X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracunweightedcommand.cpp;h=3fa44b50014de39006037771bdc9899f0bc357f3;hb=8f92612d5a69f5245e63a20657e7d93519c0769e;hp=e2b085f76a8e951886d668915306667a7de1b5f2;hpb=d97b619c4297b1274c754d73a64792ba656b0a79;p=mothur.git diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp index e2b085f..3fa44b5 100644 --- a/unifracunweightedcommand.cpp +++ b/unifracunweightedcommand.cpp @@ -16,12 +16,9 @@ UnifracUnweightedCommand::UnifracUnweightedCommand() { T = globaldata->gTree; tmap = globaldata->gTreemap; - unweightedFile = globaldata->getTreeFile() + ".unweighted"; - openOutputFile(unweightedFile, out); sumFile = globaldata->getTreeFile() + ".uwsummary"; openOutputFile(sumFile, outSum); - distFile = globaldata->getTreeFile() + ".uwdistrib"; - openOutputFile(distFile, outDist); + setGroups(); //sets users groups to analyze convert(globaldata->getIters(), iters); //how many random trees to generate unweighted = new Unweighted(tmap); @@ -39,115 +36,81 @@ UnifracUnweightedCommand::UnifracUnweightedCommand() { /***********************************************************/ int UnifracUnweightedCommand::execute() { try { - - //get unweighted for users tree - userData.resize(1,0); //data[0] = unweightedscore - randomData.resize(1,0); //data[0] = unweightedscore - - //format output - outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint); - - outDist << "Groups Used "; - for (int m = 0; m < globaldata->Groups.size(); m++) { - outDist << globaldata->Groups[m] << " "; - } - outDist << endl; - - outDist << "Tree#" << '\t' << "Iter" << '\t' << "UWScore" << endl; - + + 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(); //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"; + //column headers + outSum << "Tree# " << i+1 << endl; + outSum << "Comb" << '\t' << "UWScore" << '\t' << '\t' << "UWSig" << endl; + + //get unweighted for users tree + rscoreFreq.resize(numComp); + rCumul.resize(numComp); + utreeScores.resize(numComp); + UWScoreSig.resize(numComp); + cout << "Processing tree " << i+1 << endl; userData = unweighted->getValues(T[i]); //userData[0] = unweightedscore - //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]; - - //saves users score - utreeScores.push_back(userData[0]); - - //copy T[i]'s info. - randT->getCopy(T[i]); + //output scores for each combination + for(int k = 0; k < numComp; k++) { + //saves users score + utreeScores[k].push_back(userData[k]); + } //get unweighted scores for random trees for (int j = 0; j < iters; j++) { - //create a random tree with same topology as T[i], but different labels - randT->assembleRandomUnifracTree(); - //get pscore of random tree - randomData = unweighted->getValues(randT); - - //add trees unweighted score 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; - } + //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[randomData[0]] = randomData[0]; + 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 + rscoreFreq[k][randomData[k]]++; + }else{//first time we have seen this score + rscoreFreq[k][randomData[k]] = 1; + } - //output info to uwdistrib file - outDist << i+1 << '\t' << '\t'<< j+1 << '\t' << '\t' << randomData[0] << endl; + //add randoms score to validscores + validScores[randomData[k]] = randomData[k]; + } } - - saveRandomScores(); //save all random scores for unweighted file - - //find the signifigance of the score + + for(int a = 0; a < numComp; a++) { float rcumul = 1.0000; - for (it = rscoreFreq.begin(); it != rscoreFreq.end(); it++) { - rCumul[it->first] = rcumul; + //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 - rscoreFreq[it->first] /= iters; - rcumul-= it->second; - + 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 } - - //save the signifigance of the users score for printing later - UWScoreSig.push_back(rCumul[userData[0]]); - - - //clear random data - rscoreFreq.clear(); //you clear this because in the summary file you want the unweighted signifinance to be relative to these 1000 trees. - rCumul.clear(); - } - - 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.begin(); it != validScores.end(); it++) { - it2 = uscoreFreq.find(it->first); - //make uCumul map - uCumul[it->first] = ucumul; - //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 rscoreFreq map and rCumul - it2 = totalrscoreFreq.find(it->first); - rCumul[it->first] = rcumul; - //get percentage