#include "unifracweightedcommand.h"
/***********************************************************/
-UnifracWeightedCommand::UnifracWeightedCommand() {
+UnifracWeightedCommand::UnifracWeightedCommand(string option) {
try {
globaldata = GlobalData::getInstance();
+ abort = false;
+ Groups.clear();
- T = globaldata->gTree;
- tmap = globaldata->gTreemap;
- weightedFile = globaldata->getTreeFile() + ".weighted";
- openOutputFile(weightedFile, out);
- //column headers
- out << "Group" << '\t' << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
-
- sumFile = globaldata->getTreeFile() + ".wsummary";
- openOutputFile(sumFile, outSum);
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"groups","iters"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ parser = new OptionParser();
+ parser->parse(option, parameters); delete parser;
+
+ ValidParameters* validParameter = new ValidParameters();
+
+ //check to make sure all parameters are valid for command
+ for (it4 = parameters.begin(); it4 != parameters.end(); it4++) {
+ if (validParameter->isValidParameter(it4->first, myArray, it4->second) != true) { abort = true; }
+ }
+
+ if (globaldata->gTree.size() == 0) {//no trees were read
+ cout << "You must execute the read.tree command, before you may execute the unifrac.weighted command." << endl; abort = true; }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ groups = validParameter->validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
+ }
- setGroups(); //sets the groups the user wants to analyze
- convert(globaldata->getIters(), iters); //how many random trees to generate
- weighted = new Weighted(tmap);
-
+ itersString = validParameter->validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; }
+ convert(itersString, iters);
+
+ delete validParameter;
+
+ if (abort == false) {
+ T = globaldata->gTree;
+ tmap = globaldata->gTreemap;
+ sumFile = globaldata->getTreeFile() + ".wsummary";
+ openOutputFile(sumFile, outSum);
+
+ util = new SharedUtil();
+ string s; //to make work with setgroups
+ util->setGroups(globaldata->Groups, tmap->namesOfGroups, s, numGroups, "weighted"); //sets the groups the user wants to analyze
+ util->getCombos(groupComb, globaldata->Groups, numComp);
+
+ weighted = new Weighted(tmap);
+
+ }
+ }
+
+
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function UnifracWeightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
}
+//**********************************************************************************************************************
+
+void UnifracWeightedCommand::help(){
+ try {
+ cout << "The unifrac.weighted command can only be executed after a successful read.tree command." << "\n";
+ cout << "The unifrac.weighted command parameters are groups and iters. No parameters are required." << "\n";
+ cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups." << "\n";
+ cout << "The group names are separated by dashes. The iters parameter allows you to specify how many random trees you would like compared to your tree." << "\n";
+ cout << "The unifrac.weighted command should be in the following format: unifrac.weighted(groups=yourGroups, iters=yourIters)." << "\n";
+ cout << "Example unifrac.weighted(groups=A-B-C, iters=500)." << "\n";
+ cout << "The default value for groups is all the groups in your groupfile, and iters is 1000." << "\n";
+ cout << "The unifrac.weighted command output two files: .weighted and .wsummary their descriptions are in the manual." << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the UnifracWeightedCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
/***********************************************************/
int UnifracWeightedCommand::execute() {
try {
+
+ if (abort == true) { return 0; }
+
+ Progress* reading;
+ reading = new Progress("Comparing to random:", iters);
//get weighted for users tree
userData.resize(numComp,0); //data[0] = weightedscore AB, data[1] = weightedscore AC...
//create new tree with same num nodes and leaves as users
randT = new Tree();
- //get pscores for users trees
+ //get weighted scores for users trees
for (int i = 0; i < T.size(); i++) {
+ counter = 0;
rScores.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC...
uScores.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC...
