*/
#include "phylodiversitycommand.h"
+#include "treereader.h"
//**********************************************************************************************************************
vector<string> PhyloDiversityCommand::setParameters(){
exit(1);
}
}
-
+//**********************************************************************************************************************
+string PhyloDiversityCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "phylodiv") { outputFileName = "phylodiv"; }
+ else if (type == "rarefy") { outputFileName = "phylodiv.rarefaction"; }
+ else if (type == "summary") { outputFileName = "phylodiv.summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloDiversityCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
PhyloDiversityCommand::PhyloDiversityCommand(){
}
}
- m->runParse = true;
- m->clearGroups();
- m->clearAllGroups();
- m->Treenames.clear();
- m->names.clear();
-
//check for required parameters
treefile = validParameter.validFile(parameters, "tree", true);
- if (treefile == "not open") { abort = true; }
+ if (treefile == "not open") { treefile = ""; abort = true; }
else if (treefile == "not found") {
//if there is a current design file, use it
treefile = m->getTreeFile();
else { m->setGroupFile(groupfile); }
namefile = validParameter.validFile(parameters, "name", true);
- if (namefile == "not open") { abort = true; }
+ if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
else { m->setNameFile(namefile); }
}
if ((!collect) && (!rarefy) && (!summary)) { m->mothurOut("No outputs selected. You must set either collect, rarefy or summary to true, summary=T by default."); m->mothurOutEndLine(); abort=true; }
+
+ if (namefile == "") {
+ vector<string> files; files.push_back(treefile);
+ parser.getNameFile(files);
+ }
}
}
if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ int start = time(NULL);
+
m->setTreeFile(treefile);
-
- if (groupfile != "") {
- //read in group map info.
- tmap = new TreeMap(groupfile);
- tmap->readMap();
- }else{ //fake out by putting everyone in one group
- Tree* tree = new Tree(treefile); delete tree; //extracts names from tree to make faked out groupmap
- tmap = new TreeMap();
-
- for (int i = 0; i < m->Treenames.size(); i++) { tmap->addSeq(m->Treenames[i], "Group1"); }
- }
-
- if (namefile != "") { readNamesFile(); }
-
- read = new ReadNewickTree(treefile);
- int readOk = read->read(tmap);
-
- if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete tmap; delete read; return 0; }
-
- read->AssembleTrees();
- vector<Tree*> trees = read->getTrees();
- delete read;
-
- //make sure all files match
- //if you provide a namefile we will use the numNames in the namefile as long as the number of unique match the tree names size.
- int numNamesInTree;
- if (namefile != "") {
- if (numUniquesInName == m->Treenames.size()) { numNamesInTree = nameMap.size(); }
- else { numNamesInTree = m->Treenames.size(); }
- }else { numNamesInTree = m->Treenames.size(); }
-
-
- //output any names that are in group file but not in tree
- if (numNamesInTree < tmap->getNumSeqs()) {
- for (int i = 0; i < tmap->namesOfSeqs.size(); i++) {
- //is that name in the tree?
