X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getrelabundcommand.cpp;h=f36f1ba23a6af6c9110dc0aac103054ceefedaff;hp=037cd3ee70b970a7f0ecce05e2e0c073e449562e;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=9013e13ecfb2fda3c2664a76f76cc99b8c7fa74c diff --git a/getrelabundcommand.cpp b/getrelabundcommand.cpp index 037cd3e..f36f1ba 100644 --- a/getrelabundcommand.cpp +++ b/getrelabundcommand.cpp @@ -10,64 +10,143 @@ #include "getrelabundcommand.h" //********************************************************************************************************************** - +vector 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 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); + } +} +//********************************************************************************************************************** +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->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "GetRelAbundCommand", "getOutputPattern"); + 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 { - 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 if(option == "citation") { citation(); abort = true; calledHelp = true;} else { - //valid paramters for this command - string AlignArray[] = {"groups","label","scale","outputdir","inputdir"}; - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + 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 (map::iterator it = parameters.begin(); it != parameters.end(); it++) { + for (it = parameters.begin(); it != parameters.end(); it++) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } - //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 - } + //initialize outputTypes + vector tempOutNames; + outputTypes["relabund"] = tempOutNames; - //make sure the user has already run the read.otu command - if ((globaldata->getSharedFile() == "")) { - m->mothurOut("You must read a list and a group, or a shared file before you can use the get.relabund command."); m->mothurOutEndLine(); abort = true; + //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") { splitAtDash(label, labels); allLines = 0; } + if(label != "all") { m->splitAtDash(label, labels); allLines = 0; } else { allLines = 1; } } - //if the user has not specified any labels use the ones from read.otu - if (label == "") { - allLines = globaldata->allLines; - labels = globaldata->labels; - } - groups = validParameter.validFile(parameters, "groups", false); if (groups == "not found") { groups = ""; pickedGroups = false; } else { pickedGroups = true; - splitAtDash(groups, Groups); - globaldata->Groups = Groups; + m->splitAtDash(groups, Groups); + m->setGroups(Groups); } scale = validParameter.validFile(parameters, "scale", false); if (scale == "not found") { scale = "totalgroup"; } @@ -83,49 +162,21 @@ GetRelAbundCommand::GetRelAbundCommand(string option) { exit(1); } } - -//********************************************************************************************************************** - -void GetRelAbundCommand::help(){ - try { - m->mothurOut("The get.relabund command can only be executed after a successful read.otu command of a list and group or shared file.\n"); - m->mothurOut("The get.relabund command parameters are groups, scale and label. No parameters are required.\n"); - m->mothurOut("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"); - 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=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"); - - } - catch(exception& e) { - m->errorOut(e, "GetRelAbundCommand", "help"); - exit(1); - } -} - -//********************************************************************************************************************** - -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"; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile)); + string outputFileName = getOutputFileName("relabund", variables); 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); - input = globaldata->ginput; + input = new InputData(sharedfile, "sharedfile"); lookup = input->getSharedRAbundVectors(); string lastLabel = lookup[0]->getLabel(); @@ -136,24 +187,25 @@ 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]; } 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 ((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]; } 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()); @@ -167,13 +219,13 @@ int GetRelAbundCommand::execute(){ //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(); m->clearGroups(); delete input; out.close(); m->mothurRemove(outputFileName); 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(); m->clearGroups(); delete input; out.close(); m->mothurRemove(outputFileName); return 0; } //output error messages about any remaining user labels set::iterator it; @@ -194,25 +246,31 @@ int GetRelAbundCommand::execute(){ 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 - globaldata->Groups.clear(); - delete input; globaldata->ginput = NULL; - delete read; + m->clearGroups(); + delete input; out.close(); - if (m->control_pressed) { remove(outputFileName.c_str()); return 0;} + 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(); + 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) { @@ -224,8 +282,6 @@ int GetRelAbundCommand::execute(){ int GetRelAbundCommand::getRelAbundance(vector& thisLookUp, ofstream& out){ try { - if (pickedGroups) { eliminateZeroOTUS(thisLookUp); } - for (int i = 0; i < thisLookUp.size(); i++) { out << thisLookUp[i]->getLabel() << '\t' << thisLookUp[i]->getGroup() << '\t' << thisLookUp[i]->getNumBins() << '\t'; @@ -269,48 +325,5 @@ int GetRelAbundCommand::getRelAbundance(vector& thisLookUp, } } //********************************************************************************************************************** -int GetRelAbundCommand::eliminateZeroOTUS(vector& thislookup) { - try { - - vector 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); - } -} - -//**********************************************************************************************************************