else {
//valid paramters for this command
- string AlignArray[] = {"taxonomy","cutoff","label"};
+ string AlignArray[] = {"taxonomy","cutoff","label","outputdir","inputdir"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
ValidParameters validParameter;
+ map<string, string>::iterator it;
//check to make sure all parameters are valid for command
- for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //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 = ""; }
+ else {
+ string path;
+ it = parameters.find("taxonomy");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
+ }
+ }
+
taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
if (taxonomyFileName == "not found") {
mothurOut("taxonomy is a required parameter for the phylotype command.");
abort = true;
}else if (taxonomyFileName == "not open") { abort = true; }
+ //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 = "";
+ outputDir += hasPath(taxonomyFileName); //if user entered a file with a path then preserve it
+ }
+
string temp = validParameter.validFile(parameters, "cutoff", false);
if (temp == "not found") { temp = "-1"; }
convert(temp, cutoff);
mothurOut("The phylotype command reads a taxonomy file and outputs a .list, .rabund and .sabund file. \n");
mothurOut("The phylotype command parameter options are taxonomy, cutoff and label. The taxonomy parameter is required.\n");
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");
+ mothurOut("For example: taxonomy = Bacteria;Bacteroidetes-Chlorobi;Bacteroidetes; - cutoff=2, would truncate the taxonomy to Bacteria;Bacteroidetes-Chlorobi; \n");
+ 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");
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");
+ 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");
mothurOut("The phylotype command should be in the following format: \n");
mothurOut("phylotype(taxonomy=yourTaxonomyFile, cutoff=yourCutoff, label=yourLabels) \n");
mothurOut("Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n\n");
bool done = false;
if (tree->get(leaves[0]).parent == -1) { mothurOut("Empty Tree"); mothurOutEndLine(); done = true; }
+ string fileroot = outputDir + getRootName(getSimpleName(taxonomyFileName));
+
ofstream outList;
- string outputListFile = getRootName(taxonomyFileName) + "tax.list";
+ string outputListFile = fileroot + "tx.list";
openOutputFile(outputListFile, outList);
ofstream outSabund;
- string outputSabundFile = getRootName(taxonomyFileName) + "tax.sabund";
+ string outputSabundFile = fileroot + "tx.sabund";
openOutputFile(outputSabundFile, outSabund);
ofstream outRabund;
- string outputRabundFile = getRootName(taxonomyFileName) + "tax.rabund";
+ string outputRabundFile = fileroot + "tx.rabund";
openOutputFile(outputRabundFile, outRabund);
-
+ 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))) {
- string level = toString(tree->get(currentNodes.begin()->first).level);
+ string level = toString(count);
+ count++;
//is this a level the user want output for
if(allLines == 1 || labels.count(level) == 1){