- int count = 0;
- for (int j = 0; j < m->Treenames.size(); j++) {
- if (tmap->namesOfSeqs[i] == m->Treenames[j]) { break; } //found it
- count++;
- }
-
- if (m->control_pressed) {
- delete tmap; for (int i = 0; i < trees.size(); i++) { delete trees[i]; }
- for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
- m->clearGroups();
- return 0;
- }
-
- //then you did not find it so report it
- if (count == m->Treenames.size()) {
- //if it is in your namefile then don't remove
- map<string, string>::iterator it = nameMap.find(tmap->namesOfSeqs[i]);
-
- if (it == nameMap.end()) {
- m->mothurOut(tmap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); m->mothurOutEndLine();
- tmap->removeSeq(tmap->namesOfSeqs[i]);
- i--; //need this because removeSeq removes name from namesOfSeqs
- }
- }
- }
- }
-
- SharedUtil* util = new SharedUtil();
+ TreeReader* reader = new TreeReader(treefile, groupfile, namefile);
+ vector<Tree*> trees = reader->getTrees();
+ tmap = trees[0]->getTreeMap();
+ delete reader;
+
+ SharedUtil util;
vector<string> mGroups = m->getGroups();
vector<string> tGroups = tmap->getNamesOfGroups();
- util->setGroups(mGroups, tGroups, "phylo.diversity"); //sets the groups the user wants to analyze
- delete util;
+ util.setGroups(mGroups, tGroups, "phylo.diversity"); //sets the groups the user wants to analyze
//incase the user had some mismatches between the tree and group files we don't want group xxx to be analyzed
for (int i = 0; i < mGroups.size(); i++) { if (mGroups[i] == "xxx") { mGroups.erase(mGroups.begin()+i); break; } }
if (m->control_pressed) { delete tmap; for (int j = 0; j < trees.size(); j++) { delete trees[j]; } for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
ofstream outSum, outRare, outCollect;
- string outSumFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(i+1) + ".phylodiv.summary";
- string outRareFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(i+1) + ".phylodiv.rarefaction";
- string outCollectFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(i+1) + ".phylodiv";
+ string outSumFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(i+1) + "." + getOutputFileNameTag("summary");
+ string outRareFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(i+1) + "." + getOutputFileNameTag("rarefy");
+ string outCollectFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(i+1) + "." + getOutputFileNameTag("phylodiv");
if (summary) { m->openOutputFile(outSumFile, outSum); outputNames.push_back(outSumFile); outputTypes["summary"].push_back(outSumFile); }
if (rarefy) { m->openOutputFile(outRareFile, outRare); outputNames.push_back(outRareFile); outputTypes["rarefy"].push_back(outRareFile); }
if (numSampledList.count(diversity[mGroups[j]].size()-1) == 0) { numSampledList.insert(diversity[mGroups[j]].size()-1); }
}
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
if(processors == 1){
driver(trees[i], diversity, sumDiversity, iters, increment, randomLeaf, numSampledList, outCollect, outSum, true);
}else{
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run phylo.diversity."); 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(); }
//**********************************************************************************************************************
int PhyloDiversityCommand::createProcesses(vector<int>& procIters, Tree* t, map< string, vector<float> >& div, map<string, vector<float> >& sumDiv, int numIters, int increment, vector<int>& randomLeaf, set<int>& numSampledList, ofstream& outCollect, ofstream& outSum){
try {
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
int process = 1;
vector<int> processIDS;
try {
int numLeafNodes = randomLeaf.size();
vector<string> mGroups = m->getGroups();
-
+
+ map<string, int> rootForGroup = getRootForGroups(t); //maps groupName to root node in tree. "root" for group may not be the trees root and we don't want to include the extra branches.
+
for (int l = 0; l < numIters; l++) {
random_shuffle(randomLeaf.begin(), randomLeaf.end());
-
+
//initialize counts
map<string, int> counts;
- map< string, set<int> > countedBranch;
- for (int j = 0; j < mGroups.size(); j++) { counts[mGroups[j]] = 0; countedBranch[mGroups[j]].insert(-2); } //add dummy index to initialize countedBranch sets
