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/*
* summarycommand.cpp
* Dotur
*
* Created by Sarah Westcott on 1/2/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "summarycommand.h"
#include "ace.h"
#include "sobs.h"
#include "nseqs.h"
#include "chao1.h"
#include "bootstrap.h"
#include "simpson.h"
#include "simpsoneven.h"
#include "invsimpson.h"
#include "npshannon.h"
#include "shannon.h"
#include "heip.h"
#include "smithwilson.h"
#include "shannoneven.h"
#include "jackknife.h"
#include "geom.h"
#include "logsd.h"
#include "qstat.h"
#include "bergerparker.h"
#include "bstick.h"
#include "goodscoverage.h"
#include "coverage.h"
#include "efron.h"
#include "boneh.h"
#include "solow.h"
#include "shen.h"
#include "subsample.h"
#include "shannonrange.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 pwithreplacement("withreplacement", "Boolean", "", "F", "", "", "","",false,false,true); parameters.push_back(pwithreplacement);
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-shannonrange", "", "", "","",true,false,true); parameters.push_back(pcalc);
CommandParameter palpha("alpha", "Multiple", "0-1-2", "1", "", "", "","",false,false,true); parameters.push_back(palpha);
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 pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> tempOutNames;
outputTypes["summary"] = tempOutNames;
abort = false; calledHelp = false; allLines = true;
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 withreplacement parameter allows you to indicate you want to subsample your data allowing for the same read to be included multiple times. Default=f. \n";
helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample. Default=1000.\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 alpha parameter is used to set the alpha value for the shannonrange calculator.\n";
helpString += "The label parameter is used to analyze specific labels in your input.\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->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "SummaryCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
SummaryCommand::SummaryCommand(string option) : Command() {
try {
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
listfile = validParameter.validFile(parameters, "list");
if (listfile == "not open") { listfile = ""; abort = true; }
else if (listfile == "not found") { listfile = ""; }
else { format = "list"; inputfile = listfile; current->setListFile(listfile); }
sabundfile = validParameter.validFile(parameters, "sabund");
if (sabundfile == "not open") { sabundfile = ""; abort = true; }
else if (sabundfile == "not found") { sabundfile = ""; }
else { format = "sabund"; inputfile = sabundfile; current->setSabundFile(sabundfile); }
rabundfile = validParameter.validFile(parameters, "rabund");
if (rabundfile == "not open") { rabundfile = ""; abort = true; }
else if (rabundfile == "not found") { rabundfile = ""; }
else { format = "rabund"; inputfile = rabundfile; current->setRabundFile(rabundfile); }
sharedfile = validParameter.validFile(parameters, "shared");
if (sharedfile == "not open") { sharedfile = ""; abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
else { format = "sharedfile"; inputfile = sharedfile; current->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 = current->getSharedFile();
if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter.\n"); }
else {
listfile = current->getListFile();
if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter.\n"); }
else {
rabundfile = current->getRabundFile();
if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter.\n"); }
else {
sabundfile = current->getSabundFile();
if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter.\n"); }
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.\n");
abort = true;
}
}
}
}
}
if (outputdir == ""){ outputdir = util.hasPath(inputfile); }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
label = validParameter.valid(parameters, "label");
if (label == "not found") { label = ""; }
else {
if(label != "all") { util.splitAtDash(label, labels); allLines = false; }
else { allLines = true; }
}
calc = validParameter.valid(parameters, "calc");
if (calc == "not found") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
else {
if (calc == "default") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
}
