempOutNames; + outputTypes["rarefaction"] = tempOutNames; + outputTypes["r_chao"] = tempOutNames; + outputTypes["r_ace"] = tempOutNames; + outputTypes["r_jack"] = tempOutNames; + outputTypes["r_shannon"] = tempOutNames; + outputTypes["r_shannoneven"] = tempOutNames; + outputTypes["r_heip"] = tempOutNames; + outputTypes["r_smithwilson"] = tempOutNames; + outputTypes["r_npshannon"] = tempOutNames; + outputTypes["r_simpson"] = tempOutNames; + outputTypes["r_simpsoneven"] = tempOutNames; + outputTypes["r_invsimpson"] = tempOutNames; + outputTypes["r_bootstrap"] = tempOutNames; + outputTypes["r_coverage"] = tempOutNames; + outputTypes["r_nseqs"] = 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 = ""; } + 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; m->setListFile(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; m->setSabundFile(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; m->setRabundFile(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; m->setSharedFile(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); if (label == "not found") { label = ""; } else { - if(label != "all") { splitAtDash(label, labels); allLines = 0; } + 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"; } else { if (calc == "default") { calc = "sobs"; } } - splitAtDash(calc, Estimators); + m->splitAtDash(calc, Estimators); + if (m->inUsersGroups("citation", Estimators)) { + ValidCalculators validCalc; validCalc.printCitations(Estimators); + //remove citation from list of calcs + for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } } + } string temp; temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; } - convert(temp, freq); + m->mothurConvert(temp, freq); temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; } - convert(temp, abund); + m->mothurConvert(temp, abund); temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; } - convert(temp, nIters); + m->mothurConvert(temp, nIters); + + temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } + m->setProcessors(temp); + m->mothurConvert(temp, processors); + + temp = validParameter.validFile(parameters, "groupmode", false); if (temp == "not found") { temp = "T"; } + groupMode = m->isTrue(temp); } } @@ -103,139 +304,114 @@ 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 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 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; } - vector outputNames; - - string hadShared = ""; - if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName); } - else { hadShared = globaldata->getSharedFile(); inputFileNames = parseSharedFile(globaldata->getSharedFile()); globaldata->setFormat("rabund"); } - - if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } return 0; } + map > labelToEnds; + if ((format != "sharedfile")) { inputFileNames.push_back(inputfile); } + else { inputFileNames = parseSharedFile(sharedfile, labelToEnds); format = "rabund"; } + + if (m->control_pressed) { return 0; } + map file2Group; //index in outputNames[i] -> group for (int p = 0; p < inputFileNames.size(); p++) { - string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[p])); - globaldata->inputFileName = inputFileNames[p]; - - if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } return 0; } + string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])); + + if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->clearGroups(); 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; + map variables; + variables["[filename]"] = fileNameRoot; + 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"); + rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(getOutputFileName("rarefaction",variables)))); + outputNames.push_back(getOutputFileName("rarefaction",variables)); outputTypes["rarefaction"].push_back(getOutputFileName("rarefaction",variables)); }else if (Estimators[i] == "chao") { - rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao"))); - outputNames.push_back(fileNameRoot+"r_chao"); + rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(getOutputFileName("r_chao",variables)))); + outputNames.push_back(getOutputFileName("r_chao",variables)); outputTypes["r_chao"].push_back(getOutputFileName("r_chao",variables)); }else if (Estimators[i] == "ace") { if(abund < 5) abund = 10; - rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"r_ace"))); - outputNames.push_back(fileNameRoot+"r_ace"); + rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(getOutputFileName("r_ace",variables)))); + outputNames.push_back(getOutputFileName("r_ace",variables)); outputTypes["r_ace"].push_back(getOutputFileName("r_ace",variables)); }else if (Estimators[i] == "jack") { - rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack"))); - outputNames.push_back(fileNameRoot+"r_jack"); + rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(getOutputFileName("r_jack",variables)))); + outputNames.push_back(getOutputFileName("r_jack",variables)); outputTypes["r_jack"].push_back(getOutputFileName("r_jack",variables)); }else if (Estimators[i] == "shannon") { - rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon"))); - outputNames.push_back(fileNameRoot+"r_shannon"); + rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(getOutputFileName("r_shannon",variables)))); + outputNames.push_back(getOutputFileName("r_shannon",variables)); outputTypes["r_shannon"].push_back(getOutputFileName("r_shannon",variables)); }else if (Estimators[i] == "shannoneven") { - rDisplays.push_back(new RareDisplay(new ShannonEven(), new ThreeColumnFile(fileNameRoot+"r_shannoneven"))); - outputNames.push_back(fileNameRoot+"r_shannoneven"); + rDisplays.push_back(new RareDisplay(new ShannonEven(), new ThreeColumnFile(getOutputFileName("r_shannoneven",variables)))); + outputNames.push_back(getOutputFileName("r_shannoneven",variables)); outputTypes["r_shannoneven"].push_back(getOutputFileName("r_shannoneven",variables)); }else if (Estimators[i] == "heip") { - rDisplays.push_back(new RareDisplay(new Heip(), new ThreeColumnFile(fileNameRoot+"r_heip"))); - outputNames.push_back(fileNameRoot+"r_heip"); + rDisplays.push_back(new RareDisplay(new Heip(), new ThreeColumnFile(getOutputFileName("r_heip",variables)))); + outputNames.push_back(getOutputFileName("r_heip",variables)); outputTypes["r_heip"].push_back(getOutputFileName("r_heip",variables)); }else if (Estimators[i] == "smithwilson") { - rDisplays.push_back(new RareDisplay(new SmithWilson(), new ThreeColumnFile(fileNameRoot+"r_smithwilson"))); - outputNames.push_back(fileNameRoot+"r_smithwilson"); + rDisplays.push_back(new RareDisplay(new SmithWilson(), new ThreeColumnFile(getOutputFileName("r_smithwilson",variables)))); + outputNames.push_back(getOutputFileName("r_smithwilson",variables)); outputTypes["r_smithwilson"].push_back(getOutputFileName("r_smithwilson",variables)); }else if (Estimators[i] == "npshannon") { - rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon"))); - outputNames.push_back(fileNameRoot+"r_npshannon"); + rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(getOutputFileName("r_npshannon",variables)))); + outputNames.push_back(getOutputFileName("r_npshannon",variables)); outputTypes["r_npshannon"].push_back(getOutputFileName("r_npshannon",variables)); }else if (Estimators[i] == "simpson") { - rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson"))); - outputNames.push_back(fileNameRoot+"r_simpson"); + rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(getOutputFileName("r_simpson",variables)))); + outputNames.push_back(getOutputFileName("r_simpson",variables)); outputTypes["r_simpson"].push_back(getOutputFileName("r_simpson",variables)); }else if (Estimators[i] == "simpsoneven") { - rDisplays.push_back(new RareDisplay(new SimpsonEven(), new ThreeColumnFile(fileNameRoot+"r_simpsoneven"))); - outputNames.push_back(fileNameRoot+"r_simpsoneven"); + rDisplays.push_back(new RareDisplay(new SimpsonEven(), new ThreeColumnFile(getOutputFileName("r_simpsoneven",variables)))); + outputNames.push_back(getOutputFileName("r_simpsoneven",variables)); outputTypes["r_simpsoneven"].push_back(getOutputFileName("r_simpsoneven",variables)); }else if (Estimators[i] == "invsimpson") { - rDisplays.push_back(new RareDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+"r_invsimpson"))); - outputNames.push_back(fileNameRoot+"r_invsimpson"); + rDisplays.push_back(new RareDisplay(new InvSimpson(), new ThreeColumnFile(getOutputFileName("r_invsimpson",variables)))); + outputNames.push_back(getOutputFileName("r_invsimpson",variables)); outputTypes["r_invsimpson"].push_back(getOutputFileName("r_invsimpson",variables)); }else if (Estimators[i] == "bootstrap") { - rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap"))); - outputNames.push_back(fileNameRoot+"r_bootstrap"); + rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(getOutputFileName("r_bootstrap",variables)))); + outputNames.push_back(getOutputFileName("r_bootstrap",variables)); outputTypes["r_bootstrap"].push_back(getOutputFileName("r_bootstrap",variables)); }else if (Estimators[i] == "coverage") { - rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(fileNameRoot+"r_coverage"))); - outputNames.push_back(fileNameRoot+"r_coverage"); + rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(getOutputFileName("r_coverage",variables)))); + outputNames.push_back(getOutputFileName("r_coverage",variables)); outputTypes["r_coverage"].push_back(getOutputFileName("r_coverage",variables)); }else if (Estimators[i] == "nseqs") { - rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs"))); - outputNames.push_back(fileNameRoot+"r_nseqs"); + rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(getOutputFileName("r_nseqs",variables)))); + outputNames.push_back(getOutputFileName("r_nseqs",variables)); outputTypes["r_nseqs"].push_back(getOutputFileName("r_nseqs",variables)); } + if (inputFileNames.size() > 1) { file2Group[outputNames.size()-1] = groups[p]; } } } //if the users entered no valid calculators don't execute command - if (rDisplays.size() == 0) { for(int i=0;iinputFileName); - read->read(&*globaldata); - - order = globaldata->gorder; + 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;imothurRemove(outputNames[i]); } return 0; } //as long as you are not at the end of the file or done wih the lines you want while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { - 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;imothurRemove(outputNames[i]); } return 0; } if(allLines == 1 || labels.count(order->getLabel()) == 1){ m->mothurOut(order->getLabel()); m->mothurOutEndLine(); - rCurve = new Rarefact(order, rDisplays); + map >::iterator itEndings = labelToEnds.find(order->getLabel()); + set ends; + if (itEndings != labelToEnds.end()) { ends = itEndings->second; } + rCurve = new Rarefact(order, rDisplays, processors, ends); rCurve->getCurve(freq, nIters); delete rCurve; @@ -243,14 +419,18 @@ int RareFactCommand::execute(){ userLabels.erase(order->getLabel()); } - if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { string saveLabel = order->getLabel(); delete order; order = (input->getOrderVector(lastLabel)); m->mothurOut(order->getLabel()); m->mothurOutEndLine(); - rCurve = new Rarefact(order, rDisplays); + map >::iterator itEndings = labelToEnds.find(order->getLabel()); + set ends; + if (itEndings != labelToEnds.end()) { ends = itEndings->second; } + rCurve = new Rarefact(order, rDisplays, processors, ends); + rCurve->getCurve(freq, nIters); delete rCurve; @@ -267,7 +447,7 @@ 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;imothurRemove(outputNames[i]); } return 0; } //output error messages about any remaining user labels set::iterator it; @@ -282,7 +462,7 @@ 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;imothurRemove(outputNames[i]); } return 0; } //run last label if you need to if (needToRun == true) { @@ -290,7 +470,11 @@ int RareFactCommand::execute(){ order = (input->getOrderVector(lastLabel)); m->mothurOut(order->getLabel()); m->mothurOutEndLine(); - rCurve = new Rarefact(order, rDisplays); + map >::iterator itEndings = labelToEnds.find(order->getLabel()); + set ends; + if (itEndings != labelToEnds.end()) { ends = itEndings->second; } + rCurve = new Rarefact(order, rDisplays, processors, ends); + rCurve->getCurve(freq, nIters); delete rCurve; @@ -300,16 +484,16 @@ int RareFactCommand::execute(){ 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; } + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + + //create summary file containing all the groups data for each label - this function just combines the info from the files already created. + if ((sharedfile != "") && (groupMode)) { outputNames = createGroupFile(outputNames, file2Group); } + + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); @@ -324,26 +508,179 @@ int RareFactCommand::execute(){ } } //********************************************************************************************************************** -vector RareFactCommand::parseSharedFile(string filename) { +vector RareFactCommand::createGroupFile(vector& outputNames, map file2Group) { + try { + + vector newFileNames; + + //find different types of files + map > typesFiles; + map > > fileLabels; //combofile name to labels. each label is a vector because it may be unique lci hci. + vector groupNames; + for (int i = 0; i < outputNames.size(); i++) { + + string extension = m->getExtension(outputNames[i]); + string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + extension; + m->mothurRemove(combineFileName); //remove old file + + ifstream in; + m->openInputFile(outputNames[i], in); + + string labels = m->getline(in); + + istringstream iss (labels,istringstream::in); + string newLabel = ""; vector theseLabels; + while(!iss.eof()) { iss >> newLabel; m->gobble(iss); theseLabels.push_back(newLabel); } + vector< vector > allLabels; + vector thisSet; thisSet.push_back(theseLabels[0]); allLabels.push_back(thisSet); thisSet.clear(); //makes "numSampled" its own grouping + for (int j = 1; j < theseLabels.size()-1; j++) { + if (theseLabels[j+1] == "lci") { + thisSet.push_back(theseLabels[j]); + thisSet.push_back(theseLabels[j+1]); + thisSet.push_back(theseLabels[j+2]); + j++; j++; + }else{ //no lci or hci for this calc. + thisSet.push_back(theseLabels[j]); + } + allLabels.push_back(thisSet); + thisSet.clear(); + } + fileLabels[combineFileName] = allLabels; + + map >::iterator itfind = typesFiles.find(extension); + if (itfind != typesFiles.end()) { + (itfind->second)[outputNames[i]] = file2Group[i]; + }else { + map temp; + temp[outputNames[i]] = file2Group[i]; + typesFiles[extension] = temp; + } + if (!