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/*
* rarefactcommand.cpp
* Dotur
*
* Created by Sarah Westcott on 1/2/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "rarefactcommand.h"
#include "ace.h"
#include "sobs.h"
#include "nseqs.h"
#include "chao1.h"
#include "bootstrap.h"
#include "simpson.h"
#include "simpsoneven.h"
#include "heip.h"
#include "smithwilson.h"
#include "invsimpson.h"
#include "npshannon.h"
#include "shannoneven.h"
#include "shannon.h"
#include "jackknife.h"
#include "coverage.h"
#include "shannonrange.h"
//**********************************************************************************************************************
vector<string> RareFactCommand::setParameters(){
try {
CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(plist);
CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false); parameters.push_back(prabund);
CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false); parameters.push_back(psabund);
CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(pshared);
CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
CommandParameter pfreq("freq", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pfreq);
CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-shannonrange", "sobs", "", "", "","",true,false,true); parameters.push_back(pcalc);
CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund);
CommandParameter palpha("alpha", "Multiple", "0-1-2", "1", "", "", "","",false,false,true); parameters.push_back(palpha);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
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, "RareFactCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string RareFactCommand::getHelpString(){
try {
ValidCalculators validCalculator;
string helpString = "";
helpString += "The rarefaction.single command parameters are list, sabund, rabund, shared, label, iters, freq, calc, processors, groupmode and abund. list, sabund, rabund or shared is required unless you have a valid current file. \n";
helpString += "The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n";
helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
helpString += "The rarefaction.single command should be in the following format: \n";
helpString += "rarefaction.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n";
helpString += "Example rarefaction.single(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n";
helpString += "The default values for iters is 1000, freq is 100, and calc is rarefaction which calculates the rarefaction curve for the observed richness.\n";
helpString += "The alpha parameter is used to set the alpha value for the shannonrange calculator.\n";
validCalculator.printCalc("rarefaction");
helpString += "If you are running rarefaction.single with a shared file and would like your 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. freq), '=' and parameters (i.e.yourFreq).\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "RareFactCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string RareFactCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "rarefaction") { pattern = "[filename],rarefaction"; }
else if (type == "r_chao") { pattern = "[filename],r_chao"; }
else if (type == "r_ace") { pattern = "[filename],r_ace"; }
else if (type == "r_jack") { pattern = "[filename],r_jack"; }
else if (type == "r_shannon") { pattern = "[filename],r_shannon"; }
else if (type == "r_shannoneven") { pattern = "[filename],r_shannoneven"; }
else if (type == "r_smithwilson") { pattern = "[filename],r_smithwilson"; }
else if (type == "r_npshannon") { pattern = "[filename],r_npshannon"; }
else if (type == "r_shannonrange"){ pattern = "[filename],r_shannonrange"; }
else if (type == "r_simpson") { pattern = "[filename],r_simpson"; }
else if (type == "r_simpsoneven") { pattern = "[filename],r_simpsoneven"; }
else if (type == "r_invsimpson") { pattern = "[filename],r_invsimpson"; }
else if (type == "r_bootstrap") { pattern = "[filename],r_bootstrap"; }
else if (type == "r_coverage") { pattern = "[filename],r_coverage"; }
else if (type == "r_nseqs") { pattern = "[filename],r_nseqs"; }
else if (type == "r_heip") { pattern = "[filename],r_heip"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "RareFactCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
