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//
// makeclrcommand.cpp
// Mothur
//
// Created by Sarah Westcott on 1/20/20.
// Copyright © 2020 Schloss Lab. All rights reserved.
//
#include "makeclrcommand.hpp"
//**********************************************************************************************************************
vector<string> MakeCLRCommand::setParameters(){
try {
CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","clr",false,false,true); parameters.push_back(pshared);
CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
CommandParameter pzero("zero", "Number", "", "0.1", "", "", "","",false,false); parameters.push_back(pzero);
CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
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["clr"] = 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, "MakeCLRCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string MakeCLRCommand::getHelpString(){
try {
string helpString = "";
helpString += "The make.clr command parameters are shared, groups, zero and label. The shared file is required, unless you have a valid current file.\n";
helpString += "The groups parameter allows you to specify which of the groups in your sharedfile you would like included. The group names are separated by dashes.\n";
helpString += "The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n";
helpString += "The zero parameter allows you to set an value for zero OTUs. Default is 0.1.\n";
helpString += "The make.clr command should be in the following format: make.clr(shared=yourSharedFile).\n";
helpString += "Example make.clr(shared=final.opti_mcc.shared, zero=0.25).\n";
helpString += "The default value for groups is all the groups in your sharedfile, and all labels in your inputfile will be used.\n";
helpString += "The make.clr command outputs a .clr file.\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "MakeCLRCommand", "MakeCLRCommand");
exit(1);
}
}
//**********************************************************************************************************************
string MakeCLRCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "clr") { pattern = "[filename],[distance],clr-[filename],clr"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "MakeCLRCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
MakeCLRCommand::MakeCLRCommand(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") {
sharedfile = current->getSharedFile();
if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter.\n"); }
else { m->mothurOut("[ERROR]: No valid current shared file. You must provide a shared file, quitting.\n"); abort = true; }
}else { current->setSharedFile(sharedfile); }
if (outputdir == ""){ outputdir = util.hasPath(sharedfile); }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
label = validParameter.valid(parameters, "label");
if (label == "not found") { label = ""; }
else {
if(label != "all") { util.splitAtDash(label, labels); allLines = false; }
else { allLines = true; }
}
groups = validParameter.valid(parameters, "groups");
if (groups == "not found") { groups = ""; }
else {
util.splitAtDash(groups, Groups);
if (Groups.size() != 0) { if (Groups[0]== "all") { Groups.clear(); } }
}
string temp = validParameter.valid(parameters, "zero"); if (temp == "not found") { temp = "0.1"; }
util.mothurConvert(temp, zeroReplacementValue);
}
}
catch(exception& e) {
m->errorOut(e, "MakeCLRCommand", "MakeCLRCommand");
exit(1);
}
}
//**********************************************************************************************************************
int MakeCLRCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
InputData input(sharedfile, "sharedfile", Groups);
set<string> processedLabels;
set<string> userLabels = labels;
string lastLabel = "";
SharedRAbundVectors* lookup = util.getNextShared(input, allLines, userLabels, processedLabels, lastLabel);
Groups = lookup->getNamesGroups();
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(sharedfile));
string outputFileName = getOutputFileName("clr",variables);
bool printHeaders = true;
ofstream out;
util.openOutputFile(outputFileName, out);
outputNames.push_back(outputFileName); outputTypes["clr"].push_back(outputFileName);
while (lookup != nullptr) {
if (m->getControl_pressed()) { delete lookup; break; }
process(lookup, out, printHeaders); delete lookup;
lookup = util.getNextShared(input, allLines, userLabels, processedLabels, lastLabel);
}
out.close();
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;}
string currentName = "";
itTypes = outputTypes.find("clr");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setCLRFile(currentName); }
}
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, "MakeCLRCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
// compute geometric mean through formula
// antilog(((log(1) + log(2) + . . . + log(n))/n)
//x <- c(10, 5, 3, 1,0)
//> x[x==0] <- 0.1
//> log2(x / prod(x)^(1/4))
//[1] 2.3452054 1.3452054 0.6082399 -0.9767226 -4.2986507
void MakeCLRCommand::process(SharedRAbundVectors*& thisLookUp, ofstream& out, bool& printHeaders){
try {
vector<string> lookupGroups = thisLookUp->getNamesGroups();
vector<SharedRAbundFloatVector*> lookup = thisLookUp->getSharedRAbundFloatVectors();
vector<string> otuNames = thisLookUp->getOTUNames();
if (printHeaders) { out << "label\tGroup\tnumOtus\t" << util.getStringFromVector(otuNames, "\t") << endl; printHeaders = false; }
for (int i = 0; i < lookup.size(); i++) {
if (m->getControl_pressed()) { break; }
vector<float> abunds = lookup[i]->get();
double geoMean = util.geometricMean(abunds, zeroReplacementValue);
for (int j = 0; j < abunds.size(); j++) { lookup[i]->set(j, log2(abunds[j]/geoMean)); }
lookup[i]->print(out);
delete lookup[i];
}
}
catch(exception& e) {
m->errorOut(e, "MakeCLRCommand", "process");
exit(1);
}
}
//**********************************************************************************************************************
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