#include "phylodiversitycommand.h"
+//**********************************************************************************************************************
+vector<string> PhyloDiversityCommand::getValidParameters(){
+ try {
+ string Array[] = {"freq","rarefy","iters","groups","processors","summary","collect","scale","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloDiversityCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+PhyloDiversityCommand::PhyloDiversityCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["phylodiv"] = tempOutNames;
+ outputTypes["rarefy"] = tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloDiversityCommand", "PhyloDiversityCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> PhyloDiversityCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloDiversityCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> PhyloDiversityCommand::getRequiredFiles(){
+ try {
+ string Array[] = {"tree","group"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloDiversityCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
PhyloDiversityCommand::PhyloDiversityCommand(string option) {
try {
else {
//valid paramters for this command
- string Array[] = {"freq","rarefy","iters","groups","outputdir","inputdir"};
+ string Array[] = {"freq","rarefy","iters","groups","processors","summary","collect","scale","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["phylodiv"] = tempOutNames;
+ outputTypes["rarefy"] = tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+
//if the user changes the output directory command factory will send this info to us in the output parameter
- outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(globaldata->getTreeFile()); }
if (globaldata->gTree.size() == 0) {//no trees were read
m->mothurOut("You must execute the read.tree command, before you may execute the phylo.diversity command."); m->mothurOutEndLine(); abort = true; }
convert(temp, iters);
temp = validParameter.validFile(parameters, "rarefy", false); if (temp == "not found") { temp = "F"; }
- rarefy = isTrue(temp);
+ rarefy = m->isTrue(temp);
if (!rarefy) { iters = 1; }
+ temp = validParameter.validFile(parameters, "summary", false); if (temp == "not found") { temp = "T"; }
+ summary = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "scale", false); if (temp == "not found") { temp = "F"; }
+ scale = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "collect", false); if (temp == "not found") { temp = "F"; }
+ collect = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
+ convert(temp, processors);
+
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; Groups = globaldata->gTreemap->namesOfGroups; globaldata->Groups = Groups; }
else {
- splitAtDash(groups, Groups);
+ m->splitAtDash(groups, Groups);
globaldata->Groups = Groups;
}
+ 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; }
}
}
void PhyloDiversityCommand::help(){
try {
m->mothurOut("The phylo.diversity command can only be executed after a successful read.tree command.\n");
- m->mothurOut("The phylo.diversity command parameters are groups, iters, freq and rarefy. No parameters are required.\n");
+ m->mothurOut("The phylo.diversity command parameters are groups, iters, freq, processors, scale, rarefy, collect and summary. No parameters are required.\n");
m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. The group names are separated by dashes. By default all groups are used.\n");
m->mothurOut("The iters parameter allows you to specify the number of randomizations to preform, by default iters=1000, if you set rarefy to true.\n");
m->mothurOut("The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n");
+ m->mothurOut("The scale parameter is used indicate that you want your ouptut scaled to the number of sequences sampled, default = false. \n");
m->mothurOut("The rarefy parameter allows you to create a rarefaction curve. The default is false.\n");
+ m->mothurOut("The collect parameter allows you to create a collectors curve. The default is false.\n");
+ m->mothurOut("The summary parameter allows you to create a .summary file. The default is true.\n");
+ m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
m->mothurOut("The phylo.diversity command should be in the following format: phylo.diversity(groups=yourGroups, rarefy=yourRarefy, iters=yourIters).\n");
m->mothurOut("Example phylo.diversity(groups=A-B-C, rarefy=T, iters=500).\n");
m->mothurOut("The phylo.diversity command output two files: .phylo.diversity and if rarefy=T, .rarefaction.\n");
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
- string outFile = outputDir + getRootName(getSimpleName(globaldata->getTreeFile())) + toString(i+1) + ".phylo.diversity";
- if (rarefy) { outFile += ".rarefaction"; }
- outputNames.push_back(outFile);
+ ofstream outSum, outRare, outCollect;
+ string outSumFile = outputDir + m->getRootName(m->getSimpleName(globaldata->getTreeFile())) + toString(i+1) + ".phylodiv.summary";
+ string outRareFile = outputDir + m->getRootName(m->getSimpleName(globaldata->getTreeFile())) + toString(i+1) + ".phylodiv.rarefaction";
+ string outCollectFile = outputDir + m->getRootName(m->getSimpleName(globaldata->getTreeFile())) + toString(i+1) + ".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 (collect) { m->openOutputFile(outCollectFile, outCollect); outputNames.push_back(outCollectFile); outputTypes["phylodiv"].push_back(outCollectFile); }
int numLeafNodes = trees[i]->getNumLeaves();
//create a vector containing indexes of leaf nodes, randomize it, select nodes to send to calculator
vector<int> randomLeaf;
for (int j = 0; j < numLeafNodes; j++) {
- if (inUsersGroups(trees[i]->tree[j].getGroup(), globaldata->Groups) == true) { //is this a node from the group the user selected.
