X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=summarysharedcommand.cpp;h=59c12a03dae958f4bb199a6aad94056264c0426a;hp=8b3a63f8688e557f290aa9db1acda63ae4de5426;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=83950cc7a80a36c79dededb484daec5ec26b330f diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp index 8b3a63f..59c12a0 100644 --- a/summarysharedcommand.cpp +++ b/summarysharedcommand.cpp @@ -8,293 +8,969 @@ */ #include "summarysharedcommand.h" -#include "sharedsobscollectsummary.h" -#include "sharedchao1.h" -#include "sharedace.h" -#include "sharednseqs.h" -#include "sharedjabund.h" -#include "sharedsorabund.h" -#include "sharedjclass.h" -#include "sharedsorclass.h" -#include "sharedjest.h" -#include "sharedsorest.h" -#include "sharedthetayc.h" -#include "sharedthetan.h" -#include "sharedkstest.h" -#include "sharedbdiversity.h" -#include "sharedochiai.h" -//#include "sharedanderberg.h" -#include "sharedkulczynski.h" -#include "sharedkulczynskicody.h" -#include "sharedlennon.h" -#include "sharedmorisitahorn.h" -#include "sharedbraycurtis.h" - +#include "subsample.h" +//********************************************************************************************************************** +vector SummarySharedCommand::setParameters(){ + try { + CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pshared); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + CommandParameter psubsample("subsample", "String", "", "", "", "", "","phylip",false,false); parameters.push_back(psubsample); + CommandParameter pdistance("distance", "Boolean", "", "F", "", "", "","phylip",false,false); parameters.push_back(pdistance); + CommandParameter pcalc("calc", "Multiple", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson-jsd-rjsd", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "","",true,false,true); parameters.push_back(pcalc); + CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "","",false,false); parameters.push_back(poutput); + CommandParameter pall("all", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pall); + CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters); + CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors); + CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups); + 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, "SummarySharedCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string SummarySharedCommand::getHelpString(){ + try { + string helpString = ""; + ValidCalculators validCalculator; + helpString += "The summary.shared command parameters are shared, label, calc, distance, processors, subsample, iters and all. shared is required if there is no current sharedfile.\n"; + helpString += "The summary.shared command should be in the following format: \n"; + helpString += "summary.shared(label=yourLabel, calc=yourEstimators, groups=yourGroups).\n"; + helpString += "Example summary.shared(label=unique-.01-.03, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n"; + helpString += validCalculator.printCalc("sharedsummary"); + helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n"; + helpString += "The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group.\n"; + helpString += "The output parameter allows you to specify format of your distance matrix. Options are lt, and square. The default is lt.\n"; + helpString += "The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan\n"; + helpString += "The default value for groups is all the groups in your groupfile.\n"; + helpString += "The distance parameter allows you to indicate you would like a distance file created for each calculator for each label, default=f.\n"; + helpString += "The label parameter is used to analyze specific labels in your input.\n"; + helpString += "The all parameter is used to specify if you want the estimate of all your groups together. This estimate can only be made for sharedsobs and sharedchao calculators. The default is false.\n"; + helpString += "If you use sharedchao and run into memory issues, set all to false. \n"; + helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups.