#include "boneh.h"
#include "solow.h"
#include "shen.h"
+#include "subsample.h"
+//**********************************************************************************************************************
+vector<string> SummaryCommand::setParameters(){
+ try {
+ CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","summary",false,false,true); parameters.push_back(plist);
+ CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","summary",false,false); parameters.push_back(prabund);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","summary",false,false); parameters.push_back(psabund);
+ CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","summary",false,false,true); parameters.push_back(pshared);
+ CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false); parameters.push_back(psubsample);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "","",true,false,true); parameters.push_back(pcalc);
+ CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund);
+ CommandParameter psize("size", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psize);
+ CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pgroupmode);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string SummaryCommand::getHelpString(){
+ try {
+ string helpString = "";
+ ValidCalculators validCalculator;
+ helpString += "The summary.single command parameters are list, sabund, rabund, shared, subsample, iters, label, calc, abund and groupmode. list, sabund, rabund or shared is required unless you have a valid current file.\n";
+ helpString += "The summary.single command should be in the following format: \n";
+ helpString += "summary.single(label=yourLabel, calc=yourEstimators).\n";
+ helpString += "Example summary.single(label=unique-.01-.03, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n";
+ helpString += validCalculator.printCalc("summary");
+ helpString += "The subsample parameter allows you to enter the size of the sample or you can set subsample=T and mothur will use the size of your smallest group in the case of a shared file. With a list, sabund or rabund file you must provide a subsample size.\n";
+ helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n";
+ helpString += "The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n";
+ helpString += "If you are running summary.single with a shared file and would like your summary results collated in one file, set groupmode=t. (Default=true).\n";
+ helpString += "The label parameter is used to analyze specific labels in your input.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string SummaryCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "summary") { pattern = "[filename],summary-[filename],[tag],summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+SummaryCommand::SummaryCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryCommand", "SummaryCommand");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
SummaryCommand::SummaryCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
- labels.clear();
- Estimators.clear();
-
+
//allow user to run help
- if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"label","calc","abund","size","outputdir","groupmode","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() == "") && (globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { m->mothurOut("You must read a list, sabund, rabund or shared file before you can use the summary.single command."); m->mothurOutEndLine(); abort = true; }
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
- //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->inputFileName); //if user entered a file with a path then preserve it
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("shared");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["shared"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("rabund");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["rabund"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("sabund");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["sabund"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("list");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["list"] = inputDir + it->second; }
+ }
}
+
+ //check for required parameters
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not open") { listfile = ""; abort = true; }
+ else if (listfile == "not found") { listfile = ""; }
+ else { format = "list"; inputfile = listfile; m->setListFile(listfile); }
+
+ sabundfile = validParameter.validFile(parameters, "sabund", true);
+ if (sabundfile == "not open") { sabundfile = ""; abort = true; }
+ else if (sabundfile == "not found") { sabundfile = ""; }
+ else { format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
+
+ rabundfile = validParameter.validFile(parameters, "rabund", true);
+ if (rabundfile == "not open") { rabundfile = ""; abort = true; }
+ else if (rabundfile == "not found") { rabundfile = ""; }
+ else { format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
+
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else if (sharedfile == "not found") { sharedfile = ""; }
+ else { format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
+
+ if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) {
+ //is there are current file available for any of these?
