X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readotucommand.cpp;h=f39e8df2c382f02451848ca41ec6edb23e07aa49;hb=a6cf29fa4dac0909c7582cb1094151d34093ee76;hp=ba7eae42a668e7fa9bf3a9f8d33c4746b55ce810;hpb=753dc84cf289b1d5dc0ca5b0c043640927aa951a;p=mothur.git diff --git a/readotucommand.cpp b/readotucommand.cpp index ba7eae4..f39e8df 100644 --- a/readotucommand.cpp +++ b/readotucommand.cpp @@ -9,33 +9,129 @@ #include "readotucommand.h" + +//********************************************************************************************************************** +ReadOtuCommand::ReadOtuCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["rabund"] = tempOutNames; + outputTypes["shared"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand"); + exit(1); + } +} //********************************************************************************************************************** -ReadOtuCommand::ReadOtuCommand(string option){ +ReadOtuCommand::ReadOtuCommand(string option) { try { - globaldata = GlobalData::getInstance(); - abort = false; + 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 Array[] = {"list","order","shared", "line", "label","group","sabund", "rabund"}; + string Array[] = {"list","order","shared","relabund","label","group","sabund", "rabund","groups","ordergroup","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); 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; } } + //initialize outputTypes + vector tempOutNames; + outputTypes["rabund"] = tempOutNames; + outputTypes["shared"] = tempOutNames; + globaldata->newRead(); + //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; } + } + + it = parameters.find("order"); + //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["order"] = inputDir + it->second; } + } + + 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; } + } + + it = parameters.find("group"); + //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["group"] = inputDir + it->second; } + } + + it = parameters.find("sabund"); + //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["sabund"] = inputDir + it->second; } + } + + it = parameters.find("rabund"); + //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["rabund"] = inputDir + it->second; } + } + + it = parameters.find("ordergroup"); + //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["ordergroup"] = inputDir + it->second; } + } + + it = parameters.find("relabund"); + //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["relabund"] = 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 open") { abort = true; } @@ -52,149 +148,129 @@ ReadOtuCommand::ReadOtuCommand(string option){ else if (rabundfile == "not found") { rabundfile = ""; } else { globaldata->setRabundFile(rabundfile); globaldata->setFormat("rabund");} + ordergroupfile = validParameter.validFile(parameters, "ordergroup", true); + if (ordergroupfile == "not open") { abort = true; } + else if (ordergroupfile == "not found") { ordergroupfile = ""; } + else { globaldata->setOrderGroupFile(ordergroupfile); } + sharedfile = validParameter.validFile(parameters, "shared", true); if (sharedfile == "not open") { abort = true; } else if (sharedfile == "not found") { sharedfile = ""; } else { globaldata->setSharedFile(sharedfile); globaldata->setFormat("sharedfile"); } + relAbundfile = validParameter.validFile(parameters, "relabund", true); + if (relAbundfile == "not open") { abort = true; } + else if (relAbundfile == "not found") { relAbundfile = ""; } + else { globaldata->setRelAbundFile(relAbundfile); globaldata->setFormat("relabund"); } + + groupfile = validParameter.validFile(parameters, "group", true); if (groupfile == "not open") { abort = true; } else if (groupfile == "not found") { groupfile = ""; } else { globaldata->setGroupFile(groupfile); groupMap = new GroupMap(groupfile); - groupMap->readMap(); + + int error = groupMap->readMap(); + if (error == 1) { abort = true; } + + globaldata->gGroupmap = groupMap; + } + + groups = validParameter.validFile(parameters, "groups", false); + if (groups == "not found") { groups = ""; } + else { + m->splitAtDash(groups, Groups); + globaldata->Groups = Groups; } //you are doing a list and group shared if ((listfile != "") && (groupfile != "")) { globaldata->setFormat("shared"); } //you have not given a file - if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "")) { - cout << "You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. " << endl; abort = true; + if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "") && (relAbundfile == "")) { + m->mothurOut("You must enter either a listfile, rabundfile, sabundfile, relabund or a sharedfile with the read.otu command. "); m->mothurOutEndLine(); abort = true; } //check for optional parameter and set defaults // ...at some point should added some additional type checking... - line = validParameter.validFile(parameters, "line", false); - if (line == "not found") { line = ""; } - else { - if(line != "all") { splitAtDash(line, lines); allLines = 0; } - else { allLines = 1; } - globaldata->lines = lines; - } - 