T = globaldata->gTree;
tmap = globaldata->gTreemap;
- unweightedFile = globaldata->getTreeFile() + ".unweighted";
- openOutputFile(unweightedFile, out);
- //column headers
- out << "Comb" << '\t' << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
-
sumFile = globaldata->getTreeFile() + ".uwsummary";
openOutputFile(sumFile, outSum);
- //column headers
- outSum << "Tree#" << '\t' << "Comb" << '\t' << "UWScore" << '\t' << '\t' << "UWSig" << endl;
- setGroups(); //sets users groups to analyze
+ util = new SharedUtil();
+ util->setGroups(globaldata->Groups, tmap->namesOfGroups, allGroups, numGroups, "unweighted"); //sets the groups the user wants to analyze
+ util->getCombos(groupComb, globaldata->Groups, numComp);
+ globaldata->setGroups("");
+
+ if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
+
convert(globaldata->getIters(), iters); //how many random trees to generate
unweighted = new Unweighted(tmap);
/***********************************************************/
int UnifracUnweightedCommand::execute() {
try {
-
+
userData.resize(numComp,0); //data[0] = unweightedscore
randomData.resize(numComp,0); //data[0] = unweightedscore
//create new tree with same num nodes and leaves as users
- randT = new Tree();
-
+
+ outSum << "Tree#" << '\t' << "Groups" << '\t' << "UWScore" <<'\t' << "UWSig" << endl;
+ cout << "Tree#" << '\t' << "Groups" << '\t' << "UWScore" << '\t' << "UWSig" << endl;
+
//get pscores for users trees
for (int i = 0; i < T.size(); i++) {
+ counter = 0;
+
+ output = new ColumnFile(globaldata->getTreeFile() + toString(i+1) + ".unweighted");
+
//get unweighted for users tree
rscoreFreq.resize(numComp);
- uscoreFreq.resize(numComp);
rCumul.resize(numComp);
- uCumul.resize(numComp);
- validScores.resize(numComp);
utreeScores.resize(numComp);
UWScoreSig.resize(numComp);
- cout << "Processing tree " << i+1 << endl;
- outSum << "Tree#" << i+1 << endl;
- out << "Tree#" << i+1 << endl;
userData = unweighted->getValues(T[i]); //userData[0] = unweightedscore
//output scores for each combination
for(int k = 0; k < numComp; k++) {
- //update uscoreFreq
- it = uscoreFreq[k].find(userData[k]);
- if (it == uscoreFreq[k].end()) {//new score
- uscoreFreq[k][userData[k]] = 1;
- }else{ uscoreFreq[k][userData[k]]++; }
-
- //add users score to valid scores
- validScores[k][userData[k]] = userData[k];
-
//saves users score
utreeScores[k].push_back(userData[k]);
+
}
- //copy T[i]'s info.
- randT->getCopy(T[i]);
-
//get unweighted scores for random trees
for (int j = 0; j < iters; j++) {
//we need a different getValues because when we swap the labels we only want to swap those in each parwise comparison
- randomData = unweighted->getValues(randT, "", "");
+ randomData = unweighted->getValues(T[i], "", "");
for(int k = 0; k < numComp; k++) {
-cout << "iter " << j << " comp " << k << " = " << randomData[k] << endl;
//add trees unweighted score to map of scores
it2 = rscoreFreq[k].find(randomData[k]);
if (it2 != rscoreFreq[k].end()) {//already have that score
}
//add randoms score to validscores
- validScores[k][randomData[k]] = randomData[k];
+ validScores[randomData[k]] = randomData[k];
}
+
}
- for(int a = 0; a < numComp; a++) {
- float ucumul = 1.0000;
- 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[a].begin(); it != validScores[a].end(); it++) {
- it2 = uscoreFreq[a].find(it->first);
- //make uCumul map
- uCumul[a][it->first] = ucumul;
- //user data has that score
- if (it2 != uscoreFreq[a].end()) { uscoreFreq[a][it->first] /= T.size(); ucumul-= it2->second; }
- else { uscoreFreq[a][it->first] = 0.0000; } //no user trees with that score
-
- //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
+ 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
+ }
+ UWScoreSig[a].push_back(rCumul[a][userData[a]]);
}
- UWScoreSig[a].push_back(rCumul[a][userData[a]]);
- }
- printUnweightedFile();
- printUWSummaryFile();
- rscoreFreq.clear();
- uscoreFreq.clear();
- rCumul.clear();
- uCumul.clear();
- validScores.clear();
- utreeScores.clear();