+ vector< map<string, bool> > countedBranch;
+ for (int i = 0; i < t->getNumNodes(); i++) {
+ map<string, bool> temp;
+ for (int j = 0; j < mGroups.size(); j++) { temp[mGroups[j]] = false; }
+ countedBranch.push_back(temp);
+ }
+
+ for (int j = 0; j < mGroups.size(); j++) { counts[mGroups[j]] = 0; }
for(int k = 0; k < numLeafNodes; k++){
if (m->control_pressed) { return 0; }
//calc branch length of randomLeaf k
- vector<float> br = calcBranchLength(t, randomLeaf[k], countedBranch);
+ vector<float> br = calcBranchLength(t, randomLeaf[k], countedBranch, rootForGroup);
//for each group in the groups update the total branch length accounting for the names file
vector<string> groups = t->tree[randomLeaf[k]].getGroup();
for (int j = 0; j < groups.size(); j++) {
- int numSeqsInGroupJ = 0;
- map<string, int>::iterator it;
- it = t->tree[randomLeaf[k]].pcount.find(groups[j]);
- if (it != t->tree[randomLeaf[k]].pcount.end()) { //this leaf node contains seqs from group j
- numSeqsInGroupJ = it->second;
- }
-
- if (numSeqsInGroupJ != 0) { div[groups[j]][(counts[groups[j]]+1)] = div[groups[j]][counts[groups[j]]] + br[j]; }
-
- for (int s = (counts[groups[j]]+2); s <= (counts[groups[j]]+numSeqsInGroupJ); s++) {
- div[groups[j]][s] = div[groups[j]][s-1]; //update counts, but don't add in redundant branch lengths
- }
- counts[groups[j]] += numSeqsInGroupJ;
+
+ if (m->inUsersGroups(groups[j], mGroups)) {
+ int numSeqsInGroupJ = 0;
+ map<string, int>::iterator it;
+ it = t->tree[randomLeaf[k]].pcount.find(groups[j]);
+ if (it != t->tree[randomLeaf[k]].pcount.end()) { //this leaf node contains seqs from group j
+ numSeqsInGroupJ = it->second;
+ }
+
+ if (numSeqsInGroupJ != 0) { div[groups[j]][(counts[groups[j]]+1)] = div[groups[j]][counts[groups[j]]] + br[j]; }
+
+ for (int s = (counts[groups[j]]+2); s <= (counts[groups[j]]+numSeqsInGroupJ); s++) {
+ div[groups[j]][s] = div[groups[j]][s-1]; //update counts, but don't add in redundant branch lengths
+ }
+ counts[groups[j]] += numSeqsInGroupJ;
+ }
}
}
}
//**********************************************************************************************************************
//need a vector of floats one branch length for every group the node represents.
-vector<float> PhyloDiversityCommand::calcBranchLength(Tree* t, int leaf, map< string, set<int> >& counted){
+vector<float> PhyloDiversityCommand::calcBranchLength(Tree* t, int leaf, vector< map<string, bool> >& counted, map<string, int> roots){
try {
-
+
//calc the branch length
//while you aren't at root
vector<float> sums;
vector<string> groups = t->tree[leaf].getGroup();
sums.resize(groups.size(), 0.0);
- map<string, map<int, double> > tempTotals; //maps node to total Branch Length
- map< string, set<int> > tempCounted;
- set<int>::iterator it;
-
- //you are a leaf
+
+ //you are a leaf
if(t->tree[index].getBranchLength() != -1){
for (int k = 0; k < groups.size(); k++) {
sums[k] += abs(t->tree[index].getBranchLength());
- counted[groups[k]].insert(index);
}
}
-
- for (int k = 0; k < groups.size(); k++) {
- tempTotals[groups[k]][index] = 0.0;
- }
-
- index = t->tree[index].getParent();
-
+
+
+ index = t->tree[index].getParent();
+
//while you aren't at root
while(t->tree[index].getParent() != -1){
-
+
if (m->control_pressed) { return sums; }
- int pcountSize = 0;
for (int k = 0; k < groups.size(); k++) {
- map<string, int>::iterator itGroup = t->tree[index].pcount.find(groups[k]);
- if (itGroup != t->tree[index].pcount.end()) { pcountSize++; }
-
- //do both your chidren have have descendants from the users groups?
- int lc = t->tree[index].getLChild();
- int rc = t->tree[index].getRChild();
-
- int LpcountSize = 0;
- itGroup = t->tree[lc].pcount.find(groups[k]);
- if (itGroup != t->tree[lc].pcount.end()) { LpcountSize++; }
-
- int RpcountSize = 0;
- itGroup = t->tree[rc].pcount.find(groups[k]);
- if (itGroup != t->tree[rc].pcount.end()) { RpcountSize++; }
-
- //if yes, add your childrens tempTotals
- if ((LpcountSize != 0) && (RpcountSize != 0)) {
- sums[k] += tempTotals[groups[k]][lc] + tempTotals[groups[k]][rc];
-
- for (it = tempCounted[groups[k]].begin(); it != tempCounted[groups[k]].end(); it++) { counted[groups[k]].insert(*it); }
-