+ //give priority to shared, then list, then rabund, then sabund
+ //if there is a current shared file, use it
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else {
+ listfile = m->getListFile();
+ if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
+ else {
+ rabundfile = m->getRabundFile();
+ if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
+ else {
+ sabundfile = m->getSabundFile();
+ if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. You must provide a list, sabund, rabund or shared file before you can use the collect.single command."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
+ }
+ }
+ }
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(inputfile); }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
-
- //if the user has not specified any labels use the ones from read.otu
- if(label == "") {
- allLines = globaldata->allLines;
- labels = globaldata->labels;
- }
calc = validParameter.validFile(parameters, "calc", false);
if (calc == "not found") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
if (calc == "default") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
}
m->splitAtDash(calc, Estimators);
+ if (m->inUsersGroups("citation", Estimators)) {
+ ValidCalculators validCalc; validCalc.printCitations(Estimators);
+ //remove citation from list of calcs
+ for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } }
+ }
string temp;
temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
- convert(temp, abund);
+ m->mothurConvert(temp, abund);
temp = validParameter.validFile(parameters, "size", false); if (temp == "not found") { temp = "0"; }
- convert(temp, size);
+ m->mothurConvert(temp, size);
temp = validParameter.validFile(parameters, "groupmode", false); if (temp == "not found") { temp = "T"; }
groupMode = m->isTrue(temp);
-
+ temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
+ m->mothurConvert(temp, iters);
+
+ 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; subsampleSize = -1; }
+ }
+
+ if (subsample == false) { iters = 0; }
+ else {
+ //if you did not set a samplesize and are not using a sharedfile
+ if ((subsampleSize == -1) && (format != "sharedfile")) { m->mothurOut("[ERROR]: If you want to subsample with a list, rabund or sabund file, you must provide the sample size. You can do this by setting subsample=yourSampleSize.\n"); abort=true; }
+ }
+
}
}
catch(exception& e) {
}
//**********************************************************************************************************************
-void SummaryCommand::help(){
- try {
- m->mothurOut("The summary.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n");
- m->mothurOut("The summary.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster.\n");
- m->mothurOut("The summary.single command parameters are label, calc, abund and groupmode. No parameters are required.\n");
- m->mothurOut("The summary.single command should be in the following format: \n");
- m->mothurOut("summary.single(label=yourLabel, calc=yourEstimators).\n");
- m->mothurOut("Example summary.single(label=unique-.01-.03, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n");
- validCalculator->printCalc("summary", cout);
- m->mothurOut("The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n");
- m->mothurOut("If you are running summary.single with a shared file and would like your summary results collated in one file, set groupmode=t. (Default=true).\n");
- m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "SummaryCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-SummaryCommand::~SummaryCommand(){}
-
-//**********************************************************************************************************************
-
int SummaryCommand::execute(){
try {
- if (abort == true) { return 0; }
-
- vector<string> outputNames;
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
- string hadShared = "";
- if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName); }
- else { hadShared = globaldata->getSharedFile(); inputFileNames = parseSharedFile(globaldata->getSharedFile()); globaldata->setFormat("rabund"); }
+ if ((format != "sharedfile")) { inputFileNames.push_back(inputfile); }
+ else { inputFileNames = parseSharedFile(sharedfile); format = "rabund"; }
- if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } return 0; }
+ if (m->control_pressed) { return 0; }
int numLines = 0;
int numCols = 0;
-
+ map<string, string> groupIndex;
+
for (int p = 0; p < inputFileNames.size(); p++) {
numLines = 0;
numCols = 0;
- string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "summary";
- globaldata->inputFileName = inputFileNames[p];
- outputNames.push_back(fileNameRoot);
-
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
+ string fileNameRoot = getOutputFileName("summary",variables);
+ variables["[tag]"] = "ave-std";
+ string fileNameAve = getOutputFileName("summary",variables);
+ outputNames.push_back(fileNameRoot); outputTypes["summary"].push_back(fileNameRoot);
+
if (inputFileNames.size() > 1) {
m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
+ groupIndex[fileNameRoot] = groups[p];
}
sumCalculators.clear();
- validCalculator = new ValidCalculators();
+ ValidCalculators validCalculator;
for (int i=0; i<Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("summary", Estimators[i]) == true) {
+ if (validCalculator.isValidCalculator("summary", Estimators[i]) == true) {
if(Estimators[i] == "sobs"){
sumCalculators.push_back(new Sobs());
}else if(Estimators[i] == "chao"){
}
//if the users entered no valid calculators don't execute command
- if (sumCalculators.size() == 0) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } return 0; }
+ if (sumCalculators.size() == 0) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
ofstream outputFileHandle;
m->openOutputFile(fileNameRoot, outputFileHandle);
outputFileHandle << "label";
-
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