+ if (m->inUsersGroups(trees[i]->tree[j].getGroup(), globaldata->Groups) == true) { //is this a node from the group the user selected.
randomLeaf.push_back(j);
}
}
for (int j = 0; j < globaldata->Groups.size(); j++) {
if (numSampledList.count(diversity[globaldata->Groups[j]].size()-1) == 0) { numSampledList.insert(diversity[globaldata->Groups[j]].size()-1); }
}
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if(processors == 1){
+ driver(trees[i], diversity, sumDiversity, iters, increment, randomLeaf, numSampledList, outCollect, outSum, true);
+ }else{
+ if (rarefy) {
+ vector<int> procIters;
+
+ int numItersPerProcessor = iters / processors;
+
+ //divide iters between processes
+ for (int h = 0; h < processors; h++) {
+ if(h == processors - 1){
+ numItersPerProcessor = iters - h * numItersPerProcessor;
+ }
+ procIters.push_back(numItersPerProcessor);
+ }
+
+ createProcesses(procIters, trees[i], diversity, sumDiversity, iters, increment, randomLeaf, numSampledList, outCollect, outSum);
+
+ }else{ //no need to paralellize if you dont want to rarefy
+ driver(trees[i], diversity, sumDiversity, iters, increment, randomLeaf, numSampledList, outCollect, outSum, true);
+ }
+ }
+
+ #else
+ driver(trees[i], diversity, sumDiversity, iters, increment, randomLeaf, numSampledList, outCollect, outSum, true);
+ #endif
+
+ if (rarefy) { printData(numSampledList, sumDiversity, outRare, iters); }
+ }
+
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ 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, "PhyloDiversityCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+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)
+ int process = 1;
+ int num = 0;
+ vector<int> processIDS;
+ map< string, vector<float> >::iterator itSum;
+
+ EstOutput results;
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+
+ if (pid > 0) {
+ processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
+ process++;
+ }else if (pid == 0){
+ driver(t, div, sumDiv, procIters[process], increment, randomLeaf, numSampledList, outCollect, outSum, false);
+
+ string outTemp = outputDir + toString(getpid()) + ".sumDiv.temp";
+ ofstream out;
+ m->openOutputFile(outTemp, out);
+
+ //output the sumDIversity
+ for (itSum = sumDiv.begin(); itSum != sumDiv.end(); itSum++) {
+ out << itSum->first << '\t' << (itSum->second).size() << '\t';
+ for (int k = 0; k < (itSum->second).size(); k++) {
+ out << (itSum->second)[k] << '\t';
+ }
+ out << endl;
+ }
+
+ out.close();
+
+ exit(0);
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
+ }
+
+ driver(t, div, sumDiv, procIters[0], increment, randomLeaf, numSampledList, outCollect, outSum, true);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<(processors-1);i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ //get data created by processes
+ for (int i=0;i<(processors-1);i++) {
+
+ //input the sumDIversity
+ string inTemp = outputDir + toString(processIDS[i]) + ".sumDiv.temp";
+ ifstream in;
+ m->openInputFile(inTemp, in);
+
+ //output the sumDIversity
+ for (int j = 0; j < sumDiv.size(); j++) {
+ string group = "";
+ int size = 0;
+
+ in >> group >> size; m->gobble(in);
+
+ for (int k = 0; k < size; k++) {
+ float tempVal;
+ in >> tempVal;
+
+ sumDiv[group][k] += tempVal;
+ }
+ m->gobble(in);
+ }
+
+ in.close();
+ remove(inTemp.c_str());
+ }
+
+#endif
- for (int l = 0; l < iters; l++) {
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloDiversityCommand", "createProcesses");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int PhyloDiversityCommand::driver(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, bool doSumCollect){
+ try {
+ int numLeafNodes = randomLeaf.size();
+
+ for (int l = 0; l < numIters; l++) {
random_shuffle(randomLeaf.begin(), randomLeaf.end());
//initialize counts
map<string, int> counts;
- for (int j = 0; j < globaldata->Groups.size(); j++) { counts[globaldata->Groups[j]] = 0; }
+ map< string, set<int> > countedBranch;
+ for (int j = 0; j < globaldata->Groups.size(); j++) { counts[globaldata->Groups[j]] = 0; countedBranch[globaldata->Groups[j]].insert(-2); } //add dummy index to initialize countedBranch sets
for(int k = 0; k < numLeafNodes; k++){
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { return 0; }
//calc branch length of randomLeaf k
- float br = calcBranchLength(trees[i], randomLeaf[k]);
+ vector<float> br = calcBranchLength(t, randomLeaf[k], countedBranch);
//for each group in the groups update the total branch length accounting for the names file
