//**********************************************************************************************************************
vector<string> GetGroupsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "FNGLT-sharedGroup", "none",false,false); parameters.push_back(pshared);
- CommandParameter pname("name", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pname);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT-sharedGroup", "none",false,false); parameters.push_back(pgroup);
- CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(pfasta);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none",false,false); parameters.push_back(pshared);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "sharedGroup", "FNGLT",false,false); parameters.push_back(pgroup);
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "sharedGroup", "FNGLT",false,false); parameters.push_back(pdesign);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(plist);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(ptaxonomy);
CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
string GetGroupsCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The get.groups command selects sequences from a specfic group or set of groups from the following file types: fasta, name, group, list, taxonomy or shared file.\n";
+ helpString += "The get.groups command selects sequences from a specfic group or set of groups from the following file types: fasta, name, group, list, taxonomy, design or shared file.\n";
helpString += "It outputs a file containing the sequences in the those specified groups, or a sharedfile containing only those groups.\n";
- helpString += "The get.groups command parameters are accnos, fasta, name, group, list, taxonomy, shared and groups. The group parameter is required, unless you have a current group file, or are using a shared file.\n";
+ helpString += "The get.groups command parameters are accnos, fasta, name, group, list, taxonomy, shared, design and groups. The group parameter is required, unless you have a current group file, or are using a shared file.\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 get.groups command should be in the following format: get.groups(accnos=yourAccnos, fasta=yourFasta, group=yourGroupFile).\n";
exit(1);
}
}
+//**********************************************************************************************************************
+string GetGroupsCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "fasta") { outputFileName = "pick" + m->getExtension(inputName); }
+ else if (type == "taxonomy") { outputFileName = "pick" + m->getExtension(inputName); }
+ else if (type == "name") { outputFileName = "pick" + m->getExtension(inputName); }
+ else if (type == "group") { outputFileName = "pick" + m->getExtension(inputName); }
+ else if (type == "list") { outputFileName = "pick" + m->getExtension(inputName); }
+ else if (type == "shared") { outputFileName = "pick" + m->getExtension(inputName); }
+ else if (type == "design") { outputFileName = "pick" + m->getExtension(inputName); }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetGroupsCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
GetGroupsCommand::GetGroupsCommand(){
try {
outputTypes["group"] = tempOutNames;
outputTypes["list"] = tempOutNames;
outputTypes["shared"] = tempOutNames;
+ outputTypes["design"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "GetGroupsCommand", "GetGroupsCommand");
outputTypes["group"] = tempOutNames;
outputTypes["list"] = tempOutNames;
outputTypes["shared"] = tempOutNames;
+ outputTypes["design"] = tempOutNames;
//if the user changes the output directory command factory will send this info to us in the output parameter
//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("design");
+ //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["design"] = inputDir + it->second; }
+ }
}
else { m->setAccnosFile(accnosfile); }
fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not open") { abort = true; }
+ if (fastafile == "not open") { fastafile = ""; abort = true; }
else if (fastafile == "not found") { fastafile = ""; }
else { m->setFastaFile(fastafile); }
namefile = validParameter.validFile(parameters, "name", true);
- if (namefile == "not open") { abort = true; }
+ if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
else { m->setNameFile(namefile); }
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { groupfile = ""; abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
+
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { abort = true; }
else if (listfile == "not found") { listfile = ""; }
else { m->setListFile(listfile); }
taxfile = validParameter.validFile(parameters, "taxonomy", true);
- if (taxfile == "not open") { abort = true; }
+ if (taxfile == "not open") { taxfile = ""; abort = true; }
else if (taxfile == "not found") { taxfile = ""; }
else { m->setTaxonomyFile(taxfile); }
if (groups == "not found") { groups = ""; }
else {
m->splitAtDash(groups, Groups);
- m->Groups = Groups;
+ m->setGroups(Groups);
}
sharedfile = validParameter.validFile(parameters, "shared", true);
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { groupfile = ""; abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
- else { m->setGroupFile(groupfile); }
-
- if ((sharedfile == "") && (groupfile == "")) {
+ else { m->setGroupFile(groupfile); }
+
+ designfile = validParameter.validFile(parameters, "design", true);
+ if (designfile == "not open") { designfile = ""; abort = true; }
+ else if (designfile == "not found") { designfile = ""; }
+ else { m->setDesignFile(designfile); }
+
+ if ((sharedfile == "") && (groupfile == "") && (designfile == "")) {
//is there are current file available for any of these?
if ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != "")) {
//give priority to group, then shared
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 groupfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;
+ designfile = m->getDesignFile();
+ if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current groupfile or sharedfile or designfile and one is required."); m->mothurOutEndLine(); abort = true;
+ }
}
}
}
if ((accnosfile == "") && (Groups.size() == 0)) { m->mothurOut("You must provide an accnos file or specify groups using the groups parameter."); m->mothurOutEndLine(); abort = true; }
- if ((fastafile == "") && (namefile == "") && (groupfile == "") && (sharedfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, taxonomy, group, shared or list."); m->mothurOutEndLine(); abort = true; }
+ if ((fastafile == "") && (namefile == "") && (groupfile == "") && (designfile == "") && (sharedfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, taxonomy, group, shared, design or list."); m->mothurOutEndLine(); abort = true; }
if ((groupfile == "") && ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != ""))) { m->mothurOut("If using a fasta, name, taxonomy, group or list, then you must provide a group file."); m->mothurOutEndLine(); abort = true; }
+ if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
+ vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
+ parser.getNameFile(files);
+ }
}
}
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get groups you want to remove
- if (accnosfile != "") { readAccnos(); }
+ if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups); }
if (groupfile != "") {
groupMap = new GroupMap(groupfile);
//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;
//fill names with names of sequences that are from the groups we want to remove
if (listfile != "") { readList(); }
if (taxfile != "") { readTax(); }
if (sharedfile != "") { readShared(); }
+ if (designfile != "") { readDesign(); }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
}
+
+ itTypes = outputTypes.find("design");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setDesignFile(current); }
+ }
}
return 0;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
ofstream out;
m->openOutputFile(outputFileName, out);
currSeq.printSequence(out);
selectedCount++;
+ }else{
+ //if you are not in the accnos file check if you are a name that needs to be changed
+ map<string, string>::iterator it = uniqueToRedundant.find(name);
+ if (it != uniqueToRedundant.end()) {
+ wroteSomething = true;
+ currSeq.setName(it->second);
+ currSeq.printSequence(out);
+ selectedCount++;
+ }
}
}
m->gobble(in);
while(lookup[0] != NULL) {
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + ".pick" + m->getExtension(sharedfile);
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + "." + getOutputFileNameTag("shared", sharedfile);
ofstream out;
m->openOutputFile(outputFileName, out);
outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile);
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
ofstream out;
m->openOutputFile(outputFileName, out);
//if that name is in the .accnos file, add it
if (names.count(name) != 0) { newNames += name + ","; selectedCount++; }
+ else{
+ //if you are not in the accnos file check if you are a name that needs to be changed
+ map<string, string>::iterator it = uniqueToRedundant.find(name);
+ if (it != uniqueToRedundant.end()) {
+ newNames += it->second + ",";
+ selectedCount++;
+ }
+ }
}
//get last name
if (names.count(binnames) != 0) { newNames += binnames + ","; selectedCount++; }
+ else{
+ //if you are not in the accnos file check if you are a name that needs to be changed
+ map<string, string>::iterator it = uniqueToRedundant.find(binnames);
+ if (it != uniqueToRedundant.end()) {
+ newNames += it->second + ",";
+ selectedCount++;
+ }
+ }
//if there are names in this bin add to new list
if (newNames != "") {
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
ofstream out;
m->openOutputFile(outputFileName, out);
//you know you have at least one valid second since first column is valid
for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
out << validSecond[validSecond.size()-1] << endl;
+ uniqueToRedundant[firstCol] = validSecond[0];
}
}
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
ofstream out;
m->openOutputFile(outputFileName, out);
}
}
//**********************************************************************************************************************
-int GetGroupsCommand::readTax(){
+int GetGroupsCommand::readDesign(){
try {
string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
+ if (outputDir == "") { thisOutputDir += m->hasPath(designfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(designfile)) + getOutputFileNameTag("design", designfile);
+
ofstream out;
m->openOutputFile(outputFileName, out);
ifstream in;
- m->openInputFile(taxfile, in);
- string name, tax;
+ m->openInputFile(designfile, in);
+ string name, group;
bool wroteSomething = false;
+ int selectedCount = 0;
while(!in.eof()){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
in >> name; //read from first column
- in >> tax; //read from second column
+ in >> group; //read from second column
//if this name is in the accnos file
- if (names.count(name) != 0) {
+ if (m->inUsersGroups(name, Groups)) {
wroteSomething = true;
- out << name << '\t' << tax << endl;
+ out << name << '\t' << group << endl;
+ selectedCount++;
}
m->gobble(in);
in.close();
out.close();
- if (wroteSomething == false) { m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine(); }
- outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName);
+ if (wroteSomething == false) { m->mothurOut("Your file does NOT contain groups from the groups you wish to get."); m->mothurOutEndLine(); }
+ outputTypes["design"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ m->mothurOut("Selected " + toString(selectedCount) + " groups from your design file."); m->mothurOutEndLine();
+
return 0;
}
catch(exception& e) {
- m->errorOut(e, "GetGroupsCommand", "readTax");
+ m->errorOut(e, "GetGroupsCommand", "readDesign");
exit(1);
}
}
+
+
//**********************************************************************************************************************
-void GetGroupsCommand::readAccnos(){
+int GetGroupsCommand::readTax(){
try {
- Groups.clear();
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
ifstream in;
- m->openInputFile(accnosfile, in);
- string name;
+ m->openInputFile(taxfile, in);
+ string name, tax;
+
+ bool wroteSomething = false;
while(!in.eof()){
- in >> name;
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ in >> name; //read from first column
+ in >> tax; //read from second column
- Groups.push_back(name);
+ //if this name is in the accnos file
+ if (names.count(name) != 0) {
+ wroteSomething = true;
+ out << name << '\t' << tax << endl;
+ }else{
+ //if you are not in the accnos file check if you are a name that needs to be changed
+ map<string, string>::iterator it = uniqueToRedundant.find(name);
+ if (it != uniqueToRedundant.end()) {
+ wroteSomething = true;
+ out << it->second << '\t' << tax << endl;
+ }
+ }
m->gobble(in);
}
- in.close();
+ in.close();
+ out.close();
- m->Groups = Groups;
+ if (wroteSomething == false) { m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine(); }
+ outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName);
+ return 0;
}
catch(exception& e) {
- m->errorOut(e, "GetGroupsCommand", "readAccnos");
+ m->errorOut(e, "GetGroupsCommand", "readTax");
exit(1);
}
}
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