//**********************************************************************************************************************
vector<string> RemoveOtuLabelsCommand::setParameters(){
try {
- CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos);
- CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pconstaxonomy);
- CommandParameter potucorr("otucorr", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(potucorr);
- CommandParameter pcorraxes("corraxes", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pcorraxes);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(paccnos);
+ CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "FNGLT", "none","constaxonomy",false,false); parameters.push_back(pconstaxonomy);
+ CommandParameter potucorr("otucorr", "InputTypes", "", "", "none", "FNGLT", "none","otucorr",false,false); parameters.push_back(potucorr);
+ CommandParameter pcorraxes("corraxes", "InputTypes", "", "", "none", "FNGLT", "none","corraxes",false,false); parameters.push_back(pcorraxes);
+ 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); }
}
}
//**********************************************************************************************************************
+string RemoveOtuLabelsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "constaxonomy") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "otucorr") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "corraxes") { pattern = "[filename],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, "RemoveOtuLabelsCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
RemoveOtuLabelsCommand::RemoveOtuLabelsCommand(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
- outputTypes["contaxonomy"] = tempOutNames;
- outputTypes["otu.corr"] = tempOutNames;
- outputTypes["corr.axes"] = tempOutNames;
+ outputTypes["constaxonomy"] = tempOutNames;
+ outputTypes["otucorr"] = tempOutNames;
+ outputTypes["corraxes"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "RemoveOtuLabelsCommand", "RemoveOtuLabelsCommand");
}
vector<string> tempOutNames;
- outputTypes["contaxonomy"] = tempOutNames;
- outputTypes["otu.corr"] = tempOutNames;
- outputTypes["corr.axes"] = tempOutNames;
+ outputTypes["constaxonomy"] = tempOutNames;
+ outputTypes["otucorr"] = tempOutNames;
+ outputTypes["corraxes"] = tempOutNames;
//check for parameters
accnosfile = validParameter.validFile(parameters, "accnos", true);
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get labels you want to keep
- readAccnos();
+ labels = m->readAccnos(accnosfile);
if (m->control_pressed) { return 0; }
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(constaxonomyfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(constaxonomyfile)) + "pick.taxonomy";
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(constaxonomyfile));
+ variables["[extension]"] = m->getExtension(constaxonomyfile);
+ string outputFileName = getOutputFileName("constaxonomy", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(otucorrfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(otucorrfile)) + "pick.corr";
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(otucorrfile));
+ variables["[extension]"] = m->getExtension(otucorrfile);
+ string outputFileName = getOutputFileName("otucorr", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
out.close();
if (wroteSomething == false) { m->mothurOut("Your file only contains labels from the .accnos file."); m->mothurOutEndLine(); }
- outputNames.push_back(outputFileName); outputTypes["otu.corr"].push_back(outputFileName);
+ outputNames.push_back(outputFileName); outputTypes["otucorr"].push_back(outputFileName);
m->mothurOut("Removed " + toString(removedCount) + " lines from your otu.corr file."); m->mothurOutEndLine();
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(corraxesfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(corraxesfile)) + "pick.axes";
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(corraxesfile));
+ variables["[extension]"] = m->getExtension(corraxesfile);
+ string outputFileName = getOutputFileName("corraxes", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
out.close();
if (wroteSomething == false) { m->mothurOut("Your file only contains labels from the .accnos file."); m->mothurOutEndLine(); }
- outputNames.push_back(outputFileName); outputTypes["corr.axes"].push_back(outputFileName);
+ outputNames.push_back(outputFileName); outputTypes["corraxes"].push_back(outputFileName);
m->mothurOut("Removed " + toString(removedCount) + " lines from your corr.axes file."); m->mothurOutEndLine();
exit(1);
}
}
-
-//**********************************************************************************************************************
-int RemoveOtuLabelsCommand::readAccnos(){
- try {
-
- ifstream in;
- m->openInputFile(accnosfile, in);
- string name;
-
- while(!in.eof()){
- in >> name;
-
- labels.insert(name);
-
- m->gobble(in);
- }
- in.close();
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveOtuLabelsCommand", "readAccnos");
- exit(1);
- }
-}
//**********************************************************************************************************************