X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getlistcountcommand.cpp;h=a4d7b83397f83bf6ae3dd21627566252035b328f;hp=f14e17a951eec96494dd36a87d259f6117cc758c;hb=615301e57c25e241356a9c2380648d117709458d;hpb=c4fb347858dd8cfea4d2933f429fff4130dca65b diff --git a/getlistcountcommand.cpp b/getlistcountcommand.cpp index f14e17a..a4d7b83 100644 --- a/getlistcountcommand.cpp +++ b/getlistcountcommand.cpp @@ -10,123 +10,190 @@ #include "getlistcountcommand.h" //********************************************************************************************************************** -GetListCountCommand::GetListCountCommand(string option){ +vector GetListCountCommand::setParameters(){ try { - globaldata = GlobalData::getInstance(); - abort = false; - allLines = 1; - labels.clear(); + CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","otu",false,true, true); parameters.push_back(plist); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + CommandParameter parasort("sort", "Multiple", "name-otu", "otu", "", "", "","",false,false); parameters.push_back(parasort); + 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, "GetListCountCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string GetListCountCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The get.otulist command parameters are list, sort and label. list is required, unless you have a valid current list file.\n"; + helpString += "The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n"; + helpString += "The sort parameter allows you to select how you want the output displayed. Options are otu and name.\n"; + helpString += "If otu is selected the output will be otu number followed by the list of names in that otu.\n"; + helpString += "If name is selected the output will be a sequence name followed by its otu number.\n"; + helpString += "The get.otulist command should be in the following format: get.otulist(list=yourlistFile, label=yourLabels).\n"; + helpString += "Example get.otulist(list=amazon.fn.list, label=0.10).\n"; + helpString += "The default value for label is all lines in your inputfile.\n"; + helpString += "The get.otulist command outputs a .otu file for each distance you specify listing the bin number and the names of the sequences in that bin.\n"; + helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "GetListCountCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +string GetListCountCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "otu") { pattern = "[filename],[tag],otu"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "GetListCountCommand", "getOutputPattern"); + exit(1); + } +} +//********************************************************************************************************************** +GetListCountCommand::GetListCountCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["otu"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "GetListCountCommand", "GetListCountCommand"); + exit(1); + } +} +//********************************************************************************************************************** +GetListCountCommand::GetListCountCommand(string option) { + try { + abort = false; calledHelp = false; + allLines = 1; + //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[] = {"list","label"}; - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); ValidParameters validParameter; - + map::iterator it; + //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; } } - string ranRead = globaldata->getListFile(); + //initialize outputTypes + vector tempOutNames; + outputTypes["otu"] = 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("list"); + //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["list"] = inputDir + it->second; } + } + } + + //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 = ""; } //check for required parameters listfile = validParameter.validFile(parameters, "list", true); - if ((listfile == "not found") && (globaldata->getListFile() == "")) { mothurOut("You must read a listfile before running the get.listcount command."); mothurOutEndLine(); abort = true; } - else if ((listfile == "not found") && (globaldata->getListFile() != "")) { listfile = globaldata->getListFile(); } + if (listfile == "not found") { + listfile = m->getListFile(); + if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; } + } else if (listfile == "not open") { abort = true; } - else { globaldata->setListFile(listfile); } + else { m->setListFile(listfile); } + //check for optional parameter and set defaults // ...at some point should added some additional type checking... + sort = validParameter.validFile(parameters, "sort", false); if (sort == "not found") { sort = "otu"; } + if ((sort != "otu") && (sort != "name")) { m->mothurOut( sort + " is not a valid sort option. Options are otu and name. I will use otu."); m->mothurOutEndLine(); sort = "otu"; } 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 == "") && (ranRead != "")) { - allLines = globaldata->allLines; - labels = globaldata->labels; - } } } catch(exception& e) { - errorOut(e, "GetListCountCommand", "GetListCountCommand"); - exit(1); - } -} -//********************************************************************************************************************** - -void GetListCountCommand::help(){ - try { - mothurOut("The get.listcount command can only be executed after a successful read.otu command of a listfile or providing a list file using the list parameter.