X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarycommand.cpp;h=fbe7964e67f7eb52600bbab1bde5dc28d3ef3a1f;hb=9bc68cbe7fd7c5cf00b66d73d60624de80fb7933;hp=95f42626c9b324a0622c1ff99806384184d42714;hpb=202846c98b9eff0eca7b20a570bfffa8ee4a5f4e;p=mothur.git diff --git a/summarycommand.cpp b/summarycommand.cpp index 95f4262..fbe7964 100644 --- a/summarycommand.cpp +++ b/summarycommand.cpp @@ -14,8 +14,13 @@ #include "chao1.h" #include "bootstrap.h" #include "simpson.h" +#include "simpsoneven.h" +#include "invsimpson.h" #include "npshannon.h" #include "shannon.h" +#include "heip.h" +#include "smithwilson.h" +#include "shannoneven.h" #include "jackknife.h" #include "geom.h" #include "logsd.h" @@ -29,18 +34,65 @@ #include "solow.h" #include "shen.h" +//********************************************************************************************************************** +vector SummaryCommand::getValidParameters(){ + try { + string Array[] = {"label","calc","abund","size","outputdir","groupmode","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "SummaryCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +SummaryCommand::SummaryCommand(){ + try { + abort = true; calledHelp = true; + vector tempOutNames; + outputTypes["summary"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "SummaryCommand", "SummaryCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector SummaryCommand::getRequiredParameters(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "SummaryCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector SummaryCommand::getRequiredFiles(){ + try { + string AlignArray[] = {"shared","list","rabund","sabund","or"}; + vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "SummaryCommand", "getRequiredFiles"); + exit(1); + } +} //********************************************************************************************************************** SummaryCommand::SummaryCommand(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") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; calledHelp = true; } else { //valid paramters for this command @@ -57,13 +109,17 @@ SummaryCommand::SummaryCommand(string option) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + //initialize outputTypes + vector tempOutNames; + outputTypes["summary"] = tempOutNames; + //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 summary.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 = ""; - outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it + outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it } //check for optional parameter and set defaults @@ -71,7 +127,7 @@ SummaryCommand::SummaryCommand(string option) { 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; } } @@ -86,7 +142,7 @@ SummaryCommand::SummaryCommand(string option) { else { if (calc == "default") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; } } - splitAtDash(calc, Estimators); + m->splitAtDash(calc, Estimators); string temp; temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; } @@ -95,8 +151,8 @@ SummaryCommand::SummaryCommand(string option) { temp = validParameter.validFile(parameters, "size", false); if (temp == "not found") { temp = "0"; } convert(temp, size); - temp = validParameter.validFile(parameters, "groupmode", false); if (temp == "not found") { temp = "F"; } - groupMode = isTrue(temp); + temp = validParameter.validFile(parameters, "groupmode", false); if (temp == "not found") { temp = "T"; } + groupMode = m->isTrue(temp); } @@ -118,7 +174,7 @@ void SummaryCommand::help(){ m->mothurOut("Example summary.single(label=unique-.01-.03, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n"); validCalculator->printCalc("summary", cout); m->mothurOut("The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n"); - m->mothurOut("If you are running summary.single with a shared file and would like your summary results collated in one file, set groupmode=t. (Default=False).\n"); + m->mothurOut("If you are running summary.single with a shared file and would like your summary results collated in one file, set groupmode=t. (Default=true).\n"); 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. label), '=' and parameters (i.e.yourLabels).