#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"
//**********************************************************************************************************************
-SummaryCommand::SummaryCommand(string option){
+SummaryCommand::SummaryCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
allLines = 1;
- lines.clear();
labels.clear();
Estimators.clear();
//allow user to run help
- if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+ if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; }
else {
//valid paramters for this command
- string Array[] = {"line","label","calc","abund","size"};
+ string Array[] = {"label","calc","abund","size","outputdir","groupmode","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
}
//make sure the user has already run the read.otu command
- if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the summary.single command." << endl; abort = true; }
+ 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; }
+ //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
+ }
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
- line = validParameter.validFile(parameters, "line", false);
- if (line == "not found") { line = ""; }
- else {
- if(line != "all") { splitAtDash(line, lines); allLines = 0; }
- else { allLines = 1; }
- }
-
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
- if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
- //make sure user did not use both the line and label parameters
- if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; }
- //if the user has not specified any line or labels use the ones from read.otu
- else if((line == "") && (label == "")) {
+ //if the user has not specified any labels use the ones from read.otu
+ if(label == "") {
allLines = globaldata->allLines;
labels = globaldata->labels;
- lines = globaldata->lines;
}
calc = validParameter.validFile(parameters, "calc", false);
else {
if (calc == "default") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
}
- splitAtDash(calc, Estimators);
+ m->splitAtDash(calc, Estimators);
string temp;
temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
temp = validParameter.validFile(parameters, "size", false); if (temp == "not found") { temp = "0"; }
convert(temp, size);
-
- if (abort == false) {
- validCalculator = new ValidCalculators();
- int i;
-
- for (i=0; i<Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("summary", Estimators[i]) == true) {
- 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] == "npshannon"){
- sumCalculators.push_back(new NPShannon());
- }else if(Estimators[i] == "simpson"){
- sumCalculators.push_back(new Simpson());
- }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));
- }
- }
- }
- }
+ temp = validParameter.validFile(parameters, "groupmode", false); if (temp == "not found") { temp = "F"; }
+ groupMode = m->isTrue(temp);
+
+
}
-
-
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function SummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SummaryCommand", "SummaryCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the SummaryCommand class function SummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
void SummaryCommand::help(){
try {
- cout << "The summary.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION." << "\n";
- cout << "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";
- cout << "The summary.single command parameters are label, line, calc, abund. No parameters are required, but you may not use " << "\n";
- cout << "both the line and label parameters at the same time. The summary.single command should be in the following format: " << "\n";
- cout << "summary.single(label=yourLabel, line=yourLines, calc=yourEstimators)." << "\n";
- cout << "Example summary.single(label=unique-.01-.03, line=0,5,10, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson)." << "\n";
+ 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);
- cout << "The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson" << "\n";
- cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
- cout << "Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines)." << "\n" << "\n";
+ 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=False).\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) {
- cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SummaryCommand", "help");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the SummaryCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
-SummaryCommand::~SummaryCommand(){
- if (abort == false) {
- delete input; globaldata->ginput = NULL;
- delete read;
- delete validCalculator;
- globaldata->sabund = NULL;
- }
-}
+SummaryCommand::~SummaryCommand(){}
//**********************************************************************************************************************
if (abort == true) { return 0; }
- int count = 1;
+ vector<string> outputNames;
- //if the users entered no valid calculators don't execute command
- if (sumCalculators.size() == 0) { return 0; }
-
- outputFileName = ((getRootName(globaldata->inputFileName)) + "summary");
- openOutputFile(outputFileName, outputFileHandle);
- outputFileHandle << "label";
-
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
+ string hadShared = "";
+ if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName); }
+ else { hadShared = globaldata->getSharedFile(); inputFileNames = parseSharedFile(globaldata->getSharedFile()); globaldata->setFormat("rabund"); }
- sabund = globaldata->sabund;
- string lastLabel = sabund->getLabel();
- input = globaldata->ginput;
+ if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } return 0; }
+
+ int numLines = 0;
+ int numCols = 0;
- for(int i=0;i<sumCalculators.size();i++){
- if(sumCalculators[i]->getCols() == 1){
- outputFileHandle << '\t' << sumCalculators[i]->getName();
+ 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);
+
+ if (inputFileNames.size() > 1) {
+ m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
}
- else{
- outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
+
+ sumCalculators.clear();
+
+ validCalculator = new ValidCalculators();
+
+ for (int i=0; i<Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("summary", Estimators[i]) == true) {