util.splitAtDash(calc, Estimators);
if (util.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.valid(parameters, "abund"); if (temp == "not found") { temp = "10"; }
util.mothurConvert(temp, abund);
temp = validParameter.valid(parameters, "size"); if (temp == "not found") { temp = "0"; }
util.mothurConvert(temp, size);
temp = validParameter.valid(parameters, "groupmode"); if (temp == "not found") { temp = "T"; }
groupMode = util.isTrue(temp);
temp = validParameter.valid(parameters, "iters"); if (temp == "not found") { temp = "1000"; }
util.mothurConvert(temp, iters);
temp = validParameter.valid(parameters, "subsample"); if (temp == "not found") { temp = "F"; }
if (util.isNumeric1(temp)) { util.mothurConvert(temp, subsampleSize); subsample = true; }
else {
if (util.isTrue(temp)) { subsample = true; subsampleSize = -1; } //we will set it to smallest group later
else { subsample = false; subsampleSize = -1; }
}
temp = validParameter.valid(parameters, "withreplacement"); if (temp == "not found"){ temp = "f"; }
withReplacement = util.isTrue(temp);
temp = validParameter.valid(parameters, "alpha"); if (temp == "not found") { temp = "1"; }
util.mothurConvert(temp, alpha);
if ((alpha != 0) && (alpha != 1) && (alpha != 2)) { m->mothurOut("[ERROR]: Not a valid alpha value. Valid values are 0, 1 and 2.\n"); abort=true; }
if (!subsample) { iters = 1; }
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) {
m->errorOut(e, "SummaryCommand", "SummaryCommand");
exit(1);
}
}
//**********************************************************************************************************************
int SummaryCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
if ((format != "sharedfile")) { inputFileNames.push_back(inputfile); }
else { inputFileNames = parseSharedFile(sharedfile); format = "rabund"; }
if (m->getControl_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;
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(inputFileNames[p]));
string fileNameRoot = getOutputFileName("summary",variables);
variables["[tag]"] = "ave-std";
string fileNameAve = getOutputFileName("summary",variables);
if (inputFileNames.size() > 1) { m->mothurOut("\nProcessing group " + groups[p] + "\n\n"); groupIndex[fileNameRoot] = groups[p]; }
fillEstimators();
//if the users entered no valid calculators don't execute command
if (sumCalculators.size() == 0) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0; }
ofstream outputFileHandle; ofstream outAve;
if (subsample) {
util.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];
}
}else {
util.openOutputFile(fileNameRoot, outputFileHandle);
outputFileHandle << "label";
outputNames.push_back(fileNameRoot); outputTypes["summary"].push_back(fileNameRoot);
}
for(int i=0;i<sumCalculators.size();i++){
if(sumCalculators[i]->getCols() == 1){
if (subsample) { outAve << '\t' << sumCalculators[i]->getName(); }
else { outputFileHandle << '\t' << sumCalculators[i]->getName(); }
numCols++;
}
else{
if (subsample) { outAve << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci"; }
else { outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci"; }
numCols += 3;
}
}
if (subsample) { outAve << endl; }
else { outputFileHandle << endl; }
InputData input(inputFileNames[p], format, nullVector);
set<string> processedLabels;
set<string> userLabels = labels;
string lastLabel = "";
SAbundVector* sabund = util.getNextSAbund(input, allLines, userLabels, processedLabels, lastLabel);
if (m->getControl_pressed()) { if (!subsample) { outputFileHandle.close(); } else { outAve.close(); } for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; return 0; }
while (sabund != nullptr) {
if (m->getControl_pressed()) { delete sabund; break; }
process(sabund, outputFileHandle, outAve); delete sabund;
sabund = util.getNextSAbund(input, allLines, userLabels, processedLabels, lastLabel);
numLines++;
}
if (subsample) { outAve.close(); }
else { outputFileHandle.close(); }
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } return 0; }
for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
}
if ((format != "sharedfile")) {}
else { for (int p = 0; p < inputFileNames.size(); p++) { util.mothurRemove(inputFileNames[p]); }}
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.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 ((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->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0; }