- sabund = globaldata->sabund;
+
+ ofstream outAve;
+ if (subsample) {
+ m->openOutputFile(fileNameAve, outAve);
+ outputNames.push_back(fileNameAve); outputTypes["summary"].push_back(fileNameAve);
+ outAve << "label\tmethod";
+ outAve.setf(ios::fixed, ios::floatfield); outAve.setf(ios::showpoint);
+ if (inputFileNames.size() > 1) {
+ groupIndex[fileNameAve] = groups[p];
+ }
+ }
+
+ input = new InputData(inputFileNames[p], format);
+ sabund = input->getSAbundVector();
string lastLabel = sabund->getLabel();
- input = globaldata->ginput;
-
+
for(int i=0;i<sumCalculators.size();i++){
if(sumCalculators[i]->getCols() == 1){
outputFileHandle << '\t' << sumCalculators[i]->getName();
+ if (subsample) { outAve << '\t' << sumCalculators[i]->getName(); }
numCols++;
}
else{
outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
+ if (subsample) { outAve << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci"; }
numCols += 3;
}
}
outputFileHandle << endl;
+ if (subsample) { outAve << endl; }
//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;
- if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0; }
+
+
+ if (m->control_pressed) { outputFileHandle.close(); outAve.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0; }
+ if (m->control_pressed) { outputFileHandle.close(); outAve.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
- outputFileHandle << sabund->getLabel();
- for(int i=0;i<sumCalculators.size();i++){
- vector<double> data = sumCalculators[i]->getValues(sabund);
-
- if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0; }
-
- outputFileHandle << '\t';
- sumCalculators[i]->print(outputFileHandle);
- }
- outputFileHandle << endl;
+ process(sabund, outputFileHandle, outAve);
+
+ if (m->control_pressed) { outputFileHandle.close(); outAve.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
numLines++;
}
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
- outputFileHandle << sabund->getLabel();
- for(int i=0;i<sumCalculators.size();i++){
- vector<double> data = sumCalculators[i]->getValues(sabund);
-
- if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0; }
-
- outputFileHandle << '\t';
- sumCalculators[i]->print(outputFileHandle);
- }
- outputFileHandle << endl;
+ process(sabund, outputFileHandle, outAve);
+
+ if (m->control_pressed) { outputFileHandle.close(); outAve.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
numLines++;
//restore real lastlabel to save below
sabund = input->getSAbundVector();
}
- if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete validCalculator; delete read; delete input; globaldata->ginput = NULL; return 0; }
+ if (m->control_pressed) { outputFileHandle.close(); outAve.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete input; return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
sabund = input->getSAbundVector(lastLabel);
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
- outputFileHandle << sabund->getLabel();
- for(int i=0;i<sumCalculators.size();i++){
- vector<double> data = sumCalculators[i]->getValues(sabund);
-
- if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0; }
-
- outputFileHandle << '\t';
- sumCalculators[i]->print(outputFileHandle);
- }
- outputFileHandle << endl;
+ process(sabund, outputFileHandle, outAve);
+
+ if (m->control_pressed) { outputFileHandle.close(); outAve.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
numLines++;
delete sabund;
}
outputFileHandle.close();
+ if (subsample) { outAve.close(); }
- if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete validCalculator; delete read; delete input; globaldata->ginput = NULL; return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete input; return 0; }
- delete input; globaldata->ginput = NULL;
- delete read;
- delete validCalculator;
- globaldata->sabund = NULL;
+ delete input;
for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
}
- if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); }
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//create summary file containing all the groups data for each label - this function just combines the info from the files already created.
- if ((hadShared != "") && (groupMode)) { outputNames.push_back(createGroupSummaryFile(numLines, numCols, outputNames)); }
+ if ((sharedfile != "") && (groupMode)) { vector<string> comboNames = createGroupSummaryFile(numLines, numCols, outputNames, groupIndex); for (int i = 0; i < comboNames.size(); i++) { outputNames.push_back(comboNames[i]); } }
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
}
}
//**********************************************************************************************************************
+int SummaryCommand::process(SAbundVector*& sabund, ofstream& outputFileHandle, ofstream& outAve) {
+ try {
+
+ //calculator -> data -> values
+ vector< vector< vector<double> > > results; results.resize(sumCalculators.size());
+
+ outputFileHandle << sabund->getLabel();
+
+ SubSample sample;
+ for (int thisIter = 0; thisIter < iters+1; thisIter++) {
+
+ SAbundVector* thisIterSabund = sabund;
+
+ //we want the summary results for the whole dataset, then the subsampling
+ if ((thisIter > 0) && subsample) { //subsample sabund and run it
+ //copy sabund since getSample destroys it
+ RAbundVector rabund = sabund->getRAbundVector();
+ SAbundVector* newSabund = new SAbundVector();
+ *newSabund = rabund.getSAbundVector();
+
+ sample.getSample(newSabund, subsampleSize);
+ thisIterSabund = newSabund;
+ }
+
+ for(int i=0;i<sumCalculators.size();i++){
+ vector<double> data = sumCalculators[i]->getValues(thisIterSabund);
+
+ if (m->control_pressed) { return 0; }
+
+ if (thisIter == 0) {
+ outputFileHandle << '\t';
+ sumCalculators[i]->print(outputFileHandle);
+ }else {
+ //some of the calc have hci and lci need to make room for that
+ if (results[i].size() == 0) { results[i].resize(data.size()); }
+ //save results for ave and std.
