sumFile = globaldata->getTreeFile() + ".wsummary";
openOutputFile(sumFile, outSum);
- setGroups(); //sets the groups the user wants to analyze
+ 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);
+ globaldata->setGroups("");
+
convert(globaldata->getIters(), iters); //how many random trees to generate
weighted = new Weighted(tmap);
/***********************************************************/
int UnifracWeightedCommand::execute() {
try {
+ 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...
counter = 0;
rScores.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC...
uScores.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC...
- weightedFile = globaldata->getTreeFile() + toString(i+1) + ".weighted";
- weightedFileout = globaldata->getTreeFile() + "temp." + toString(i+1) + ".weighted";
-
- cout << "Processing tree " << i+1 << endl;
+
+ output = new ColumnFile(globaldata->getTreeFile() + toString(i+1) + ".weighted");
+
userData = weighted->getValues(T[i]); //userData[0] = weightedscore
//save users score
count++;
}
}
+
+ //update progress bar
+ reading->update(j);
+
}
//removeValidScoresDuplicates();
calculateFreqsCumuls();
printWeightedFile();
+ delete output;
+
//clear data
rScores.clear();
uScores.clear();
validScores.clear();
}
+ //finish progress bar
+ reading->finish();
+ delete reading;
+
printWSummaryFile();
//clear out users groups
void UnifracWeightedCommand::printWeightedFile() {
try {
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++) {
- initFile(groupComb[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(data);
+ output->output(data);
data.clear();
}
- resetFile();
+ output->resetFile();
}
-
- out.close();
- inFile.close();
- remove(weightedFileout.c_str());
-
}
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(globaldata->getIters().length()) << i+1 << '\t' << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << WScoreSig[count] << endl;
- cout << setprecision(globaldata->getIters().length()) << 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(globaldata->getIters().length()) << WScoreSig[count] << endl;
+ cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(globaldata->getIters().length()) << WScoreSig[count] << endl;
+ }else{
+ outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << endl;
+ cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << endl;
+ }
count++;
}
}
}
}
-/***********************************************************/
-void UnifracWeightedCommand::setGroups() {
- try {
- //if the user has not entered specific groups to analyze then do them all
- if (globaldata->Groups.size() == 0) {
- numGroups = tmap->getNumGroups();
- for (int i=0; i < numGroups; i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
- }
- }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);
- }
- }
-
- //if the user only entered invalid groups
- if (globaldata->Groups.size() == 0) {
- numGroups = tmap->getNumGroups();
- for (int i=0; i < numGroups; i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
- }
- 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();
- for (int i=0; i < numGroups; i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
- }
- }else { numGroups = globaldata->Groups.size(); }
- }else { //users wants all groups
- numGroups = tmap->getNumGroups();
- globaldata->Groups.clear();
- globaldata->setGroups("");
- for (int i=0; i < numGroups; i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
- }
- }
- }
-
- //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
- numComp = 0;
- for (int i=0; i<numGroups; i++) {
- numComp += i;
- for (int l = i+1; l < numGroups; l++) {
- //set group comparison labels
- groupComb.push_back(globaldata->Groups[i]+globaldata->Groups[l]);
- }
- }
- }
- 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";
- 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";
- exit(1);
- }
-}
-
/***********************************************************/
void UnifracWeightedCommand::calculateFreqsCumuls() {
}
-/*****************************************************************/
-
-void UnifracWeightedCommand::initFile(string label){
- try {
- if(counter != 0){
- openOutputFile(weightedFileout, out);
- openInputFile(weightedFile, inFile);
-
- string inputBuffer;
- getline(inFile, inputBuffer);
-
- out << inputBuffer << '\t' << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
- }else{
- openOutputFile(weightedFileout, 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 UnifracWeightedCommand class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracWeightedCommand class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-
-/***********************************************************************/
+/***********************************************************/
-void UnifracWeightedCommand::output(vector<double> data){
- try {
- if(counter != 0){
- string inputBuffer;
- getline(inFile, inputBuffer);
-
- out << inputBuffer << setprecision(globaldata->getIters().length()) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
- }
- else{
- out << setprecision(globaldata->getIters().length()) << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
- }
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracWeightedCommand class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-};
-/***********************************************************************/
-void UnifracWeightedCommand::resetFile(){
- try {
- if(counter != 0){
- out.close();
- inFile.close();
- }
- else{
- out.close();
- }
- counter = 1;
-
- remove(weightedFile.c_str());
- rename(weightedFileout.c_str(), weightedFile.c_str());
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracWeightedCommand class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
projects / mothur.git / blobdiff