X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readotucommand.cpp;h=8683fc3fa80154729ea5228fcaa38fb03726603a;hb=995238e9aa4455e3b59053e3dfe497b89caed79e;hp=1b2ec9e750445f7b256b978fec0298d42b3f825c;hpb=37a229b590342d94cd22bb1f7f4127e85197a27f;p=mothur.git diff --git a/readotucommand.cpp b/readotucommand.cpp index 1b2ec9e..8683fc3 100644 --- a/readotucommand.cpp +++ b/readotucommand.cpp @@ -10,56 +10,313 @@ #include "readotucommand.h" //********************************************************************************************************************** -ReadOtuCommand::ReadOtuCommand(){ +vector ReadOtuCommand::getValidParameters(){ try { - globaldata = GlobalData::getInstance(); - filename = globaldata->inputFileName; - read = new ReadOTUFile(filename); - if (globaldata->getFormat() == "shared") { - //read in group map info. - groupMap = new GroupMap(globaldata->getGroupFile()); - } + string Array[] = {"list","order","shared","relabund","label","group","sabund", "rabund","groups","ordergroup","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; } 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"; + m->errorOut(e, "ReadOtuCommand", "getValidParameters"); 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"; +} +//********************************************************************************************************************** +ReadOtuCommand::ReadOtuCommand(){ + try { + abort = true; + //initialize outputTypes + vector tempOutNames; + outputTypes["rabund"] = tempOutNames; + outputTypes["shared"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand"); exit(1); } } +//********************************************************************************************************************** +vector ReadOtuCommand::getRequiredParameters(){ + try { + string Array[] = {"list","shared","relabund","sabund","rabund","or"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ChopSeqsCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector ReadOtuCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ReadOtuCommand", "getRequiredFiles"); + exit(1); + } +} +//********************************************************************************************************************** +ReadOtuCommand::ReadOtuCommand(string option) { + try { + globaldata = GlobalData::getInstance(); + abort = false; + allLines = 1; + + //allow user to run help + if(option == "help") { help(); abort = true; } + + else { + //valid paramters for this command + 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 (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; } + else if (listfile == "not found") { listfile = ""; } + else { globaldata->setListFile(listfile); globaldata->setFormat("list"); } + + sabundfile = validParameter.validFile(parameters, "sabund", true); + if (sabundfile == "not open") { abort = true; } + else if (sabundfile == "not found") { sabundfile = ""; } + else { globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); } + + rabundfile = validParameter.validFile(parameters, "rabund", true); + if (rabundfile == "not open") { abort = true; } + 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); + + 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 == "") && (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... + label = validParameter.validFile(parameters, "label", false); + if (label == "not found") { label = ""; } + else { + if(label != "all") { m->splitAtDash(label, labels); allLines = 0; } + else { allLines = 1; } + globaldata->labels = labels; + } + + globaldata->allLines = allLines; + + 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; + } + } + + } + catch(exception& e) { + m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand"); + exit(1); + } +} //********************************************************************************************************************** -ReadOtuCommand::~ReadOtuCommand(){ - delete read; +void ReadOtuCommand::help(){ + try { + m->mothurOut("The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, \n"); + m->mothurOut("collect.shared, rarefaction.shared, summary.shared heatmap.bin, heatmap.sim or venn command. Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command \n"); + m->mothurOut("or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, relabund, group, order, ordergroup, label and groups.\n"); + m->mothurOut("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"); + m->mothurOut("For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels).\n"); + m->mothurOut("The list, rabund or sabund parameter is required, but you may only use one of them.\n"); + m->mothurOut("The label parameter is used to read specific labels in your input.\n"); + m->mothurOut("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"); + m->mothurOut("In this case the read.otu command should be in the following format: read.otu(list=yourListFile, group=yourGroupFile) or read.otu(shared=yourSharedFile). \n"); + m->mothurOut("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"); + m->mothurOut("and separates it into groups. It outputs a .shared file containing the OTU information for each group. The read.otu command also outputs a .rabund file for each group. \n"); + m->mothurOut("You can use the groups parameter to choose only specific groups to be used in the .shared and .rabund files. \n"); + m->mothurOut("You can use the ordergroup parameter to provide a file containing a list of group names in the order you would like them to appear in your shared file. \n"); + m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n"); + + } + catch(exception& e) { + m->errorOut(e, "ReadOtuCommand", "help"); + exit(1); + } } + + +//********************************************************************************************************************** +ReadOtuCommand::~ReadOtuCommand(){} //********************************************************************************************************************** int ReadOtuCommand::execute(){ try { - read->read(&*globaldata); + + if (abort == true) { return 0; } + if (globaldata->getFormat() == "shared") { - groupMap->readMap(); - //if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap; } - globaldata->gGroupmap = groupMap; - shared = new SharedCommand(); - shared->execute(); - - parselist = new ParseListCommand(); - parselist->execute(); + 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(); + } + + outputTypes = shared->getOutputFiles(); + + 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); } }