*/
#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 "whittaker.h"
-#include "sharedochiai.h"
-#include "sharedanderbergs.h"
-#include "sharedkulczynski.h"
-#include "sharedkulczynskicody.h"
-#include "sharedlennon.h"
-#include "sharedmorisitahorn.h"
-#include "sharedbraycurtis.h"
-#include "sharedjackknife.h"
-#include "whittaker.h"
-
+#include "subsample.h"
+//**********************************************************************************************************************
+vector<string> 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<string> 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<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummarySharedCommand", "SummarySharedCommand");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
SummarySharedCommand::SummarySharedCommand(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(); 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[] = {"label","calc","groups","all","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
+ map<string, string>::iterator it;
ValidParameters validParameter;
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
- //make sure the user has already run the read.otu command
- if (globaldata->getSharedFile() == "") {
- m->mothurOut("You must read a list and a group, or a shared before you can use the summary.shared command."); m->mothurOutEndLine(); abort = true;
+ //initialize outputTypes
+ vector<string> 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; }
+ }
}
+ //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 = "";
- outputDir += m->hasPath(globaldata->getSharedFile()); //if user entered a file with a path then preserve it
- }
+ 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...
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 = "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);
- globaldata->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) {
- validCalculator = new ValidCalculators();
+ ValidCalculators validCalculator;
int i;
for (i=0; i<Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("sharedsummary", Estimators[i]) == true) {
+ if (validCalculator.isValidCalculator("sharedsummary", Estimators[i]) == true) {
if (Estimators[i] == "sharedsobs") {
sumCalculators.push_back(new SharedSobsCS());
}else if (Estimators[i] == "sharedchao") {
sumCalculators.push_back(new BrayCurtis());
}else if (Estimators[i] == "whittaker") {
sumCalculators.push_back(new Whittaker());
+ }else if (Estimators[i] == "odum") {
+ sumCalculators.push_back(new Odum());
+ }else if (Estimators[i] == "canberra") {
+ sumCalculators.push_back(new Canberra());
+ }else if (Estimators[i] == "structeuclidean") {
+ sumCalculators.push_back(new StructEuclidean());
+ }else if (Estimators[i] == "structchord") {
+ sumCalculators.push_back(new StructChord());
+ }else if (Estimators[i] == "hellinger") {
+ sumCalculators.push_back(new Hellinger());
+ }else if (Estimators[i] == "manhattan") {
+ sumCalculators.push_back(new Manhattan());
+ }else if (Estimators[i] == "structpearson") {
+ sumCalculators.push_back(new StructPearson());
+ }else if (Estimators[i] == "soergel") {
+ sumCalculators.push_back(new Soergel());
+ }else if (Estimators[i] == "spearman") {
+ sumCalculators.push_back(new Spearman());
+ }else if (Estimators[i] == "structkulczynski") {
+ sumCalculators.push_back(new StructKulczynski());
+ }else if (Estimators[i] == "speciesprofile") {
+ sumCalculators.push_back(new SpeciesProfile());
+ }else if (Estimators[i] == "hamming") {
+ sumCalculators.push_back(new Hamming());
+ }else if (Estimators[i] == "structchi2") {
+ sumCalculators.push_back(new StructChi2());
+ }else if (Estimators[i] == "gower") {
+ sumCalculators.push_back(new Gower());
+ }else if (Estimators[i] == "memchi2") {
+ sumCalculators.push_back(new MemChi2());
+ }else if (Estimators[i] == "memchord") {
+ sumCalculators.push_back(new MemChord());
+ }else if (Estimators[i] == "memeuclidean") {
+ sumCalculators.push_back(new MemEuclidean());
+ }else if (Estimators[i] == "mempearson") {
+ sumCalculators.push_back(new MemPearson());
+ }else if (Estimators[i] == "jsd") {
+ sumCalculators.push_back(new JSD());
+ }else if (Estimators[i] == "rjsd") {
+ sumCalculators.push_back(new RJSD());
}
}
}
- outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "shared.summary";
- m->openOutputFile(outputFileName, outputFileHandle);
- outputNames.push_back(outputFileName);
-
mult = false;
}
}
exit(1);
}
}
-
-//**********************************************************************************************************************
-
-void SummarySharedCommand::help(){
- try {
- m->mothurOut("The summary.shared command can only be executed after a successful read.otu command.\n");
- m->mothurOut("The summary.shared command parameters are label, calc and all. No parameters are required.\n");
- m->mothurOut("The summary.shared command should be in the following format: \n");
- m->mothurOut("summary.shared(label=yourLabel, calc=yourEstimators, groups=yourGroups).\n");
- m->mothurOut("Example summary.shared(label=unique-.01-.03, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n");
- validCalculator->printCalc("sharedsummary", cout);
- m->mothurOut("The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan\n");
- m->mothurOut("The default value for groups is all the groups in your groupfile.\n");
- m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
- m->mothurOut("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");
- m->mothurOut("If you use sharedchao and run into memory issues, set all to false. \n");
- m->mothurOut("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");
