#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"
//**********************************************************************************************************************
-RareFactCommand::RareFactCommand(string option){
+RareFactCommand::RareFactCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
allLines = 1;
labels.clear();
Estimators.clear();
-
+
//allow user to run help
if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; }
else {
//valid paramters for this command
- string Array[] = {"iters","freq","label","calc","abund","outputdir","inputdir"};
+ string Array[] = {"iters","freq","label","calc","abund","processors","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
//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 += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
}
//make sure the user has already run the read.otu command
- if ((globaldata->getSharedFile() == "") && (globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { mothurOut("You must read a list, sabund, rabund or shared file before you can use the rarefact.single command."); mothurOutEndLine(); 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 rarefact.single command."); m->mothurOutEndLine(); abort = true; }
//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") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
else {
if (calc == "default") { calc = "sobs"; }
}
- splitAtDash(calc, Estimators);
+ m->splitAtDash(calc, Estimators);
string temp;
temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
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"; }
+ convert(temp, processors);
}
}
catch(exception& e) {
- errorOut(e, "RareFactCommand", "RareFactCommand");
+ m->errorOut(e, "RareFactCommand", "RareFactCommand");
exit(1);
}
}
void RareFactCommand::help(){
try {
- mothurOut("The rarefaction.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n");
- 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");
- mothurOut("The rarefaction.single command parameters are label, iters, freq, calc and abund. No parameters are required. \n");
- mothurOut("The rarefaction.single command should be in the following format: \n");
- mothurOut("rarefaction.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
- mothurOut("Example rarefaction.single(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n");
- 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");
+ 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);
- mothurOut("The label parameter is used to analyze specific labels in your input.\n");
- mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\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. freq), '=' and parameters (i.e.yourFreq).\n\n");
}
catch(exception& e) {
- errorOut(e, "RareFactCommand", "help");
+ m->errorOut(e, "RareFactCommand", "help");
exit(1);
}
}
if (abort == true) { return 0; }
+ vector<string> outputNames;
+
+ string hadShared = "";
if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName); }
- else { inputFileNames = parseSharedFile(globaldata->getSharedFile()); globaldata->setFormat("rabund"); }
+ else { hadShared = globaldata->getSharedFile(); inputFileNames = parseSharedFile(globaldata->getSharedFile()); globaldata->setFormat("rabund"); }
+
+ if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } return 0; }
for (int p = 0; p < inputFileNames.size(); p++) {
- string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[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 (inputFileNames.size() > 1) {
- mothurOutEndLine(); mothurOut("Processing group " + groups[p]); mothurOutEndLine(); mothurOutEndLine();
+ m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
}
int i;
validCalculator = new ValidCalculators();
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");
}else if (Estimators[i] == "chao") {
rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao")));
+ outputNames.push_back(fileNameRoot+"r_chao");
}else if (Estimators[i] == "ace") {
if(abund < 5)
abund = 10;
rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"r_ace")));
+ outputNames.push_back(fileNameRoot+"r_ace");
}else if (Estimators[i] == "jack") {
rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));
+ outputNames.push_back(fileNameRoot+"r_jack");
}else if (Estimators[i] == "shannon") {
rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon")));
+ outputNames.push_back(fileNameRoot+"r_shannon");
+ }else if (Estimators[i] == "shannoneven") {
+ rDisplays.push_back(new RareDisplay(new ShannonEven(), new ThreeColumnFile(fileNameRoot+"r_shannoneven")));
+ outputNames.push_back(fileNameRoot+"r_shannoneven");
+ }else if (Estimators[i] == "heip") {
+ rDisplays.push_back(new RareDisplay(new Heip(), new ThreeColumnFile(fileNameRoot+"r_heip")));
+ outputNames.push_back(fileNameRoot+"r_heip");
+ }else if (Estimators[i] == "smithwilson") {
+ rDisplays.push_back(new RareDisplay(new SmithWilson(), new ThreeColumnFile(fileNameRoot+"r_smithwilson")));
+ outputNames.push_back(fileNameRoot+"r_smithwilson");
}else if (Estimators[i] == "npshannon") {
rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon")));
+ outputNames.push_back(fileNameRoot+"r_npshannon");
}else if (Estimators[i] == "simpson") {
rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson")));
+ outputNames.push_back(fileNameRoot+"r_simpson");
+ }else if (Estimators[i] == "simpsoneven") {
+ rDisplays.push_back(new RareDisplay(new SimpsonEven(), new ThreeColumnFile(fileNameRoot+"r_simpsoneven")));
+ outputNames.push_back(fileNameRoot+"r_simpsoneven");
+ }else if (Estimators[i] == "invsimpson") {
+ rDisplays.push_back(new RareDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+"r_invsimpson")));
+ outputNames.push_back(fileNameRoot+"r_invsimpson");
}else if (Estimators[i] == "bootstrap") {
rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap")));
+ outputNames.push_back(fileNameRoot+"r_bootstrap");
}else if (Estimators[i] == "coverage") {
rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(fileNameRoot+"r_coverage")));
+ outputNames.push_back(fileNameRoot+"r_coverage");
}else if (Estimators[i] == "nseqs") {
rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs")));
+ outputNames.push_back(fileNameRoot+"r_nseqs");
}
}
}
//if the users entered no valid calculators don't execute command
- if (rDisplays.size() == 0) { return 0; }
+ 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);
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; }
+
//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(allLines == 1 || labels.count(order->getLabel()) == 1){
- rCurve = new Rarefact(order, rDisplays);
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+ rCurve = new Rarefact(order, rDisplays, processors);
rCurve->getCurve(freq, nIters);
delete rCurve;
- mothurOut(order->getLabel()); mothurOutEndLine();
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
}
- if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = order->getLabel();
delete order;
order = (input->getOrderVector(lastLabel));
- rCurve = new Rarefact(order, rDisplays);
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+ rCurve = new Rarefact(order, rDisplays, processors);
rCurve->getCurve(freq, nIters);
delete rCurve;
- mothurOut(order->getLabel()); mothurOutEndLine();
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
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; }
+
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
- mothurOut("Your file does not include the label " + *it);
+ m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
- mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
- mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
+ 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; }
+
//run last label if you need to
if (needToRun == true) {
if (order != NULL) { delete order; }
order = (input->getOrderVector(lastLabel));
- rCurve = new Rarefact(order, rDisplays);
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+ rCurve = new Rarefact(order, rDisplays, processors);
rCurve->getCurve(freq, nIters);
delete rCurve;
- mothurOut(order->getLabel()); mothurOutEndLine();
delete order;
}
}
+ 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; }
+
+ 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) {
- errorOut(e, "RareFactCommand", "execute");
+ m->errorOut(e, "RareFactCommand", "execute");
exit(1);
}
}
input = globaldata->ginput;
vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
- string sharedFileRoot = getRootName(filename);
+ string sharedFileRoot = m->getRootName(filename);
//clears file before we start to write to it below
for (int i=0; i<lookup.size(); i++) {
for (int i = 0; i < lookup.size(); i++) {
RAbundVector rav = lookup[i]->getRAbundVector();
- openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
+ m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
rav.print(*(filehandles[lookup[i]->getGroup()]));
(*(filehandles[lookup[i]->getGroup()])).close();
}
return filenames;
}
catch(exception& e) {
- errorOut(e, "RareFactCommand", "parseSharedFile");
+ m->errorOut(e, "RareFactCommand", "parseSharedFile");
exit(1);
}
}
projects / mothur.git / blobdiff