//**********************************************************************************************************************
-vector<string> GetOtusCommand::getValidParameters(){
+vector<string> GetOtusCommand::setParameters(){
try {
- string Array[] = { "group", "accnos","label", "groups","list","outputdir","inputdir" };
- vector<string> 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<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "GetOtusCommand", "getValidParameters");
+ m->errorOut(e, "GetOtusCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-GetOtusCommand::GetOtusCommand(){
+string GetOtusCommand::getHelpString(){
try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["group"] = tempOutNames;
- outputTypes["list"] = tempOutNames;
+ string helpString = "";
+ helpString += "The get.otus command selects otus containing sequences from a specfic group or set of groups.\n";
+ helpString += "It outputs a new list file containing the otus containing sequences from in the those specified groups.\n";
+ helpString += "The get.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 get.otus command should be in the following format: get.otus(accnos=yourAccnos, list=yourListFile, group=yourGroupFile, label=yourLabel).\n";
+ helpString += "Example get.otus(accnos=amazon.accnos, list=amazon.fn.list, group=amazon.groups, label=0.03).\n";
+ helpString += "or get.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\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "GetOtusCommand", "GetOtusCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> GetOtusCommand::getRequiredParameters(){
- try {
- string Array[] = {"group","label", "list"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "GetOtusCommand", "getRequiredParameters");
+ m->errorOut(e, "GetOtusCommand", "getHelpString");
exit(1);
}
}
+
//**********************************************************************************************************************
-vector<string> GetOtusCommand::getRequiredFiles(){
+GetOtusCommand::GetOtusCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["list"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "GetOtusCommand", "getRequiredFiles");
+ m->errorOut(e, "GetOtusCommand", "GetOtusCommand");
exit(1);
}
}
if(option == "help") { help(); abort = true; calledHelp = true; }
else {
- //valid paramters for this command
- string Array[] = { "group", "accnos","label", "groups", "list","outputdir","inputdir" };
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
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 = ""; }
}
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; }
}
}
//**********************************************************************************************************************
-void GetOtusCommand::help(){
- try {
- m->mothurOut("The get.otus command selects 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 from in the those specified groups.\n");
- m->mothurOut("The get.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 get.otus command should be in the following format: get.otus(accnos=yourAccnos, list=yourListFile, group=yourGroupFile, label=yourLabel).\n");
- m->mothurOut("Example get.otus(accnos=amazon.accnos, list=amazon.fn.list, group=amazon.groups, label=0.03).\n");
- m->mothurOut("or get.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, "GetOtusCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
int GetOtusCommand::execute(){
try {
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<string> labels; labels.insert(label);
set<string> processedLabels;
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