- m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "SummarySharedCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-SummarySharedCommand::~SummarySharedCommand(){
- if (abort == false) {
- delete read;
- delete validCalculator;
- }
-}
-
//**********************************************************************************************************************
int SummarySharedCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ ofstream outputFileHandle, outAll;
+ map<string, string> 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; }
}
}
}
-
- //read first line
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
- input = globaldata->ginput;
+ 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;i<sumCalculators.size();i++){
outputFileHandle << '\t' << sumCalculators[i]->getName();
- if (sumCalculators[i]->getCols() == 3) { outputFileHandle << "\tlci\thci"; }
+ 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) {
- outAllFileName = ((m->getRootName(globaldata->inputFileName)) + "sharedmultiple.summary");
m->openOutputFile(outAllFileName, outAll);
outputNames.push_back(outAllFileName);
}
}
outAll << endl;
+ outAll.close();
}
if (lookup.size() < 2) {
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
//close files and clean up
- outputFileHandle.close(); remove(outputFileName.c_str());
- if (mult == true) { outAll.close(); remove(outAllFileName.c_str()); }
+ 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;
- outAll.close();
- remove(outAllFileName.c_str());
+ m->mothurRemove(outAllFileName);
outputNames.pop_back();
}
if (m->control_pressed) {
- if (mult) { outAll.close(); remove(outAllFileName.c_str()); }
- outputFileHandle.close(); remove(outputFileName.c_str());
- delete input; globaldata->ginput = NULL;
+ 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;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
- globaldata->Groups.clear();
+ m->clearGroups();
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<SharedRAbundVector*> 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; }
+ }
+
+
+ /******************************************************/
+ //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<string> processedLabels;
set<string> 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) { outAll.close(); remove(outAllFileName.c_str()); }
- outputFileHandle.close(); remove(outputFileName.c_str());
- delete input; globaldata->ginput = NULL;
+ 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;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
- globaldata->Groups.clear();
+ m->clearGroups();
return 0;
}
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- process(lookup);
+ process(lookup, outputFileName, outAllFileName);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
lookup = input->getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- process(lookup);
+ process(lookup, outputFileName, outAllFileName);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
}
if (m->control_pressed) {
- if (mult) { outAll.close(); remove(outAllFileName.c_str()); }
- outputFileHandle.close(); remove(outputFileName.c_str());
- delete input; globaldata->ginput = NULL;
+ if (mult) { m->mothurRemove(outAllFileName); }
+ m->mothurRemove(outputFileName);
+ delete input;
for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
- globaldata->Groups.clear();
+ m->clearGroups();
return 0;
}
lookup = input->getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- process(lookup);
+ process(lookup, outputFileName, outAllFileName);
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
//reset groups parameter
- globaldata->Groups.clear();
-
- //close files
- outputFileHandle.close();
- if (mult == true) { outAll.close(); }
+ m->clearGroups();
for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
- delete input; globaldata->ginput = NULL;
+ delete input;
if (m->control_pressed) {
- remove(outAllFileName.c_str());
- remove(outputFileName.c_str());
+ m->mothurRemove(outAllFileName);
+ m->mothurRemove(outputFileName);
return 0;
}
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); 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;
exit(1);
}
}
-
/***********************************************************/
-int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup) {
+int SummarySharedCommand::printSims(ostream& out, vector< vector<double> >& simMatrix) {
+ try {
+
+ 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) {
+ m->errorOut(e, "SummarySharedCommand", "printSims");
+ exit(1);
+ }
+}
+/***********************************************************/
+int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string sumFileName, string sumAllFileName) {
+ try {
+ vector< vector< vector<seqDist> > > calcDistsTotals; //each iter, one for each calc, then each groupCombos dists. this will be used to make .dist files
+ vector< vector<seqDist> > calcDists; calcDists.resize(sumCalculators.size());
+
+ for (int thisIter = 0; thisIter < iters+1; thisIter++) {
+
+ vector<SharedRAbundVector*> thisItersLookup = thisLookup;
+
+ if (subsample && (thisIter != 0)) { //we want the summary results for the whole dataset, then the subsampling
+ SubSample sample;
+ vector<string> tempLabels; //dont need since we arent printing the sampled sharedRabunds
+
+ //make copy of lookup so we don't get access violations
+ vector<SharedRAbundVector*> 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<int> 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<summarySharedData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+
+ //Create processor worker threads.