\n"; + helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "SummarySharedCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +string SummarySharedCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "summary") { pattern = "[filename],summary-[filename],[tag],summary"; } + else if (type == "phylip") { pattern = "[filename],[calc],[distance],[outputtag],[tag2],dist"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "SummarySharedCommand", "getOutputPattern"); + exit(1); + } +} +//********************************************************************************************************************** +SummarySharedCommand::SummarySharedCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["summary"] = tempOutNames; + outputTypes["phylip"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "SummarySharedCommand", "SummarySharedCommand"); + exit(1); + } +} //********************************************************************************************************************** -SummarySharedCommand::SummarySharedCommand(){ +SummarySharedCommand::SummarySharedCommand(string option) { try { - globaldata = GlobalData::getInstance(); - outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary"); - openOutputFile(outputFileName, outputFileHandle); - format = globaldata->getFormat(); - validCalculator = new ValidCalculators(); + abort = false; calledHelp = false; + allLines = 1; + + //allow user to run help + if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} - int i; - for (i=0; iEstimators.size(); i++) { - if (validCalculator->isValidCalculator("sharedsummary", globaldata->Estimators[i]) == true) { - if (globaldata->Estimators[i] == "sharedsobs") { - sumCalculators.push_back(new SharedSobsCS()); - }else if (globaldata->Estimators[i] == "sharedchao") { - sumCalculators.push_back(new SharedChao1()); - }else if (globaldata->Estimators[i] == "sharedace") { - sumCalculators.push_back(new SharedAce()); - }else if (globaldata->Estimators[i] == "sharedjabund") { - sumCalculators.push_back(new SharedJAbund()); - }else if (globaldata->Estimators[i] == "sharedsorensonabund") { - sumCalculators.push_back(new SharedSorAbund()); - }else if (globaldata->Estimators[i] == "sharedjclass") { - sumCalculators.push_back(new SharedJclass()); - }else if (globaldata->Estimators[i] == "sharedsorclass") { - sumCalculators.push_back(new SharedSorClass()); - }else if (globaldata->Estimators[i] == "sharedjest") { - sumCalculators.push_back(new SharedJest()); - }else if (globaldata->Estimators[i] == "sharedsorest") { - sumCalculators.push_back(new SharedSorEst()); - }else if (globaldata->Estimators[i] == "sharedthetayc") { - sumCalculators.push_back(new SharedThetaYC()); - }else if (globaldata->Estimators[i] == "sharedthetan") { - sumCalculators.push_back(new SharedThetaN()); - }else if (globaldata->Estimators[i] == "sharedkstest") { - sumCalculators.push_back(new SharedKSTest()); - }else if (globaldata->Estimators[i] == "sharednseqs") { - sumCalculators.push_back(new SharedNSeqs()); - }else if (globaldata->Estimators[i] == "sharedochiai") { - sumCalculators.push_back(new SharedOchiai()); - //}else if (globaldata->Estimators[i] == "sharedanderberg") { - //sumCalculators.push_back(new SharedAnderberg()); - }else if (globaldata->Estimators[i] == "sharedkulczynski") { - sumCalculators.push_back(new SharedKulczynski()); - }else if (globaldata->Estimators[i] == "sharedkulczynskicody") { - sumCalculators.push_back(new SharedKulczynskiCody()); - }else if (globaldata->Estimators[i] == "sharedlennon") { - sumCalculators.push_back(new SharedLennon()); - }else if (globaldata->Estimators[i] == "sharedmorisitahorn") { - sumCalculators.push_back(new SharedMorHorn()); - }else if (globaldata->Estimators[i] == "sharedbraycurtis") { - sumCalculators.push_back(new SharedBrayCurtis()); + else { + 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++) { + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + } + + //initialize outputTypes + vector tempOutNames; + outputTypes["summary"] = tempOutNames; + outputTypes["phylip"] = 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; } } - else if (globaldata->Estimators[i] == "sharedbdiversity") { - sumCalculators.push_back(new SharedBDiversity()); + } + + //get shared file + sharedfile = validParameter.validFile(parameters, "shared", true); + if (sharedfile == "not open") { sharedfile = ""; abort = true; } + else if (sharedfile == "not found") { + //if there is a current shared file, use it + sharedfile = m->getSharedFile(); + if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; } + }else { m->setSharedFile(sharedfile); } + + + //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(sharedfile); } + + + //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") { m->splitAtDash(label, labels); allLines = 0; } + else { allLines = 1; } + } + + + calc = validParameter.validFile(parameters, "calc", false); + if (calc == "not found") { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; } + else { + if (calc == "default") { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; } + } + 