--- /dev/null
+/*
+ * rawTrainingDataMaker.cpp
+ * Mothur
+ *
+ * Created by westcott on 4/21/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "phylosummary.h"
+
+/**************************************************************************************************/
+
+PhyloSummary::PhyloSummary(string refTfile, string groupFile){
+ try {
+ m = MothurOut::getInstance();
+ maxLevel = 0;
+ ignore = false;
+
+ if (groupFile != "") {
+ groupmap = new GroupMap(groupFile);
+ groupmap->readMap();
+ }else{
+ groupmap = NULL;
+ }
+
+ //check for necessary files
+ string taxFileNameTest = m->getFullPathName((refTfile.substr(0,refTfile.find_last_of(".")+1) + "tree.sum"));
+ ifstream FileTest(taxFileNameTest.c_str());
+
+ if (!FileTest) {
+ m->mothurOut("Error: can't find " + taxFileNameTest + "."); m->mothurOutEndLine(); exit(1);
+ }else{
+ readTreeStruct(FileTest);
+ }
+
+ tree[0].rank = "0";
+ assignRank(0);
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloSummary", "PhyloSummary");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+PhyloSummary::PhyloSummary(string groupFile){
+ try {
+ m = MothurOut::getInstance();
+ maxLevel = 0;
+ ignore = true;
+
+ if (groupFile != "") {
+ groupmap = new GroupMap(groupFile);
+ groupmap->readMap();
+ }else{
+ groupmap = NULL;
+ }
+
+ tree.push_back(rawTaxNode("Root"));
+ tree[0].rank = "0";
+
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloSummary", "PhyloSummary");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+int PhyloSummary::summarize(string userTfile){
+ try {
+
+ ifstream in;
+ m->openInputFile(userTfile, in);
+
+ //read in users taxonomy file and add sequences to tree
+ string name, tax;
+ int numSeqs = 0;
+ while(!in.eof()){
+ in >> name >> tax; m->gobble(in);
+
+ addSeqToTree(name, tax);
+ numSeqs++;
+
+ if (m->control_pressed) { break; }
+ }
+ in.close();
+
+ return numSeqs;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloSummary", "summarize");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+string PhyloSummary::getNextTaxon(string& heirarchy){
+ try {
+ string currentLevel = "";
+ if(heirarchy != ""){
+ int pos = heirarchy.find_first_of(';');
+ currentLevel=heirarchy.substr(0,pos);
+ if (pos != (heirarchy.length()-1)) { heirarchy=heirarchy.substr(pos+1); }
+ else { heirarchy = ""; }
+ }
+ return currentLevel;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloSummary", "getNextTaxon");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){
+ try {
+
+ numSeqs++;
+
+ map<string, int>::iterator childPointer;
+
+ int currentNode = 0;
+ string taxon;
+
+ int level = 0;
+
+ //are there confidence scores, if so remove them
+ if (seqTaxonomy.find_first_of('(') != -1) { m->removeConfidences(seqTaxonomy); }
+
+ while (seqTaxonomy != "") {
+
+ if (m->control_pressed) { return 0; }
+
+ //somehow the parent is getting one too many accnos
+ //use print to reassign the taxa id
+ taxon = getNextTaxon(seqTaxonomy);
+
+ childPointer = tree[currentNode].children.find(taxon);
+
+ if(childPointer != tree[currentNode].children.end()){ //if the node already exists, update count and move on
+ if (groupmap != NULL) {
+ //find out the sequences group
+ string group = groupmap->getGroup(seqName);
+
+ if (group == "not found") { m->mothurOut("[WARNING]: " + seqName + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine(); }
+
+ //do you have a count for this group?
+ map<string, int>::iterator itGroup = tree[childPointer->second].groupCount.find(group);
+
+ //if yes, increment it - there should not be a case where we can't find it since we load group in read
+ if (itGroup != tree[childPointer->second].groupCount.end()) {
+ tree[childPointer->second].groupCount[group]++;
+ }
+ }
+
+ tree[childPointer->second].total++;
+
+ currentNode = childPointer->second;
+ }else{
+ if (ignore) {
+
+ tree.push_back(rawTaxNode(taxon));
+ int index = tree.size() - 1;
+
+ tree[index].parent = currentNode;
+ tree[index].level = (level+1);
+ tree[index].total = 1;
+ tree[currentNode].children[taxon] = index;
+
+ //initialize groupcounts
+ if (groupmap != NULL) {
+ vector<string> mGroups = groupmap->getNamesOfGroups();
+ for (int j = 0; j < mGroups.size(); j++) {
+ tree[index].groupCount[mGroups[j]] = 0;
+ }
+
+ //find out the sequences group
+ string group = groupmap->getGroup(seqName);
+
+ if (group == "not found") { m->mothurOut("[WARNING]: " + seqName + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine(); }
+
+ //do you have a count for this group?