\n\n"); } @@ -137,9 +193,7 @@ SummaryCommand::~SummaryCommand(){} int SummaryCommand::execute(){ try { - if (abort == true) { return 0; } - - vector outputNames; + if (abort == true) { if (calledHelp) { return 0; } return 2; } string hadShared = ""; if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName); } @@ -155,9 +209,9 @@ int SummaryCommand::execute(){ numLines = 0; numCols = 0; - string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[p])) + "summary"; + string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "summary"; globaldata->inputFileName = inputFileNames[p]; - outputNames.push_back(fileNameRoot); + outputNames.push_back(fileNameRoot); outputTypes["summary"].push_back(fileNameRoot); if (inputFileNames.size() > 1) { m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine(); @@ -193,10 +247,20 @@ int SummaryCommand::execute(){ sumCalculators.push_back(new Jackknife()); }else if(Estimators[i] == "shannon"){ sumCalculators.push_back(new Shannon()); + }else if(Estimators[i] == "shannoneven"){ + sumCalculators.push_back(new ShannonEven()); }else if(Estimators[i] == "npshannon"){ sumCalculators.push_back(new NPShannon()); + }else if(Estimators[i] == "heip"){ + sumCalculators.push_back(new Heip()); + }else if(Estimators[i] == "smithwilson"){ + sumCalculators.push_back(new SmithWilson()); }else if(Estimators[i] == "simpson"){ sumCalculators.push_back(new Simpson()); + }else if(Estimators[i] == "simpsoneven"){ + sumCalculators.push_back(new SimpsonEven()); + }else if(Estimators[i] == "invsimpson"){ + sumCalculators.push_back(new InvSimpson()); }else if(Estimators[i] == "bootstrap"){ sumCalculators.push_back(new Bootstrap()); }else if (Estimators[i] == "nseqs") { @@ -219,7 +283,7 @@ int SummaryCommand::execute(){ if (sumCalculators.size() == 0) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } return 0; } ofstream outputFileHandle; - openOutputFile(fileNameRoot, outputFileHandle); + m->openOutputFile(fileNameRoot, outputFileHandle); outputFileHandle << "label"; read = new ReadOTUFile(globaldata->inputFileName); @@ -270,7 +334,7 @@ int SummaryCommand::execute(){ numLines++; } - if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { string saveLabel = sabund->getLabel(); delete sabund; @@ -386,7 +450,7 @@ vector SummaryCommand::parseSharedFile(string filename) { input = globaldata->ginput; 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; i SummaryCommand::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(); } @@ -430,63 +494,78 @@ vector SummaryCommand::parseSharedFile(string filename) { } } //********************************************************************************************************************** -string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector outputNames) { +string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector& outputNames) { try { ofstream out; - string combineFileName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "groups.summary"; + string combineFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "groups.summary"; //open combined file - openOutputFile(combineFileName, out); + m->openOutputFile(combineFileName, out); //open each groups summary file string newLabel = ""; - ifstream* temp; - map filehandles; + map > files; for (int i=0; i thisFilesLines; + + ifstream temp; + m->openInputFile(outputNames[i], temp); //read through first line - labels string tempLabel; if (i == 0) { //we want to save the labels to output below for (int j = 0; j < numCols+1; j++) { - *(temp) >> tempLabel; + temp >> tempLabel; if (j == 1) { newLabel += "group\t" + tempLabel + '\t'; }else{ newLabel += tempLabel + '\t'; } } - }else{ for (int j = 0; j < numCols+1; j++) { *(temp) >> tempLabel; } } + }else{ for (int j = 0; j < numCols+1; j++) { temp >> tempLabel; } } + + m->gobble(temp); + + //for each label + for (int k = 0; k < numLines; k++) { + + string thisLine = ""; + string tempLabel; + + for (int j = 0; j < numCols+1; j++) { + temp >> tempLabel; + + //save for later + if (j == 1) { thisLine += groups[i] + "\t" + tempLabel + "\t"; } + else{ thisLine += tempLabel + "\t"; } + } + + thisLine += "\n"; + + thisFilesLines.push_back(thisLine); + + m->gobble(temp); + } + + files[outputNames[i]] = thisFilesLines; - gobble(*(temp)); + temp.close(); + remove(outputNames[i].c_str()); } //output label line to new file out << newLabel << endl; //for each label - for (int i = 0; i < numLines; i++) { + for (int k = 0; k < numLines; k++) { //grab summary data for each group for (int i=0; i> tempLabel; - - //print to combined file - if (j == 1) { out << groups[i] << '\t' << tempLabel << '\t'; } - else{ out << tempLabel << '\t'; } - } - - out << endl; - gobble(*(filehandles[outputNames[i]])); + out << files[outputNames[i]][k]; } } - //close each groups summary file - for (int i=0; i