#include "shen.h"
//**********************************************************************************************************************
-vector<string> SummaryCommand::getValidParameters(){
+vector<string> SummaryCommand::setParameters(){
try {
- string Array[] = {"label","calc","abund","size","outputdir","groupmode","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); 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); parameters.push_back(pshared);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-np_shannon-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); 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", "getValidParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-SummaryCommand::SummaryCommand(){
- try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["summary"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "SummaryCommand", "SummaryCommand");
+ m->errorOut(e, "SummaryCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> SummaryCommand::getRequiredParameters(){
+string SummaryCommand::getHelpString(){
try {
- vector<string> myArray;
- return myArray;
+ string helpString = "";
+ ValidCalculators validCalculator;
+ helpString += "The summary.single command parameters are list, sabund, rabund, shared, 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 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\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "SummaryCommand", "getRequiredParameters");
+ m->errorOut(e, "SummaryCommand", "getHelpString");
exit(1);
}
}
+
//**********************************************************************************************************************
-vector<string> SummaryCommand::getRequiredFiles(){
+SummaryCommand::SummaryCommand(){
try {
- string AlignArray[] = {"shared","list","rabund","sabund","or"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "SummaryCommand", "getRequiredFiles");
+ m->errorOut(e, "SummaryCommand", "SummaryCommand");
exit(1);
}
}
SummaryCommand::SummaryCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
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; calledHelp = true; }
+ if(option == "help") { help(); 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;
vector<string> tempOutNames;
outputTypes["summary"] = tempOutNames;
- //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; }
+ //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; }
+ }
+ }
- //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 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; }
+
+ sabundfile = validParameter.validFile(parameters, "sabund", true);
+ if (sabundfile == "not open") { sabundfile = ""; abort = true; }
+ else if (sabundfile == "not found") { sabundfile = ""; }
+ else { format = "sabund"; inputfile = 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; }
+
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else if (sharedfile == "not found") { sharedfile = ""; }
+ else { format = "sharedfile"; inputfile = 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"; }
}
//**********************************************************************************************************************
-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) { 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;
numCols = 0;
string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "summary";
- globaldata->inputFileName = inputFileNames[p];
outputNames.push_back(fileNameRoot); outputTypes["summary"].push_back(fileNameRoot);
if (inputFileNames.size() > 1) {
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++) { remove(outputNames[i].c_str()); } return 0; }
ofstream outputFileHandle;
m->openOutputFile(fileNameRoot, outputFileHandle);
outputFileHandle << "label";
-
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
- sabund = globaldata->sabund;
+
+ 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();
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(); 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 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(); 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 sabund; delete input; return 0; }
if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
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; }
+ if (m->control_pressed) { 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 sabund; delete input; return 0; }
outputFileHandle << '\t';
sumCalculators[i]->print(outputFileHandle);
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; }
+ if (m->control_pressed) { 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 sabund; delete input; return 0; }
outputFileHandle << '\t';
sumCalculators[i]->print(outputFileHandle);
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(); 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 input; return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
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; }
+ if (m->control_pressed) { 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 sabund; delete input; return 0; }
outputFileHandle << '\t';
sumCalculators[i]->print(outputFileHandle);
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; }
+ if (m->control_pressed) { 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 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; }
//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)) { 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; }
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);
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
delete it3->second;
}
- delete read;
+
delete input;
- globaldata->ginput = NULL;
return filenames;
}
try {
ofstream out;
- string combineFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "groups.summary";
+ string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups.summary";
//open combined file
m->openOutputFile(combineFileName, out);
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