of random trees with that info - if (it2 != totalrscoreFreq.end()) { totalrscoreFreq[it->first] /= (iters*T.size()); rcumul-= it2->second; } - else { totalrscoreFreq[it->first] = 0.0000; } //no random trees with that score - + UWScoreSig[a].push_back(rCumul[a][userData[a]]); } printUnweightedFile(); printUWSummaryFile(); + rscoreFreq.clear(); + rCumul.clear(); + validScores.clear(); + utreeScores.clear(); + UWScoreSig.clear(); + } //reset groups parameter - globaldata->Groups.clear(); - - delete randT; + globaldata->Groups.clear(); globaldata->setGroups(""); + outSum.close(); return 0; @@ -164,25 +127,22 @@ int UnifracUnweightedCommand::execute() { /***********************************************************/ void UnifracUnweightedCommand::printUnweightedFile() { try { - //column headers + vector data; - out << "Groups Used "; - for (int m = 0; m < globaldata->Groups.size(); m++) { - out << globaldata->Groups[m] << " "; + for(int a = 0; a < numComp; a++) { + initFile(groupComb[a]); + //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); + data.clear(); + } + resetFile(); } - out << endl; - - out << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl; - - //format output - out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint); - - //print each line - for (it = validScores.begin(); it != validScores.end(); it++) { - out << setprecision(6) << it->first << '\t' << '\t' << uscoreFreq[it->first] << '\t' << uCumul[it->first] << '\t' << totalrscoreFreq[it->first] << '\t' << rCumul[it->first] << endl; - } out.close(); + inFile.close(); + remove(unweightedFileout.c_str()); } catch(exception& e) { @@ -198,25 +158,16 @@ void UnifracUnweightedCommand::printUnweightedFile() { /***********************************************************/ void UnifracUnweightedCommand::printUWSummaryFile() { try { - //column headers - - outSum << "Groups Used "; - for (int m = 0; m < globaldata->Groups.size(); m++) { - outSum << globaldata->Groups[m] << " "; - } - outSum << endl; - - outSum << "Tree#" << '\t' << "UWScore" << '\t' << '\t' << "UWSig" << 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' << utreeScores[i] << '\t' << UWScoreSig[i] << endl; + for(int a = 0; a < numComp; a++) { + outSum << setprecision(6) << groupComb[a] << '\t' << '\t' << utreeScores[a][0] << '\t' << UWScoreSig[a][0] << endl; + cout << setprecision(6) << groupComb[a] << '\t' << '\t' << utreeScores[a][0] << '\t' << UWScoreSig[a][0] << 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"; @@ -227,57 +178,66 @@ void UnifracUnweightedCommand::printUWSummaryFile() { exit(1); } } -/***********************************************************/ -void UnifracUnweightedCommand::saveRandomScores() { - try { - for (it = rscoreFreq.begin(); it != rscoreFreq.end(); it++) { - //does this score already exist in the total map - it2 = totalrscoreFreq.find(it->first); - //if yes then add them - if (it2 != totalrscoreFreq.end()) { - totalrscoreFreq[it->first] += rscoreFreq[it->first]; - }else{ //its a new score - totalrscoreFreq[it->first] = rscoreFreq[it->first]; - } - } - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function saveRandomScores. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the UnifracUnweightedCommand class function saveRandomScores. 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) { - //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 (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; + //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++) { - globaldata->Groups.push_back(tmap->namesOfGroups[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) { @@ -292,3 +252,82 @@ void UnifracUnweightedCommand::setGroups() { } /*****************************************************************/ +void UnifracUnweightedCommand::initFile(string label){ + try { + if(counter != 0){ + openOutputFile(unweightedFileout, out); + openInputFile(unweightedFile, inFile); + + string inputBuffer; + getline(inFile, inputBuffer); + + out << inputBuffer << '\t' << label + "Score" << '\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 data){ + try { + if(counter != 0){ + string inputBuffer; + getline(inFile, inputBuffer); + + out << inputBuffer << setprecision(6) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl; + } + else{ + out << setprecision(6) << data[0] << '\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); + } +} +