//**********************************************************************************************************************
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", "", "", "NameCount", "none", "ColumnName","rabund-sabund",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pcount);
+ 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); }
try {
string helpString = "";
helpString += "The phylotype command reads a taxonomy file and outputs a .list, .rabund and .sabund file. \n";
- helpString += "The phylotype command parameter options are taxonomy, cutoff and label. The taxonomy parameter is required.\n";
+ helpString += "The phylotype command parameter options are taxonomy, name, count, cutoff and label. The taxonomy parameter is required.\n";
helpString += "The cutoff parameter allows you to specify the level you want to stop at. The default is the highest level in your taxonomy file. \n";
helpString += "For example: taxonomy = Bacteria;Bacteroidetes-Chlorobi;Bacteroidetes; - cutoff=2, would truncate the taxonomy to Bacteria;Bacteroidetes-Chlorobi; \n";
helpString += "For the cutoff parameter levels count up from the root of the phylotree. This enables you to look at the grouping down to a specific resolution, say the genus level.\n";
exit(1);
}
}
-
+//**********************************************************************************************************************
+string PhylotypeCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "list") { pattern = "[filename],[clustertag],list-[filename],[clustertag],[tag2],list"; }
+ else if (type == "rabund") { pattern = "[filename],[clustertag],rabund"; }
+ else if (type == "sabund") { pattern = "[filename],[clustertag],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 {
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["name"] = inputDir + it->second; }
}
+
+ it = parameters.find("count");
+ //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["count"] = inputDir + it->second; }
+ }
}
taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
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 { readNamesFile(); m->setNameFile(namefile); }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { abort = true; countfile = ""; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
outputDir += m->hasPath(taxonomyFileName); //if user entered a file with a path then preserve it
}
+ if ((countfile != "") && (namefile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
+
string temp = validParameter.validFile(parameters, "cutoff", false);
if (temp == "not found") { temp = "-1"; }
m->mothurConvert(temp, cutoff);
else { allLines = 1; }
}
+ if (countfile == "") {
+ 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";
- m->openOutputFile(outputListFile, outList);
- ofstream outSabund;
- string outputSabundFile = fileroot + "tx.sabund";
- m->openOutputFile(outputSabundFile, outSabund);
- ofstream outRabund;
- string outputRabundFile = fileroot + "tx.rabund";
- m->openOutputFile(outputRabundFile, outRabund);
-
- outputNames.push_back(outputListFile); outputTypes["list"].push_back(outputListFile);
- outputNames.push_back(outputSabundFile); outputTypes["sabund"].push_back(outputSabundFile);
- outputNames.push_back(outputRabundFile); outputTypes["rabund"].push_back(outputRabundFile);
-
+ ofstream outList, outRabund, outSabund;
+ map<string, string> variables;
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(taxonomyFileName));
+ variables["[filename]"] = fileroot;
+ variables["[clustertag]"] = "tx";
+ string sabundFileName = getOutputFileName("sabund", variables);
+ string rabundFileName = getOutputFileName("rabund", variables);
+ if (countfile != "") { variables["[tag2]"] = "unique_list"; }
+ string listFileName = getOutputFileName("list", variables);
+
+ if (countfile == "") {
+ m->openOutputFile(sabundFileName, outSabund);
+ m->openOutputFile(rabundFileName, outRabund);
+ outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName);
+ outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName);
+
+ }
+ m->openOutputFile(listFileName, outList);
+ outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName);
+
+
int count = 1;
//start at leaves of tree and work towards root, processing the labels the user wants
while((!done) && ((allLines == 1) || (labels.size() != 0))) {
count++;
if (m->control_pressed) {
- outRabund.close(); outSabund.close(); outList.close();
+ if (countfile == "") { outRabund.close(); outSabund.close(); } outList.close();
for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
delete tree; return 0;
}
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
- list.print(outList);
- //print rabund
- list.getRAbundVector().print(outRabund);
- //print sabund
- list.getSAbundVector().print(outSabund);
-
+ if (!m->printedListHeaders) { list.printHeaders(outList); }
+ list.print(outList);
+
+ if (countfile == "") {
+ //print rabund
+ list.getRAbundVector().print(outRabund);
+ //print sabund
+ list.getSAbundVector().print(outSabund);
+ }
labels.erase(level);
}else {
}
outList.close();
- outSabund.close();
- outRabund.close();
+ if (countfile == "") {
+ outSabund.close();
+ outRabund.close();
+ }
delete tree;
projects / mothur.git / blobdiff