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; } } + } + + groups = validParameter.validFile(parameters, "groups", false); + if (groups == "not found") { groups = ""; } + else { + m->splitAtDash(groups, Groups); + m->setGroups(Groups); + } + + string temp = validParameter.validFile(parameters, "all", false); if (temp == "not found") { temp = "false"; } + all = m->isTrue(temp); + + temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; } + m->mothurConvert(temp, iters); + + output = validParameter.validFile(parameters, "output", false); + if(output == "not found"){ output = "lt"; } + else { createPhylip = true; } + if ((output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are lt and square. I will use lt."); m->mothurOutEndLine(); output = "lt"; } + + temp = validParameter.validFile(parameters, "subsample", false); if (temp == "not found") { temp = "F"; } + if (m->isNumeric1(temp)) { m->mothurConvert(temp, subsampleSize); subsample = true; } + else { + if (m->isTrue(temp)) { subsample = true; subsampleSize = -1; } //we will set it to smallest group later + else { subsample = false; } + } + + if (subsample == false) { iters = 0; } + + temp = validParameter.validFile(parameters, "distance", false); if (temp == "not found") { temp = "false"; } + createPhylip = m->isTrue(temp); + if (subsample) { createPhylip = true; } + + temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } + m->setProcessors(temp); + m->mothurConvert(temp, processors); + + if (abort == false) { + + ValidCalculators validCalculator; + int i; + + for (i=0; isetCalc(""); - } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function SummarySharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SummarySharedCommand", "SummarySharedCommand"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the SummarySharedCommand class function SummarySharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //********************************************************************************************************************** -SummarySharedCommand::~SummarySharedCommand(){ - delete input; - delete read; -} - -//********************************************************************************************************************** - int SummarySharedCommand::execute(){ try { - int count = 1; + + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + ofstream outputFileHandle, outAll; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile)); + string outputFileName = getOutputFileName("summary",variables); //if the users entered no valid calculators don't execute command if (sumCalculators.size() == 0) { return 0; } - - if (format == "sharedfile") { - read = new ReadPhilFile(globaldata->inputFileName); - read->read(&*globaldata); - - input = globaldata->ginput; - order = input->getSharedOrderVector(); - }else { - //you are using a list and a groupfile - read = new ReadPhilFile(globaldata->inputFileName); - read->read(&*globaldata); - - input = globaldata->ginput; - SharedList = globaldata->gSharedList; - order = SharedList->getSharedOrderVector(); + //check if any calcs can do multiples + else{ + if (all){ + for (int i = 0; i < sumCalculators.size(); i++) { + if (sumCalculators[i]->getMultiple() == true) { mult = true; } + } + } } - - //set users groups - setGroups(); - + + input = new InputData(sharedfile, "sharedfile"); + lookup = input->getSharedRAbundVectors(); + string lastLabel = lookup[0]->getLabel(); + + /******************************************************/ + //output headings for files + /******************************************************/ //output estimator names as column headers + m->openOutputFile(outputFileName, outputFileHandle); outputFileHandle << "label" <<'\t' << "comparison" << '\t'; for(int i=0;igetName(); + if (sumCalculators[i]->getCols() == 3) { outputFileHandle << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci"; } } outputFileHandle << endl; + outputFileHandle.close(); + + //create file and put column headers for multiple groups file + variables["[tag]"]= "multiple"; + string outAllFileName = getOutputFileName("summary",variables); + if (mult == true) { + m->openOutputFile(outAllFileName, outAll); + outputNames.push_back(outAllFileName); + + outAll << "label" <<'\t' << "comparison" << '\t'; + for(int i=0;igetMultiple() == true) { + outAll << '\t' << sumCalculators[i]->getName(); + } + } + outAll << endl; + outAll.close(); + } - while(order != NULL){ + if (lookup.size() < 2) { + m->mothurOut("I cannot run the command without at least 2 valid groups."); + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + + //close files