#include "sharedlennon.h"
#include "sharedmorisitahorn.h"
#include "sharedbraycurtis.h"
+#include "sharedjackknife.h"
+#include "whittaker.h"
//**********************************************************************************************************************
-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();
- util = new SharedUtil();
-
- int i;
- for (i=0; i<globaldata->Estimators.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] == "jabund") {
- sumCalculators.push_back(new JAbund());
- }else if (globaldata->Estimators[i] == "sorabund") {
- sumCalculators.push_back(new SorAbund());
- }else if (globaldata->Estimators[i] == "jclass") {
- sumCalculators.push_back(new Jclass());
- }else if (globaldata->Estimators[i] == "sorclass") {
- sumCalculators.push_back(new SorClass());
- }else if (globaldata->Estimators[i] == "jest") {
- sumCalculators.push_back(new Jest());
- }else if (globaldata->Estimators[i] == "sorest") {
- sumCalculators.push_back(new SorEst());
- }else if (globaldata->Estimators[i] == "thetayc") {
- sumCalculators.push_back(new ThetaYC());
- }else if (globaldata->Estimators[i] == "thetan") {
- sumCalculators.push_back(new ThetaN());
- }else if (globaldata->Estimators[i] == "kstest") {
- sumCalculators.push_back(new KSTest());
- }else if (globaldata->Estimators[i] == "sharednseqs") {
- sumCalculators.push_back(new SharedNSeqs());
- }else if (globaldata->Estimators[i] == "ochiai") {
- sumCalculators.push_back(new Ochiai());
- }else if (globaldata->Estimators[i] == "anderberg") {
- sumCalculators.push_back(new Anderberg());
- }else if (globaldata->Estimators[i] == "kulczynski") {
- sumCalculators.push_back(new Kulczynski());
- }else if (globaldata->Estimators[i] == "kulczynskicody") {
- sumCalculators.push_back(new KulczynskiCody());
- }else if (globaldata->Estimators[i] == "lennon") {
- sumCalculators.push_back(new Lennon());
- }else if (globaldata->Estimators[i] == "morisitahorn") {
- sumCalculators.push_back(new MorHorn());
- }else if (globaldata->Estimators[i] == "braycurtis") {
- sumCalculators.push_back(new BrayCurtis());
- }else if (globaldata->Estimators[i] == "whittaker") {
- sumCalculators.push_back(new Whittaker());
+ abort = false;
+ allLines = 1;
+ lines.clear();
+ labels.clear();
+ Estimators.clear();
+
+ //allow user to run help
+ if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"line","label","calc","groups"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ 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() == "") {
+ mothurOut("You must read a list and a group, or a shared before you can use the summary.shared command."); mothurOutEndLine(); abort = true;
+ }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ line = validParameter.validFile(parameters, "line", false);
+ if (line == "not found") { line = ""; }
+ else {
+ if(line != "all") { splitAtDash(line, lines); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; }
+ else {
+ if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ //make sure user did not use both the line and label parameters
+ if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; }
+ //if the user has not specified any line or labels use the ones from read.otu
+ else if((line == "") && (label == "")) {
+ allLines = globaldata->allLines;
+ labels = globaldata->labels;
+ lines = globaldata->lines;
+ }
+
+ 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"; }
+ }
+ splitAtDash(calc, Estimators);
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
+ }
+
+ if (abort == false) {
+
+ validCalculator = new ValidCalculators();
+ int i;
+
+ for (i=0; i<Estimators.size(); i++) {
+ 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 SharedChao1());
+ }else if (Estimators[i] == "sharedace") {
+ sumCalculators.push_back(new SharedAce());
+ }else if (Estimators[i] == "jabund") {
+ sumCalculators.push_back(new JAbund());
+ }else if (Estimators[i] == "sorabund") {
+ sumCalculators.push_back(new SorAbund());
+ }else if (Estimators[i] == "jclass") {
+ sumCalculators.push_back(new Jclass());
+ }else if (Estimators[i] == "sorclass") {
+ sumCalculators.push_back(new SorClass());
+ }else if (Estimators[i] == "jest") {
+ sumCalculators.push_back(new Jest());
+ }else if (Estimators[i] == "sorest") {
+ sumCalculators.push_back(new SorEst());
+ }else if (Estimators[i] == "thetayc") {
+ sumCalculators.push_back(new ThetaYC());
+ }else if (Estimators[i] == "thetan") {
+ sumCalculators.push_back(new ThetaN());
+ }else if (Estimators[i] == "kstest") {
+ sumCalculators.push_back(new KSTest());
+ }else if (Estimators[i] == "sharednseqs") {
+ sumCalculators.push_back(new SharedNSeqs());
+ }else if (Estimators[i] == "ochiai") {
