2 * phylodiversitycommand.cpp
5 * Created by westcott on 4/30/10.
6 * Copyright 2010 Schloss Lab. All rights reserved.
10 #include "phylodiversitycommand.h"
12 //**********************************************************************************************************************
13 PhyloDiversityCommand::PhyloDiversityCommand(string option) {
15 globaldata = GlobalData::getInstance();
18 //allow user to run help
19 if(option == "help") { help(); abort = true; }
22 //valid paramters for this command
23 string Array[] = {"freq","rarefy","iters","groups","summary","collect","scale","outputdir","inputdir"};
24 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
26 OptionParser parser(option);
27 map<string,string> parameters = parser.getParameters();
29 ValidParameters validParameter;
31 //check to make sure all parameters are valid for command
32 for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
33 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
36 //if the user changes the output directory command factory will send this info to us in the output parameter
37 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = hasPath(globaldata->getTreeFile()); }
39 if (globaldata->gTree.size() == 0) {//no trees were read
40 m->mothurOut("You must execute the read.tree command, before you may execute the phylo.diversity command."); m->mothurOutEndLine(); abort = true; }
43 temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
46 temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
49 temp = validParameter.validFile(parameters, "rarefy", false); if (temp == "not found") { temp = "F"; }
50 rarefy = isTrue(temp);
51 if (!rarefy) { iters = 1; }
53 temp = validParameter.validFile(parameters, "summary", false); if (temp == "not found") { temp = "T"; }
54 summary = isTrue(temp);
56 temp = validParameter.validFile(parameters, "scale", false); if (temp == "not found") { temp = "F"; }
59 temp = validParameter.validFile(parameters, "collect", false); if (temp == "not found") { temp = "F"; }
60 collect = isTrue(temp);
62 groups = validParameter.validFile(parameters, "groups", false);
63 if (groups == "not found") { groups = ""; Groups = globaldata->gTreemap->namesOfGroups; globaldata->Groups = Groups; }
65 splitAtDash(groups, Groups);
66 globaldata->Groups = Groups;
69 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; }
74 m->errorOut(e, "PhyloDiversityCommand", "PhyloDiversityCommand");
78 //**********************************************************************************************************************
80 void PhyloDiversityCommand::help(){
82 m->mothurOut("The phylo.diversity command can only be executed after a successful read.tree command.\n");
83 m->mothurOut("The phylo.diversity command parameters are groups, iters, freq, scale, rarefy, collect and summary. No parameters are required.\n");
84 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");
85 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");
86 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");
87 m->mothurOut("The scale parameter is used indicate that you want your ouptut scaled to the number of sequences sampled, default = false. \n");
88 m->mothurOut("The rarefy parameter allows you to create a rarefaction curve. The default is false.\n");
89 m->mothurOut("The collect parameter allows you to create a collectors curve. The default is false.\n");
90 m->mothurOut("The summary parameter allows you to create a .summary file. The default is true.\n");
91 m->mothurOut("The phylo.diversity command should be in the following format: phylo.diversity(groups=yourGroups, rarefy=yourRarefy, iters=yourIters).\n");
92 m->mothurOut("Example phylo.diversity(groups=A-B-C, rarefy=T, iters=500).\n");
93 m->mothurOut("The phylo.diversity command output two files: .phylo.diversity and if rarefy=T, .rarefaction.\n");
94 m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
98 m->errorOut(e, "PhyloDiversityCommand", "help");
103 //**********************************************************************************************************************
