T = globaldata->gTree;
tmap = globaldata->gTreemap;
parsFile = globaldata->getTreeFile() + ".parsimony";
- openOutputFile(parsFile, out);
+ parsFileout = globaldata->getTreeFile() + "temp" + ".parsimony";
sumFile = globaldata->getTreeFile() + ".psummary";
openOutputFile(sumFile, outSum);
- distFile = globaldata->getTreeFile() + ".pdistrib";
- openOutputFile(distFile, outDist);
-
- //if the user has not entered specific groups to analyze then do them all
- if (globaldata->Groups.size() != 0) {
- //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]);
- }
- }
- }else {
- for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
- }
- }
-
}else { //user wants random distribution
savetmap = globaldata->gTreemap;
getUserInput();
- parsFile = randomtree + ".rd_parsimony";
- openOutputFile(parsFile, out);
+ parsFile = randomtree;
+ parsFileout = globaldata->getTreeFile() + "temp";
}
+ //set users groups to analyze
+ setGroups();
convert(globaldata->getIters(), iters); //how many random trees to generate
pars = new Parsimony(tmap);
+ counter = 0;
}
catch(exception& e) {
/***********************************************************/
int ParsimonyCommand::execute() {
try {
-
+
//get pscore for users tree
- userData.resize(1,0); //data[0] = pscore.
- randomData.resize(1,0); //data[0] = pscore.
-
- //format output
- outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
- outDist << "RandomTree#" << '\t' << "ParsScore" << endl;
-
+ userData.resize(numComp,0); //data = AB, AC, BC, ABC.
+ randomData.resize(numComp,0); //data = AB, AC, BC, ABC.
+ rscoreFreq.resize(numComp);
+ uscoreFreq.resize(numComp);
+ rCumul.resize(numComp);
+ uCumul.resize(numComp);
+ userTreeScores.resize(numComp);
+ UScoreSig.resize(numComp);
+
if (randomtree == "") {
//get pscores for users trees
for (int i = 0; i < T.size(); i++) {
- cout << "Processing tree " << i+1 << endl;
- userData = pars->getValues(T[i]); //userData[0] = pscore
- //update uscoreFreq
- it = uscoreFreq.find(userData[0]);
- if (it == uscoreFreq.end()) {//new score
- uscoreFreq[userData[0]] = 1;
- }else{ uscoreFreq[userData[0]]++; }
-
- //add users score to valid scores
- validScores[userData[0]] = userData[0];
+ userData = pars->getValues(T[i]); //data = AB, AC, BC, ABC.
- //save score for summary file
- userTreeScores.push_back(userData[0]);
-
+ //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[userData[k]] = userData[k];
+
+ //save score for summary file
+ userTreeScores[k].push_back(userData[k]);
+ }
}
//get pscores for random trees
randT->assembleRandomTree();
//get pscore of random tree
randomData = pars->getValues(randT);
+
+ for(int r = 0; r < numComp; r++) {
+ //add trees pscore to map of scores
+ it2 = rscoreFreq[r].find(randomData[r]);
+ if (it2 != rscoreFreq[r].end()) {//already have that score
+ rscoreFreq[r][randomData[r]]++;
+ }else{//first time we have seen this score
+ rscoreFreq[r][randomData[r]] = 1;
+ }
- //add trees pscore to map of scores
- it2 = rscoreFreq.find(randomData[0]);
- if (it2 != rscoreFreq.end()) {//already have that score
- rscoreFreq[randomData[0]]++;
- }else{//first time we have seen this score
- rscoreFreq[randomData[0]] = 1;
+ //add randoms score to validscores
+ validScores[randomData[r]] = randomData[r];
}
-
- //add randoms score to validscores
- validScores[randomData[0]] = randomData[0];
- //output info to pdistrib file
- outDist << j+1 << '\t'<< '\t' << randomData[0] << endl;
-
delete randT;
}
}else {
randT->assembleRandomTree();
//get pscore of random tree
randomData = pars->getValues(randT);
+
+ for(int r = 0; r < numComp; r++) {
+ //add trees pscore to map of scores
+ it2 = rscoreFreq[r].find(randomData[r]);
+ if (it2 != rscoreFreq[r].end()) {//already have that score
+ rscoreFreq[r][randomData[r]]++;
+ }else{//first time we have seen this score
+ rscoreFreq[r][randomData[r]] = 1;
+ }
- //add trees pscore to map of scores
- it2 = rscoreFreq.find(randomData[0]);
- if (it2 != rscoreFreq.end()) {//already have that score
- rscoreFreq[randomData[0]]++;
- }else{//first time we have seen this score
