--- /dev/null
+//
+// classifytreecommand.cpp
+// Mothur
+//
+// Created by Sarah Westcott on 2/20/12.
+// Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+#include "classifytreecommand.h"
+#include "phylotree.h"
+#include "treereader.h"
+
+//**********************************************************************************************************************
+vector<string> ClassifyTreeCommand::setParameters(){
+ 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 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);
+
+ 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, "ClassifyTreeCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ClassifyTreeCommand::getHelpString(){
+ try {
+ string helpString = "";
+ 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 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 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";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifyTreeCommand", "getHelpString");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+ClassifyTreeCommand::ClassifyTreeCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["tree"] = tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifyTreeCommand", "ClassifyTreeCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ClassifyTreeCommand::ClassifyTreeCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+ vector<string> myArray = setParameters();
+
+ 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 (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ vector<string> tempOutNames;
+ outputTypes["tree"] = tempOutNames;
+ outputTypes["summary"] = 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 = ""; }
+ else {
+ string path;
+ it = parameters.find("tree");
+ //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["tree"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //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["name"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("group");
+ //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["group"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("taxonomy");
+ //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["taxonomy"] = inputDir + it->second; }
+ }
+ }
+
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
+
+ //check for required parameters
+ treefile = validParameter.validFile(parameters, "tree", true);
+ if (treefile == "not open") { treefile = ""; abort = true; }
+ else if (treefile == "not found") { treefile = "";
+ treefile = m->getTreeFile();
+ if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("No valid current files. You must provide a tree file."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setTreeFile(treefile); }
+
+ taxonomyfile = validParameter.validFile(parameters, "taxonomy", true);
+ if (taxonomyfile == "not open") { taxonomyfile = ""; abort = true; }
+ else if (taxonomyfile == "not found") { taxonomyfile = "";
+ taxonomyfile = m->getTaxonomyFile();
+ if (taxonomyfile != "") { m->mothurOut("Using " + taxonomyfile + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("No valid current files. You must provide a taxonomy file."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setTaxonomyFile(taxonomyfile); }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { namefile = ""; abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { groupfile = ""; abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
+
+ 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);
+ }
+
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifyTreeCommand", "ClassifyTreeCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int ClassifyTreeCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
+
+ int start = time(NULL);
+
+ /***************************************************/
+ // reading tree info //
+ /***************************************************/
+ m->setTreeFile(treefile);
+
+ TreeReader* reader = new TreeReader(treefile, groupfile, namefile);
+ vector<Tree*> T = reader->getTrees();
+ TreeMap* tmap = T[0]->getTreeMap();
+ Tree* outputTree = T[0];
+ delete reader;
+
+ if (namefile != "") { readNamesFile(); }
+
+ if (m->control_pressed) { delete tmap; delete outputTree; return 0; }
+
+ readTaxonomyFile();
+
+ /***************************************************/
+ // get concensus taxonomies //
