//**********************************************************************************************************************
vector<string> PhylotypeCommand::setParameters(){
try {
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptaxonomy);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcutoff("cutoff", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pcutoff);
- 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);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","list-rabund-sabund",false,true,true); parameters.push_back(ptaxonomy);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcutoff("cutoff", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(pcutoff);
+ 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); }
exit(1);
}
}
-
+//**********************************************************************************************************************
+string PhylotypeCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "list") { pattern = "[filename],[tag],list"; }
+ else if (type == "rabund") { pattern = "[filename],[tag],rabund"; }
+ else if (type == "sabund") { pattern = "[filename],[tag],sabund"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhylotypeCommand", "getOutputPattern");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
PhylotypeCommand::PhylotypeCommand(){
try {
m->mothurOut("No valid current files. taxonomy is a required parameter."); m->mothurOutEndLine();
abort = true;
}
- }else if (taxonomyFileName == "not open") { abort = true; }
+ }else if (taxonomyFileName == "not open") { taxonomyFileName = ""; abort = true; }
else { m->setTaxonomyFile(taxonomyFileName); }
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 { readNamesFile(); m->setNameFile(namefile); }
else { allLines = 1; }
}
+ if (namefile == "") {
+ vector<string> files; files.push_back(taxonomyFileName);
+ parser.getNameFile(files);
+ }
+
}
}
catch(exception& e) {
if (m->control_pressed) { delete tree; return 0; }
string fileroot = outputDir + m->getRootName(m->getSimpleName(taxonomyFileName));
-
- ofstream outList;
- string outputListFile = fileroot + "tx.list";
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[tag]"] = "tx";
+ ofstream outList;
+ string outputListFile = getOutputFileName("list",variables);
m->openOutputFile(outputListFile, outList);
ofstream outSabund;
- string outputSabundFile = fileroot + "tx.sabund";
+ string outputSabundFile = getOutputFileName("sabund",variables);
m->openOutputFile(outputSabundFile, outSabund);
ofstream outRabund;
- string outputRabundFile = fileroot + "tx.rabund";
+ string outputRabundFile = getOutputFileName("rabund",variables);
m->openOutputFile(outputRabundFile, outRabund);
outputNames.push_back(outputListFile); outputTypes["list"].push_back(outputListFile);
ListVector list;
list.setLabel(level);
+
//go through nodes and build listvector
for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
//make the names compatable with listvector
string name = "";
for (int i = 0; i < names.size(); i++) {
- if (namefile != "") {
- map<string, string>::iterator itNames = namemap.find(names[i]); //make sure this name is in namefile
-
- if (itNames != namemap.end()) { name += namemap[names[i]] + ","; } //you found it in namefile
- else { m->mothurOut(names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); exit(1); }
-
- }else{ name += names[i] + ","; }
+
+ if (names[i] != "unknown") {
+ if (namefile != "") {
+ map<string, string>::iterator itNames = namemap.find(names[i]); //make sure this name is in namefile
+
+ if (itNames != namemap.end()) { name += namemap[names[i]] + ","; } //you found it in namefile
+ else { m->mothurOut("[ERROR]: " + names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ }else{ name += names[i] + ","; }
+ }
}
+
+ if (m->control_pressed) { break; }
+
name = name.substr(0, name.length()-1); //rip off extra ','
-
//add bin to list vector
- list.push_back(name);
+ if (name != "") { list.push_back(name); } //caused by unknown
}
//print listvector