- validScores.resize(numComp);
-
- cout << "Processing tree " << i+1 << endl;
+
+ output = new ColumnFile(globaldata->getTreeFile() + toString(i+1) + ".weighted", itersString);
+
userData = weighted->getValues(T[i]); //userData[0] = weightedscore
//save users score
//add users score to vector of user scores
uScores[s].push_back(userData[s]);
- //add users score to vector of valid scores
- validScores[s].push_back(userData[s]);
-
//save users tree score for summary file
utreeScores.push_back(userData[s]);
}
//copy T[i]'s info.
randT->getCopy(T[i]);
- if (globaldata->Groups.size() != 0) {
- //create a random tree with same topology as T[i], but different labels
- randT->assembleRandomUnifracTree(globaldata->Groups[r], globaldata->Groups[l]);
- //get wscore of random tree
- randomData = weighted->getValues(randT, globaldata->Groups[r], globaldata->Groups[l]);
- }else {
- //create a random tree with same topology as T[i], but different labels
- randT->assembleRandomUnifracTree(tmap->namesOfGroups[r], tmap->namesOfGroups[l]);
- //get wscore of random tree
- randomData = weighted->getValues(randT, tmap->namesOfGroups[r], tmap->namesOfGroups[l]);
- }
+ //create a random tree with same topology as T[i], but different labels
+ randT->assembleRandomUnifracTree(globaldata->Groups[r], globaldata->Groups[l]);
+ //get wscore of random tree
+ randomData = weighted->getValues(randT, globaldata->Groups[r], globaldata->Groups[l]);
+
//save scores
rScores[count].push_back(randomData[0]);
- validScores[count][randomData[0]] = randomData[0];
count++;
}
}
+
+ //update progress bar
+ reading->update(j);
+
}
- removeValidScoresDuplicates();
+ //removeValidScoresDuplicates();
//find the signifigance of the score for summary file
for (int f = 0; f < numComp; f++) {
//sort random scores
WScoreSig.push_back((iters-index)/(float)iters);
}
- out << "Tree# " << i << endl;
- //printWeightedFile();
+ //out << "Tree# " << i << endl;
+ calculateFreqsCumuls();
+ printWeightedFile();
+
+ delete output;
//clear data
rScores.clear();
validScores.clear();
}
+ //finish progress bar
+ reading->finish();
+ delete reading;
+
printWSummaryFile();
//clear out users groups
exit(1);
}
}
-/***********************************************************
+/***********************************************************/
void UnifracWeightedCommand::printWeightedFile() {
try {
-
- //format output
- out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+ vector<double> data;
+ vector<string> tags;
+ tags.push_back("Score"); tags.push_back("RandFreq"); tags.push_back("RandCumul");
- //for each group
- for (int e = 0; e < numComp; e++) {
- //print each line in that group
- for (i = 0; i < validScores[e].size(); i++) {
- out << setprecision(6) << groupComb[e] << '\t' << validScores[e][i] << '\t' << '\t' << uscoreFreq[e][it->first] << '\t' << uCumul[e][it->first] << '\t' << rscoreFreq[e][it->first] << '\t' << rCumul[e][it->first] << endl;
+ for(int a = 0; a < numComp; a++) {
+ output->initFile(groupComb[a], tags);
+ //print each line
+ for (it = validScores.begin(); it != validScores.end(); it++) {
+ data.push_back(it->first); data.push_back(rScoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
+ output->output(data);
+ data.clear();
}
+ output->resetFile();
}
-
- out.close();
-
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
void UnifracWeightedCommand::printWSummaryFile() {
try {
//column headers
- outSum << "Tree#" << '\t' << "Groups" << '\t' << '\t' << "WScore" << '\t' << '\t' << "WSig" << endl;
- cout << "Tree#" << '\t' << "Groups" << '\t' << '\t' << "WScore" << '\t' << '\t' << "WSig" << endl;
+ outSum << "Tree#" << '\t' << "Groups" << '\t' << "WScore" << '\t' << "WSig" << endl;
+ cout << "Tree#" << '\t' << "Groups" << '\t' << "WScore" << '\t' << "WSig" << endl;
//format output
outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
int count = 0;
for (int i = 0; i < T.size(); i++) {
for (int j = 0; j < numComp; j++) {
- outSum << setprecision(6) << i+1 << '\t' << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << WScoreSig[count] << endl;
- cout << setprecision(6) << i+1 << '\t' << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << WScoreSig[count] << endl;
+ if (WScoreSig[count] > (1/(float)iters)) {
+ outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << WScoreSig[count] << endl;
+ cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << WScoreSig[count] << endl;
+ }else{
+ outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
+ cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
+ }
count++;
}
}
}
}
-/***********************************************************/
-void UnifracWeightedCommand::removeValidScoresDuplicates() {
- try {
- for (int e = 0; e < numComp; e++) {
- //sort valid scores
- sort(validScores[e].begin(), validScores[e].end());
-
- for (int i = 0; i< validScores[e].size()-1; i++) {
- if (validScores[e][i] == validScores[e][i+1]) { validScores[e].erase(validScores[e].begin()+i); }
- }
- }
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function removeValidScoresDuplicates. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracWeightedCommand class function removeValidScoresDuplicates. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-
/***********************************************************/
int UnifracWeightedCommand::findIndex(float score, int index) {
try{
}
/***********************************************************/
-void UnifracWeightedCommand::setGroups() {
+
+void UnifracWeightedCommand::calculateFreqsCumuls() {
try {
- //if the user has not entered specific groups to analyze then do them all
- if (globaldata->Groups.size() == 0) {
- numGroups = tmap->getNumGroups();
- }else {
- if (globaldata->getGroups() != "all") {
- //check that groups are valid
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- if (tmap->isValidGroup(globaldata->Groups[i]) != true) {
- cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
- // erase the invalid group from globaldata->Groups
- globaldata->Groups.erase (globaldata->Groups.begin()+i);
- }
+ //clear out old tree values
+ rScoreFreq.clear();
+ rScoreFreq.resize(numComp);
+ rCumul.clear();
+ rCumul.resize(numComp);
+ validScores.clear();
+
+ //calculate frequency
+ for (int f = 0; f < numComp; f++) {
+ for (int i = 0; i < rScores[f].size(); i++) { //looks like 0,0,1,1,1,2,4,7... you want to make a map that say rScoreFreq[0] = 2, rScoreFreq[1] = 3...
+ validScores[rScores[f][i]] = rScores[f][i];
+ it = rScoreFreq[f].find(rScores[f][i]);
+ if (it != rScoreFreq[f].end()) {
+ rScoreFreq[f][rScores[f][i]]++;
+ }else{
+ rScoreFreq[f][rScores[f][i]] = 1;
}
-
- //if the user only entered invalid groups
- if (globaldata->Groups.size() == 0) {
- numGroups = tmap->getNumGroups();
- cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
- }else if (globaldata->Groups.size() == 1) {
- cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
- numGroups = tmap->getNumGroups();
- globaldata->Groups.clear();
- }else { numGroups = globaldata->Groups.size(); }
- }else { //users wants all groups
- numGroups = tmap->getNumGroups();
- globaldata->Groups.clear();
- globaldata->setGroups("");
}
}
- //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
- numComp = 0;
- int n = 1;
- for (int i=1; i<numGroups; i++) {
- numComp += i;
- for (int l = n; l < numGroups; l++) {
- //set group comparison labels
- if (globaldata->Groups.size() != 0) {
- groupComb.push_back(globaldata->Groups[i-1]+globaldata->Groups[l]);
- }else {
- groupComb.push_back(tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]);
- }
+ //calculate rcumul
+ for(int a = 0; a < numComp; a++) {
+ float rcumul = 1.0000;
+ //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
+ for (it = validScores.begin(); it != validScores.end(); it++) {
+ //make rscoreFreq map and rCumul
+ it2 = rScoreFreq[a].find(it->first);
+ rCumul[a][it->first] = rcumul;
+ //get percentage of random trees with that info
+ if (it2 != rScoreFreq[a].end()) { rScoreFreq[a][it->first] /= iters; rcumul-= it2->second; }
+ else { rScoreFreq[a][it->first] = 0.0000; } //no random trees with that score
}
- n++;
}
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function calculateFreqsCums. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
catch(...) {
- cout << "An unknown error has occurred in the UnifracWeightedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "An unknown error has occurred in the UnifracWeightedCommand class function calculateFreqsCums. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
+
}
+/***********************************************************/
+
+
+
+
+
projects / mothur.git / blobdiff