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/*
* getrelabundcommand.cpp
* Mothur
*
* Created by westcott on 6/21/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "getrelabundcommand.h"
//**********************************************************************************************************************
vector<string> GetRelAbundCommand::setParameters(){
try {
CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","relabund",false,true, true); parameters.push_back(pshared);
CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
CommandParameter pscale("scale", "Multiple", "totalgroup-totalotu-averagegroup-averageotu", "totalgroup", "", "", "","",false,false); parameters.push_back(pscale);
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["relabund"] = 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, "GetRelAbundCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string GetRelAbundCommand::getHelpString(){
try {
string helpString = "";
helpString += "The get.relabund command parameters are shared, groups, scale and label. shared is required, unless you have a valid current file.\n";
helpString += "The groups parameter allows you to specify which of the groups in your groupfile 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 scale parameter allows you to select what scale you would like to use. Choices are totalgroup, totalotu, averagegroup, averageotu, default is totalgroup.\n";
helpString += "The get.relabund command should be in the following format: get.relabund(groups=yourGroups, label=yourLabels).\n";
helpString += "Example get.relabund(groups=A-B-C, scale=averagegroup).\n";
helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
helpString += "The get.relabund command outputs a .relabund file.\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "GetRelAbundCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string GetRelAbundCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "relabund") { pattern = "[filename],relabund"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "GetRelAbundCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
GetRelAbundCommand::GetRelAbundCommand(string option) : Command() {
try {
//allow user to run help
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); }
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 = ""; pickedGroups = false; }
else {
pickedGroups = true;
util.splitAtDash(groups, Groups);
if (Groups.size() != 0) { if (Groups[0]== "all") { Groups.clear(); } }
}
scale = validParameter.valid(parameters, "scale"); if (scale == "not found") { scale = "totalgroup"; }
if ((scale != "totalgroup") && (scale != "totalotu") && (scale != "averagegroup") && (scale != "averageotu")) {
m->mothurOut(scale + " is not a valid scaling option for the get.relabund command. Choices are totalgroup, totalotu, averagegroup, averageotu.\n"); abort = true;
}
}
}
catch(exception& e) {
m->errorOut(e, "GetRelAbundCommand", "GetRelAbundCommand");
exit(1);
}
}
//**********************************************************************************************************************
int GetRelAbundCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(sharedfile));
string outputFileName = getOutputFileName("relabund", variables);
ofstream out;
util.openOutputFile(outputFileName, out);
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
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();
vector<string> binLabels = lookup->getOTUNames();
out << "label\tGroup\tnumOtus";
for (int i = 0; i < binLabels.size(); i++) { out << '\t' << binLabels[i]; } out << endl;
while (lookup != nullptr) {
if (m->getControl_pressed()) { delete lookup; break; }
getRelAbundance(lookup, out); delete lookup;
lookup = util.getNextShared(input, allLines, userLabels, processedLabels, lastLabel);
}
out.close();
if (m->getControl_pressed()) { outputTypes.clear(); util.mothurRemove(outputFileName); return 0; }
m->mothurOut("\nOutput File Names: \n");
m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["relabund"].push_back(outputFileName);
m->mothurOutEndLine();
//set relabund file as new current relabundfile
string currentName = "";
itTypes = outputTypes.find("relabund");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setRelAbundFile(currentName); }
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetRelAbundCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
int GetRelAbundCommand::getRelAbundance(SharedRAbundVectors*& thisLookUp, ofstream& out){
try {
vector<string> groups = thisLookUp->getNamesGroups();
vector<string> binLabels = thisLookUp->getOTUNames();
for (int i = 0; i < thisLookUp->size(); i++) {
out << thisLookUp->getLabel() << '\t' << groups[i] << '\t' << thisLookUp->getNumBins();
for (int j = 0; j < thisLookUp->getNumBins(); j++) {
if (m->getControl_pressed()) { return 0; }
int abund = thisLookUp->get(j, groups[i]);
float relabund = 0.0;
if (scale == "totalgroup") {
relabund = abund / (float) thisLookUp->getNumSeqs(groups[i]);
}else if (scale == "totalotu") {
//calc the total in this otu
int totalOtu = thisLookUp->getOTUTotal(j);
relabund = abund / (float) totalOtu;
}else if (scale == "averagegroup") {
relabund = abund / (float) (thisLookUp->getNumSeqs(groups[i]) / (float) thisLookUp->getNumBins());
}else if (scale == "averageotu") {
//calc the total in this otu
int totalOtu = thisLookUp->getOTUTotal(j);
float averageOtu = totalOtu / (float) thisLookUp->size();
relabund = abund / (float) averageOtu;
}else{ m->mothurOut(scale + " is not a valid scaling option.\n"); m->setControl_pressed(true); return 0; }
out << '\t' << relabund;
}
out << endl;
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetRelAbundCommand", "getRelAbundance");
exit(1);
}
}
//**********************************************************************************************************************
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