\n"); - mothurOut("The get.listcount command parameters are list and label. No parameters are required.\n"); - mothurOut("The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n"); - mothurOut("The get.listcount command should be in the following format: get.listcount(list=yourlistFile, label=yourLabels).\n"); - mothurOut("Example get.listcount(list=amazon.fn.list, label=0.10).\n"); - mothurOut("The default value for label is all lines in your inputfile.\n"); - mothurOut("The get.listcount command outputs a .otu file for each distance you specify listing the bin number and the names of the sequences in that bin.\n"); - mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n"); - } - catch(exception& e) { - errorOut(e, "GetListCountCommand", "help"); + m->errorOut(e, "GetListCountCommand", "GetListCountCommand"); exit(1); } } - -//********************************************************************************************************************** - -GetListCountCommand::~GetListCountCommand(){} - //********************************************************************************************************************** int GetListCountCommand::execute(){ try { - if (abort == true) { return 0; } - - globaldata->setFormat("list"); - - //read list file - read = new ReadOTUFile(listfile); - read->read(&*globaldata); + if (abort == true) { if (calledHelp) { return 0; } return 2; } - input = globaldata->ginput; - list = globaldata->gListVector; + input = new InputData(listfile, "list"); + list = input->getListVector(); string lastLabel = list->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; - + + if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { if(allLines == 1 || labels.count(list->getLabel()) == 1){ process(list); + + if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } processedLabels.insert(list->getLabel()); userLabels.erase(list->getLabel()); } - if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = list->getLabel(); + delete list; list = input->getListVector(lastLabel); process(list); + + if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + processedLabels.insert(list->getLabel()); userLabels.erase(list->getLabel()); + + //restore real lastlabel to save below + list->setLabel(saveLabel); } lastLabel = list->getLabel(); @@ -140,12 +207,12 @@ int GetListCountCommand::execute(){ set::iterator it; bool needToRun = false; for (it = userLabels.begin(); it != userLabels.end(); it++) { - mothurOut("Your file does not include the label " + *it); + m->mothurOut("Your file does not include the label " + *it); if (processedLabels.count(lastLabel) != 1) { - mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine(); + m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); needToRun = true; }else { - mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine(); + m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); } } @@ -154,17 +221,24 @@ int GetListCountCommand::execute(){ if (list != NULL) { delete list; } list = input->getListVector(lastLabel); - process(list); + process(list); + + if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + delete list; } - delete read; - globaldata->gListVector = NULL; + delete input; + + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } + m->mothurOutEndLine(); return 0; } catch(exception& e) { - errorOut(e, "GetListCountCommand", "execute"); + m->errorOut(e, "GetListCountCommand", "execute"); exit(1); } } @@ -173,22 +247,40 @@ int GetListCountCommand::execute(){ //return 1 if error, 0 otherwise void GetListCountCommand::process(ListVector* list) { try { - string binnames, name, sequence; - string outputFileName = getRootName(listfile) + list->getLabel() + ".otu"; - openOutputFile(outputFileName, out); + string binnames; + if (outputDir == "") { outputDir += m->hasPath(listfile); } + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile)); + variables["[tag]"] = list->getLabel(); + string outputFileName = getOutputFileName("otu", variables); + + m->openOutputFile(outputFileName, out); + outputNames.push_back(outputFileName); outputTypes["otu"].push_back(outputFileName); - mothurOut(list->getLabel()); mothurOutEndLine(); + m->mothurOut(list->getLabel()); m->mothurOutEndLine(); //for each bin in the list vector for (int i = 0; i < list->getNumBins(); i++) { + if (m->control_pressed) { break; } + binnames = list->get(i); - out << i+1 << '\t' << binnames << endl; + + if (sort == "otu") { + out << i+1 << '\t' << binnames << endl; + }else{ //sort = name + vector names; + m->splitAtComma(binnames, names); + + for (int j = 0; j < names.size(); j++) { + out << names[j] << '\t' << i+1 << endl; + } + } } out.close(); } catch(exception& e) { - errorOut(e, "GetListCountCommand", "process"); + m->errorOut(e, "GetListCountCommand", "process"); exit(1); } }