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/*
* File: kruskalwalliscommand.cpp
* Author: kiverson
*
* Created on June 26, 2012, 11:06 AM
*/
#include "kruskalwalliscommand.h"
#include "linearalgebra.h"
//**********************************************************************************************************************
vector<string> KruskalWallisCommand::setParameters(){
try {
CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pdesign);
CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pshared);
CommandParameter pclass("class", "String", "", "", "", "", "","",false,false); parameters.push_back(pclass);
CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
//every command must have inputdir and outputdir. This allows mothur users to redirect input and output files.
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
abort = false; calledHelp = false; allLines = true;
vector<string> tempOutNames;
outputTypes["kruskall-wallis"] = tempOutNames;
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, "KruskalWallisCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string KruskalWallisCommand::getHelpString(){
try {
string helpString = "";
helpString += "The kruskal.wallis command allows you to ....\n";
helpString += "The kruskal.wallis command parameters are: shared, design, class, label and classes.\n";
helpString += "The class parameter is used to indicate the which category you would like used for the Kruskal Wallis analysis. If none is provided first category is used.\n";
helpString += "The label parameter is used to indicate which distances in the shared file you would like to use. labels are separated by dashes.\n";
helpString += "The kruskal.wallis command should be in the following format: kruskal.wallis(shared=final.an.shared, design=final.design, class=treatment).\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "KruskalWallisCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string KruskalWallisCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "kruskall-wallis") { pattern = "[filename],[distance],kruskall_wallis"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "KruskalWallisCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
KruskalWallisCommand::KruskalWallisCommand(string option) : Command() {
try {
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
sharedfile = validParameter.validFile(parameters, "shared");
if (sharedfile == "not open") { sharedfile = ""; abort = true; }
else if (sharedfile == "not found") {
//if there is a current shared file, use it
sharedfile = current->getSharedFile();
if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter.\n"); }
else { m->mothurOut("You have no current sharedfile and the shared parameter is required.\n"); abort = true; }
}else { current->setSharedFile(sharedfile); }
//get shared file, it is required
designfile = validParameter.validFile(parameters, "design");
if (designfile == "not open") { designfile = ""; abort = true; }
else if (designfile == "not found") {
//if there is a current shared file, use it
designfile = current->getDesignFile();
if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter.\n"); }
else { m->mothurOut("You have no current design file and the design parameter is required.\n"); abort = true; }
}else { current->setDesignFile(designfile); }
if (outputdir == ""){
outputdir = util.hasPath(sharedfile);
}
string label = validParameter.valid(parameters, "label");
if (label == "not found") { label = ""; }
else {
if(label != "all") { util.splitAtDash(label, labels); allLines = false; }
else { allLines = true; }
}
mclass = validParameter.valid(parameters, "class");
if (mclass == "not found") { mclass = ""; }
}
}
catch(exception& e) {
m->errorOut(e, "KruskalWallisCommand", "KruskalWallisCommand");
exit(1);
}
}
//**********************************************************************************************************************
int KruskalWallisCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
DesignMap designMap(designfile); if (m->getControl_pressed()) { return 0; }
//if user did not select class use first column
if (mclass == "") { mclass = designMap.getDefaultClass(); m->mothurOut("\nYou did not provide a class, using " + mclass +".\n\n"); }
InputData input(sharedfile, "sharedfile", nullVector);
set<string> processedLabels;
set<string> userLabels = labels;
string lastLabel = "";
SharedRAbundVectors* lookup = util.getNextShared(input, allLines, userLabels, processedLabels, lastLabel);
vector<string> currentLabels = lookup->getOTUNames();
while (lookup != nullptr) {
if (m->getControl_pressed()) { delete lookup; break; }
vector<SharedRAbundVector*> data = lookup->getSharedRAbundVectors();
process(data, designMap, currentLabels);
for (int i = 0; i < data.size(); i++) { delete data[i]; } data.clear();
delete lookup;
lookup = util.getNextShared(input, allLines, userLabels, processedLabels, lastLabel);
}
//output files created by command
m->mothurOut("\nOutput File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i] +"\n"); } m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "KruskalWallisCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
int KruskalWallisCommand::process(vector<SharedRAbundVector*>& lookup, DesignMap& designMap, vector<string> currentLabels) {
try {
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(sharedfile));
variables["[distance]"] = lookup[0]->getLabel();
string outputFileName = getOutputFileName("kruskall-wallis",variables);
ofstream out;
util.openOutputFile(outputFileName, out);
outputNames.push_back(outputFileName); outputTypes["kruskall-wallis"].push_back(outputFileName);
out << "OTULabel\tKW\tPvalue\n";
int numBins = lookup[0]->getNumBins();
//sanity check to make sure each treatment has a group in the shared file
set<string> treatments;
for (int j = 0; j < lookup.size(); j++) {
string group = lookup[j]->getGroup();
string treatment = designMap.get(group, mclass); //get value for this group in this category
treatments.insert(treatment);
}
if (treatments.size() < 2) { m->mothurOut("[ERROR]: need at least 2 things for classes to compare, quitting.\n"); m->setControl_pressed(true); }
LinearAlgebra linear;
for (int i = 0; i < numBins; i++) {
if (m->getControl_pressed()) { break; }
vector<spearmanRank> values;
for (int j = 0; j < lookup.size(); j++) {
string group = lookup[j]->getGroup();
string treatment = designMap.get(group, mclass); //get value for this group in this category
spearmanRank temp(treatment, lookup[j]->get(i));
values.push_back(temp);
}
double pValue = 0.0;
double H = linear.calcKruskalWallis(values, pValue);
//output H and signifigance
out << currentLabels[i] << '\t' << H << '\t' << pValue << endl;
}
out.close();
return 0;
}
catch(exception& e) {
m->errorOut(e, "KruskalWallisCommand", "process");
exit(1);
}
}
//**********************************************************************************************************************
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