X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removeotuscommand.cpp;h=30f337bf7fffc90bcdf7d9ebb8cc97611c6ebd29;hb=e150b0b0664caec517485ee6d69dcdade6dcae77;hp=0e7d302ecc065c00a364dfe8e58b0b6e46750a6a;hpb=fd5f17bcbe5fadab2c525f3d1fcfd1d79a60ae72;p=mothur.git diff --git a/removeotuscommand.cpp b/removeotuscommand.cpp index 0e7d302..30f337b 100644 --- a/removeotuscommand.cpp +++ b/removeotuscommand.cpp @@ -11,68 +11,74 @@ #include "inputdata.h" #include "sharedutilities.h" - //********************************************************************************************************************** -vector RemoveOtusCommand::getValidParameters(){ +vector RemoveOtusCommand::setParameters(){ try { - string Array[] = { "group", "accnos","label", "groups","list","outputdir","inputdir" }; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup); + CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist); + CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos); + CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups); + 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, "RemoveOtusCommand", "getValidParameters"); + m->errorOut(e, "RemoveOtusCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -RemoveOtusCommand::RemoveOtusCommand(){ +string RemoveOtusCommand::getHelpString(){ try { - abort = true; - //initialize outputTypes - vector tempOutNames; - outputTypes["group"] = tempOutNames; - outputTypes["list"] = tempOutNames; + string helpString = ""; + helpString += "The remove.otus command removes otus containing sequences from a specfic group or set of groups.\n"; + helpString += "It outputs a new list file containing the otus containing sequences NOT from in the those specified groups.\n"; + helpString += "The remove.otus command parameters are accnos, group, list, label and groups. The group and list parameters are required, unless you have valid current files.\n"; + helpString += "You must also provide an accnos containing the list of groups to get or set the groups parameter to the groups you wish to select.\n"; + helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like. You can separate group names with dashes.\n"; + helpString += "The label parameter allows you to specify which distance you want to process.\n"; + helpString += "The remove.otus command should be in the following format: remove.otus(accnos=yourAccnos, list=yourListFile, group=yourGroupFile, label=yourLabel).\n"; + helpString += "Example remove.otus(accnos=amazon.accnos, list=amazon.fn.list, group=amazon.groups, label=0.03).\n"; + helpString += "or remove.otus(groups=pasture, list=amazon.fn.list, amazon.groups, label=0.03).\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, "RemoveOtusCommand", "RemoveOtusCommand"); + m->errorOut(e, "RemoveOtusCommand", "getHelpString"); exit(1); } } -//********************************************************************************************************************** -vector RemoveOtusCommand::getRequiredParameters(){ - try { - string Array[] = {"group","label", "list"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; - } - catch(exception& e) { - m->errorOut(e, "RemoveOtusCommand", "getRequiredParameters"); - exit(1); - } -} -//********************************************************************************************************************** -vector RemoveOtusCommand::getRequiredFiles(){ + +///********************************************************************************************************************** +RemoveOtusCommand::RemoveOtusCommand(){ try { - vector myArray; - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["group"] = tempOutNames; + outputTypes["list"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "RemoveOtusCommand", "getRequiredFiles"); + m->errorOut(e, "RemoveOtusCommand", "RemoveOtusCommand"); exit(1); } } + //********************************************************************************************************************** RemoveOtusCommand::RemoveOtusCommand(string option) { try { - abort = false; + abort = false; calledHelp = false; //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[] = { "group", "accnos","label", "groups", "list","outputdir","inputdir" }; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -132,11 +138,19 @@ RemoveOtusCommand::RemoveOtusCommand(string option) { groupfile = validParameter.validFile(parameters, "group", true); if (groupfile == "not open") { abort = true; } - else if (groupfile == "not found") { groupfile = ""; m->mothurOut("You must provide a group file."); m->mothurOutEndLine(); abort = true; } + else if (groupfile == "not found") { + groupfile = m->getGroupFile(); + if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current group file and the group parameter is required."); m->mothurOutEndLine(); abort = true; } + } listfile = validParameter.validFile(parameters, "list", true); if (listfile == "not open") { abort = true; } - else if (listfile == "not found") { listfile = ""; m->mothurOut("You must provide a list file."); m->mothurOutEndLine(); abort = true; } + else 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; } + } groups = validParameter.validFile(parameters, "groups", false); if (groups == "not found") { groups = ""; } @@ -145,7 +159,7 @@ RemoveOtusCommand::RemoveOtusCommand(string option) { } label = validParameter.validFile(parameters, "label", false); - if (label == "not found") { label = ""; m->mothurOut("You must provide a label to process."); m->mothurOutEndLine(); abort = true; } + if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); label=""; } if ((accnosfile == "") && (Groups.size() == 0)) { m->mothurOut("You must provide an accnos file or specify groups using the groups parameter."); m->mothurOutEndLine(); abort = true; } } @@ -158,31 +172,10 @@ RemoveOtusCommand::RemoveOtusCommand(string option) { } //********************************************************************************************************************** -void RemoveOtusCommand::help(){ - try { - m->mothurOut("The remove.otus command removes otus containing sequences from a specfic group or set of groups.\n"); - m->mothurOut("It outputs a new list file containing the otus containing sequences NOT from in the those specified groups.\n"); - m->mothurOut("The remove.otus command parameters are accnos, group, list, label and groups. The group, list and label parameters are required.\n"); - m->mothurOut("You must also provide an accnos containing the list of groups to get or set the groups parameter to the groups you wish to select.\n"); - m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like. You can separate group names with dashes.\n"); - m->mothurOut("The label parameter allows you to specify which distance you want to process.\n"); - m->mothurOut("The remove.otus command should be in the following format: remove.otus(accnos=yourAccnos, list=yourListFile, group=yourGroupFile, label=yourLabel).\n"); - m->mothurOut("Example remove.otus(accnos=amazon.accnos, list=amazon.fn.list, group=amazon.groups, label=0.03).\n"); - m->mothurOut("or remove.otus(groups=pasture, list=amazon.fn.list, amazon.groups, label=0.03).\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, "RemoveOtusCommand", "help"); - exit(1); - } -} - -//********************************************************************************************************************** - int RemoveOtusCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } groupMap = new GroupMap(groupfile); groupMap->readMap(); @@ -208,6 +201,18 @@ int RemoveOtusCommand::execute(){ m->mothurOut("Output File names: "); m->mothurOutEndLine(); for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } m->mothurOutEndLine(); + + //set fasta file as new current fastafile + string current = ""; + itTypes = outputTypes.find("group"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); } + } + + itTypes = outputTypes.find("list"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); } + } } return 0; @@ -239,6 +244,9 @@ int RemoveOtusCommand::readListGroup(){ ListVector* list = input->getListVector(); string lastLabel = list->getLabel(); + //using first label seen if none is provided + if (label == "") { label = lastLabel; } + //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. set labels; labels.insert(label); set processedLabels; @@ -388,6 +396,7 @@ int RemoveOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstr m->mothurOut(newList.getLabel() + " - removed " + toString(numOtus) + " of the " + toString(list->getNumBins()) + " OTUs."); m->mothurOutEndLine(); + return 0; } catch(exception& e) {