and clean up + m->mothurRemove(outputFileName); + if (mult == true) { m->mothurRemove(outAllFileName); } + return 0; + //if you only have 2 groups you don't need a .sharedmultiple file + }else if ((lookup.size() == 2) && (mult == true)) { + mult = false; + m->mothurRemove(outAllFileName); + outputNames.pop_back(); + } - if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){ - - cout << order->getLabel() << '\t' << count << endl; - getSharedVectors(); //fills group vectors from order vector. - - //randomize group order - if (globaldata->getJumble() == "1") { random_shuffle(lookup.begin(), lookup.end()); } + if (m->control_pressed) { + if (mult) { m->mothurRemove(outAllFileName); } + m->mothurRemove(outputFileName); + delete input; + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + for(int i=0;iclearGroups(); + return 0; + } + /******************************************************/ + if (subsample) { + if (subsampleSize == -1) { //user has not set size, set size = smallest samples size + subsampleSize = lookup[0]->getNumSeqs(); + for (int i = 1; i < lookup.size(); i++) { + int thisSize = lookup[i]->getNumSeqs(); + + if (thisSize < subsampleSize) { subsampleSize = thisSize; } + } + }else { + m->clearGroups(); + Groups.clear(); + vector temp; + for (int i = 0; i < lookup.size(); i++) { + if (lookup[i]->getNumSeqs() < subsampleSize) { + m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine(); + delete lookup[i]; + }else { + Groups.push_back(lookup[i]->getGroup()); + temp.push_back(lookup[i]); + } + } + lookup = temp; + m->setGroups(Groups); + } + + if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; delete input; return 0; } + } - int n = 1; - for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare - for (int l = n; l < lookup.size(); l++) { - outputFileHandle << order->getLabel() << '\t' << (lookup[k]->getGroup() + lookup[l]->getGroup()) << '\t' << '\t'; //print out label and group - outputFileHandle << order->getLabel() << '\t'; - - //sort groups to be alphanumeric - if (lookup[k]->getGroup() > lookup[l]->getGroup()) { - outputFileHandle << (lookup[l]->getGroup() +'\t' + lookup[k]->getGroup()) << '\t'; //print out groups - }else{ - outputFileHandle << (lookup[k]->getGroup() +'\t' + lookup[l]->getGroup()) << '\t'; //print out groups - } - - for(int i=0;igetValues(lookup[k], lookup[l]); //saves the calculator outputs - outputFileHandle << '\t'; - sumCalculators[i]->print(outputFileHandle); - } - outputFileHandle << endl; - } - n++; - } + + /******************************************************/ + //comparison breakup to be used by different processes later + numGroups = lookup.size(); + lines.resize(processors); + for (int i = 0; i < processors; i++) { + lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups); + lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups); + } + /******************************************************/ + + //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; + + //as long as you are not at the end of the file or done wih the lines you want + while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { + if (m->control_pressed) { + if (mult) { m->mothurRemove(outAllFileName); } + m->mothurRemove(outputFileName); + delete input; + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + for(int i=0;iclearGroups(); + return 0; } + + if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + process(lookup, outputFileName, outAllFileName); + + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + } + + if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = lookup[0]->getLabel(); + + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + lookup = input->getSharedRAbundVectors(lastLabel); + + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + process(lookup, outputFileName, outAllFileName); + + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + + //restore real lastlabel to save below + lookup[0]->setLabel(saveLabel); + } + + lastLabel = lookup[0]->getLabel(); + //get next line to process - if (format == "sharedfile") { - order = input->getSharedOrderVector(); + //prevent memory leak + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + lookup = input->getSharedRAbundVectors(); + } + + if (m->control_pressed) { + if (mult) { m->mothurRemove(outAllFileName); } + m->mothurRemove(outputFileName); + delete input; + for(int i=0;iclearGroups(); + return 0; + } + + //output error messages about any remaining user labels + set::iterator it; + bool needToRun = false; + for (it = userLabels.begin(); it != userLabels.end(); it++) { + m->mothurOut("Your file does not