vector<string> PhyloDiversityCommand::setParameters(){
try {
- CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptree);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter prarefy("rarefy", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(prarefy);
- CommandParameter psummary("summary", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(psummary);
- CommandParameter pcollect("collect", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pcollect);
- CommandParameter pscale("scale", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pscale);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none","phylodiv",false,true,true); parameters.push_back(ptree);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pfreq("freq", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pfreq);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter prarefy("rarefy", "Boolean", "", "F", "", "", "","rarefy",false,false); parameters.push_back(prarefy);
+ CommandParameter psummary("summary", "Boolean", "", "T", "", "", "","summary",false,false); parameters.push_back(psummary);
+ CommandParameter pcollect("collect", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pcollect);
+ CommandParameter pscale("scale", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pscale);
+ 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); }
string PhyloDiversityCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The phylo.diversity command parameters are tree, group, name, groups, iters, freq, processors, scale, rarefy, collect and summary. tree and group are required, unless you have valid current files.\n";
+ helpString += "The phylo.diversity command parameters are tree, group, name, count, groups, iters, freq, processors, scale, rarefy, collect and summary. tree and group are required, unless you have valid current files.\n";
helpString += "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";
helpString += "The iters parameter allows you to specify the number of randomizations to preform, by default iters=1000, if you set rarefy to true.\n";
helpString += "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";
}
}
//**********************************************************************************************************************
-string PhyloDiversityCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string PhyloDiversityCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //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);
- }
+ if (type == "phylodiv") { pattern = "[filename],[tag],phylodiv"; }
+ else if (type == "rarefy") { pattern = "[filename],[tag],phylodiv.rarefaction"; }
+ else if (type == "summary") { pattern = "[filename],[tag],phylodiv.summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloDiversityCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
//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("count");
+ //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["count"] = inputDir + it->second; }
+ }
}
//check for required parameters
else if (namefile == "not found") { namefile = ""; }
else { m->setNameFile(namefile); }
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { countfile = ""; abort = true; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
+
+ if ((namefile != "") && (countfile != "")) {
+ m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
+ }
+
+ if ((groupfile != "") && (countfile != "")) {
+ m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
+ }
+
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(treefile); }
string temp;
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 (countfile=="") {
+ if (namefile == "") {
+ vector<string> files; files.push_back(treefile);
+ parser.getNameFile(files);
+ }
+ }
}
}
int start = time(NULL);
m->setTreeFile(treefile);
- TreeReader* reader = new TreeReader(treefile, groupfile, namefile);
+ TreeReader* reader;
+ if (countfile == "") { reader = new TreeReader(treefile, groupfile, namefile); }
+ else { reader = new TreeReader(treefile, countfile); }
vector<Tree*> trees = reader->getTrees();
- tmap = trees[0]->getTreeMap();
+ ct = trees[0]->getCountTable();
delete reader;
SharedUtil util;
vector<string> mGroups = m->getGroups();
- vector<string> tGroups = tmap->getNamesOfGroups();
+ vector<string> tGroups = ct->getNamesOfGroups();
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 each of the users trees
for(int i = 0; i < trees.size(); i++) {
- 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; }
+ if (m->control_pressed) { delete ct; 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) + "." + 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");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(treefile));
+ variables["[tag]"] = toString(i+1);
+ string outSumFile = getOutputFileName("summary",variables);
+ string outRareFile = getOutputFileName("rarefy",variables);
+ string outCollectFile = getOutputFileName("phylodiv",variables);
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); }
randomLeaf.push_back(j);
}
}
+
+ /* float sum = 0;
+ vector<float> sums; sums.resize(m->getGroups().size(), 0);
+ vector<float> sumsAboveRoot; sumsAboveRoot.resize(m->getGroups().size(), 0);
+ for (int j = 0; j < trees[i]->getNumNodes(); j++) {
+ if (trees[i]->tree[j].getBranchLength() < 0) { cout << j << '\t' << trees[i]->tree[j].getName() << '\t' << trees[i]->tree[j].getBranchLength() << endl; }
