+++ /dev/null
-/*
- * 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",false,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 pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
-
- 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";
- helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "GetRelAbundCommand", "getHelpString");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-GetRelAbundCommand::GetRelAbundCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["relabund"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "GetRelAbundCommand", "GetRelAbundCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-GetRelAbundCommand::GetRelAbundCommand(string option) {
- try {
- abort = false; calledHelp = false;
- allLines = 1;
-
- //allow user to run help
- if(option == "help") { help(); abort = true; calledHelp = true; }
- else if(option == "citation") { citation(); abort = true; calledHelp = true;}
-
- else {
- vector<string> myArray = setParameters();
-
- OptionParser parser(option);
- map<string,string> parameters = parser.getParameters();
- map<string,string>::iterator it;
-
- ValidParameters validParameter;
-
- //check to make sure all parameters are valid for command
- for (it = parameters.begin(); it != parameters.end(); it++) {
- if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
- }
-
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["relabund"] = tempOutNames;
-
- //if the user changes the input directory command factory will send this info to us in the output parameter
- string inputDir = validParameter.validFile(parameters, "inputdir", false);
- if (inputDir == "not found"){ inputDir = ""; }
- else {
- string path;
- it = parameters.find("shared");
- //user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["shared"] = inputDir + it->second; }
- }
- }
-
- //get shared file
- sharedfile = validParameter.validFile(parameters, "shared", true);
- if (sharedfile == "not open") { sharedfile = ""; abort = true; }
- else if (sharedfile == "not found") {
- //if there is a current shared file, use it
- sharedfile = m->getSharedFile();
- if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
- else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
- }else { m->setSharedFile(sharedfile); }
-
-
- //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 = m->hasPath(sharedfile); }
-
- //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") { m->splitAtDash(label, labels); allLines = 0; }
- else { allLines = 1; }
- }
-
- groups = validParameter.validFile(parameters, "groups", false);
- if (groups == "not found") { groups = ""; pickedGroups = false; }
- else {
- pickedGroups = true;
- m->splitAtDash(groups, Groups);
- m->setGroups(Groups);
- }
-
- scale = validParameter.validFile(parameters, "scale", false); 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."); m->mothurOutEndLine(); abort = true;
- }
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "GetRelAbundCommand", "GetRelAbundCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int GetRelAbundCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "relabund";
- ofstream out;
- m->openOutputFile(outputFileName, out);
- out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-
- input = new InputData(sharedfile, "sharedfile");
- lookup = input->getSharedRAbundVectors();
- string lastLabel = lookup[0]->getLabel();
-
- //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
- set<string> processedLabels;
- set<string> userLabels = labels;
-
- //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) { outputTypes.clear(); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); delete input; out.close(); m->mothurRemove(outputFileName); return 0; }
-
- if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
-
- m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
- getRelAbundance(lookup, out);
-
- processedLabels.insert(lookup[0]->getLabel());
- userLabels.erase(lookup[0]->getLabel());
- }
-
- 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]; }
- lookup = input->getSharedRAbundVectors(lastLabel);
- m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
- getRelAbundance(lookup, out);
-
- processedLabels.insert(lookup[0]->getLabel());
- userLabels.erase(lookup[0]->getLabel());
-
- //restore real lastlabel to save below
- lookup[0]->setLabel(saveLabel);
- }
-
- lastLabel = lookup[0]->getLabel();
- //prevent memory leak
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
-
- if (m->control_pressed) { outputTypes.clear(); m->clearGroups(); delete input; out.close(); m->mothurRemove(outputFileName); return 0; }
-
- //get next line to process
- lookup = input->getSharedRAbundVectors();
- }
-
- if (m->control_pressed) { outputTypes.clear(); m->clearGroups(); delete input; out.close(); m->mothurRemove(outputFileName); 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++) {
- m->mothurOut("Your file does not include the label " + *it);
- if (processedLabels.count(lastLabel) != 1) {
- m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
- needToRun = true;
- }else {
- m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
- }
- }
-
- //run last label if you need to
- if (needToRun == true) {
- for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
- lookup = input->getSharedRAbundVectors(lastLabel);
-
- m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
- getRelAbundance(lookup, out);
-
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
- }
-
- //reset groups parameter
- m->clearGroups();
- delete input;
- out.close();
-
- if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0;}
-
- m->mothurOutEndLine();
- m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["relabund"].push_back(outputFileName);
- m->mothurOutEndLine();
-
- //set relabund file as new current relabundfile
- string current = "";
- itTypes = outputTypes.find("relabund");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRelAbundFile(current); }
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "GetRelAbundCommand", "execute");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int GetRelAbundCommand::getRelAbundance(vector<SharedRAbundVector*>& thisLookUp, ofstream& out){
- try {
-
- for (int i = 0; i < thisLookUp.size(); i++) {
- out << thisLookUp[i]->getLabel() << '\t' << thisLookUp[i]->getGroup() << '\t' << thisLookUp[i]->getNumBins() << '\t';
-
- for (int j = 0; j < thisLookUp[i]->getNumBins(); j++) {
-
- if (m->control_pressed) { return 0; }
-
- int abund = thisLookUp[i]->getAbundance(j);
-
- float relabund = 0.0;
-
- 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) (thisLookUp[i]->getNumSeqs() / (float) thisLookUp[i]->getNumBins());
- }else if (scale == "averageotu") {
- //calc the total in this otu
- int totalOtu = 0;
- for (int l = 0; l < thisLookUp.size(); l++) { totalOtu += thisLookUp[l]->getAbundance(j); }
- float averageOtu = totalOtu / (float) thisLookUp.size();
-
- relabund = abund / (float) averageOtu;
- }else{ m->mothurOut(scale + " is not a valid scaling option."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
-
- out << relabund << '\t';
- }
- out << endl;
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "GetRelAbundCommand", "getRelAbundance");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-
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