include the label " + *it); + if (processedLabels.count(lastLabel) != 1) { + m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); + needToRun = true; }else { - //you are using a list and a groupfile - SharedList = input->getSharedListVector(); //get new list vector to process - if (SharedList != NULL) { - order = SharedList->getSharedOrderVector(); //gets new order vector with group info. - }else { - break; - } + m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); } - count++; } + //run last label if you need to + if (needToRun == true) { + for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } } + lookup = input->getSharedRAbundVectors(lastLabel); + + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + process(lookup, outputFileName, outAllFileName); + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + } + + //reset groups parameter - globaldata->Groups.clear(); globaldata->setGroups(""); + m->clearGroups(); + + for(int i=0;icontrol_pressed) { + m->mothurRemove(outAllFileName); + m->mothurRemove(outputFileName); + return 0; + } + + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + m->mothurOut(outputFileName); m->mothurOutEndLine(); + if (mult) { m->mothurOut(outAllFileName); m->mothurOutEndLine(); outputTypes["summary"].push_back(outAllFileName); } + for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } outputTypes["summary"].push_back(outputFileName); + m->mothurOutEndLine(); return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SummarySharedCommand", "execute"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the SummarySharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } - -//********************************************************************************************************************** - -void SummarySharedCommand::getSharedVectors(){ -try { - lookup.clear(); - //create and initialize vector of sharedvectors, one for each group - for (int i = 0; i < globaldata->Groups.size(); i++) { - SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins()); - temp->setLabel(order->getLabel()); - temp->setGroup(globaldata->Groups[i]); - lookup.push_back(temp); - } +/***********************************************************/ +int SummarySharedCommand::printSims(ostream& out, vector< vector >& simMatrix) { + try { - int numSeqs = order->size(); - //sample all the members - for(int i=0;iget(i); - int abundance; - - //set info for sharedvector in chosens group - for (int j = 0; j < lookup.size(); j++) { - if (chosen.group == lookup[j]->getGroup()) { - abundance = lookup[j]->getAbundance(chosen.bin); - lookup[j]->set(chosen.bin, (abundance + 1), chosen.group); - break; + out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint); + + //output num seqs + out << simMatrix.size() << endl; + + if (output == "lt") { + for (int b = 0; b < simMatrix.size(); b++) { + out << lookup[b]->getGroup() << '\t'; + for (int n = 0; n < b; n++) { + if (m->control_pressed) { return 0; } + out << simMatrix[b][n] << '\t'; } + out << endl; + } + }else{ + for (int b = 0; b < simMatrix.size(); m++) { + out << lookup[b]->getGroup() << '\t'; + for (int n = 0; n < simMatrix[b].size(); n++) { + if (m->control_pressed) { return 0; } + out << simMatrix[b][n] << '\t'; + } + out << endl; } } + + return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SummarySharedCommand", "printSims"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the SummarySharedCommand class function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +/***********************************************************/ +int SummarySharedCommand::process(vector thisLookup, string sumFileName, string sumAllFileName) { + try { + vector< vector< vector > > calcDistsTotals; //each iter, one for each calc, then each groupCombos dists. this will be used to make .dist files + vector< vector > calcDists; calcDists.resize(sumCalculators.size()); + + for (int thisIter = 0; thisIter < iters+1; thisIter++) { + + vector thisItersLookup = thisLookup; + + if (subsample && (thisIter != 0)) { //we want the summary results for the whole dataset, then the subsampling + SubSample sample; + vector tempLabels; //dont need since we arent printing the sampled sharedRabunds + + //make copy of lookup so we don't get access violations + vector newLookup; + for (int k = 0; k < thisItersLookup.size(); k++) { + SharedRAbundVector* temp = new SharedRAbundVector(); + temp->setLabel(thisItersLookup[k]->getLabel()); + temp->setGroup(thisItersLookup[k]->getGroup()); + newLookup.push_back(temp); + } + + //for each bin + for (int k = 0; k < thisItersLookup[0]->getNumBins(); k++) { + if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; } + for (int j = 0; j < thisItersLookup.size(); j++) { newLookup[j]->push_back(thisItersLookup[j]->getAbundance(k), thisItersLookup[j]->getGroup()); } + } + + tempLabels = sample.getSample(newLookup, subsampleSize); + thisItersLookup = newLookup; + } + + + if(processors == 1){ + driver(thisLookup, 0, numGroups, sumFileName+".temp", sumAllFileName+".temp", calcDists); + m->appendFiles((sumFileName + ".temp"), sumFileName); + m->mothurRemove((sumFileName + ".temp")); + if (mult) { + m->appendFiles((sumAllFileName + ".temp"), sumAllFileName); + m->mothurRemove((sumAllFileName + ".temp")); + } + }else{ + + int process = 1; + vector processIDS; + +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + //loop through and create all the processes you want + while (process != processors) { + int pid = fork(); + + if (pid > 0) { + processIDS.push_back(pid); + process++; + }else if (pid == 0){ + driver(thisLookup, lines[process].start, lines[process].end, sumFileName + toString(getpid()) + ".temp", sumAllFileName + toString(getpid()) + ".temp", calcDists); + + //only do this if you want a distance file + if (createPhylip) { + string tempdistFileName = m->getRootName(m->getSimpleName(sumFileName)) + toString(getpid()) + ".dist"; + ofstream outtemp; + m->openOutputFile(tempdistFileName, outtemp); + + for (int i = 0; i < calcDists.size(); i++) { + outtemp << calcDists[i].size() << endl; + + for (int j = 0; j < calcDists[i].size(); j++) { + outtemp << calcDists[i][j].seq1 << '\t' << calcDists[i][j].seq2 << '\t' << calcDists[i][j].dist << endl; + } + } + outtemp.close(); + } + + exit(0); + }else { + m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); + for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); } + exit(0); + } + } + + //parent do your part + driver(thisLookup, lines[0].start, lines[0].end, sumFileName + toString(getpid()) + ".temp", sumAllFileName + toString(getpid()) + ".temp", calcDists); + m->appendFiles((sumFileName + toString(getpid()) + ".temp"), sumFileName); + m->mothurRemove((sumFileName + toString(getpid()) + ".temp")); + if (mult) { m->appendFiles((sumAllFileName + toString(getpid()) + ".temp"), sumAllFileName); } + + //force parent to wait until all the processes are done + for (int i = 0; i < processIDS.size(); i++) { + int temp = processIDS[i]; + wait(&temp); + } + + for (int i = 0; i < processIDS.size(); i++) { + m->appendFiles((sumFileName + toString(processIDS[i]) + ".temp"), sumFileName); + m->mothurRemove((sumFileName + toString(processIDS[i]) + ".temp")); + if (mult) { m->mothurRemove((sumAllFileName + toString(processIDS[i]) + ".temp")); } + + if (createPhylip) { + string tempdistFileName = m->getRootName(m->getSimpleName(sumFileName)) + toString(processIDS[i]) + ".dist"; + ifstream intemp; + m->openInputFile(tempdistFileName, intemp); + + for (int k = 0; k < calcDists.size(); k++) { + int size = 0; + intemp >> size; m->gobble(intemp); + + for (int j = 0; j < size; j++) { + int seq1 = 0; + int seq2 = 0; + float dist = 1.0; + + intemp >> seq1 >> seq2 >> dist; m->gobble(intemp); + + seqDist tempDist(seq1, seq2, dist); + calcDists[k].push_back(tempDist); + } + } + intemp.close(); + m->mothurRemove(tempdistFileName); + } + } +#else + ////////////////////////////////////////////////////////////////////////////////////////////////////// + //Windows version shared memory, so be careful when passing variables through the summarySharedData struct. + //Above fork() will clone, so memory is separate, but that's not the case with windows, + //Taking advantage of shared memory to pass results vectors. + ////////////////////////////////////////////////////////////////////////////////////////////////////// + + vector pDataArray; + DWORD dwThreadIdArray[processors-1]; + HANDLE hThreadArray[processors-1]; + + //Create processor worker threads. + for( int i=1; i newLookup; + for (int k = 0; k < thisLookup.size(); k++) { + SharedRAbundVector* temp = new SharedRAbundVector(); + temp->setLabel(thisLookup[k]->getLabel()); + temp->setGroup(thisLookup[k]->getGroup()); + newLookup.push_back(temp); + } + + + //for each bin + for (int k = 0; k < thisLookup[0]->getNumBins(); k++) { + if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; } + for (int j = 0; j < thisLookup.size(); j++) { newLookup[j]->push_back(thisLookup[j]->getAbundance(k), thisLookup[j]->getGroup()); } + } + + // Allocate memory for thread data. + summarySharedData* tempSum = new