X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getrelabundcommand.cpp;fp=getrelabundcommand.cpp;h=8c8d8e1539b8be7e76656be1304ee1f1f01f9a02;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git diff --git a/getrelabundcommand.cpp b/getrelabundcommand.cpp new file mode 100644 index 0000000..8c8d8e1 --- /dev/null +++ b/getrelabundcommand.cpp @@ -0,0 +1,312 @@ +/* + * getrelabundcommand.cpp + * Mothur + * + * Created by westcott on 6/21/10. + * Copyright 2010 Schloss Lab. All rights reserved. + * + */ + +#include "getrelabundcommand.h" + +//********************************************************************************************************************** +vector 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 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 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 myArray = setParameters(); + + OptionParser parser(option); + map parameters = parser.getParameters(); + map::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 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 processedLabels; + set 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::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& 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); + } +} +//********************************************************************************************************************** + +