From: westcott Date: Tue, 3 Mar 2009 17:39:03 +0000 (+0000) Subject: parsimony output changed X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=847cf1477867e920eddf68e1af64838cfc318386 parsimony output changed --- diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp index a527a18..4529f77 100644 --- a/parsimonycommand.cpp +++ b/parsimonycommand.cpp @@ -22,7 +22,7 @@ ParsimonyCommand::ParsimonyCommand() { 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); }else { //user wants random distribution @@ -36,6 +36,7 @@ ParsimonyCommand::ParsimonyCommand() { setGroups(); convert(globaldata->getIters(), iters); //how many random trees to generate pars = new Parsimony(tmap); + counter = 0; } catch(exception& e) { @@ -58,7 +59,6 @@ int ParsimonyCommand::execute() { uscoreFreq.resize(numComp); rCumul.resize(numComp); uCumul.resize(numComp); - validScores.resize(numComp); userTreeScores.resize(numComp); UScoreSig.resize(numComp); @@ -77,7 +77,7 @@ int ParsimonyCommand::execute() { }else{ uscoreFreq[k][userData[k]]++; } //add users score to valid scores - validScores[k][userData[k]] = userData[k]; + validScores[userData[k]] = userData[k]; //save score for summary file userTreeScores[k].push_back(userData[k]); @@ -103,7 +103,7 @@ int ParsimonyCommand::execute() { } //add randoms score to validscores - validScores[r][randomData[r]] = randomData[r]; + validScores[randomData[r]] = randomData[r]; } delete randT; @@ -128,26 +128,25 @@ int ParsimonyCommand::execute() { } //add randoms score to validscores - validScores[r][randomData[r]] = randomData[r]; + validScores[randomData[r]] = randomData[r]; } delete randT; } } - float rcumul = 0.0000; - float ucumul = 0.0000; - for(int a = 0; a < numComp; a++) { - //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++) { + 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-a; + uCumul[a][it->first] = ucumul; } //make rscoreFreq map and rCumul @@ -155,7 +154,7 @@ int ParsimonyCommand::execute() { //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-a; + rCumul[a][it->first] = rcumul; } //find the signifigance of each user trees score when compared to the random trees and save for printing the summary file @@ -191,28 +190,29 @@ int ParsimonyCommand::execute() { /***********************************************************/ void ParsimonyCommand::printParsimonyFile() { try { - //column headers - if (randomtree == "") { - out << "Comb" << '\t' << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl; - }else { - out << "Comb" << '\t' << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl; - } + vector data; //format output out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint); - + for(int a = 0; a < numComp; a++) { + initFile(groupComb[a]); //print each line - for (it = validScores[a].begin(); it != validScores[a].end(); it++) { + for (it = validScores.begin(); it != validScores.end(); it++) { if (randomtree == "") { - 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; + 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{ - out << setprecision(6) << groupComb[a] << '\t' << it->first << '\t' << '\t' << rscoreFreq[a][it->first] << '\t' << rCumul[a][it->first] << endl; + 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(); + 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"; @@ -375,4 +375,100 @@ void ParsimonyCommand::setGroups() { } /*****************************************************************/ +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' << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "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 << 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 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 data){ + try { + if(counter != 0){ + string inputBuffer; + getline(inFile, inputBuffer); + + if (randomtree == "") { + out << inputBuffer << '\t' << setprecision(6) << data[0] << '\t' << data[1] << '\t' << data[2] << '\t' << data[3] << '\t' << data[4] << endl; + }else{ + out << inputBuffer << '\t' << setprecision(6) << data[0] << '\t' << data[1] << '\t' << data[2] << endl; + } + } + else{ + if (randomtree == "") { + out << setprecision(6) << data[0] << '\t' << data[1] << '\t' << data[2] << '\t' << data[3] << '\t' << data[4] << 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 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); + } +} + diff --git a/parsimonycommand.h b/parsimonycommand.h index db062c6..8907e21 100644 --- a/parsimonycommand.h +++ b/parsimonycommand.h @@ -33,14 +33,14 @@ class ParsimonyCommand : public Command { TreeMap* savetmap; Parsimony* pars; vector groupComb; // AB. AC, BC... - string parsFile, sumFile, randomtree; - int iters, numGroups, numComp; + string parsFile, parsFileout, sumFile, randomtree; + int iters, numGroups, numComp, counter; vector numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib. vector< vector > userTreeScores; //scores for users trees for each comb. vector< vector > UScoreSig; //tree score signifigance when compared to random trees - percentage of random trees with that score or lower. EstOutput userData; //pscore info for user tree EstOutput randomData; //pscore info for random trees - vector< map > validScores; //map contains scores from both user and random + map validScores; //map contains scores from both user and random vector< map > rscoreFreq; //map -vector entry for each combination. vector< map > uscoreFreq; //map -vector entry for each combination. vector< map > rCumul; //map -vector entry for each combination. @@ -49,11 +49,16 @@ class ParsimonyCommand : public Command { map::iterator it2; ofstream out, outSum; + ifstream inFile; void printParsimonyFile(); void printUSummaryFile(); void getUserInput(); void setGroups(); + void initFile(string); + void output(vector); + void resetFile(); + }; diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp index 5a7cc36..2a169d0 100644 --- a/unifracunweightedcommand.cpp +++ b/unifracunweightedcommand.cpp @@ -22,6 +22,7 @@ UnifracUnweightedCommand::UnifracUnweightedCommand() { setGroups(); //sets users groups to analyze convert(globaldata->getIters(), iters); //how many random trees to generate unweighted = new Unweighted(tmap); + counter = 0; } catch(exception& e) {