+ /***************************************************/
+ getClassifications(outputTree);
+ delete outputTree; delete tmap;
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ //set tree file as new current treefile
+ if (treefile != "") {
+ string current = "";
+ itTypes = outputTypes.find("tree");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTreeFile(current); }
+ }
+ }
+
+ m->mothurOutEndLine(); m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to find the concensus taxonomies."); m->mothurOutEndLine();
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifyTreeCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//traverse tree finding concensus taxonomy at each node
+//label node with a number to relate to output summary file
+//report all concensus taxonomies to file
+int ClassifyTreeCommand::getClassifications(Tree*& T){
+ try {
+
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(treefile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(treefile)) + "taxonomy.summary";
+ outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+
+ //print headings
+ out << "TreeNode\t";
+ if (groupfile != "") { out << "Group\t"; }
+ out << "NumRep\tTaxonomy" << endl;
+
+ string treeOutputDir = outputDir;
+ if (outputDir == "") { treeOutputDir += m->hasPath(treefile); }
+ string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + "taxonomy.tre";
+
+ //create a map from tree node index to names of descendants, save time later
+ map<int, map<string, set<string> > > nodeToDescendants; //node# -> (groupName -> groupMembers)
+ for (int i = 0; i < T->getNumNodes(); i++) {
+ if (m->control_pressed) { return 0; }
+
+ nodeToDescendants[i] = getDescendantList(T, i, nodeToDescendants);
+ }
+
+ //for each node
+ for (int i = T->getNumLeaves(); i < T->getNumNodes(); i++) {
+
+ if (m->control_pressed) { out.close(); return 0; }
+
+ string tax = "not classifed";
+ int size;
+ if (groupfile != "") {
+ for (map<string, set<string> >::iterator itGroups = nodeToDescendants[i].begin(); itGroups != nodeToDescendants[i].end(); itGroups++) {
+ if (itGroups->first != "AllGroups") {
+ tax = getTaxonomy(itGroups->second, size);
+ out << (i+1) << '\t' << itGroups->first << '\t' << size << '\t' << tax << endl;
+ }
+ }
+ }else {
+ string group = "AllGroups";
+ tax = getTaxonomy(nodeToDescendants[i][group], size);
+ out << (i+1) << '\t' << size << '\t' << tax << endl;
+ }
+
+ T->tree[i].setLabel((i+1));
+ }
+ out.close();
+
+ ofstream outTree;
+ m->openOutputFile(outputTreeFileName, outTree);
+ outputNames.push_back(outputTreeFileName); outputTypes["tree"].push_back(outputTreeFileName);
+ T->print(outTree, "both");
+ outTree.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifyTreeCommand", "GetConcensusTaxonomies");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ClassifyTreeCommand::getTaxonomy(set<string> names, int& size) {
+ try{
+ string conTax = "";
+ size = 0;
+
+ //create a tree containing sequences from this bin
+ PhyloTree* phylo = new PhyloTree();
+
+ for (set<string>::iterator it = names.begin(); it != names.end(); it++) {
+
+
+ //if namesfile include the names
+ if (namefile != "") {
+
+ //is this sequence in the name file - namemap maps seqName -> repSeqName
+ map<string, string>::iterator it2 = nameMap.find(*it);
+
+ if (it2 == nameMap.end()) { //this name is not in name file, skip it
+ m->mothurOut((*it) + " is not in your name file. I will not include it in the consensus."); m->mothurOutEndLine();
+ }else{
+
+ //is this sequence in the taxonomy file - look for repSeqName since we are assuming the taxonomy file is unique
+ map<string, string>::iterator itTax = taxMap.find((it2->second));
+
+ if (itTax == taxMap.end()) { //this name is not in taxonomy file, skip it
+
+ if ((*it) != (it2->second)) { m->mothurOut((*it) + " is represented by " + it2->second + " and is not in your taxonomy file. I will not include it in the consensus."); m->mothurOutEndLine(); }
+ else { m->mothurOut((*it) + " is not in your taxonomy file. I will not include it in the consensus."); m->mothurOutEndLine(); }
+ }else{
+ //add seq to tree
+ int num = nameCount[(*it)]; // we know its there since we found it in nameMap
+ for (int i = 0; i < num; i++) { phylo->addSeqToTree((*it)+toString(i), it2->second); }
+ size += num;
+ }
+ }
+
+ }else{