m->mothurOut("\nOutput File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i] +"\n"); } m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "SummaryCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
void SummaryCommand::fillEstimators() {
try {
sumCalculators.clear();
ValidCalculators validCalculator;
for (int i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("summary", Estimators[i]) ) {
if(Estimators[i] == "sobs"){
sumCalculators.push_back(new Sobs());
}else if(Estimators[i] == "chao"){
sumCalculators.push_back(new Chao1());
}else if(Estimators[i] == "coverage"){
sumCalculators.push_back(new Coverage());
}else if(Estimators[i] == "geometric"){
sumCalculators.push_back(new Geom());
}else if(Estimators[i] == "logseries"){
sumCalculators.push_back(new LogSD());
}else if(Estimators[i] == "qstat"){
sumCalculators.push_back(new QStat());
}else if(Estimators[i] == "bergerparker"){
sumCalculators.push_back(new BergerParker());
}else if(Estimators[i] == "bstick"){
sumCalculators.push_back(new BStick());
}else if(Estimators[i] == "ace"){
if(abund < 5)
abund = 10;
sumCalculators.push_back(new Ace(abund));
}else if(Estimators[i] == "jack"){
sumCalculators.push_back(new Jackknife());
}else if(Estimators[i] == "shannon"){
sumCalculators.push_back(new Shannon());
}else if(Estimators[i] == "shannoneven"){
sumCalculators.push_back(new ShannonEven());
}else if(Estimators[i] == "shannonrange"){
sumCalculators.push_back(new RangeShannon(alpha));
}else if(Estimators[i] == "npshannon"){
sumCalculators.push_back(new NPShannon());
}else if(Estimators[i] == "heip"){
sumCalculators.push_back(new Heip());
}else if(Estimators[i] == "smithwilson"){
sumCalculators.push_back(new SmithWilson());
}else if(Estimators[i] == "simpson"){
sumCalculators.push_back(new Simpson());
}else if(Estimators[i] == "simpsoneven"){
sumCalculators.push_back(new SimpsonEven());
}else if(Estimators[i] == "invsimpson"){
sumCalculators.push_back(new InvSimpson());
}else if(Estimators[i] == "bootstrap"){
sumCalculators.push_back(new Bootstrap());
}else if (Estimators[i] == "nseqs") {
sumCalculators.push_back(new NSeqs());
}else if (Estimators[i] == "goodscoverage") {
sumCalculators.push_back(new GoodsCoverage());
}else if (Estimators[i] == "efron") {
sumCalculators.push_back(new Efron(size));
}else if (Estimators[i] == "boneh") {
sumCalculators.push_back(new Boneh(size));
}else if (Estimators[i] == "solow") {
sumCalculators.push_back(new Solow(size));
}else if (Estimators[i] == "shen") {
sumCalculators.push_back(new Shen(size, abund));
}
}
}
}
catch(exception& e) {
m->errorOut(e, "SummaryCommand", "fillEstimators");
exit(1);
}
}
//**********************************************************************************************************************
int SummaryCommand::process(SAbundVector*& sabund, ofstream& outputFileHandle, ofstream& outAve) {
try {
//calculator -> data -> values
vector< vector< vector<double> > > results; results.resize(sumCalculators.size());
if (!subsample) { outputFileHandle << sabund->getLabel(); }
SubSample sample;
for (int thisIter = 0; thisIter < iters; thisIter++) {
SAbundVector* thisIterSabund = sabund;
//we want the summary results for the whole dataset, then the subsampling
if (subsample) { //subsample sabund and run it
//copy sabund since getSample destroys it
RAbundVector rabund = sabund->getRAbundVector();
SAbundVector* newSabund = new SAbundVector();
*newSabund = rabund.getSAbundVector();
if (withReplacement) { sample.getSampleWithReplacement(newSabund, subsampleSize); }
else { sample.getSample(newSabund, subsampleSize); }
thisIterSabund = newSabund;
}
for(int i=0;i<sumCalculators.size();i++){
vector<double> data = sumCalculators[i]->getValues(thisIterSabund);
if (m->getControl_pressed()) { return 0; }
if (!subsample) {
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->getControl_pressed()) { return 0; }
results[i][j].push_back(data[j]);
}
}
}
//cleanup memory
if (subsample) { delete thisIterSabund; }
}
if (!subsample) { outputFileHandle << endl; }
if (subsample) {
outAve << sabund->getLabel() << '\t' << "ave";
//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 << '\t' << calcAverages[i][j];
}
}
//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";
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 << '\t' << stdDev[i][j];