+ for (int j = 0; j < data.size(); j++) {
+ if (m->control_pressed) { return 0; }
+ results[i][j].push_back(data[j]);
+ }
+ }
+ }
+
+ //cleanup memory
+ if ((thisIter > 0) && subsample) { delete thisIterSabund; }
+ }
+ outputFileHandle << endl;
+
+ if (subsample) {
+ outAve << sabund->getLabel() << '\t' << "ave\t";
+ //find ave and std for this label and output
+ //will need to modify the createGroupSummary to combine results and not mess with the .summary file.
+
+ //calcs -> values
+ vector< vector<double> > calcAverages; calcAverages.resize(sumCalculators.size());
+ for (int i = 0; i < calcAverages.size(); i++) { calcAverages[i].resize(results[i].size(), 0); }
+
+ for (int thisIter = 0; thisIter < iters; thisIter++) { //sum all groups dists for each calculator
+ for (int i = 0; i < calcAverages.size(); i++) { //initialize sums to zero.
+ for (int j = 0; j < calcAverages[i].size(); j++) {
+ calcAverages[i][j] += results[i][j][thisIter];
+ }
+ }
+ }
+
+ for (int i = 0; i < calcAverages.size(); i++) { //finds average.
+ for (int j = 0; j < calcAverages[i].size(); j++) {
+ calcAverages[i][j] /= (float) iters;
+ outAve << calcAverages[i][j] << '\t';
+ }
+ }
+
+ //find standard deviation
+ vector< vector<double> > stdDev; stdDev.resize(sumCalculators.size());
+ for (int i = 0; i < stdDev.size(); i++) { stdDev[i].resize(results[i].size(), 0); }
+
+ for (int thisIter = 0; thisIter < iters; thisIter++) { //compute the difference of each dist from the mean, and square the result of each
+ for (int i = 0; i < stdDev.size(); i++) {
+ for (int j = 0; j < stdDev[i].size(); j++) {
+ stdDev[i][j] += ((results[i][j][thisIter] - calcAverages[i][j]) * (results[i][j][thisIter] - calcAverages[i][j]));
+ }
+ }
+ }
+
+ outAve << endl << sabund->getLabel() << '\t' << "std\t";
+ for (int i = 0; i < stdDev.size(); i++) { //finds average.
+ for (int j = 0; j < stdDev[i].size(); j++) {
+ stdDev[i][j] /= (float) iters;
+ stdDev[i][j] = sqrt(stdDev[i][j]);
+ outAve << stdDev[i][j] << '\t';
+ }
+ }
+ outAve << endl;
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryCommand", "process");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
vector<string> SummaryCommand::parseSharedFile(string filename) {
try {
vector<string> filenames;
map<string, ofstream*> filehandles;
map<string, ofstream*>::iterator it3;
-
- //read first line
- read = new ReadOTUFile(filename);
- read->read(&*globaldata);
-
- input = globaldata->ginput;
+ input = new InputData(filename, "sharedfile");
vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
string sharedFileRoot = m->getRootName(filename);
- //clears file before we start to write to it below
+ /******************************************************/
+ 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();
+ vector<string> Groups;
+ 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() < 1) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; delete input; return filenames; }
+ }
+
+
+ /******************************************************/
+
+ //clears file before we start to write to it below
for (int i=0; i<lookup.size(); i++) {
- remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
+ m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
}
-
+
ofstream* temp;
for (int i=0; i<lookup.size(); i++) {
temp = new ofstream;
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
delete it3->second;
}
- delete read;
+
delete input;
- globaldata->ginput = NULL;
return filenames;
}
}
}
//**********************************************************************************************************************
-string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<string>& outputNames) {
+vector<string> SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<string>& outputNames, map<string, string> groupIndex) {
try {
-
- ofstream out;
- string combineFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "groups.summary";
-
- //open combined file
- m->openOutputFile(combineFileName, out);
-
+
//open each groups summary file
- string newLabel = "";
- ifstream* temp;
