X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getrelabundcommand.cpp;h=e79ccc9a3b3c9ec4812dc219af6dbe0428d5ece9;hb=b663591fb57c9508f017fd0891911fd959530125;hp=4fd95b2ba54c079b62a2cec8409d2dff661bff76;hpb=4ee9d3c973fb056f3105c26306da3b5d7dfb8108;p=mothur.git diff --git a/getrelabundcommand.cpp b/getrelabundcommand.cpp index 4fd95b2..e79ccc9 100644 --- a/getrelabundcommand.cpp +++ b/getrelabundcommand.cpp @@ -10,16 +10,62 @@ #include "getrelabundcommand.h" //********************************************************************************************************************** - +vector GetRelAbundCommand::getValidParameters(){ + try { + string Array[] = {"groups","label","scale","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "GetRelAbundCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +GetRelAbundCommand::GetRelAbundCommand(){ + try { + abort = true; calledHelp = true; + vector tempOutNames; + outputTypes["relabund"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "GetRelAbundCommand", "GetRelAbundCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector GetRelAbundCommand::getRequiredParameters(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "GetRelAbundCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector GetRelAbundCommand::getRequiredFiles(){ + try { + string Array[] = {"shared"}; + vector 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(); - abort = false; + abort = false; calledHelp = false; allLines = 1; labels.clear(); //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true; } else { //valid paramters for this command @@ -36,10 +82,14 @@ GetRelAbundCommand::GetRelAbundCommand(string option) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + //initialize outputTypes + vector 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 @@ -52,7 +102,7 @@ GetRelAbundCommand::GetRelAbundCommand(string option) { 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; } } @@ -63,15 +113,16 @@ GetRelAbundCommand::GetRelAbundCommand(string option) { } groups = validParameter.validFile(parameters, "groups", false); - if (groups == "not found") { groups = ""; } + if (groups == "not found") { groups = ""; pickedGroups = false; } else { - splitAtDash(groups, Groups); + pickedGroups = true; + m->splitAtDash(groups, Groups); globaldata->Groups = Groups; } scale = validParameter.validFile(parameters, "scale", false); if (scale == "not found") { scale = "totalgroup"; } - if ((scale != "totalgroup") && (scale != "totalgroup") && (scale != "totalgroup") && (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; } } @@ -93,7 +144,7 @@ void GetRelAbundCommand::help(){ 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"); @@ -115,11 +166,12 @@ GetRelAbundCommand::~GetRelAbundCommand(){ int GetRelAbundCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } - 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); read->read(&*globaldata); @@ -134,7 +186,7 @@ int GetRelAbundCommand::execute(){ //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){ @@ -145,7 +197,7 @@ int GetRelAbundCommand::execute(){ 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]; } @@ -164,12 +216,14 @@ int GetRelAbundCommand::execute(){ 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(); 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::iterator it; @@ -202,13 +256,20 @@ int GetRelAbundCommand::execute(){ 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(); + //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) { @@ -218,10 +279,44 @@ int GetRelAbundCommand::execute(){ } //********************************************************************************************************************** -int GetRelAbundCommand::getRelAbundance(vector thisLookUp, ofstream& out){ +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");