}
}
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, string> files;
map<string, string>::iterator it3;
InputData input(filename, "sharedfile", groups);
SharedRAbundVectors* lookup = input.getSharedRAbundVectors();
/******************************************************/
//user has not set size, set size = smallest samples size
if (subsample) {
if (subsampleSize == -1) { subsampleSize = lookup->getNumSeqsSmallestGroup(); m->mothurOut("\nSetting subsample size to " + toString(subsampleSize) + ".\n"); }
else { lookup->removeGroups(subsampleSize); }
if (lookup->size() < 1) { m->mothurOut("You have not provided enough valid groups. I cannot run the command.\n"); m->setControl_pressed(true); return filenames; }
}
/******************************************************/
groups = lookup->getNamesGroups();
//clears file before we start to write to it below
string sharedFileRoot = util.getRootName(filename);
for (int i=0; i<groups.size(); i++) {
ofstream temp;
string group = groups[i];
util.openOutputFile((sharedFileRoot + group + ".rabund"), temp);
filenames.push_back((sharedFileRoot + group + ".rabund"));
files[group] = (sharedFileRoot + group + ".rabund");
}
while(lookup != nullptr) {
vector<SharedRAbundVector*> data = lookup->getSharedRAbundVectors();
for (int i = 0; i < data.size(); i++) {
ofstream temp;
string group = data[i]->getGroup();
util.openOutputFileAppend(files[group], temp);
data[i]->getRAbundVector().print(temp);
temp.close();
delete data[i];
}
delete lookup;
lookup = input.getSharedRAbundVectors();
}
return filenames;
}
catch(exception& e) {
m->errorOut(e, "SummaryCommand", "parseSharedFile");
exit(1);
}
}
//**********************************************************************************************************************
vector<string> SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<string>& outputNames, map<string, string> groupIndex) {
try {
//open each groups summary file
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++) {
vector<string> thisFilesLines;
ifstream temp;
util.openInputFile(outputNames[i], temp);
//read through first line - labels
string labelsLine = util.getline(temp);
vector<string> theseLabels = util.splitWhiteSpace(labelsLine);
string newLabel = "";
for (int j = 0; j < theseLabels.size(); j++) {
if (j == 1) { newLabel += "group\t" + theseLabels[j]; }
else if (j == 0) { newLabel += theseLabels[j] + "\t"; }
else{ newLabel += '\t' + theseLabels[j]; }
}
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;
for (int j = 0; j < theseLabels.size(); j++) {
temp >> tempLabel;
//save for later
if (j == 1) { thisLine += groupIndex[outputNames[i]] + "\t" + tempLabel; }
else if (j == 0) { thisLine += tempLabel + "\t"; }
else{ thisLine += "\t" + tempLabel; }
}
thisLine += "\n";
thisFilesLines.push_back(thisLine);
gobble(temp);
}
string extension = util.getExtension(outputNames[i]);
if (theseLabels.size() != numCols+1) { extension = ".ave-std" + extension; }
string combineFileName = outputdir + util.getRootName(util.getSimpleName(sharedfile)) + "groups" + extension;
util.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;
}
temp.close();
util.mothurRemove(outputNames[i]);
}
for (map<string, map<string, vector<string> > >::iterator itFiles = files.begin(); itFiles != files.end(); itFiles++) {
if (m->getControl_pressed()) { break; }
string extension = itFiles->first;
map<string, vector<string> > thisType = itFiles->second;
string combineFileName = outputdir + util.getRootName(util.getSimpleName(sharedfile)) + "groups" + extension;
newComboNames.push_back(combineFileName);
//open combined file
ofstream out;
util.openOutputFile(combineFileName, out);
//output label line to new file
out << filesTypesLabels[extension] << endl;
//for each label
for (int k = 0; k < filesTypesNumLines[extension]; k++) {
//grab summary data for each group
for (map<string, vector<string> >::iterator itType = thisType.begin(); itType != thisType.end(); itType++) {
out << (itType->second)[k];
}
}
outputNames.clear();
out.close();
}
//return combine file name
return newComboNames;
}
catch(exception& e) {
m->errorOut(e, "SummaryCommand", "createGroupSummaryFile");
exit(1);
}
}
//**********************************************************************************************************************
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