RareFactCommand::RareFactCommand(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
outputTypes["rarefaction"] = tempOutNames;
outputTypes["r_chao"] = tempOutNames;
outputTypes["r_ace"] = tempOutNames;
outputTypes["r_jack"] = tempOutNames;
outputTypes["r_shannon"] = tempOutNames;
outputTypes["r_shannoneven"] = tempOutNames;
outputTypes["r_shannonrange"] = tempOutNames;
outputTypes["r_heip"] = tempOutNames;
outputTypes["r_smithwilson"] = tempOutNames;
outputTypes["r_npshannon"] = tempOutNames;
outputTypes["r_simpson"] = tempOutNames;
outputTypes["r_simpsoneven"] = tempOutNames;
outputTypes["r_invsimpson"] = tempOutNames;
outputTypes["r_bootstrap"] = tempOutNames;
outputTypes["r_coverage"] = tempOutNames;
outputTypes["r_nseqs"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "RareFactCommand", "RareFactCommand");
exit(1);
}
}
//**********************************************************************************************************************
RareFactCommand::RareFactCommand(string option) {
try {
abort = false; calledHelp = false;
allLines = 1;
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
map<string,string>::iterator it;
ValidParameters validParameter;
//check to make sure all parameters are valid for command
for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["rarefaction"] = tempOutNames;
outputTypes["r_chao"] = tempOutNames;
outputTypes["r_ace"] = tempOutNames;
outputTypes["r_jack"] = tempOutNames;
outputTypes["r_shannon"] = tempOutNames;
outputTypes["r_shannoneven"] = tempOutNames;
outputTypes["r_shannonrange"] = tempOutNames;
outputTypes["r_heip"] = tempOutNames;
outputTypes["r_smithwilson"] = tempOutNames;
outputTypes["r_npshannon"] = tempOutNames;
outputTypes["r_simpson"] = tempOutNames;
outputTypes["r_simpsoneven"] = tempOutNames;
outputTypes["r_invsimpson"] = tempOutNames;
outputTypes["r_bootstrap"] = tempOutNames;
outputTypes["r_coverage"] = tempOutNames;
outputTypes["r_nseqs"] = 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; }
}
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...
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
calc = validParameter.validFile(parameters, "calc", false);
if (calc == "not found") { calc = "sobs"; }
else {
if (calc == "default") { calc = "sobs"; }
}
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, "freq", false); if (temp == "not found") { temp = "100"; }
m->mothurConvert(temp, freq);
temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
m->mothurConvert(temp, abund);
temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
m->mothurConvert(temp, nIters);
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
m->mothurConvert(temp, processors);
temp = validParameter.validFile(parameters, "alpha", false); if (temp == "not found") { temp = "1"; }
m->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."); m->mothurOutEndLine(); abort=true; }
temp = validParameter.validFile(parameters, "groupmode", false); if (temp == "not found") { temp = "T"; }
groupMode = m->isTrue(temp);
}
}
catch(exception& e) {
m->errorOut(e, "RareFactCommand", "RareFactCommand");
exit(1);
}
}
//**********************************************************************************************************************
int RareFactCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
map<string, set<int> > labelToEnds;
if ((format != "sharedfile")) { inputFileNames.push_back(inputfile); }
else { inputFileNames = parseSharedFile(sharedfile, labelToEnds); format = "rabund"; }
if (m->control_pressed) { return 0; }
map<int, string> file2Group; //index in outputNames[i] -> group
for (int p = 0; p < inputFileNames.size(); p++) {
string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0; }
if (inputFileNames.size() > 1) {
m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
}
int i;
ValidCalculators validCalculator;
map<string, string> variables;
variables["[filename]"] = fileNameRoot;
for (i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("rarefaction", Estimators[i]) == true) {
if (Estimators[i] == "sobs") {
rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(getOutputFileName("rarefaction",variables))));
outputNames.push_back(getOutputFileName("rarefaction",variables)); outputTypes["rarefaction"].push_back(getOutputFileName("rarefaction",variables));