- vector<string> groups = trees[i]->tree[randomLeaf[k]].getGroup();
+ 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 = trees[i]->tree[randomLeaf[k]].pcount.find(groups[j]);
- if (it != trees[i]->tree[randomLeaf[k]].pcount.end()) { //this leaf node contains seqs from group j
+ 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;
}
-
- for (int s = (counts[groups[j]]+1); s <= (counts[groups[j]]+numSeqsInGroupJ); s++) {
- diversity[groups[j]][s] = diversity[groups[j]][s-1] + (numSeqsInGroupJ * br);
+
+ 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 (rarefy) {
//add this diversity to the sum
for (int j = 0; j < globaldata->Groups.size(); j++) {
- for (int g = 0; g < diversity[globaldata->Groups[j]].size(); g++) {
- sumDiversity[globaldata->Groups[j]][g] += diversity[globaldata->Groups[j]][g];
+ for (int g = 0; g < div[globaldata->Groups[j]].size(); g++) {
+ sumDiv[globaldata->Groups[j]][g] += div[globaldata->Groups[j]][g];
}
}
}
+
+ if ((collect) && (l == 0) && doSumCollect) { printData(numSampledList, div, outCollect, 1); }
+ if ((summary) && (l == 0) && doSumCollect) { printSumData(div, outSum, 1); }
}
- if (rarefy) {
- printData(numSampledList, sumDiversity, outFile);
- }else{
- printData(numSampledList, diversity, outFile);
- }
+ return 0;
- }
-
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloDiversityCommand", "driver");
+ exit(1);
+ }
+}
- 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();
+//**********************************************************************************************************************
+void PhyloDiversityCommand::printSumData(map< string, vector<float> >& div, ofstream& out, int numIters){
+ try {
+
+ out << "Groups\tnumSampled\tphyloDiversity" << endl;
+
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+
+ for (int j = 0; j < globaldata->Groups.size(); j++) {
+ int numSampled = (div[globaldata->Groups[j]].size()-1);
+ out << globaldata->Groups[j] << '\t' << numSampled << '\t';
+
+
+ float score;
+ if (scale) { score = (div[globaldata->Groups[j]][numSampled] / (float)numIters) / (float)numSampled; }
+ else { score = div[globaldata->Groups[j]][numSampled] / (float)numIters; }
+
+ out << setprecision(4) << score << endl;
+ }
+
+ out.close();
- return 0;
}
catch(exception& e) {
- m->errorOut(e, "PhyloDiversityCommand", "execute");
+ m->errorOut(e, "PhyloDiversityCommand", "printSumData");
exit(1);
}
}
//**********************************************************************************************************************
-void PhyloDiversityCommand::printData(set<int>& num, map< string, vector<float> >& div, string file){
+void PhyloDiversityCommand::printData(set<int>& num, map< string, vector<float> >& div, ofstream& out, int numIters){
try {
- ofstream out;
- openOutputFile(file, out);
out << "numSampled\t";
for (int i = 0; i < globaldata->Groups.size(); i++) { out << globaldata->Groups[i] << '\t'; }
for (int j = 0; j < globaldata->Groups.size(); j++) {
if (numSampled < div[globaldata->Groups[j]].size()) {
- float score = div[globaldata->Groups[j]][numSampled] / (float)iters;
- out << setprecision(6) << score << '\t';
+ float score;
+ if (scale) { score = (div[globaldata->Groups[j]][numSampled] / (float)numIters) / (float)numSampled; }
+ else { score = div[globaldata->Groups[j]][numSampled] / (float)numIters; }
+
+ out << setprecision(4) << score << '\t';
}else { out << "NA" << '\t'; }
}
out << endl;
exit(1);
}
}
-
//**********************************************************************************************************************
-float PhyloDiversityCommand::calcBranchLength(Tree* t, int leaf){
+//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){
try {
//calc the branch length
//while you aren't at root
- float sum = 0.0;
+ vector<float> sums;
int index = leaf;
-
+
+ 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
+ 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();
+
+ //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();
- //if you have a BL
- if(t->tree[index].getBranchLength() != -1){
- sum += abs(t->tree[index].getBranchLength());
+ 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();
- }
- //get last breanch length added
- if(t->tree[index].getBranchLength() != -1){
- sum += abs(t->tree[index].getBranchLength());
+ index = t->tree[index].getParent();
}
-
- return sum;
+
+ return sums;
+
}
catch(exception& e) {
m->errorOut(e, "PhyloDiversityCommand", "calcBranchLength");
projects / mothur.git / blobdiff