#include "jackknife.h"
#include "coverage.h"
+
//**********************************************************************************************************************
-vector<string> RareFactCommand::getValidParameters(){
- try {
- string Array[] = {"iters","freq","label","calc","abund","processors","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "RareFactCommand", "getValidParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> RareFactCommand::getRequiredParameters(){
+vector<string> RareFactCommand::setParameters(){
try {
+ 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 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", "sobs", "", "", "",true,false); parameters.push_back(pcalc);
+ CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+ 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", "getRequiredParameters");
+ m->errorOut(e, "RareFactCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> RareFactCommand::getRequiredFiles(){
+string RareFactCommand::getHelpString(){
try {
- string AlignArray[] = {"shared","list","rabund","sabund","or"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
- return myArray;
+ ValidCalculators validCalculator;
+ string helpString = "";
+ helpString += "The rarefaction.single command parameters are list, sabund, rabund, shared, label, iters, freq, calc, processors 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";
+ validCalculator.printCalc("rarefaction");
+ 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\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "RareFactCommand", "getRequiredFiles");
+ m->errorOut(e, "RareFactCommand", "getHelpString");
exit(1);
}
}
+
//**********************************************************************************************************************
RareFactCommand::RareFactCommand(){
try {
abort = true; calledHelp = true;
+ setParameters();
vector<string> tempOutNames;
outputTypes["rarefaction"] = tempOutNames;
outputTypes["r_chao"] = tempOutNames;
//**********************************************************************************************************************
RareFactCommand::RareFactCommand(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") { abort = true; calledHelp = true; }
else {
- //valid paramters for this command
- string Array[] = {"iters","freq","label","calc","abund","processors","outputdir","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;
//check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
outputTypes["r_coverage"] = tempOutNames;
outputTypes["r_nseqs"] = tempOutNames;
- //if the user changes the output directory command factory will send this info to us in the output parameter
- outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
- outputDir = "";
- outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("shared");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["shared"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("rabund");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["rabund"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("sabund");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["sabund"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("list");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["list"] = inputDir + it->second; }
+ }
}
-
- //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 rarefact.single command."); m->mothurOutEndLine(); abort = true; }
+ //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...
label = validParameter.validFile(parameters, "label", false);
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"; }
temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
convert(temp, nIters);
- temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
convert(temp, processors);
}
}
//**********************************************************************************************************************
-void RareFactCommand::help(){
- try {
- m->mothurOut("The rarefaction.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n");
- m->mothurOut("The rarefaction.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 rarefaction.single command parameters are label, iters, freq, calc, processors and abund. No parameters are required. \n");
- m->mothurOut("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");
- m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
- m->mothurOut("The rarefaction.single command should be in the following format: \n");
- m->mothurOut("rarefaction.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
- m->mothurOut("Example rarefaction.single(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n");
- m->mothurOut("The default values for iters is 1000, freq is 100, and calc is rarefaction which calculates the rarefaction curve for the observed richness.\n");
- validCalculator->printCalc("rarefaction", cout);
- 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. freq), '=' and parameters (i.e.yourFreq).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "RareFactCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-RareFactCommand::~RareFactCommand(){}
-
-//**********************************************************************************************************************
-
int RareFactCommand::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; }
for (int p = 0; p < inputFileNames.size(); p++) {
string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
- globaldata->inputFileName = inputFileNames[p];
-
- if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } return 0; }
+
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } m->Groups.clear(); return 0; }
if (inputFileNames.size() > 1) {
m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
}
int i;
- validCalculator = new ValidCalculators();
-
+ ValidCalculators validCalculator;
+
for (i=0; i<Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("rarefaction", Estimators[i]) == true) {
+ if (validCalculator.isValidCalculator("rarefaction", Estimators[i]) == true) {
if (Estimators[i] == "sobs") {
rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction")));
outputNames.push_back(fileNameRoot+"rarefaction"); outputTypes["rarefaction"].push_back(fileNameRoot+"rarefaction");
//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]; } delete validCalculator; return 0; }
-
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
+ if (rDisplays.size() == 0) { for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; } return 0; }
- order = globaldata->gorder;
+ input = new InputData(inputFileNames[p], format);
+ order = input->getOrderVector();
string lastLabel = order->getLabel();
- input = globaldata->ginput;
//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"); } for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; } delete validCalculator; delete read; delete input; globaldata->ginput = NULL; delete order; globaldata->gorder = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 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++) { remove(outputNames[i].c_str()); } 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) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; } delete validCalculator; delete read; delete input; globaldata->ginput = NULL; delete order; globaldata->gorder = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 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++) { remove(outputNames[i].c_str()); } return 0; }
if(allLines == 1 || labels.count(order->getLabel()) == 1){
order = (input->getOrderVector());
}
- if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; } delete validCalculator; delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ 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++) { remove(outputNames[i].c_str()); } return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
}
}
- if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; } delete validCalculator; delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ 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++) { remove(outputNames[i].c_str()); } return 0; }
//run last label if you need to
if (needToRun == true) {
for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
rDisplays.clear();
- globaldata->gorder = NULL;
- delete input; globaldata->ginput = NULL;
- delete read;
- delete validCalculator;
-
+ delete input;
}
- 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; }
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;
+ m->Groups.clear();
return filenames;
}
projects / mothur.git / blobdiff