- //cout << "added to total " << tempTotals[lc] << '\t' << tempTotals[rc] << endl;
- if (t->tree[index].getBranchLength() != -1) {
- if (counted[groups[k]].count(index) == 0) {
- tempTotals[groups[k]][index] = abs(t->tree[index].getBranchLength());
- tempCounted[groups[k]].insert(index);
- }else{
- tempTotals[groups[k]][index] = 0.0;
- }
- }else {
- tempTotals[groups[k]][index] = 0.0;
- }
- }else { //if no, your tempTotal is your childrens temp totals + your branch length
- tempTotals[groups[k]][index] = tempTotals[groups[k]][lc] + tempTotals[groups[k]][rc];
-
- if (counted[groups[k]].count(index) == 0) {
- tempTotals[groups[k]][index] += abs(t->tree[index].getBranchLength());
- tempCounted[groups[k]].insert(index);
- }
-
- }
- //cout << "temptotal = "<< tempTotals[i] << endl;
- }
-
- index = t->tree[index].getParent();
- }
-
+
+ if (index >= roots[groups[k]]) { counted[index][groups[k]] = true; } //if you are at this groups "root", then say we are done
+
+ if (!counted[index][groups[k]]){ //if counted[index][groups[k] is true this groups has already added all br from here to root, so quit early
+ if (t->tree[index].getBranchLength() != -1) {
+ sums[k] += abs(t->tree[index].getBranchLength());
+ }
+ counted[index][groups[k]] = true;
+ }
+ }
+ index = t->tree[index].getParent();
+ }
+
return sums;
-
+
}
catch(exception& e) {
m->errorOut(e, "PhyloDiversityCommand", "calcBranchLength");
exit(1);
}
}
-/*****************************************************************/
-int PhyloDiversityCommand::readNamesFile() {
+//**********************************************************************************************************************
+map<string, int> PhyloDiversityCommand::getRootForGroups(Tree* t){
try {
- m->names.clear();
- numUniquesInName = 0;
-
- ifstream in;
- m->openInputFile(namefile, in);
-
- string first, second;
- map<string, string>::iterator itNames;
-
- while(!in.eof()) {
- in >> first >> second; m->gobble(in);
-
- numUniquesInName++;
-
- itNames = m->names.find(first);
- if (itNames == m->names.end()) {
- m->names[first] = second;
-
- //we need a list of names in your namefile to use above when removing extra seqs above so we don't remove them
- vector<string> dupNames;
- m->splitAtComma(second, dupNames);
-
- for (int i = 0; i < dupNames.size(); i++) {
- nameMap[dupNames[i]] = dupNames[i];
- if ((groupfile == "") && (i != 0)) { tmap->addSeq(dupNames[i], "Group1"); }
- }
- }else { m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); m->names.clear(); namefile = ""; return 1; }
- }
- in.close();
-
- return 0;
+ map<string, int> roots; //maps group to root for group, may not be root of tree
+ map<string, bool> done;
+
+ //initialize root for all groups to -1
+ for (int k = 0; k < (t->getTreeMap())->getNamesOfGroups().size(); k++) { done[(t->getTreeMap())->getNamesOfGroups()[k]] = false; }
+
+ for (int i = 0; i < t->getNumLeaves(); i++) {
+
+ vector<string> groups = t->tree[i].getGroup();
+
+ int index = t->tree[i].getParent();
+
+ for (int j = 0; j < groups.size(); j++) {
+
+ if (done[groups[j]] == false) { //we haven't found the root for this group yet
+
+ done[groups[j]] = true;
+ roots[groups[j]] = i; //set root to self to start
+
+ //while you aren't at root
+ while(t->tree[index].getParent() != -1){
+
+ if (m->control_pressed) { return roots; }
+
+ //do both your chidren have have descendants from the users groups?
+ int lc = t->tree[index].getLChild();
+ int rc = t->tree[index].getRChild();
+
+ int LpcountSize = 0;
+ map<string, int>:: iterator itGroup = t->tree[lc].pcount.find(groups[j]);
+ if (itGroup != t->tree[lc].pcount.end()) { LpcountSize++; }
+
+ int RpcountSize = 0;
+ itGroup = t->tree[rc].pcount.find(groups[j]);
+ if (itGroup != t->tree[rc].pcount.end()) { RpcountSize++; }
+
+ if ((LpcountSize != 0) && (RpcountSize != 0)) { //possible root
+ roots[groups[j]] = index;
+ }else { ;}
+
+ index = t->tree[index].getParent();
+ }
+ }
+ }
+ }
+
+ return roots;
+
}
catch(exception& e) {
- m->errorOut(e, "PhyloDiversityCommand", "readNamesFile");
+ m->errorOut(e, "PhyloDiversityCommand", "getRootForGroups");
exit(1);
}
}
-
//**********************************************************************************************************************
projects / mothur.git / blobdiff