X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracunweightedcommand.cpp;h=fcff253fc4812bafea60669dcb07c301dfa8de62;hb=31c6076fe649829d9b8f773f6f12b627d3ef5d9b;hp=c345ca16bc478ee9635846c54abb8ab68ec67b69;hpb=fc7cf3aac8fd6106fd725b43baa8ab5ca6f836f8;p=mothur.git diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp index c345ca1..fcff253 100644 --- a/unifracunweightedcommand.cpp +++ b/unifracunweightedcommand.cpp @@ -16,17 +16,16 @@ UnifracUnweightedCommand::UnifracUnweightedCommand() { 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); @@ -43,106 +42,85 @@ UnifracUnweightedCommand::UnifracUnweightedCommand() { /***********************************************************/ 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++) { - int count = 0; - for (int r=0; rgetValues(randT, "", ""); - - //add trees unweighted score to map of scores - it2 = rscoreFreq[count].find(randomData[count]); - if (it2 != rscoreFreq[count].end()) {//already have that score - rscoreFreq[count][randomData[count]]++; - }else{//first time we have seen this score - rscoreFreq[count][randomData[count]] = 1; - } + //we need a different getValues because when we swap the labels we only want to swap those in each parwise comparison + randomData = unweighted->getValues(T[i], "", ""); - //add randoms score to validscores - validScores[count][randomData[count]] = randomData[count]; - count++; + for(int k = 0; k < numComp; k++) { + //add trees unweighted score to map of scores + it2 = rscoreFreq[k].find(randomData[k]); + if (it2 != rscoreFreq[k].end()) {//already have that score + rscoreFreq[k][randomData[k]]++; + }else{//first time we have seen this score + rscoreFreq[k][randomData[k]] = 1; } + + //add randoms score to validscores + 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; @@ -159,17 +137,20 @@ int UnifracUnweightedCommand::execute() { /***********************************************************/ void UnifracUnweightedCommand::printUnweightedFile() { try { - //format output - out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint); + vector data; + vector 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"; @@ -182,21 +163,27 @@ void UnifracUnweightedCommand::printUnweightedFile() { } /***********************************************************/ -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"; @@ -207,77 +194,7 @@ void UnifracUnweightedCommand::printUWSummaryFile() { 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 += tmap->namesOfGroups[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; rGroups[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); - } +/***********************************************************/ -} -/*****************************************************************/