#include "rabundvector.hpp"
#include "sabundvector.hpp"
+//**********************************************************************************************************************
+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);
+
+ 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, "PhylotypeCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string PhylotypeCommand::getHelpString(){
+ 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 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";
+ helpString += "The label parameter allows you to specify which level you would like, and are separated by dashes. The default all levels in your taxonomy file. \n";
+ helpString += "For the label parameter, levels count down from the root to keep the output similiar to mothur's other commands which report information from finer resolution to coarser resolutions.\n";
+ helpString += "The phylotype command should be in the following format: \n";
+ helpString += "phylotype(taxonomy=yourTaxonomyFile, cutoff=yourCutoff, label=yourLabels) \n";
+ helpString += "Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhylotypeCommand", "getHelpString");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+PhylotypeCommand::PhylotypeCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ outputTypes["sabund"] = tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhylotypeCommand", "PhylotypeCommand");
+ exit(1);
+ }
+}
/**********************************************************************************************************************/
PhylotypeCommand::PhylotypeCommand(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 AlignArray[] = {"taxonomy","cutoff","label","name","outputdir","inputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ outputTypes["sabund"] = tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
if (taxonomyFileName == "not found") {
- m->mothurOut("taxonomy is a required parameter for the phylotype command.");
- m->mothurOutEndLine();
- abort = true;
+ taxonomyFileName = m->getTaxonomyFile();
+ if (taxonomyFileName != "") { m->mothurOut("Using " + taxonomyFileName + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. taxonomy is a required parameter."); m->mothurOutEndLine();
+ abort = true;
+ }
}else if (taxonomyFileName == "not open") { abort = true; }
+ else { m->setTaxonomyFile(taxonomyFileName); }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { namefile = ""; }
- else { readNamesFile(); }
+ else { readNamesFile(); m->setNameFile(namefile); }
//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"){
}
/**********************************************************************************************************************/
-void PhylotypeCommand::help(){
- try {
- m->mothurOut("The phylotype command reads a taxonomy file and outputs a .list, .rabund and .sabund file. \n");
- m->mothurOut("The phylotype command parameter options are taxonomy, cutoff and label. The taxonomy parameter is required.\n");
- m->mothurOut("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");
- m->mothurOut("For example: taxonomy = Bacteria;Bacteroidetes-Chlorobi;Bacteroidetes; - cutoff=2, would truncate the taxonomy to Bacteria;Bacteroidetes-Chlorobi; \n");
- m->mothurOut("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");
- m->mothurOut("The label parameter allows you to specify which level you would like, and are separated by dashes. The default all levels in your taxonomy file. \n");
- m->mothurOut("For the label parameter, levels count down from the root to keep the output similiar to mothur's other commands which report information from finer resolution to coarser resolutions.\n");
- m->mothurOut("The phylotype command should be in the following format: \n");
- m->mothurOut("phylotype(taxonomy=yourTaxonomyFile, cutoff=yourCutoff, label=yourLabels) \n");
- m->mothurOut("Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "PhylotypeCommand", "help");
- exit(1);
- }
-}
-/**********************************************************************************************************************/
-
-PhylotypeCommand::~PhylotypeCommand(){}
-
-/**********************************************************************************************************************/
-
int PhylotypeCommand::execute(){
try {
- if (abort == true) { return 0; }
-
- vector<string> outputNames;
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//reads in taxonomy file and makes all the taxonomies the same length
//by appending the last taxon to a given taxonomy as many times as needed to
string outputRabundFile = fileroot + "tx.rabund";
m->openOutputFile(outputRabundFile, outRabund);
- outputNames.push_back(outputListFile);
- outputNames.push_back(outputSabundFile);
- outputNames.push_back(outputRabundFile);
+ 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);
int count = 1;
//start at leaves of tree and work towards root, processing the labels the user wants
return 0;
}
+ //set list file as new current listfile
+ string current = "";
+ itTypes = outputTypes.find("list");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
+ }
+
+ //set rabund file as new current rabundfile
+ itTypes = outputTypes.find("rabund");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
+ }
+
+ //set sabund file as new current sabundfile
+ itTypes = outputTypes.find("sabund");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
+ }
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
projects / mothur.git / blobdiff