//**********************************************************************************************************************
-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","group",false,true, true); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","list",false,true, 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;
- //initialize outputTypes
- 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";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "GetOtusCommand", "GetOtusCommand");
+ m->errorOut(e, "GetOtusCommand", "getHelpString");
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");
- exit(1);
- }
+string GetOtusCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "group") { pattern = "[filename],[tag],pick,[extension]"; }
+ else if (type == "list") { pattern = "[filename],[tag],pick,[extension]"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetOtusCommand", "getOutputPattern");
+ 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);
}
}
//**********************************************************************************************************************
GetOtusCommand::GetOtusCommand(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<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
//check for required parameters
accnosfile = validParameter.validFile(parameters, "accnos", true);
if (accnosfile == "not open") { abort = true; }
- else if (accnosfile == "not found") { accnosfile = ""; }
+ else if (accnosfile == "not found") { accnosfile = ""; }
+ else { m->setAccnosFile(accnosfile); }
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; }
+ }else { m->setGroupFile(groupfile); }
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; }
+ }else { m->setListFile(listfile); }
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 {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
groupMap = new GroupMap(groupfile);
groupMap->readMap();
- //get groups you want to remove
- if (accnosfile != "") { readAccnos(); }
+ //get groups you want to get
+ if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups); }
//make sure groups are valid
//takes care of user setting groupNames that are invalid or setting groups=all
SharedUtil* util = new SharedUtil();
- util->setGroups(Groups, groupMap->namesOfGroups);
+ vector<string> gNamesOfGroups = groupMap->getNamesOfGroups();
+ util->setGroups(Groups, gNamesOfGroups);
+ groupMap->setNamesOfGroups(gNamesOfGroups);
delete util;
if (m->control_pressed) { delete groupMap; return 0; }
//read through the list file keeping any otus that contain any sequence from the groups selected
readListGroup();
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if (outputNames.size() != 0) {
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();
+
+ //set list file as new current listfile
+ 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;
//**********************************************************************************************************************
int GetOtusCommand::readListGroup(){
try {
- string thisOutputDir = outputDir;
+ InputData* input = new InputData(listfile, "list");
+ ListVector* list = input->getListVector();
+ string lastLabel = list->getLabel();
+
+ //using first label seen if none is provided
+ if (label == "") { label = lastLabel; }
+
+ string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick." + label + m->getExtension(listfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[tag]"] = label;
+ variables["[extension]"] = m->getExtension(listfile);
+ string outputFileName = getOutputFileName("list", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
-
- string GroupOutputDir = outputDir;
+
+ string GroupOutputDir = outputDir;
if (outputDir == "") { GroupOutputDir += m->hasPath(groupfile); }
- string outputGroupFileName = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick." + label + m->getExtension(groupfile);
+ variables["[filename]"] = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string outputGroupFileName = getOutputFileName("group", variables);
ofstream outGroup;
m->openOutputFile(outputGroupFileName, outGroup);
-
- InputData* input = new InputData(listfile, "list");
- ListVector* 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<string> labels; labels.insert(label);
//as long as you are not at the end of the file or done wih the lines you want
while((list != NULL) && (userLabels.size() != 0)) {
- if (m->control_pressed) { delete list; delete input; out.close(); outGroup.close(); remove(outputFileName.c_str()); remove(outputGroupFileName.c_str());return 0; }
+ if (m->control_pressed) { delete list; delete input; out.close(); outGroup.close(); m->mothurRemove(outputFileName); m->mothurRemove(outputGroupFileName);return 0; }
if(labels.count(list->getLabel()) == 1){
processList(list, groupMap, out, outGroup, wroteSomething);
}
- if (m->control_pressed) { if (list != NULL) { delete list; } delete input; out.close(); outGroup.close(); remove(outputFileName.c_str()); remove(outputGroupFileName.c_str()); return 0; }
+ if (m->control_pressed) { if (list != NULL) { delete list; } delete input; out.close(); outGroup.close(); m->mothurRemove(outputFileName); m->mothurRemove(outputGroupFileName); return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
int numOtus = 0;
//for each bin
+ vector<string> binLabels = list->getLabels();
+ vector<string> newBinLabels;
for (int i = 0; i < list->getNumBins(); i++) {
if (m->control_pressed) { return 0; }
//if there are sequences from the groups we want in this bin add to new list, output to groupfile
if (keepBin) {
- newList.push_back(binnames);
+ newList.push_back(binnames);
+ newBinLabels.push_back(binLabels[i]);
outGroup << groupFileOutput;
numOtus++;
}
//print new listvector
if (newList.getNumBins() != 0) {
wroteSomething = true;
- newList.print(out);
+ newList.setLabels(newBinLabels);
+ newList.printHeaders(out);
+ newList.print(out);
}
m->mothurOut(newList.getLabel() + " - selected " + toString(numOtus) + " of the " + toString(list->getNumBins()) + " OTUs."); m->mothurOutEndLine();
}
}
//**********************************************************************************************************************
-void GetOtusCommand::readAccnos(){
- try {
- Groups.clear();
-
- ifstream in;
- m->openInputFile(accnosfile, in);
- string name;
-
- while(!in.eof()){
- in >> name;
-
- Groups.push_back(name);
-
- m->gobble(in);
- }
- in.close();
-
- }
- catch(exception& e) {
- m->errorOut(e, "GetOtusCommand", "readAccnos");
- exit(1);
- }
-}
-//**********************************************************************************************************************
projects / mothur.git / blobdiff