- UWScoreSig.clear();
- }
- //reset groups parameter
- globaldata->Groups.clear(); globaldata->setGroups("");
- delete randT;
+ printUnweightedFile();
+ printUWSummaryFile(i);
+
+ delete output;
+ rscoreFreq.clear();
+ rCumul.clear();
+ validScores.clear();
+ utreeScores.clear();
+ UWScoreSig.clear();
+ }
+
+ //reset groups parameter
+ globaldata->Groups.clear();
+ outSum.close();
return 0;
/***********************************************************/
void UnifracUnweightedCommand::printUnweightedFile() {
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(int a = 0; a < numComp; a++) {
+ output->initFile(groupComb[a], tags);
//print each line
- for (it = validScores[a].begin(); it != validScores[a].end(); it++) {
- out << setprecision(6) << groupComb[a] << '\t' << it->first << '\t' << '\t' << uscoreFreq[a][it->first] << '\t' << uCumul[a][it->first] << '\t' << rscoreFreq[a][it->first] << '\t' << rCumul[a][it->first] << endl;
+ 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 UnifracUnweightedCommand class Function printUnweightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
}
/***********************************************************/
-void UnifracUnweightedCommand::printUWSummaryFile() {
+void UnifracUnweightedCommand::printUWSummaryFile(int i) {
try {
//format output
outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
-
+
//print each line
- for (int i = 0; i< T.size(); i++) {
- for(int a = 0; a < numComp; a++) {
- outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << '\t' << utreeScores[a][i] << '\t' << UWScoreSig[a][i] << endl;
- cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << '\t' << utreeScores[a][i] << '\t' << UWScoreSig[a][i] << endl;
- }
+
+ for(int a = 0; a < numComp; a++) {
+ outSum << i+1 << '\t';
+ cout << i+1 << '\t';
+
+ if (UWScoreSig[a][0] > (1/(float)iters)) {
+ outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << UWScoreSig[a][0] << endl;
+ cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << UWScoreSig[a][0] << endl;
+ }else {
+ outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << endl;
+ cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << endl;
+ }
}
- outSum.close();
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function printUWSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
}
-/***********************************************************/
-void UnifracUnweightedCommand::setGroups() {
- try {
- string allGroups = "";
- numGroups = 0;
- //if the user has not entered specific groups to analyze then do them all
- if (globaldata->Groups.size() != 0) {
- if (globaldata->Groups[0] != "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);
- }
- }
-
- //if the user only entered invalid groups
- if (globaldata->Groups.size() == 0) {
- cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile." << endl;
- for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
- numGroups++;
- allGroups += tmap->namesOfGroups[i];
- }
- }else {
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- allGroups += globaldata->Groups[i];
- numGroups++;
- }
- }
- }else{//user has enter "all" and wants the default groups
- for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
- numGroups++;
- allGroups += tmap->namesOfGroups[i];
- }
- globaldata->setGroups("");
- }
- }else {
- for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- allGroups += tmap->namesOfGroups[i];
- }
- numGroups = 1;
- }
-
- //calculate number of comparsions
- numComp = 0;
- for (int r=0; r<numGroups; r++) {
- for (int l = r+1; l < numGroups; l++) {
- groupComb.push_back(globaldata->Groups[r]+globaldata->Groups[l]);
- numComp++;
- }
- }
-
- //ABC
- if (numComp != 1) {
- groupComb.push_back(allGroups);
- numComp++;
- }
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracUnweightedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
+/***********************************************************/
-}
-/*****************************************************************/
projects / mothur.git / blobdiff