summarySharedData((sumFileName+toString(i)+".temp"), m, lines[i].start, lines[i].end, Estimators, newLookup); + pDataArray.push_back(tempSum); + processIDS.push_back(i); + + hThreadArray[i-1] = CreateThread(NULL, 0, MySummarySharedThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]); + } + + //parent do your part + driver(thisLookup, lines[0].start, lines[0].end, sumFileName +"0.temp", sumAllFileName + "0.temp", calcDists); + m->appendFiles((sumFileName + "0.temp"), sumFileName); + m->mothurRemove((sumFileName + "0.temp")); + if (mult) { m->appendFiles((sumAllFileName + "0.temp"), sumAllFileName); } + + //Wait until all threads have terminated. + WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE); + + //Close all thread handles and free memory allocations. + for(int i=0; i < pDataArray.size(); i++){ + if (pDataArray[i]->count != (pDataArray[i]->end-pDataArray[i]->start)) { + m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end-pDataArray[i]->start) + " groups assigned to it, quitting. \n"); m->control_pressed = true; + } + m->appendFiles((sumFileName + toString(processIDS[i]) + ".temp"), sumFileName); + m->mothurRemove((sumFileName + toString(processIDS[i]) + ".temp")); + + for (int j = 0; j < pDataArray[i]->thisLookup.size(); j++) { delete pDataArray[i]->thisLookup[j]; } + + if (createPhylip) { + for (int k = 0; k < calcDists.size(); k++) { + int size = pDataArray[i]->calcDists[k].size(); + for (int j = 0; j < size; j++) { calcDists[k].push_back(pDataArray[i]->calcDists[k][j]); } + } + } + + CloseHandle(hThreadArray[i]); + delete pDataArray[i]; + } + +#endif + } + + if (subsample && (thisIter != 0)) { //we want the summary results for the whole dataset, then the subsampling + + calcDistsTotals.push_back(calcDists); + //clean up memory + for (int i = 0; i < thisItersLookup.size(); i++) { delete thisItersLookup[i]; } + thisItersLookup.clear(); + }else { + if (createPhylip) { + for (int i = 0; i < calcDists.size(); i++) { + if (m->control_pressed) { break; } + + //initialize matrix + vector< vector > matrix; //square matrix to represent the distance + matrix.resize(thisLookup.size()); + for (int k = 0; k < thisLookup.size(); k++) { matrix[k].resize(thisLookup.size(), 0.0); } + + for (int j = 0; j < calcDists[i].size(); j++) { + int row = calcDists[i][j].seq1; + int column = calcDists[i][j].seq2; + double dist = calcDists[i][j].dist; + + matrix[row][column] = dist; + matrix[column][row] = dist; + } + + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile)); + variables["[calc]"] = sumCalculators[i]->getName(); + variables["[distance]"] = thisLookup[0]->getLabel(); + variables["[outputtag]"] = output; + variables["[tag2]"] = ""; + string distFileName = getOutputFileName("phylip",variables); + outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName); + ofstream outDist; + m->openOutputFile(distFileName, outDist); + outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint); + + printSims(outDist, matrix); + + outDist.close(); + } + } + } + for (int i = 0; i < calcDists.size(); i++) { calcDists[i].clear(); } + } + + if (iters != 0) { + //we need to find the average distance and standard deviation for each groups distance + vector< vector > calcAverages = m->getAverages(calcDistsTotals); + + //find standard deviation + vector< vector > stdDev = m->getStandardDeviation(calcDistsTotals, calcAverages); + + //print results + for (int i = 0; i < calcDists.size(); i++) { + vector< vector > matrix; //square matrix to represent the distance + matrix.resize(thisLookup.size()); + for (int k = 0; k < thisLookup.size(); k++) { matrix[k].resize(thisLookup.size(), 0.0); } + + vector< vector > stdmatrix; //square matrix to represent the stdDev + stdmatrix.resize(thisLookup.size()); + for (int k = 0; k < thisLookup.size(); k++) { stdmatrix[k].resize(thisLookup.size(), 0.0); } + + + for (int j = 0; j < calcAverages[i].size(); j++) { + int row = calcAverages[i][j].seq1; + int column = calcAverages[i][j].seq2; + float dist = calcAverages[i][j].dist; + float stdDist = stdDev[i][j].dist; + + matrix[row][column] = dist; + matrix[column][row] = dist; + stdmatrix[row][column] = stdDist; + stdmatrix[column][row] = stdDist; + } + + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile)); + variables["[calc]"] = sumCalculators[i]->getName(); + variables["[distance]"] = thisLookup[0]->getLabel(); + variables["[outputtag]"] = output; + variables["[tag2]"] = "ave"; + string distFileName = getOutputFileName("phylip",variables); + outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName); + ofstream outAve; + m->openOutputFile(distFileName, outAve); + outAve.setf(ios::fixed, ios::floatfield); outAve.setf(ios::showpoint); + + printSims(outAve, matrix); + + outAve.close(); + + variables["[tag2]"] = "std"; + distFileName = getOutputFileName("phylip",variables); + outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName); + ofstream outSTD; + m->openOutputFile(distFileName, outSTD); + outSTD.setf(ios::fixed, ios::floatfield); outSTD.setf(ios::showpoint); + + printSims(outSTD, stdmatrix); + + outSTD.close(); + + } + } + + return 0; + } + catch(exception& e) { + m->errorOut(e, "SummarySharedCommand", "process"); exit(1); } - } - -//********************************************************************************************************************** -void SummarySharedCommand::setGroups() { +/**************************************************************************************************/ +int SummarySharedCommand::driver(vector thisLookup, int start, int end, string sumFile, string sumAllFile, vector< vector >& calcDists) { try { - //if the user has not entered specific groups to analyze then do them all - if (globaldata->Groups.size() != 0) { - if (globaldata->Groups[0] != "all") { - //check that groups are valid - for (int i = 0; i < globaldata->Groups.size(); i++) { - if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) { - cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl; - // erase the invalid group from globaldata->Groups - globaldata->Groups.erase(globaldata->Groups.begin()+i); - } - } + + //loop through calculators and add to file all for all calcs that can do mutiple groups + if (mult == true) { + ofstream outAll; + m->openOutputFile(sumAllFile, outAll); - //if the user only entered invalid groups - if ((globaldata->Groups.size() == 0) || (globaldata->Groups.size() == 1)) { - cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl; - for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) { - globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]); - } - } - }else{//user has enter "all" and wants the default groups - globaldata->Groups.clear(); - for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) { - globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]); + //output label + outAll << thisLookup[0]->getLabel() << '\t'; + + //output groups names + string outNames = ""; + for (int j = 0; j < thisLookup.size(); j++) { + outNames += thisLookup[j]->getGroup() + "-"; + } + outNames = outNames.substr(0, outNames.length()-1); //rip off extra '-'; + outAll << outNames << '\t'; + + for(int i=0;igetMultiple() == true) { + sumCalculators[i]->getValues(thisLookup); + + if (m->control_pressed) { outAll.close(); return 1; } + + outAll << '\t'; + sumCalculators[i]->print(outAll); } - globaldata->setGroups(""); } - }else { - for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) { - globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]); + outAll << endl; + outAll.close(); + } + + ofstream outputFileHandle; + m->openOutputFile(sumFile, outputFileHandle); + + vector subset; + for (int k = start; k < end; k++) { // pass cdd each set of groups to compare + + for (int l = 0; l < k; l++) { + + outputFileHandle << thisLookup[0]->getLabel() << '\t'; + + subset.clear(); //clear out old pair of sharedrabunds + //add new pair of sharedrabunds + subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]); + + //sort groups to be alphanumeric + if (thisLookup[k]->getGroup() > thisLookup[l]->getGroup()) { + outputFileHandle << (thisLookup[l]->getGroup() +'\t' + thisLookup[k]->getGroup()) << '\t'; //print out groups + }else{ + outputFileHandle << (thisLookup[k]->getGroup() +'\t' + thisLookup[l]->getGroup()) << '\t'; //print out groups + } + + for(int i=0;igetNeedsAll()) { + //load subset with rest of lookup for those calcs that need everyone to calc for a pair + for (int w = 0; w < thisLookup.size(); w++) { + if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); } + } + } + + vector tempdata = sumCalculators[i]->getValues(subset); //saves the calculator outputs + + if (m->control_pressed) { outputFileHandle.close(); return 1; } + + outputFileHandle << '\t'; + sumCalculators[i]->print(outputFileHandle); + + seqDist temp(l, k, tempdata[0]); + calcDists[i].push_back(temp); + } + outputFileHandle << endl; } } + outputFileHandle.close(); + + return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SummarySharedCommand", "driver"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the SummarySharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - } -/***********************************************************/ +/**************************************************************************************************/ + +