- map<string, ifstream*> filehandles;
+ vector<string> newComboNames;
+
+ map<string, map<string, vector<string> > > files;
+ map<string, string> filesTypesLabels;
+ map<string, int> filesTypesNumLines;
for (int i=0; i<outputNames.size(); i++) {
- temp = new ifstream;
- filehandles[outputNames[i]] = temp;
- m->openInputFile(outputNames[i], *(temp));
+ vector<string> thisFilesLines;
+
+ ifstream temp;
+ m->openInputFile(outputNames[i], temp);
//read through first line - labels
- string tempLabel;
- if (i == 0) { //we want to save the labels to output below
- for (int j = 0; j < numCols+1; j++) {
- *(temp) >> tempLabel;
+ string labelsLine = m->getline(temp);
+ vector<string> theseLabels = m->splitWhiteSpace(labelsLine);
+
+ string newLabel = "";
+ for (int j = 0; j < theseLabels.size(); j++) {
+ if (j == 1) { newLabel += "group\t" + theseLabels[j] + '\t';
+ }else{ newLabel += theseLabels[j] + '\t'; }
+ }
+
+ m->gobble(temp);
+
+ int stop = numLines;
+ if (theseLabels.size() != numCols+1) { stop = numLines*2; }
+ //for each label
+ for (int k = 0; k < stop; k++) {
+
+ string thisLine = "";
+ string tempLabel;
- if (j == 1) { newLabel += "group\t" + tempLabel + '\t';
- }else{ newLabel += tempLabel + '\t'; }
+ for (int j = 0; j < theseLabels.size(); j++) {
+ temp >> tempLabel;
+
+ //save for later
+ if (j == 1) { thisLine += groupIndex[outputNames[i]] + "\t" + tempLabel + "\t"; }
+ else{ thisLine += tempLabel + "\t"; }
}
- }else{ for (int j = 0; j < numCols+1; j++) { *(temp) >> tempLabel; } }
+
+ thisLine += "\n";
+
+ thisFilesLines.push_back(thisLine);
+
+ m->gobble(temp);
+ }
+
+ string extension = m->getExtension(outputNames[i]);
+ if (theseLabels.size() != numCols+1) { extension = ".ave-std" + extension; }
+ string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + extension;
+ m->mothurRemove(combineFileName); //remove old file
+ filesTypesLabels[extension] = newLabel;
+ filesTypesNumLines[extension] = stop;
+
+ map<string, map<string, vector<string> > >::iterator itFiles = files.find(extension);
+ if (itFiles != files.end()) { //add new files info to existing type
+ files[extension][outputNames[i]] = thisFilesLines;
+ }else {
+ map<string, vector<string> > thisFile;
+ thisFile[outputNames[i]] = thisFilesLines;
+ files[extension] = thisFile;
+ }
- m->gobble(*(temp));
+ temp.close();
+ m->mothurRemove(outputNames[i]);
}
- //output label line to new file
- out << newLabel << endl;
+
+ for (map<string, map<string, vector<string> > >::iterator itFiles = files.begin(); itFiles != files.end(); itFiles++) {
+
+ if (m->control_pressed) { break; }
+
+ string extension = itFiles->first;
+ map<string, vector<string> > thisType = itFiles->second;
+ string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + extension;
+ newComboNames.push_back(combineFileName);
+ //open combined file
+ ofstream out;
+ m->openOutputFile(combineFileName, out);
+
+ //output label line to new file
+ out << filesTypesLabels[extension] << endl;
- //for each label
- for (int i = 0; i < numLines; i++) {
+ //for each label
+ for (int k = 0; k < filesTypesNumLines[extension]; k++) {
- //grab summary data for each group
- for (int i=0; i<outputNames.size(); i++) {
- string tempLabel;
-
- for (int j = 0; j < numCols+1; j++) {
- *(filehandles[outputNames[i]]) >> tempLabel;
-
- //print to combined file
- if (j == 1) { out << groups[i] << '\t' << tempLabel << '\t'; }
- else{ out << tempLabel << '\t'; }
- }
-
- out << endl;
- m->gobble(*(filehandles[outputNames[i]]));
- }
- }
+ //grab summary data for each group
+ for (map<string, vector<string> >::iterator itType = thisType.begin(); itType != thisType.end(); itType++) {
+ out << (itType->second)[k];
+ }
+ }
- //close each groups summary file
- for (int i=0; i<outputNames.size(); i++) { (*(filehandles[outputNames[i]])).close(); remove(outputNames[i].c_str()); }
- outputNames.clear();
+ outputNames.clear();
- out.close();
+ out.close();
+ }
//return combine file name
- return combineFileName;
+ return newComboNames;
}
catch(exception& e) {
projects / mothur.git / blobdiff