}else if (Estimators[i] == "chao") {
rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(getOutputFileName("r_chao",variables))));
outputNames.push_back(getOutputFileName("r_chao",variables)); outputTypes["r_chao"].push_back(getOutputFileName("r_chao",variables));
}else if (Estimators[i] == "ace") {
if(abund < 5)
abund = 10;
rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(getOutputFileName("r_ace",variables))));
outputNames.push_back(getOutputFileName("r_ace",variables)); outputTypes["r_ace"].push_back(getOutputFileName("r_ace",variables));
}else if (Estimators[i] == "jack") {
rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(getOutputFileName("r_jack",variables))));
outputNames.push_back(getOutputFileName("r_jack",variables)); outputTypes["r_jack"].push_back(getOutputFileName("r_jack",variables));
}else if (Estimators[i] == "shannon") {
rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(getOutputFileName("r_shannon",variables))));
outputNames.push_back(getOutputFileName("r_shannon",variables)); outputTypes["r_shannon"].push_back(getOutputFileName("r_shannon",variables));
}else if (Estimators[i] == "shannoneven") {
rDisplays.push_back(new RareDisplay(new ShannonEven(), new ThreeColumnFile(getOutputFileName("r_shannoneven",variables))));
outputNames.push_back(getOutputFileName("r_shannoneven",variables)); outputTypes["r_shannoneven"].push_back(getOutputFileName("r_shannoneven",variables));
}else if (Estimators[i] == "heip") {
rDisplays.push_back(new RareDisplay(new Heip(), new ThreeColumnFile(getOutputFileName("r_heip",variables))));
outputNames.push_back(getOutputFileName("r_heip",variables)); outputTypes["r_heip"].push_back(getOutputFileName("r_heip",variables));
}else if (Estimators[i] == "r_shannonrange") {
rDisplays.push_back(new RareDisplay(new RangeShannon(alpha), new ThreeColumnFile(getOutputFileName("r_shannonrange", variables))));
outputNames.push_back(getOutputFileName("r_shannonrange", variables)); outputTypes["r_shannoneven"].push_back(getOutputFileName("r_shannonrange", variables));
}else if (Estimators[i] == "smithwilson") {
rDisplays.push_back(new RareDisplay(new SmithWilson(), new ThreeColumnFile(getOutputFileName("r_smithwilson",variables))));
outputNames.push_back(getOutputFileName("r_smithwilson",variables)); outputTypes["r_smithwilson"].push_back(getOutputFileName("r_smithwilson",variables));
}else if (Estimators[i] == "npshannon") {
rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(getOutputFileName("r_npshannon",variables))));
outputNames.push_back(getOutputFileName("r_npshannon",variables)); outputTypes["r_npshannon"].push_back(getOutputFileName("r_npshannon",variables));
}else if (Estimators[i] == "simpson") {
rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(getOutputFileName("r_simpson",variables))));
outputNames.push_back(getOutputFileName("r_simpson",variables)); outputTypes["r_simpson"].push_back(getOutputFileName("r_simpson",variables));
}else if (Estimators[i] == "simpsoneven") {
rDisplays.push_back(new RareDisplay(new SimpsonEven(), new ThreeColumnFile(getOutputFileName("r_simpsoneven",variables))));
outputNames.push_back(getOutputFileName("r_simpsoneven",variables)); outputTypes["r_simpsoneven"].push_back(getOutputFileName("r_simpsoneven",variables));
}else if (Estimators[i] == "invsimpson") {
rDisplays.push_back(new RareDisplay(new InvSimpson(), new ThreeColumnFile(getOutputFileName("r_invsimpson",variables))));
outputNames.push_back(getOutputFileName("r_invsimpson",variables)); outputTypes["r_invsimpson"].push_back(getOutputFileName("r_invsimpson",variables));
}else if (Estimators[i] == "bootstrap") {
rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(getOutputFileName("r_bootstrap",variables))));
outputNames.push_back(getOutputFileName("r_bootstrap",variables)); outputTypes["r_bootstrap"].push_back(getOutputFileName("r_bootstrap",variables));
}else if (Estimators[i] == "coverage") {
rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(getOutputFileName("r_coverage",variables))));
outputNames.push_back(getOutputFileName("r_coverage",variables)); outputTypes["r_coverage"].push_back(getOutputFileName("r_coverage",variables));
}else if (Estimators[i] == "nseqs") {
rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(getOutputFileName("r_nseqs",variables))));