+ map<string, int>::iterator itGroup = tree[index].groupCount.find(group);
+
+ //if yes, increment it - there should not be a case where we can't find it since we load group in read
+ if (itGroup != tree[index].groupCount.end()) {
+ tree[index].groupCount[group]++;
+ }
+ }
+
+ currentNode = index;
+
+ }else{ //otherwise, error
+ m->mothurOut("Warning: cannot find taxon " + taxon + " in reference taxonomy tree at level " + toString(tree[currentNode].level) + " for " + seqName + ". This may cause totals of daughter levels not to add up in summary file."); m->mothurOutEndLine();
+ break;
+ }
+ }
+
+ level++;
+
+ if ((seqTaxonomy == "") && (level < maxLevel)) { //if you think you are done and you are not.
+ for (int k = level; k < maxLevel; k++) { seqTaxonomy += "unclassified;"; }
+ }
+ }
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloSummary", "addSeqToTree");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+int PhyloSummary::addSeqToTree(string seqTaxonomy, vector<string> names){
+ try {
+ numSeqs++;
+
+ map<string, int>::iterator childPointer;
+
+ int currentNode = 0;
+ string taxon;
+
+ int level = 0;
+
+ //are there confidence scores, if so remove them
+ if (seqTaxonomy.find_first_of('(') != -1) { m->removeConfidences(seqTaxonomy); }
+
+ while (seqTaxonomy != "") {
+
+ if (m->control_pressed) { return 0; }
+
+ //somehow the parent is getting one too many accnos
+ //use print to reassign the taxa id
+ taxon = getNextTaxon(seqTaxonomy);
+
+ childPointer = tree[currentNode].children.find(taxon);
+
+ if(childPointer != tree[currentNode].children.end()){ //if the node already exists, update count and move on
+ if (groupmap != NULL) {
+
+ map<string, bool> containsGroup;
+ vector<string> mGroups = groupmap->getNamesOfGroups();
+ for (int j = 0; j < mGroups.size(); j++) {
+ containsGroup[mGroups[j]] = false;
+ }
+
+ for (int k = 0; k < names.size(); k++) {
+ //find out the sequences group
+ string group = groupmap->getGroup(names[k]);
+
+ if (group == "not found") { m->mothurOut("[WARNING]: " + names[k] + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine(); }
+ else {
+ containsGroup[group] = true;
+ }
+ }
+
+ for (map<string, bool>::iterator itGroup = containsGroup.begin(); itGroup != containsGroup.end(); itGroup++) {
+ if (itGroup->second == true) {
+ tree[childPointer->second].groupCount[itGroup->first]++;
+ }
+ }
+
+ }
+
+ tree[childPointer->second].total++;
+
+ currentNode = childPointer->second;
+ }else{
+ if (ignore) {
+
+ tree.push_back(rawTaxNode(taxon));
+ int index = tree.size() - 1;
+
+ tree[index].parent = currentNode;
+ tree[index].level = (level+1);
+ tree[index].total = 1;
+ tree[currentNode].children[taxon] = index;
+
+ //initialize groupcounts
+ if (groupmap != NULL) {
+ map<string, bool> containsGroup;
+ vector<string> mGroups = groupmap->getNamesOfGroups();
+ for (int j = 0; j < mGroups.size(); j++) {
+ tree[index].groupCount[mGroups[j]] = 0;
+ containsGroup[mGroups[j]] = false;
+ }
+
+
+ for (int k = 0; k < names.size(); k++) {
+ //find out the sequences group
+ string group = groupmap->getGroup(names[k]);
+
+ if (group == "not found") { m->mothurOut("[WARNING]: " + names[k] + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine(); }
+ else {
+ containsGroup[group] = true;
+ }
+ }
+
+ for (map<string, bool>::iterator itGroup = containsGroup.begin(); itGroup != containsGroup.end(); itGroup++) {
+ if (itGroup->second == true) {
+ tree[index].groupCount[itGroup->first]++;
+ }
+ }
+ }
+
+ currentNode = index;
+
+ }else{ //otherwise, error
+ m->mothurOut("Warning: cannot find taxon " + taxon + " in reference taxonomy tree at level " + toString(tree[currentNode].level) + ". This may cause totals of daughter levels not to add up in summary file."); m->mothurOutEndLine();
+ break;
+ }
+ }
+
+ level++;
+
+ if ((seqTaxonomy == "") && (level < maxLevel)) { //if you think you are done and you are not.