105 PhyloDiversityCommand::~PhyloDiversityCommand(){}
107 //**********************************************************************************************************************
109 int PhyloDiversityCommand::execute(){
112 if (abort == true) { return 0; }
114 //incase the user had some mismatches between the tree and group files we don't want group xxx to be analyzed
115 for (int i = 0; i < globaldata->Groups.size(); i++) { if (globaldata->Groups[i] == "xxx") { globaldata->Groups.erase(globaldata->Groups.begin()+i); break; } }
117 vector<string> outputNames;
119 vector<Tree*> trees = globaldata->gTree;
121 //for each of the users trees
122 for(int i = 0; i < trees.size(); i++) {
124 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
126 ofstream outSum, outRare, outCollect;
127 string outSumFile = outputDir + getRootName(getSimpleName(globaldata->getTreeFile())) + toString(i+1) + ".phylodiv.summary";
128 string outRareFile = outputDir + getRootName(getSimpleName(globaldata->getTreeFile())) + toString(i+1) + ".phylodiv.rarefaction";
129 string outCollectFile = outputDir + getRootName(getSimpleName(globaldata->getTreeFile())) + toString(i+1) + ".phylodiv";
131 if (summary) { openOutputFile(outSumFile, outSum); outputNames.push_back(outSumFile); }
132 if (rarefy) { openOutputFile(outRareFile, outRare); outputNames.push_back(outRareFile); }
133 if (collect) { openOutputFile(outCollectFile, outCollect); outputNames.push_back(outCollectFile); }
135 int numLeafNodes = trees[i]->getNumLeaves();
137 //create a vector containing indexes of leaf nodes, randomize it, select nodes to send to calculator
138 vector<int> randomLeaf;
139 for (int j = 0; j < numLeafNodes; j++) {
140 if (inUsersGroups(trees[i]->tree[j].getGroup(), globaldata->Groups) == true) { //is this a node from the group the user selected.
141 randomLeaf.push_back(j);
145 numLeafNodes = randomLeaf.size(); //reset the number of leaf nodes you are using
147 //each group, each sampling, if no rarefy iters = 1;
148 map<string, vector<float> > diversity;
150 //each group, each sampling, if no rarefy iters = 1;
151 map<string, vector<float> > sumDiversity;
153 //find largest group total
154 int largestGroup = 0;
155 for (int j = 0; j < globaldata->Groups.size(); j++) {
156 if (globaldata->gTreemap->seqsPerGroup[globaldata->Groups[j]] > largestGroup) { largestGroup = globaldata->gTreemap->seqsPerGroup[globaldata->Groups[j]]; }
158 //initialize diversity
159 diversity[globaldata->Groups[j]].resize(globaldata->gTreemap->seqsPerGroup[globaldata->Groups[j]]+1, 0.0); //numSampled
162 //initialize sumDiversity
163 sumDiversity[globaldata->Groups[j]].resize(globaldata->gTreemap->seqsPerGroup[globaldata->Groups[j]]+1, 0.0);
166 //convert freq percentage to number
168 if (freq < 1.0) { increment = largestGroup * freq;
169 }else { increment = freq; }
171 //initialize sampling spots
172 set<int> numSampledList;
173 for(int k = 1; k <= largestGroup; k++){ if((k == 1) || (k % increment == 0)){ numSampledList.insert(k); } }
174 if(largestGroup % increment != 0){ numSampledList.insert(largestGroup); }
176 //add other groups ending points
177 for (int j = 0; j < globaldata->Groups.size(); j++) {
178 if (numSampledList.count(diversity[globaldata->Groups[j]].size()-1) == 0) { numSampledList.insert(diversity[globaldata->Groups[j]].size()-1); }
181 for (int l = 0; l < iters; l++) {
182 random_shuffle(randomLeaf.begin(), randomLeaf.end());
185 map<string, int> counts;
186 for (int j = 0; j < globaldata->Groups.size(); j++) { counts[globaldata->Groups[j]] = 0; }
188 for(int k = 0; k < numLeafNodes; k++){
190 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
192 //calc branch length of randomLeaf k
193 float br = calcBranchLength(trees[i], randomLeaf[k]);
195 //for each group in the groups update the total branch length accounting for the names file
196 vector<string> groups = trees[i]->tree[randomLeaf[k]].getGroup();
197 for (int j = 0; j < groups.size(); j++) {
198 int numSeqsInGroupJ = 0;
199 map<string, int>::iterator it;
200 it = trees[i]->tree[randomLeaf[k]].pcount.find(groups[j]);