- rscoreFreq[randomData[0]] = 1;
+ //add randoms score to validscores
+ validScores[randomData[r]] = randomData[r];
}
-
- //add randoms score to validscores
- validScores[randomData[0]] = randomData[0];
-
+
delete randT;
}
}
- float rcumul = 0.0000;
- float ucumul = 0.0000;
-
- //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++) {
- if (randomtree == "") {
- it2 = uscoreFreq.find(it->first);
- //user data has that score
- if (it2 != uscoreFreq.end()) { uscoreFreq[it->first] /= T.size(); ucumul+= it2->second; }
- else { uscoreFreq[it->first] = 0.0000; } //no user trees with that score
- //make uCumul map
- uCumul[it->first] = ucumul;
+ for(int a = 0; a < numComp; a++) {
+ float rcumul = 0.0000;
+ float ucumul = 0.0000;
+ //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++) {
+ if (randomtree == "") {
+ it2 = uscoreFreq[a].find(it->first);
+ //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 uCumul map
+ uCumul[a][it->first] = ucumul;
+ }
+
+ //make rscoreFreq map and rCumul
+ it2 = rscoreFreq[a].find(it->first);
+ //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
+ rCumul[a][it->first] = rcumul;
}
- //make rscoreFreq map and rCumul
- it2 = rscoreFreq.find(it->first);
- //get percentage of random trees with that info
- if (it2 != rscoreFreq.end()) { rscoreFreq[it->first] /= iters; rcumul+= it2->second; }
- else { rscoreFreq[it->first] = 0.0000; } //no random trees with that score
- rCumul[it->first] = rcumul;
+ //find the signifigance of each user trees score when compared to the random trees and save for printing the summary file
+ for (int h = 0; h < userTreeScores[a].size(); h++) {
+ UScoreSig[a].push_back(rCumul[a][userTreeScores[a][h]]);
+ }
}
- //find the signifigance of each user trees score when compared to the random trees and save for printing the summary file
- for (int h = 0; h < userTreeScores.size(); h++) {
- UScoreSig.push_back(rCumul[userTreeScores[h]]);
- }
-
printParsimonyFile();
- printUSummaryFile();
+ if (randomtree == "") { printUSummaryFile(); }
//reset globaldata's treemap if you just did random distrib
if (randomtree != "") { globaldata->gTreemap = savetmap; }
//reset randomTree parameter to ""
globaldata->setRandomTree("");
//reset groups parameter
- globaldata->Groups.clear();
+ globaldata->Groups.clear(); globaldata->setGroups("");
return 0;
/***********************************************************/
void ParsimonyCommand::printParsimonyFile() {
try {
- //column headers
- if (randomtree == "") {
- out << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
- }else {
- out << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
- }
+ vector<double> data;
//format output
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-
- //print each line
- for (it = validScores.begin(); it != validScores.end(); it++) {
- if (randomtree == "") {
- out << setprecision(6) << it->first << '\t' << '\t' << uscoreFreq[it->first] << '\t' << uCumul[it->first] << '\t' << rscoreFreq[it->first] << '\t' << rCumul[it->first] << endl;
- }else{
- out << setprecision(6) << it->first << '\t' << '\t' << rscoreFreq[it->first] << '\t' << rCumul[it->first] << endl;
- }
- }
+
+ for(int a = 0; a < numComp; a++) {
+ initFile(groupComb[a]);
+ //print each line
+ for (it = validScores.begin(); it != validScores.end(); it++) {
+ if (randomtree == "") {
+ data.push_back(it->first); data.push_back(uscoreFreq[a][it->first]); data.push_back(uCumul[a][it->first]); data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
+ }else{
+ 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(parsFileout.c_str());
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function printParsimonyFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
void ParsimonyCommand::printUSummaryFile() {
try {
//column headers
- outSum << "Tree#" << '\t' << "ParsScore" << '\t' << '\t' << "ParsSig" << endl;
+ outSum << "Tree#" << '\t' << "Groups" << '\t' << "ParsScore" << '\t' << "ParsSig" << endl;
+ cout << "Tree#" << '\t' << "Groups" << '\t' << "ParsScore" << '\t' << "ParsSig" << endl;
//format output
outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
+
//print each line
for (int i = 0; i< T.size(); i++) {
- outSum << setprecision(6) << i+1 << '\t' << '\t' << userTreeScores[i] << '\t' << UScoreSig[i] << endl;
+ for(int a = 0; a < numComp; a++) {
+ if (UScoreSig[a][i] > (1/(float)iters)) {
+ outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << '\t' << userTreeScores[a][i] << setprecision(globaldata->getIters().length()) << '\t' << UScoreSig[a][i] << endl;
+ cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << '\t' << userTreeScores[a][i] << setprecision(globaldata->getIters().length()) << '\t' << UScoreSig[a][i] << endl;
+ }else {
+ outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(globaldata->getIters().length()) << '\t' << "<" << (1/float(iters)) << endl;
+ cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(globaldata->getIters().length()) << '\t' << "<" << (1/float(iters)) << endl;
+ }
+ }
}
outSum.close();
//set tmaps seqsPerGroup
tmap->seqsPerGroup[toString(i)] = num;
+ tmap->namesOfGroups.push_back(toString(i));
//set tmaps namesOfSeqs
for (int j = 0; j < num; j++) {
}
/***********************************************************/
+void ParsimonyCommand::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] + "-";
+ }
+ allGroups = allGroups.substr(0, allGroups.length()-1);
+ }else {
+ for (int i = 0; i < globaldata->Groups.size(); 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 = allGroups.substr(0, allGroups.length()-1);
+ globaldata->setGroups("");
+ }
+ }else {
+ for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
+ allGroups += tmap->namesOfGroups[i] + "-";
+ }
+ allGroups = allGroups.substr(0, allGroups.length()-1);
+ 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 ParsimonyCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ParsimonyCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+}
+/*****************************************************************/
+
+void ParsimonyCommand::initFile(string label){
+ try {
+ if(counter != 0){
+ openOutputFile(parsFileout, out);
+ openInputFile(parsFile, inFile);
+
+ string inputBuffer;
+ getline(inFile, inputBuffer);
+
+ if (randomtree == "") {
+ out << inputBuffer << '\t' << label + "Score" << '\t' << label + "UserFreq" << '\t' << label + "UserCumul" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
+ }else {
+ out << inputBuffer << '\t' << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
+ }
+ }else{
+ openOutputFile(parsFileout, out);
+ //column headers
+ if (randomtree == "") {
+ out << label + "Score" << '\t' << label + "UserFreq" << '\t' << label + "UserCumul" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
+ }else {
+ out << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
+ }
+ }
+
+ out.setf(ios::fixed, ios::floatfield);
+ out.setf(ios::showpoint);
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ParsimonyCommand class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void ParsimonyCommand::output(vector<double> data){
+ try {
+ if(counter != 0){
+ string inputBuffer;
+ getline(inFile, inputBuffer);
+
+ if (randomtree == "") {
+ out << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << '\t' << data[3] << '\t' << data[4] << endl;
+ }else{
+ out << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << endl;
+ }
+ }
+ else{
+ if (randomtree == "") {
+ out << setprecision(6) << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << '\t' << data[3] << '\t' << data[4] << 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 ParsimonyCommand class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ParsimonyCommand class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void ParsimonyCommand::resetFile(){
+ try {
+ if(counter != 0){
+ out.close();
+ inFile.close();
+ }
+ else{
+ out.close();
+ }
+ counter = 1;
+
+ remove(parsFile.c_str());
+ rename(parsFileout.c_str(), parsFile.c_str());
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ParsimonyCommand class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+
projects / mothur.git / blobdiff