+ //is this sequence in the taxonomy file - look for repSeqName since we are assuming the taxonomy file is unique
+ map<string, string>::iterator itTax = taxMap.find((*it));
+
+ 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 (m->control_pressed) { delete phylo; return conTax; }
+
+ }
+
+ //build tree
+ phylo->assignHeirarchyIDs(0);
+
+ TaxNode currentNode = phylo->get(0);
+ int myLevel = 0;
+ //at each level
+ while (currentNode.children.size() != 0) { //you still have more to explore
+
+ TaxNode bestChild;
+ int bestChildSize = 0;
+
+ //go through children
+ for (map<string, int>::iterator itChild = currentNode.children.begin(); itChild != currentNode.children.end(); itChild++) {
+
+ TaxNode temp = phylo->get(itChild->second);
+
+ //select child with largest accesions - most seqs assigned to it
+ if (temp.accessions.size() > bestChildSize) {
+ bestChild = phylo->get(itChild->second);
+ bestChildSize = temp.accessions.size();
+ }
+
+ }
+
+ //is this taxonomy above cutoff
+ int consensusConfidence = ceil((bestChildSize / (float) size) * 100);
+
+ if (consensusConfidence >= cutoff) { //if yes, add it
+ conTax += bestChild.name + "(" + toString(consensusConfidence) + ");";
+ myLevel++;
+ }else{ //if no, quit
+ break;
+ }
+
+ //move down a level
+ currentNode = bestChild;
+ }
+
+ if (myLevel != phylo->getMaxLevel()) {
+ while (myLevel != phylo->getMaxLevel()) {
+ conTax += "unclassified;";
+ myLevel++;
+ }
+ }
+ if (conTax == "") { conTax = "no_consensus;"; }
+
+ delete phylo;
+
+ return conTax;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifyTreeCommand", "getTaxonomy");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+map<string, set<string> > ClassifyTreeCommand::getDescendantList(Tree*& T, int i, map<int, map<string, set<string> > > descendants){
+ try {
+ map<string ,set<string> > names;
+
+ map<string ,set<string> >::iterator it;
+ map<string ,set<string> >::iterator it2;
+
+ int lc = T->tree[i].getLChild();
+ int rc = T->tree[i].getRChild();
+ TreeMap* tmap = T->getTreeMap();
+
+ if (lc == -1) { //you are a leaf your only descendant is yourself
+ string group = tmap->getGroup(T->tree[i].getName());
+ set<string> mynames; mynames.insert(T->tree[i].getName());
+ names[group] = mynames; //mygroup -> me
+ names["AllGroups"] = mynames;
+ }else{ //your descedants are the combination of your childrens descendants
+ names = descendants[lc];
+ for (it = descendants[rc].begin(); it != descendants[rc].end(); it++) {
+ it2 = names.find(it->first); //do we already have this group
+ if (it2 == names.end()) { //nope, so add it
+ names[it->first] = it->second;
+ }else {
+ for (set<string>::iterator it3 = (it->second).begin(); it3 != (it->second).end(); it3++) {
+ names[it->first].insert(*it3);
+ }
+ }
+
+ }
+ }
+
+ return names;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifyTreeCommand", "getDescendantList");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int ClassifyTreeCommand::readTaxonomyFile() {
+ try {
+
+ ifstream in;
+ m->openInputFile(taxonomyfile, in);
+
+ string name, tax;
+
+ while(!in.eof()){
+ in >> name >> tax;
+ m->gobble(in);
+
+ //are there confidence scores, if so remove them
+ if (tax.find_first_of('(') != -1) { m->removeConfidences(tax); }
+
+ taxMap[name] = tax;
+
+ if (m->control_pressed) { in.close(); taxMap.clear(); return 0; }
+ }
+ in.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifyTreeCommand", "readTaxonomyFile");
+ exit(1);
+ }
+}
+
+/*****************************************************************/
+int ClassifyTreeCommand::readNamesFile() {
+ try {
+ ifstream inNames;
+ m->openInputFile(namefile, inNames);
+
+ string name, names;
+
+ while(!inNames.eof()){
+ inNames >> name; //read from first column A
+ inNames >> names; //read from second column A,B,C,D
+ m->gobble(inNames);
+
+ //parse names into vector
+ vector<string> theseNames;
+ m->splitAtComma(names, theseNames);
+
+ for (int i = 0; i < theseNames.size(); i++) { nameMap[theseNames[i]] = name; }
+ nameCount[name] = theseNames.size();
+
+ if (m->control_pressed) { inNames.close(); nameMap.clear(); return 0; }
+ }
+ inNames.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifyTreeCommand", "readNamesFile");
+ exit(1);
+ }
+}
+
+/*****************************************************************/
+
+
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