+ for (int k = level; k < maxLevel; k++) { seqTaxonomy += "unclassified;"; }
+ }
+ }
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloSummary", "addSeqToTree");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+void PhyloSummary::assignRank(int index){
+ try {
+ map<string,int>::iterator it;
+ int counter = 1;
+
+ for(it=tree[index].children.begin();it!=tree[index].children.end();it++){
+ tree[it->second].rank = tree[index].rank + '.' + toString(counter);
+ counter++;
+
+ assignRank(it->second);
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloSummary", "assignRank");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+void PhyloSummary::print(ofstream& out){
+ try {
+
+ if (ignore) { assignRank(0); }
+
+ //print labels
+ out << "taxlevel\t rankID\t taxon\t daughterlevels\t total\t";
+ if (groupmap != NULL) {
+ //so the labels match the counts below, since the map sorts them automatically...
+ //sort(groupmap->namesOfGroups.begin(), groupmap->namesOfGroups.end());
+ vector<string> mGroups = groupmap->getNamesOfGroups();
+ for (int i = 0; i < mGroups.size(); i++) {
+ out << mGroups[i] << '\t';
+ }
+ }
+
+ out << endl;
+
+ int totalChildrenInTree = 0;
+ map<string, int>::iterator itGroup;
+
+ map<string,int>::iterator it;
+ for(it=tree[0].children.begin();it!=tree[0].children.end();it++){
+ if (tree[it->second].total != 0) {
+ totalChildrenInTree++;
+ tree[0].total += tree[it->second].total;
+
+ if (groupmap != NULL) {
+ vector<string> mGroups = groupmap->getNamesOfGroups();
+ for (int i = 0; i < mGroups.size(); i++) { tree[0].groupCount[mGroups[i]] += tree[it->second].groupCount[mGroups[i]]; }
+ }
+ }
+ }
+
+ //print root
+ out << tree[0].level << "\t" << tree[0].rank << "\t" << tree[0].name << "\t" << totalChildrenInTree << "\t" << tree[0].total << "\t";
+
+
+ if (groupmap != NULL) {
+ //for (itGroup = tree[0].groupCount.begin(); itGroup != tree[0].groupCount.end(); itGroup++) {
+ // out << itGroup->second << '\t';
+ //}
+ vector<string> mGroups = groupmap->getNamesOfGroups();
+ for (int i = 0; i < mGroups.size(); i++) { out << tree[0].groupCount[mGroups[i]] << '\t'; }
+ }
+ out << endl;
+
+ //print rest
+ print(0, out);
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloSummary", "print");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+void PhyloSummary::print(int i, ofstream& out){
+ try {
+ map<string,int>::iterator it;
+ for(it=tree[i].children.begin();it!=tree[i].children.end();it++){
+
+ if (tree[it->second].total != 0) {
+
+ int totalChildrenInTree = 0;
+
+ map<string,int>::iterator it2;
+ for(it2=tree[it->second].children.begin();it2!=tree[it->second].children.end();it2++){
+ if (tree[it2->second].total != 0) { totalChildrenInTree++; }
+ }
+
+ out << tree[it->second].level << "\t" << tree[it->second].rank << "\t" << tree[it->second].name << "\t" << totalChildrenInTree << "\t" << tree[it->second].total << "\t";
+
+ map<string, int>::iterator itGroup;
+ if (groupmap != NULL) {
+ //for (itGroup = tree[it->second].groupCount.begin(); itGroup != tree[it->second].groupCount.end(); itGroup++) {
+ // out << itGroup->second << '\t';
+ //}
+ vector<string> mGroups = groupmap->getNamesOfGroups();
+ for (int i = 0; i < mGroups.size(); i++) { out << tree[it->second].groupCount[mGroups[i]] << '\t'; }
+ }
+ out << endl;
+
+ }
+
+ print(it->second, out);
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloSummary", "print");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+void PhyloSummary::readTreeStruct(ifstream& in){
+ try {
+
+ //read version
+ string line = m->getline(in); m->gobble(in);
+
+ int num;
+
+ in >> num; m->gobble(in);
+
+ tree.resize(num);
+
+ in >> maxLevel; m->gobble(in);
+
+ //read the tree file
+ for (int i = 0; i < tree.size(); i++) {
+
+ in >> tree[i].level >> tree[i].name >> num; //num contains the number of children tree[i] has
+
+ //set children
+ string childName;
+ int childIndex;
+ for (int j = 0; j < num; j++) {
+ in >> childName >> childIndex;
+ tree[i].children[childName] = childIndex;
+ }
+
+ //initialize groupcounts
+ if (groupmap != NULL) {
+ for (int j = 0; j < (groupmap->getNamesOfGroups()).size(); j++) {
+ tree[i].groupCount[(groupmap->getNamesOfGroups())[j]] = 0;
+ }
+ }
+
+ tree[i].total = 0;
+
+ m->gobble(in);
+
+ //if (tree[i].level > maxLevel) { maxLevel = tree[i].level; }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloSummary", "readTreeStruct");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+
+
projects / mothur.git / blobdiff