+ 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] == "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));
+ }
+ }
}
- }
- outputFileHandle << 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;
- set<int> userLines = lines;
-
- while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
- if(allLines == 1 || lines.count(count) == 1 || labels.count(sabund->getLabel()) == 1){
-
- cout << sabund->getLabel() << '\t' << count << endl;
- processedLabels.insert(sabund->getLabel());
- userLabels.erase(sabund->getLabel());
- userLines.erase(count);
+ //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; }
+
+ ofstream outputFileHandle;
+ m->openOutputFile(fileNameRoot, outputFileHandle);
+ outputFileHandle << "label";
+
+ read = new ReadOTUFile(globaldata->inputFileName);
+ read->read(&*globaldata);
+
+ sabund = globaldata->sabund;
+ 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();
+ numCols++;
+ }
+ else{
+ outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
+ numCols += 3;
+ }
+ }
+ outputFileHandle << 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; }
+
+ 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(allLines == 1 || labels.count(sabund->getLabel()) == 1){
+
+ m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
+ 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;
+ numLines++;
+ }
- outputFileHandle << sabund->getLabel();
- for(int i=0;i<sumCalculators.size();i++){
- vector<double> data = sumCalculators[i]->getValues(sabund);
- outputFileHandle << '\t';
- sumCalculators[i]->print(outputFileHandle);
+ if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = sabund->getLabel();
+
+ delete sabund;
+ sabund = input->getSAbundVector(lastLabel);
+
+ m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
+ 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;
+ numLines++;
+
+ //restore real lastlabel to save below
+ sabund->setLabel(saveLabel);
+ }
+
+ lastLabel = sabund->getLabel();
+
+ delete sabund;
+ 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; }
+
+ //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();
}
- outputFileHandle << endl;
}
- if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- delete sabund;
+ //run last label if you need to
+ if (needToRun == true) {
+ if (sabund != NULL) { delete sabund; }
sabund = input->getSAbundVector(lastLabel);
- cout << sabund->getLabel() << '\t' << count << endl;
- processedLabels.insert(sabund->getLabel());
- userLabels.erase(sabund->getLabel());
-
+ 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;
- }
+ numLines++;
+ delete sabund;
+ }
+
+ outputFileHandle.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; }
- lastLabel = sabund->getLabel();
- delete sabund;
- sabund = input->getSAbundVector();
- count++;
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ delete validCalculator;
+ globaldata->sabund = NULL;
+ for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
}
- //output error messages about any remaining user labels
- set<string>::iterator it;
- bool needToRun = false;
- for (it = userLabels.begin(); it != userLabels.end(); it++) {
- cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastLabel) != 1) {
- cout << ". I will use " << lastLabel << "." << endl;
- needToRun = true;
- }else {
- cout << ". Please refer to " << lastLabel << "." << endl;
+ 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; }
+
+ //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 (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } 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, "SummaryCommand", "execute");
+ 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;
+ 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++) {
+ remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
+ 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();
}
+
+ 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 read;
+ delete input;
+ globaldata->ginput = NULL;
+
+ return filenames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryCommand", "parseSharedFile");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<string>& outputNames) {
+ try {
+
+ ofstream out;
+ string combineFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "groups.summary";
- //run last line if you need to
- if (needToRun == true) {
- delete sabund;
- sabund = input->getSAbundVector(lastLabel);
+ //open combined file
+ m->openOutputFile(combineFileName, out);
+
+ //open each groups summary file
+ string newLabel = "";
+ ifstream* temp;
+ map<string, ifstream*> filehandles;
+ for (int i=0; i<outputNames.size(); i++) {
+ temp = new ifstream;
+ filehandles[outputNames[i]] = temp;
+ m->openInputFile(outputNames[i], *(temp));
- cout << sabund->getLabel() << '\t' << count << endl;
- outputFileHandle << sabund->getLabel();
- for(int i=0;i<sumCalculators.size();i++){
- vector<double> data = sumCalculators[i]->getValues(sabund);
- outputFileHandle << '\t';
- sumCalculators[i]->print(outputFileHandle);
- }
- outputFileHandle << endl;
- delete sabund;
+ //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;
+
+ if (j == 1) { newLabel += "group\t" + tempLabel + '\t';
+ }else{ newLabel += tempLabel + '\t'; }
+ }
+ }else{ for (int j = 0; j < numCols+1; j++) { *(temp) >> tempLabel; } }
+
+ m->gobble(*(temp));
}
- outputFileHandle.close();
+ //output label line to new file
+ out << newLabel << endl;
+
+ //for each label
+ for (int i = 0; i < numLines; i++) {
+
+ //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]]));
+ }
+ }
+
+ //close each groups summary file
+ for (int i=0; i<outputNames.size(); i++) { (*(filehandles[outputNames[i]])).close(); remove(outputNames[i].c_str()); }
+ outputNames.clear();
+
+ out.close();
+
+ //return combine file name
+ return combineFileName;
- return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SummaryCommand", "createGroupSummaryFile");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the SummaryCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
-
//**********************************************************************************************************************
projects / mothur.git / blobdiff