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
convert(globaldata->getIters(), iters); //how many random trees to generate
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;
+ unweightedFile = globaldata->getTreeFile() + toString(i+1) + ".unweighted";
+ unweightedFileout = globaldata->getTreeFile() + "temp." + toString(i+1) + ".unweighted";
+
+ outSum << i+1 << '\t';
+ cout << i+1 << '\t';
+
//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
-
+ for (it = validScores.begin(); it != validScores.end(); it++) {
//make rscoreFreq map and rCumul
it2 = rscoreFreq[a].find(it->first);
rCumul[a][it->first] = rcumul;
printUnweightedFile();
printUWSummaryFile();
- rscoreFreq.clear();
- uscoreFreq.clear();
+ rscoreFreq.clear();
rCumul.clear();
- uCumul.clear();
validScores.clear();
utreeScores.clear();
UWScoreSig.clear();
}
//reset groups parameter
globaldata->Groups.clear(); globaldata->setGroups("");
-
- delete randT;
+ outSum.close();
return 0;
/***********************************************************/
void UnifracUnweightedCommand::printUnweightedFile() {
try {
- //format output
- out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+ vector<double> data;
for(int a = 0; a < numComp; a++) {
+ initFile(groupComb[a]);
//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(data);
+ data.clear();
}
+ resetFile();
}
+
out.close();
+ inFile.close();
+ remove(unweightedFileout.c_str());
}
catch(exception& e) {
//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++) {
+ 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";
for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
globaldata->Groups.push_back(tmap->namesOfGroups[i]);
numGroups++;
- allGroups += tmap->namesOfGroups[i];
+ allGroups += tmap->namesOfGroups[i] + "-";
}
+ allGroups = allGroups.substr(0, allGroups.length()-1);
}else {
for (int i = 0; i < globaldata->Groups.size(); i++) {
- allGroups += globaldata->Groups[i];
+ allGroups += globaldata->Groups[i] + "-";
numGroups++;
}
+ allGroups = allGroups.substr(0, allGroups.length()-1);
}
}else{//user has enter "all" and wants the default groups
+ globaldata->Groups.clear();
for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
globaldata->Groups.push_back(tmap->namesOfGroups[i]);
numGroups++;
- allGroups += tmap->namesOfGroups[i];
+ allGroups += tmap->namesOfGroups[i] + "-";
}
+ allGroups = allGroups.substr(0, allGroups.length()-1);
globaldata->setGroups("");
}
}else {
for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- allGroups += tmap->namesOfGroups[i];
+ allGroups += tmap->namesOfGroups[i] + "-";
}
+ allGroups = allGroups.substr(0, allGroups.length()-1);
numGroups = 1;
}
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]);
+ groupComb.push_back(globaldata->Groups[r]+ "-" + globaldata->Groups[l]);
numComp++;
}
}
}
/*****************************************************************/
+void UnifracUnweightedCommand::initFile(string label){
+ try {
+ if(counter != 0){
+ openOutputFile(unweightedFileout, out);
+ openInputFile(unweightedFile, inFile);
+
+ string inputBuffer;
+ getline(inFile, inputBuffer);
+
+ out << inputBuffer << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
+ }else{
+ openOutputFile(unweightedFileout, out);
+ out << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
+ }
+
+ out.setf(ios::fixed, ios::floatfield);
+ out.setf(ios::showpoint);
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the UnifracUnweightedCommand class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void UnifracUnweightedCommand::output(vector<double> data){
+ try {
+ if(counter != 0){
+ string inputBuffer;
+ getline(inFile, inputBuffer);
+// out << inputBuffer << setprecision(6) << '\t' << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << endl;
+
+ out << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << endl;
+ }
+ else{
+ out << setprecision(6) << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << endl;
+ }
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the UnifracUnweightedCommand class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+};
+
+/***********************************************************************/
+
+void UnifracUnweightedCommand::resetFile(){
+ try {
+ if(counter != 0){
+ out.close();
+ inFile.close();
+ }
+ else{
+ out.close();
+ }
+ counter = 1;
+
+ remove(unweightedFile.c_str());
+ rename(unweightedFileout.c_str(), unweightedFile.c_str());
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the UnifracUnweightedCommand class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
projects / mothur.git / blobdiff