+ for( int i=1; i<processors; i++ ){
+
+ //make copy of lookup so we don't get access violations
+ vector<SharedRAbundVector*> 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<double> > 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<string, string> 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<seqDist> > calcAverages = m->getAverages(calcDistsTotals);
+
+ //find standard deviation
+ vector< vector<seqDist> > stdDev = m->getStandardDeviation(calcDistsTotals, calcAverages);
+
+ //print results
+ for (int i = 0; i < calcDists.size(); i++) {
+ vector< vector<double> > 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<double> > 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<string, string> 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);
+ }
+}
+/**************************************************************************************************/
+int SummarySharedCommand::driver(vector<SharedRAbundVector*> thisLookup, int start, int end, string sumFile, string sumAllFile, vector< vector<seqDist> >& calcDists) {
try {
- //loop through calculators and add to file all for all calcs that can do mutiple groups
- if (mult == true) {
- //output label
- outAll << thisLookup[0]->getLabel() << '\t';
+
+ //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);
+
+ //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;i<sumCalculators.size();i++){
+ if (sumCalculators[i]->getMultiple() == true) {
+ sumCalculators[i]->getValues(thisLookup);
- //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';
+ if (m->control_pressed) { outAll.close(); return 1; }
- for(int i=0;i<sumCalculators.size();i++){
- if (sumCalculators[i]->getMultiple() == true) {
- sumCalculators[i]->getValues(thisLookup);
-
- if (m->control_pressed) { return 1; }
-
- outAll << '\t';
- sumCalculators[i]->print(outAll);
- }
- }
- outAll << endl;
+ outAll << '\t';
+ sumCalculators[i]->print(outAll);
}
-
- int n = 1;
- vector<SharedRAbundVector*> subset;
- for (int k = 0; k < (thisLookup.size() - 1); k++) { // pass cdd each set of groups to commpare
- for (int l = n; l < thisLookup.size(); 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;i<sumCalculators.size();i++) {
+ }
+ outAll << endl;
+ outAll.close();
+ }
+
+ ofstream outputFileHandle;
+ m->openOutputFile(sumFile, outputFileHandle);
+
+ vector<SharedRAbundVector*> subset;
+ for (int k = start; k < end; k++) { // pass cdd each set of groups to compare
- sumCalculators[i]->getValues(subset); //saves the calculator outputs
-
- if (m->control_pressed) { return 1; }
-
- outputFileHandle << '\t';
- sumCalculators[i]->print(outputFileHandle);
+ 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;i<sumCalculators.size();i++) {
+
+ //if this calc needs all groups to calculate the pair load all groups
+ if (sumCalculators[i]->getNeedsAll()) {
+ //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]); }
}
- outputFileHandle << endl;
}
- n++;
+
+ vector<double> 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);
}
- return 0;
+ outputFileHandle << endl;
+ }
+ }
+
+ outputFileHandle.close();
+
+ return 0;
}
catch(exception& e) {
- m->errorOut(e, "SummarySharedCommand", "process");
+ m->errorOut(e, "SummarySharedCommand", "driver");
exit(1);
}
}
+/**************************************************************************************************/
+
-/***********************************************************/
projects / mothur.git / blobdiff