outputNames.push_back(getOutputFileName("r_nseqs",variables)); outputTypes["r_nseqs"].push_back(getOutputFileName("r_nseqs",variables));
}
if (inputFileNames.size() > 1) { file2Group[outputNames.size()-1] = groups[p]; }
}
}
//if the users entered no valid calculators don't execute command
if (rDisplays.size() == 0) { for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; } return 0; }
input = new InputData(inputFileNames[p], format);
order = input->getOrderVector();
string lastLabel = order->getLabel();
//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) { for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; } delete input; delete order; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//as long as you are not at the end of the file or done wih the lines you want
while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; } delete input; delete order; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if(allLines == 1 || labels.count(order->getLabel()) == 1){
m->mothurOut(order->getLabel()); m->mothurOutEndLine();
map<string, set<int> >::iterator itEndings = labelToEnds.find(order->getLabel());
set<int> ends;
if (itEndings != labelToEnds.end()) { ends = itEndings->second; }
rCurve = new Rarefact(order, rDisplays, processors, ends);
rCurve->getCurve(freq, nIters);
delete rCurve;
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
}
if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = order->getLabel();
delete order;
order = (input->getOrderVector(lastLabel));
m->mothurOut(order->getLabel()); m->mothurOutEndLine();
map<string, set<int> >::iterator itEndings = labelToEnds.find(order->getLabel());
set<int> ends;
if (itEndings != labelToEnds.end()) { ends = itEndings->second; }
rCurve = new Rarefact(order, rDisplays, processors, ends);
rCurve->getCurve(freq, nIters);
delete rCurve;
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
//restore real lastlabel to save below
order->setLabel(saveLabel);
}
lastLabel = order->getLabel();
delete order;
order = (input->getOrderVector());
}
if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; } delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; } delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//run last label if you need to
if (needToRun == true) {
if (order != NULL) { delete order; }
order = (input->getOrderVector(lastLabel));
m->mothurOut(order->getLabel()); m->mothurOutEndLine();
map<string, set<int> >::iterator itEndings = labelToEnds.find(order->getLabel());
set<int> ends;
if (itEndings != labelToEnds.end()) { ends = itEndings->second; }
rCurve = new Rarefact(order, rDisplays, processors, ends);
rCurve->getCurve(freq, nIters);
delete rCurve;
delete order;
}
for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
rDisplays.clear();
delete input;
}
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 ((sharedfile != "") && (groupMode)) { outputNames = createGroupFile(outputNames, file2Group); }
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();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "RareFactCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map<int, string> file2Group) {
try {
vector<string> newFileNames;
//find different types of files
map<string, map<string, string> > typesFiles;
map<string, vector< vector<string> > > fileLabels; //combofile name to labels. each label is a vector because it may be unique lci hci.
vector<string> groupNames;
for (int i = 0; i < outputNames.size(); i++) {
string extension = m->getExtension(outputNames[i]);
string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + extension;
m->mothurRemove(combineFileName); //remove old file
ifstream in;
m->openInputFile(outputNames[i], in);
string labels = m->getline(in);
istringstream iss (labels,istringstream::in);
string newLabel = ""; vector<string> theseLabels;
while(!iss.eof()) { iss >> newLabel; m->gobble(iss); theseLabels.push_back(newLabel); }
vector< vector<string> > allLabels;
vector<string> thisSet; thisSet.push_back(theseLabels[0]); allLabels.push_back(thisSet); thisSet.clear(); //makes "numSampled" its own grouping
for (int j = 1; j < theseLabels.size()-1; j++) {
if (theseLabels[j+1] == "lci") {
thisSet.push_back(theseLabels[j]);
thisSet.push_back(theseLabels[j+1]);
thisSet.push_back(theseLabels[j+2]);
j++; j++;
}else{ //no lci or hci for this calc.