(m->inUsersGroups(file2Group[i], groupNames))) { groupNames.push_back(file2Group[i]); } + } + + //for each type create a combo file + + for (map >::iterator it = typesFiles.begin(); it != typesFiles.end(); it++) { + + ofstream out; + string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + it->first; + m->openOutputFileAppend(combineFileName, out); + newFileNames.push_back(combineFileName); + map thisTypesFiles = it->second; //it->second maps filename to group + set numSampledSet; + + //open each type summary file + map > > > files; //maps file name to lines in file + int maxLines = 0; + for (map::iterator itFileNameGroup = thisTypesFiles.begin(); itFileNameGroup != thisTypesFiles.end(); itFileNameGroup++) { + + string thisfilename = itFileNameGroup->first; + string group = itFileNameGroup->second; + + ifstream temp; + m->openInputFile(thisfilename, temp); + + //read through first line - labels + m->getline(temp); m->gobble(temp); + + map > > thisFilesLines; + while (!temp.eof()){ + int numSampled = 0; + temp >> numSampled; m->gobble(temp); + + vector< vector > theseReads; + vector thisSet; thisSet.push_back(toString(numSampled)); theseReads.push_back(thisSet); thisSet.clear(); + for (int k = 1; k < fileLabels[combineFileName].size(); k++) { //output thing like 0.03-A lci-A hci-A + vector reads; + string next = ""; + for (int l = 0; l < fileLabels[combineFileName][k].size(); l++) { //output modified labels + temp >> next; m->gobble(temp); + reads.push_back(next); + } + theseReads.push_back(reads); + } + thisFilesLines[numSampled] = theseReads; + m->gobble(temp); + + numSampledSet.insert(numSampled); + } + + files[group] = thisFilesLines; + + //save longest file for below + if (maxLines < thisFilesLines.size()) { maxLines = thisFilesLines.size(); } + + temp.close(); + m->mothurRemove(thisfilename); + } + + //output new labels line + out << fileLabels[combineFileName][0][0] << '\t'; + for (int k = 1; k < fileLabels[combineFileName].size(); k++) { //output thing like 0.03-A lci-A hci-A + for (int n = 0; n < groupNames.size(); n++) { // for each group + for (int l = 0; l < fileLabels[combineFileName][k].size(); l++) { //output modified labels + out << fileLabels[combineFileName][k][l] << '-' << groupNames[n] << '\t'; + } + } + } + out << endl; + + //for each label + for (set::iterator itNumSampled = numSampledSet.begin(); itNumSampled != numSampledSet.end(); itNumSampled++) { + + out << (*itNumSampled) << '\t'; + + if (m->control_pressed) { break; } + + for (int k = 1; k < fileLabels[combineFileName].size(); k++) { //each chunk + //grab data for each group + for (map > > >::iterator itFileNameGroup = files.begin(); itFileNameGroup != files.end(); itFileNameGroup++) { + + string group = itFileNameGroup->first; + + map > >::iterator itLine = files[group].find(*itNumSampled); + if (itLine != files[group].end()) { + for (int l = 0; l < (itLine->second)[k].size(); l++) { + out << (itLine->second)[k][l] << '\t'; + + } + }else { + for (int l = 0; l < fileLabels[combineFileName][k].size(); l++) { + out << "NA" << '\t'; + } + } + } + } + out << endl; + } + out.close(); + } + + //return combine file name + return newFileNames; + + } + catch(exception& e) { + m->errorOut(e, "RareFactCommand", "createGroupFile"); + exit(1); + } +} +//********************************************************************************************************************** +vector RareFactCommand::parseSharedFile(string filename, map >& label2Ends) { try { vector filenames; 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 = getRootName(filename); + string sharedFileRoot = m->getRootName(filename); //clears file before we start to write to it below for (int i=0; igetGroup() + ".rabund").c_str()); + m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".rabund")); filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund")); } @@ -358,9 +695,10 @@ vector RareFactCommand::parseSharedFile(string filename) { for (int i = 0; i < lookup.size(); i++) { RAbundVector rav = lookup[i]->getRAbundVector(); - openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()])); + m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()])); rav.print(*(filehandles[lookup[i]->getGroup()])); (*(filehandles[lookup[i]->getGroup()])).close(); + label2Ends[lookup[i]->getLabel()].insert(rav.getNumSeqs()); } for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } @@ -371,9 +709,9 @@ vector RareFactCommand::parseSharedFile(string filename) { for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; } - delete read; + delete input; - globaldata->ginput = NULL; + m->clearGroups(); return filenames; }