#include "getrelabundcommand.h"
//**********************************************************************************************************************
-
+vector<string> GetRelAbundCommand::getValidParameters(){
+ try {
+ string Array[] = {"groups","label","scale","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRelAbundCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetRelAbundCommand::GetRelAbundCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["relabund"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRelAbundCommand", "GetRelAbundCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetRelAbundCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRelAbundCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetRelAbundCommand::getRequiredFiles(){
+ try {
+ string Array[] = {"shared"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRelAbundCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
GetRelAbundCommand::GetRelAbundCommand(string option) {
try {
globaldata = GlobalData::getInstance();
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["relabund"] = 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 += 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
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; }
}
if (groups == "not found") { groups = ""; pickedGroups = false; }
else {
pickedGroups = true;
- splitAtDash(groups, Groups);
+ m->splitAtDash(groups, Groups);
globaldata->Groups = Groups;
}
m->mothurOut("The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n");
m->mothurOut("The scale parameter allows you to select what scale you would like to use. Choices are totalgroup, totalotu, averagegroup, averageotu, default is totalgroup.\n");
m->mothurOut("The get.relabund command should be in the following format: get.relabund(groups=yourGroups, label=yourLabels).\n");
- m->mothurOut("Example get.relabund(groups=A-B-C, scale=log10).\n");
+ m->mothurOut("Example get.relabund(groups=A-B-C, scale=averagegroup).\n");
m->mothurOut("The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n");
m->mothurOut("The get.relabund command outputs a .relabund file.\n");
m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
if (abort == true) { return 0; }
- string outputFileName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "relabund";
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "relabund";
ofstream out;
- openOutputFile(outputFileName, out);
+ m->openOutputFile(outputFileName, out);
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
read = new ReadOTUFile(globaldata->inputFileName);
//as long as you are not at the end of the file or done wih the lines you want
while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } globaldata->Groups.clear(); delete read; out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } globaldata->Groups.clear(); delete read; out.close(); remove(outputFileName.c_str()); return 0; }
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
userLabels.erase(lookup[0]->getLabel());
}
- if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = lookup[0]->getLabel();
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
//prevent memory leak
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
- if (m->control_pressed) { globaldata->Groups.clear(); delete read; out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); globaldata->Groups.clear(); delete read; out.close(); remove(outputFileName.c_str()); return 0; }
//get next line to process
lookup = input->getSharedRAbundVectors();
}
- if (m->control_pressed) { globaldata->Groups.clear(); delete read; out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); globaldata->Groups.clear(); delete read; out.close(); remove(outputFileName.c_str()); return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
delete read;
out.close();
- if (m->control_pressed) { remove(outputFileName.c_str()); return 0;}
+ if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0;}
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- m->mothurOut(outputFileName); m->mothurOutEndLine();
+ m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["relabund"].push_back(outputFileName);
m->mothurOutEndLine();
return 0;
int GetRelAbundCommand::getRelAbundance(vector<SharedRAbundVector*>& thisLookUp, ofstream& out){
try {
- if (pickedGroups) { eliminateZeroOTUS(thisLookUp); }
-
- int totalNumSeqs = 0;
- if ((scale == "totalgroup") || (scale == "averagegroup")) {
- for (int i = 0; i < thisLookUp.size(); i++) {
- //find total number of sequences in all samples
- totalNumSeqs += thisLookUp[i]->getNumSeqs();
- }
- }
- float averageNumSeqs = totalNumSeqs / (float) thisLookUp.size();
for (int i = 0; i < thisLookUp.size(); i++) {
out << thisLookUp[i]->getLabel() << '\t' << thisLookUp[i]->getGroup() << '\t' << thisLookUp[i]->getNumBins() << '\t';
float relabund = 0.0;
- if (scale == "totalgroup") { //abund of this otu compared to total number of sequence in my group
- relabund = abund / (float) totalNumSeqs;
+ if (scale == "totalgroup") {
+ relabund = abund / (float) thisLookUp[i]->getNumSeqs();
}else if (scale == "totalotu") {
//calc the total in this otu
int totalOtu = 0;
for (int l = 0; l < thisLookUp.size(); l++) { totalOtu += thisLookUp[l]->getAbundance(j); }
-
relabund = abund / (float) totalOtu;
}else if (scale == "averagegroup") {
- relabund = abund / (float) averageNumSeqs;
+ relabund = abund / (float) (thisLookUp[i]->getNumSeqs() / (float) thisLookUp[i]->getNumBins());
}else if (scale == "averageotu") {
//calc the total in this otu
int totalOtu = 0;
}
}
//**********************************************************************************************************************
-int GetRelAbundCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
- try {
-
- vector<SharedRAbundVector*> newLookup;
- for (int i = 0; i < thislookup.size(); i++) {
- SharedRAbundVector* temp = new SharedRAbundVector();
- temp->setLabel(thislookup[i]->getLabel());
- temp->setGroup(thislookup[i]->getGroup());
- newLookup.push_back(temp);
- }
-
- //for each bin
- for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
- if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
-
- //look at each sharedRabund and make sure they are not all zero
- bool allZero = true;
- for (int j = 0; j < thislookup.size(); j++) {
- if (thislookup[j]->getAbundance(i) != 0) { allZero = false; break; }
- }
-
- //if they are not all zero add this bin
- if (!allZero) {
- for (int j = 0; j < thislookup.size(); j++) {
- newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
- }
- }
- }
-
- for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; }
-
- thislookup = newLookup;
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "GetRelAbundCommand", "eliminateZeroOTUS");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
projects / mothur.git / blobdiff