thisSet.push_back(theseLabels[j]);
}
allLabels.push_back(thisSet);
thisSet.clear();
}
fileLabels[combineFileName] = allLabels;
map<string, map<string, string> >::iterator itfind = typesFiles.find(extension);
if (itfind != typesFiles.end()) {
(itfind->second)[outputNames[i]] = file2Group[i];
}else {
map<string, string> temp;
temp[outputNames[i]] = file2Group[i];
typesFiles[extension] = temp;
}
if (!(m->inUsersGroups(file2Group[i], groupNames))) { groupNames.push_back(file2Group[i]); }
}
//for each type create a combo file
for (map<string, map<string, string> >::iterator it = typesFiles.begin(); it != typesFiles.end(); it++) {
ofstream out;
string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + it->first;
m->openOutputFileAppend(combineFileName, out);
newFileNames.push_back(combineFileName);
map<string, string> thisTypesFiles = it->second; //it->second maps filename to group
set<int> numSampledSet;
//open each type summary file
map<string, map<int, vector< vector<string> > > > files; //maps file name to lines in file
int maxLines = 0;
for (map<string, string>::iterator itFileNameGroup = thisTypesFiles.begin(); itFileNameGroup != thisTypesFiles.end(); itFileNameGroup++) {
string thisfilename = itFileNameGroup->first;
string group = itFileNameGroup->second;
ifstream temp;
m->openInputFile(thisfilename, temp);
//read through first line - labels
m->getline(temp); m->gobble(temp);
map<int, vector< vector<string> > > thisFilesLines;
while (!temp.eof()){
int numSampled = 0;
temp >> numSampled; m->gobble(temp);
vector< vector<string> > theseReads;
vector<string> thisSet; thisSet.push_back(toString(numSampled)); theseReads.push_back(thisSet); thisSet.clear();
for (int k = 1; k < fileLabels[combineFileName].size(); k++) { //output thing like 0.03-A lci-A hci-A
vector<string> reads;
string next = "";
for (int l = 0; l < fileLabels[combineFileName][k].size(); l++) { //output modified labels
temp >> next; m->gobble(temp);
reads.push_back(next);
}
theseReads.push_back(reads);
}
thisFilesLines[numSampled] = theseReads;
m->gobble(temp);
numSampledSet.insert(numSampled);
}
files[group] = thisFilesLines;
//save longest file for below
if (maxLines < thisFilesLines.size()) { maxLines = thisFilesLines.size(); }
temp.close();
m->mothurRemove(thisfilename);
}
//output new labels line
out << fileLabels[combineFileName][0][0] << '\t';
for (int k = 1; k < fileLabels[combineFileName].size(); k++) { //output thing like 0.03-A lci-A hci-A
for (int n = 0; n < groupNames.size(); n++) { // for each group
for (int l = 0; l < fileLabels[combineFileName][k].size(); l++) { //output modified labels
out << fileLabels[combineFileName][k][l] << '-' << groupNames[n] << '\t';
}
}
}
out << endl;
//for each label
for (set<int>::iterator itNumSampled = numSampledSet.begin(); itNumSampled != numSampledSet.end(); itNumSampled++) {
out << (*itNumSampled) << '\t';
if (m->control_pressed) { break; }
for (int k = 1; k < fileLabels[combineFileName].size(); k++) { //each chunk
//grab data for each group
for (int n = 0; n < groupNames.size(); n++) {
string group = groupNames[n];
map<int, vector< vector<string> > >::iterator itLine = files[group].find(*itNumSampled);
if (itLine != files[group].end()) {
for (int l = 0; l < (itLine->second)[k].size(); l++) {
out << (itLine->second)[k][l] << '\t';
}
}else {
for (int l = 0; l < fileLabels[combineFileName][k].size(); l++) {
out << "NA" << '\t';
}
}
}
}
out << endl;
}
out.close();
}
//return combine file name
return newFileNames;
}
catch(exception& e) {
m->errorOut(e, "RareFactCommand", "createGroupFile");
exit(1);
}
}
//**********************************************************************************************************************
vector<string> RareFactCommand::parseSharedFile(string filename, map<string, set<int> >& label2Ends) {
try {
vector<string> filenames;
map<string, ofstream*> filehandles;
map<string, ofstream*>::iterator it3;
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
for (int i=0; i<lookup.size(); i++) {
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;
filehandles[lookup[i]->getGroup()] = temp;
groups.push_back(lookup[i]->getGroup());
}
while(lookup[0] != NULL) {
for (int i = 0; i < lookup.size(); i++) {
RAbundVector rav = lookup[i]->getRAbundVector();
m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
rav.print(*(filehandles[lookup[i]->getGroup()]));
(*(filehandles[lookup[i]->getGroup()])).close();
label2Ends[lookup[i]->getLabel()].insert(rav.getNumSeqs());
}
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors();
}
//free memory
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
delete it3->second;
}
delete input;
m->clearGroups();
return filenames;
}
catch(exception& e) {
m->errorOut(e, "RareFactCommand", "parseSharedFile");
exit(1);
}
}
//**********************************************************************************************************************
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