+ sumCalculators.push_back(new Ochiai());
+ }else if (Estimators[i] == "anderberg") {
+ sumCalculators.push_back(new Anderberg());
+ }else if (Estimators[i] == "kulczynski") {
+ sumCalculators.push_back(new Kulczynski());
+ }else if (Estimators[i] == "kulczynskicody") {
+ sumCalculators.push_back(new KulczynskiCody());
+ }else if (Estimators[i] == "lennon") {
+ sumCalculators.push_back(new Lennon());
+ }else if (Estimators[i] == "morisitahorn") {
+ sumCalculators.push_back(new MorHorn());
+ }else if (Estimators[i] == "braycurtis") {
+ sumCalculators.push_back(new BrayCurtis());
+ }else if (Estimators[i] == "whittaker") {
+ sumCalculators.push_back(new Whittaker());
+ }
+ }
}
+ outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary");
+ openOutputFile(outputFileName, outputFileHandle);
+ mult = false;
}
}
- //reset calc for next command
- globaldata->setCalc("");
-
}
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";
+ 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";
+}
+
+//**********************************************************************************************************************
+
+void SummarySharedCommand::help(){
+ try {
+ mothurOut("The summary.shared command can only be executed after a successful read.otu command.\n");
+ mothurOut("The summary.shared command parameters are label, line and calc. No parameters are required, but you may not use \n");
+ mothurOut("both the line and label parameters at the same time. The summary.shared command should be in the following format: \n");
+ mothurOut("summary.shared(label=yourLabel, line=yourLines, calc=yourEstimators, groups=yourGroups).\n");
+ mothurOut("Example summary.shared(label=unique-.01-.03, line=0,5,10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n");
+ validCalculator->printCalc("sharedsummary", cout);
+ mothurOut("The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan\n");
+ mothurOut("The default value for groups is all the groups in your groupfile.\n");
+ mothurOut("The label and line parameters are used to analyze specific lines in your input.\n");
+ 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");
+ mothurOut("Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines).\n\n");
+ }
+ catch(exception& e) {
+ errorOut(e, "SummarySharedCommand", "help");
exit(1);
- }
+ }
}
+
//**********************************************************************************************************************
SummarySharedCommand::~SummarySharedCommand(){
- delete input;
- delete read;
- delete util;
+ if (abort == false) {
+ delete read;
+ delete validCalculator;
+ }
}
//**********************************************************************************************************************
int SummarySharedCommand::execute(){
try {
- int count = 1;
+
+ if (abort == true) { return 0; }
+ int count = 1;
+
//if the users entered no valid calculators don't execute command
if (sumCalculators.size() == 0) { return 0; }
-
- if (format == "sharedfile") {
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
- input = globaldata->ginput;
- order = input->getSharedOrderVector();
- }else {
- //you are using a list and a groupfile
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
- input = globaldata->ginput;
- SharedList = globaldata->gSharedList;
- order = SharedList->getSharedOrderVector();
+ //check if any calcs can do multiples
+ else{
+ for (int i = 0; i < sumCalculators.size(); i++) {
+ if (sumCalculators[i]->getMultiple() == true) { mult = true; }
+ }
}
- //set users groups
- util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "summary");
+ //read first line
+ read = new ReadOTUFile(globaldata->inputFileName);
+ read->read(&*globaldata);
+
+ input = globaldata->ginput;
+ lookup = input->getSharedRAbundVectors();
+ string lastLabel = lookup[0]->getLabel();
//output estimator names as column headers
outputFileHandle << "label" <<'\t' << "comparison" << '\t';
}
outputFileHandle << endl;
- while(order != NULL){
+ //create file and put column headers for multiple groups file
+ if (mult == true) {
+ outAllFileName = ((getRootName(globaldata->inputFileName)) + "sharedmultiple.summary");
+ openOutputFile(outAllFileName, outAll);
+
+ outAll << "label" <<'\t' << "comparison" << '\t';
+ for(int i=0;i<sumCalculators.size();i++){
+ if (sumCalculators[i]->getMultiple() == true) {
+ outAll << '\t' << sumCalculators[i]->getName();
+ }
+ }
+ outAll << endl;
+ }
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
-
- cout << order->getLabel() << '\t' << count << endl;
- util->getSharedVectors(globaldata->Groups, lookup, order); //fills group vectors from order vector. //fills group vectors from order vector.