201 if (it != trees[i]->tree[randomLeaf[k]].pcount.end()) { //this leaf node contains seqs from group j
202 numSeqsInGroupJ = it->second;
205 for (int s = (counts[groups[j]]+1); s <= (counts[groups[j]]+numSeqsInGroupJ); s++) {
206 diversity[groups[j]][s] = diversity[groups[j]][s-1] + ((float) numSeqsInGroupJ * br);
208 counts[groups[j]] += numSeqsInGroupJ;
213 //add this diversity to the sum
214 for (int j = 0; j < globaldata->Groups.size(); j++) {
215 for (int g = 0; g < diversity[globaldata->Groups[j]].size(); g++) {
216 sumDiversity[globaldata->Groups[j]][g] += diversity[globaldata->Groups[j]][g];
221 if ((collect) && (l == 0)) { printData(numSampledList, diversity, outCollect, 1); }
222 if ((summary) && (l == 0)) { printSumData(diversity, outSum, 1); }
225 if (rarefy) { printData(numSampledList, sumDiversity, outRare, iters); }
229 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
231 m->mothurOutEndLine();
232 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
233 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
234 m->mothurOutEndLine();
239 catch(exception& e) {
240 m->errorOut(e, "PhyloDiversityCommand", "execute");
244 //**********************************************************************************************************************
246 void PhyloDiversityCommand::printSumData(map< string, vector<float> >& div, ofstream& out, int numIters){
249 out << "numSampled\t";
250 for (int i = 0; i < globaldata->Groups.size(); i++) { out << globaldata->Groups[i] << '\t'; }
253 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
256 //find end points to output
257 for (map<string, vector<float> >::iterator itEnds = div.begin(); itEnds != div.end(); itEnds++) { num.insert(itEnds->second.size()-1); }
259 for (set<int>::iterator it = num.begin(); it != num.end(); it++) {
260 int numSampled = *it;
262 out << numSampled << '\t';
264 for (int j = 0; j < globaldata->Groups.size(); j++) {
265 if (numSampled < div[globaldata->Groups[j]].size()) {
267 if (scale) { score = (div[globaldata->Groups[j]][numSampled] / (float)numIters) / (float)numSampled; }
268 else { score = div[globaldata->Groups[j]][numSampled] / (float)numIters; }
270 out << setprecision(4) << score << '\t';
271 }else { out << "NA" << '\t'; }
279 catch(exception& e) {
280 m->errorOut(e, "PhyloDiversityCommand", "printSumData");
284 //**********************************************************************************************************************
286 void PhyloDiversityCommand::printData(set<int>& num, map< string, vector<float> >& div, ofstream& out, int numIters){
289 out << "numSampled\t";
290 for (int i = 0; i < globaldata->Groups.size(); i++) { out << globaldata->Groups[i] << '\t'; }
293 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
295 for (set<int>::iterator it = num.begin(); it != num.end(); it++) {
296 int numSampled = *it;
298 out << numSampled << '\t';
300 for (int j = 0; j < globaldata->Groups.size(); j++) {
301 if (numSampled < div[globaldata->Groups[j]].size()) {
303 if (scale) { score = (div[globaldata->Groups[j]][numSampled] / (float)numIters) / (float)numSampled; }
304 else { score = div[globaldata->Groups[j]][numSampled] / (float)numIters; }
306 out << setprecision(4) << score << '\t';
307 }else { out << "NA" << '\t'; }
315 catch(exception& e) {
316 m->errorOut(e, "PhyloDiversityCommand", "printData");
320 //**********************************************************************************************************************
321 float PhyloDiversityCommand::calcBranchLength(Tree* t, int leaf){
324 //calc the branch length
325 //while you aren't at root
329 while(t->tree[index].getParent() != -1){
332 if(t->tree[index].getBranchLength() != -1){
333 sum += abs(t->tree[index].getBranchLength());
335 index = t->tree[index].getParent();
338 //get last breanch length added
339 if(t->tree[index].getBranchLength() != -1){
340 sum += abs(t->tree[index].getBranchLength());
345 catch(exception& e) {
346 m->errorOut(e, "PhyloDiversityCommand", "calcBranchLength");
350 //**********************************************************************************************************************