+++ /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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