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; } globaldata->labels = labels; } globaldata->allLines = allLines; - - //make sure user did not use both the line and label parameters - if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; } - + orderfile = validParameter.validFile(parameters, "order", true); if (orderfile == "not open") { abort = true; } else if (orderfile == "not found") { orderfile = ""; } else { globaldata->setOrderFile(orderfile); } - + if (abort == false) { //gets whichever one of the above is set filename = globaldata->inputFileName; - //read = new ReadOTUFile(filename); } - + */ } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function ReadOtuCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ReadOtuCommand class function ReadOtuCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } -} -//********************************************************************************************************************** - -void ReadOtuCommand::help(){ - try { - cout << "The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, " << "\n"; - cout << "collect.shared, rarefaction.shared or summary.shared command. Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command " << "\n"; - cout << "or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, group, order, line and label." << "\n"; - cout << "The read.otu command can be used in two ways. The first is to read a list, rabund or sabund and run the collect.single, rarefaction.single or summary.single." << "\n"; - cout << "For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels)." << "\n"; - cout << "The list, rabund or sabund parameter is required, but you may only use one of them." << "\n"; - cout << "The line and label parameters are optional but you may not use both the line and label parameters at the same time." << "\n"; - cout << "The label and line parameters are used to read specific lines in your input." << "\n"; - cout << "The second way to use the read.otu command is to read a list and a group, or a shared so you can use the collect.shared, rarefaction.shared or summary.shared commands." << "\n"; - cout << "In this case the read.otu command should be in the following format: read.otu(list=yourListFile, group=yourGroupFile, line=yourLines) or read.otu(shared=yourSharedFile). " << "\n"; - cout << "The list parameter and group paramaters or the shared paremeter is required. When using the command the second way with a list and group file read.otu command parses the .list file" << "\n"; - cout << "and separates it into groups. It outputs a .shared file containing the OTU information for each group. The read.otu command also outputs a .list file for each group. " << "\n"; - cout << "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile)." << "\n" << "\n"; - - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the ReadOtuCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } - - - -//********************************************************************************************************************** - -ReadOtuCommand::~ReadOtuCommand(){ - if (abort == false) { //delete read; - } -} - -//********************************************************************************************************************** +///********************************************************************************************************************** int ReadOtuCommand::execute(){ try { - if (abort == true) { return 0; } - - //read->read(&*globaldata); + if (abort == true) { if (calledHelp) { return 0; } return 2; } + m->mothurOut(getHelpString()); m->mothurOutEndLine(); + + /* if (globaldata->getFormat() == "shared") { - groupMap->readMap(); - //if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap; } - globaldata->gGroupmap = groupMap; + shared = new SharedCommand(outputDir); + int okay = shared->execute(); + + //problem with shared + if (okay == 1) { + globaldata->setListFile(""); + globaldata->setGroupFile(""); + globaldata->setSharedFile(""); + }else { //shared command outputs the filenames + //m->mothurOutEndLine(); + //m->mothurOut("Output File Name: "); m->mothurOutEndLine(); + //m->mothurOut(globaldata->getSharedFile()); m->mothurOutEndLine(); + //m->mothurOutEndLine(); + } - parselist = new ParseListCommand(); - parselist->execute(); - delete parselist; + outputTypes = shared->getOutputFiles(); - shared = new SharedCommand(); - shared->execute(); - delete shared; + //set rabund file as new current rabundfile + string current = ""; + itTypes = outputTypes.find("rabund"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); } + } + + itTypes = outputTypes.find("shared"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); } + } - //change format to shared to speed up commands - globaldata->setFormat("sharedfile"); - globaldata->setListFile(""); - globaldata->setGroupFile(""); - globaldata->setSharedFile(getRootName(filename) + "shared"); + delete shared; } + */ + return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ReadOtuCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ReadOtuCommand", "execute"); exit(1); } }