+ if (lookup.size() < 2) {
+ 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
+ outputFileHandle.close(); remove(outputFileName.c_str());
+ if (mult == true) { outAll.close(); remove(outAllFileName.c_str()); }
+ 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());
+ }
+
+ //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;
+ set<int> userLines = lines;
+
+ //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) || (userLines.size() != 0))) {
+
+ if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
+ mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ process(lookup);
- //randomize group order
- if (globaldata->getJumble() == "1") { random_shuffle(lookup.begin(), lookup.end()); }
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+ userLines.erase(count);
+ }
+
+ if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ process(lookup);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+ }
+
+
+
+ lastLabel = lookup[0]->getLabel();
+
+ //get next line to process
+ //prevent memory leak
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors();
+ count++;
+ }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ needToRun = true;
+ }else {
+ mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ }
+ }
+
+ //run last line if you need to
+ if (needToRun == true) {
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ process(lookup);
+ 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(); }
+
+ for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
+
+ delete input; globaldata->ginput = NULL;
+
+ return 0;
+ }
+ catch(exception& e) {
+ errorOut(e, "SummarySharedCommand", "execute");
+ exit(1);
+ }
+}
+/***********************************************************/
+void SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup) {
+ 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';
+
+ //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);
+ outAll << '\t';
+ sumCalculators[i]->print(outAll);
+ }
+ }
+ outAll << endl;
+ }
+
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++) {
+ 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';
- outputFileHandle << order->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 (lookup[k]->getGroup() > lookup[l]->getGroup()) {
- outputFileHandle << (lookup[l]->getGroup() +'\t' + lookup[k]->getGroup()) << '\t'; //print out groups
+ if (thisLookup[k]->getGroup() > thisLookup[l]->getGroup()) {
+ outputFileHandle << (thisLookup[l]->getGroup() +'\t' + thisLookup[k]->getGroup()) << '\t'; //print out groups
}else{
- outputFileHandle << (lookup[k]->getGroup() +'\t' + lookup[l]->getGroup()) << '\t'; //print out groups
+ outputFileHandle << (thisLookup[k]->getGroup() +'\t' + thisLookup[l]->getGroup()) << '\t'; //print out groups
}
- for(int i=0;i<sumCalculators.size();i++){
- sumCalculators[i]->getValues(lookup[k], lookup[l]); //saves the calculator outputs
+ for(int i=0;i<sumCalculators.size();i++) {
+
+ sumCalculators[i]->getValues(subset); //saves the calculator outputs
outputFileHandle << '\t';
sumCalculators[i]->print(outputFileHandle);
}
}
n++;
}
- }
-
- //get next line to process
- if (format == "sharedfile") {
- order = input->getSharedOrderVector();
- }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;
- }
- }
- count++;
- }
-
- //reset groups parameter
- globaldata->Groups.clear(); globaldata->setGroups("");
- 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";
+ errorOut(e, "SummarySharedCommand", "process");
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);
- }
}
/***********************************************************/
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