+
+ sum += abs(trees[i]->tree[j].getBranchLength());
+ for (int k = 0; k < m->getGroups().size(); k++) {
+ map<string, int>::iterator itGroup = trees[i]->tree[j].pcount.find(m->getGroups()[k]);
+ if (itGroup != trees[i]->tree[j].pcount.end()) { //this branch belongs to a group we care about
+ if (j < rootForGroup[m->getGroups()[k]]) {
+ sums[k] += abs(trees[i]->tree[j].getBranchLength());
+ }else {
+ sumsAboveRoot[k] += abs(trees[i]->tree[j].getBranchLength());
+ }
+ }
+ }
+ }
+ cout << sum << endl; //exit(1);
+
+ for (int k = 0; k < m->getGroups().size(); k++) {
+ cout << m->getGroups()[k] << "root node = " << rootForGroup[m->getGroups()[k]] << "sum below root = " << sums[k] << "sum above root = " << sumsAboveRoot[k] << endl;
+ }
+ exit(1); */
numLeafNodes = randomLeaf.size(); //reset the number of leaf nodes you are using
//find largest group total
int largestGroup = 0;
- for (int j = 0; j < mGroups.size(); j++) {
- if (tmap->seqsPerGroup[mGroups[j]] > largestGroup) { largestGroup = tmap->seqsPerGroup[mGroups[j]]; }
+ for (int j = 0; j < mGroups.size(); j++) {
+ int numSeqsThisGroup = ct->getGroupCount(mGroups[j]);
+ if (numSeqsThisGroup > largestGroup) { largestGroup = numSeqsThisGroup; }
//initialize diversity
- diversity[mGroups[j]].resize(tmap->seqsPerGroup[mGroups[j]]+1, 0.0); //numSampled
+ diversity[mGroups[j]].resize(numSeqsThisGroup+1, 0.0); //numSampled
//groupA 0.0 0.0
//initialize sumDiversity
- sumDiversity[mGroups[j]].resize(tmap->seqsPerGroup[mGroups[j]]+1, 0.0);
+ sumDiversity[mGroups[j]].resize(numSeqsThisGroup+1, 0.0);
}
//convert freq percentage to number
if (numSampledList.count(diversity[mGroups[j]].size()-1) == 0) { numSampledList.insert(diversity[mGroups[j]].size()-1); }
}
- #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 (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) {
+ 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);
+ }
+
if (rarefy) { printData(numSampledList, sumDiversity, outRare, iters); }
}
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 unifrac.unweighted."); m->mothurOutEndLine();
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run phylo.diversity."); m->mothurOutEndLine();
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) || (__linux__) || (__unix__) || (__unix)
- int process = 1;
+ int process = 1;
vector<int> processIDS;
map< string, vector<float> >::iterator itSum;
-
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+
//loop through and create all the processes you want
while (process != processors) {
int pid = fork();
in.close();
m->mothurRemove(inTemp);
}
+#else
+
+ //fill in functions
+ vector<phylodivData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+ vector<CountTable*> cts;
+ vector<Tree*> trees;
+ map<string, int> rootForGroup = getRootForGroups(t);
+
+ //Create processor worker threads.
+ for( int i=1; i<processors; i++ ){
+ CountTable* copyCount = new CountTable();
+ copyCount->copy(ct);
+ Tree* copyTree = new Tree(copyCount);
+ copyTree->getCopy(t);
+
+ cts.push_back(copyCount);
+ trees.push_back(copyTree);
+
+ map<string, vector<float> > copydiv = div;
+ map<string, vector<float> > copysumDiv = sumDiv;
+ vector<int> copyrandomLeaf = randomLeaf;
+ set<int> copynumSampledList = numSampledList;
+ map<string, int> copyRootForGrouping = rootForGroup;
+
+ phylodivData* temp = new phylodivData(m, procIters[i], copydiv, copysumDiv, copyTree, copyCount, increment, copyrandomLeaf, copynumSampledList, copyRootForGrouping);
+ pDataArray.push_back(temp);
+ processIDS.push_back(i);
+
+ hThreadArray[i-1] = CreateThread(NULL, 0, MyPhyloDivThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
+ }
+
+ driver(t, div, sumDiv, procIters[0], increment, randomLeaf, numSampledList, outCollect, outSum, true);
+
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ for (itSum = pDataArray[i]->sumDiv.begin(); itSum != pDataArray[i]->sumDiv.end(); itSum++) {
+ for (int k = 0; k < (itSum->second).size(); k++) {
+ sumDiv[itSum->first][k] += (itSum->second)[k];
+ }
+ }
+ delete cts[i];
+ delete trees[i];
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
#endif
for (int l = 0; l < numIters; l++) {
random_shuffle(randomLeaf.begin(), randomLeaf.end());
- cout << l << endl;
+
//initialize counts
map<string, int> counts;
vector< map<string, bool> > countedBranch;
else { score = div[mGroups[j]][numSampled] / (float)numIters; }
out << setprecision(4) << score << endl;
+ //cout << mGroups[j] << '\t' << numSampled << '\t'<< setprecision(4) << score << endl;
}
out.close();
//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());
+ sums[k] += abs(t->tree[index].getBranchLength());
}
}
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 k = 0; k < (t->getCountTable())->getNamesOfGroups().size(); k++) { done[(t->getCountTable())->getNamesOfGroups()[k]] = false; }
for (int i = 0; i < t->getNumLeaves(); i++) {
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
+ if (done[groups[j]] == false) { //we haven't found the root for this group yet, initialize it
+ 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 (itGroup != t->tree[rc].pcount.end()) { RpcountSize++; }
if ((LpcountSize != 0) && (RpcountSize != 0)) { //possible root
- roots[groups[j]] = index;
+ if (index > roots[groups[j]]) { roots[groups[j]] = index; }
}else { ;}
index = t->tree[index].getParent();
}
- }
+ //}
}
}
+
+
return roots;
}
projects / mothur.git / blobdiff