try {
CommandParameter ptree("tree", "InputTypes", "", "", "", "", "none",false,true); parameters.push_back(ptree);
CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "", "", "none",false,true); parameters.push_back(ptaxonomy);
- CommandParameter pname("name", "InputTypes", "", "", "", "", "none",false,false); parameters.push_back(pname);
- CommandParameter pgroup("group", "InputTypes", "", "", "", "", "none",false,false); parameters.push_back(pgroup);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
CommandParameter pcutoff("cutoff", "Number", "", "51", "", "", "",false,true); parameters.push_back(pcutoff);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
helpString += "The classify.tree command reads a tree and taxonomy file and output the consensus taxonomy for each node on the tree. \n";
helpString += "If you provide a group file, the concensus for each group will also be provided. \n";
helpString += "The new tree contains labels at each internal node. The label is the node number so you can relate the tree to the summary file.\n";
+ helpString += "The count parameter allows you add a count file so you can have the summary totals broken up by group.\n";
helpString += "The summary file lists the concensus taxonomy for the descendants of each node.\n";
- helpString += "The classify.tree command parameters are tree, group, name and taxonomy. The tree and taxonomy files are required.\n";
+ helpString += "The classify.tree command parameters are tree, group, name, count and taxonomy. The tree and taxonomy files are required.\n";
helpString += "The cutoff parameter allows you to specify a consensus confidence threshold for your taxonomy. The default is 51, meaning 51%. Cutoff cannot be below 51.\n";
helpString += "The classify.tree command should be used in the following format: classify.tree(tree=test.tre, group=test.group, taxonomy=test.taxonomy)\n";
helpString += "Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n";
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["taxonomy"] = 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; }
+ }
}
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
else if (groupfile == "not found") { groupfile = ""; }
else { m->setGroupFile(groupfile); }
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { countfile = ""; abort = true; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
+
+ if ((namefile != "") && (countfile != "")) {
+ m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
+ }
+
+ if ((groupfile != "") && (countfile != "")) {
+ m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
+ }
+
string temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "51"; }
m->mothurConvert(temp, cutoff);
if ((cutoff < 51) || (cutoff > 100)) { m->mothurOut("cutoff must be above 50, and no greater than 100."); m->mothurOutEndLine(); abort = true; }
- if (namefile == "") {
- vector<string> files; files.push_back(treefile);
- parser.getNameFile(files);
+ if (countfile == "") {
+ if (namefile == "") {
+ vector<string> files; files.push_back(treefile);
+ parser.getNameFile(files);
+ }
}
-
}
}
catch(exception& e) {
TreeReader* reader = new TreeReader(treefile, groupfile, namefile);
vector<Tree*> T = reader->getTrees();
- TreeMap* tmap = T[0]->getTreeMap();
+ CountTable* tmap = T[0]->getCountTable();
Tree* outputTree = T[0];
delete reader;
if (itTax == taxMap.end()) { //this name is not in taxonomy file, skip it
m->mothurOut((*it) + " is not in your taxonomy file. I will not include it in the consensus."); m->mothurOutEndLine();
}else{
- //add seq to tree
- phylo->addSeqToTree((*it), itTax->second);
- size++;
- }
+ if (countfile != "") {
+ int numDups = ct->getNumSeqs((*it));
+ for (int j = 0; j < numDups; j++) { phylo->addSeqToTree((*it), itTax->second); }
+ size += numDups;
+ }else{
+ //add seq to tree
+ phylo->addSeqToTree((*it), itTax->second);
+ size++;
+ } }
}
if (m->control_pressed) { delete phylo; return conTax; }
int lc = T->tree[i].getLChild();
int rc = T->tree[i].getRChild();
- TreeMap* tmap = T->getTreeMap();
+ // TreeMap* tmap = T->getTreeMap();
if (lc == -1) { //you are a leaf your only descendant is yourself
- string group = tmap->getGroup(T->tree[i].getName());
+ vector<string> groups = T->tree[i].getGroup();
set<string> mynames; mynames.insert(T->tree[i].getName());
- names[group] = mynames; //mygroup -> me
+ for (int j = 0; j < groups.size(); j++) { names[groups[j]] = mynames; } //mygroup -> me
names["AllGroups"] = mynames;
}else{ //your descedants are the combination of your childrens descendants
names = descendants[lc];
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