X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.cpp;h=cd7fec12320e3ee50e415a348df4a5b503e35763;hb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;hp=4ec2773d38eba93933015d8be8a77b8d078124bc;hpb=3c5c4e255ee8c36feb9e97aebc4e792e6ff8c440;p=mothur.git diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp index 4ec2773..cd7fec1 100644 --- a/unifracweightedcommand.cpp +++ b/unifracweightedcommand.cpp @@ -10,189 +10,293 @@ #include "unifracweightedcommand.h" /***********************************************************/ -UnifracWeightedCommand::UnifracWeightedCommand() { +UnifracWeightedCommand::UnifracWeightedCommand(string option) { try { globaldata = GlobalData::getInstance(); + abort = false; + Groups.clear(); + + //allow user to run help + if(option == "help") { help(); abort = true; } + + else { + //valid paramters for this command + string Array[] = {"groups","iters","distance","random","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + + OptionParser parser(option); + map parameters=parser.getParameters(); + + ValidParameters validParameter; - T = globaldata->gTree; - tmap = globaldata->gTreemap; - weightedFile = globaldata->getTreeFile() + ".weighted"; - openOutputFile(weightedFile, out); - sumFile = globaldata->getTreeFile() + ".wsummary"; - openOutputFile(sumFile, outSum); + //check to make sure all parameters are valid for command + for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + } + + if (globaldata->gTree.size() == 0) {//no trees were read + m->mothurOut("You must execute the read.tree command, before you may execute the unifrac.weighted command."); m->mothurOutEndLine(); abort = true; } + + //if the user changes the output directory command factory will send this info to us in the output parameter + outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ + outputDir = ""; + outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it + } + + //check for optional parameter and set defaults + // ...at some point should added some additional type checking... + groups = validParameter.validFile(parameters, "groups", false); + if (groups == "not found") { groups = ""; } + else { + splitAtDash(groups, Groups); + globaldata->Groups = Groups; + } - setGroups(); //sets the groups the user wants to analyze - convert(globaldata->getIters(), iters); //how many random trees to generate - weighted = new Weighted(tmap); + itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; } + convert(itersString, iters); + + string temp = validParameter.validFile(parameters, "distance", false); if (temp == "not found") { temp = "false"; } + phylip = isTrue(temp); + + temp = validParameter.validFile(parameters, "random", false); if (temp == "not found") { temp = "true"; } + random = isTrue(temp); + + if (!random) { iters = 0; } //turn off random calcs + + if (abort == false) { + T = globaldata->gTree; + tmap = globaldata->gTreemap; + sumFile = outputDir + getSimpleName(globaldata->getTreeFile()) + ".wsummary"; + openOutputFile(sumFile, outSum); + outputNames.push_back(sumFile); + + 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); + + weighted = new Weighted(tmap); + + } + } + + } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function UnifracWeightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "UnifracWeightedCommand", "UnifracWeightedCommand"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the UnifracWeightedCommand class function UnifracWeightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +//********************************************************************************************************************** + +void UnifracWeightedCommand::help(){ + try { + m->mothurOut("The unifrac.weighted command can only be executed after a successful read.tree command.\n"); + m->mothurOut("The unifrac.weighted command parameters are groups, iters, distance and random. No parameters are required.\n"); + m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups.\n"); + m->mothurOut("The group names are separated by dashes. The iters parameter allows you to specify how many random trees you would like compared to your tree.\n"); + m->mothurOut("The distance parameter allows you to create a distance file from the results. The default is false.\n"); + m->mothurOut("The random parameter allows you to shut off the comparison to random trees. The default is true, meaning compare your trees with randomly generated trees.\n"); + m->mothurOut("The unifrac.weighted command should be in the following format: unifrac.weighted(groups=yourGroups, iters=yourIters).\n"); + m->mothurOut("Example unifrac.weighted(groups=A-B-C, iters=500).\n"); + m->mothurOut("The default value for groups is all the groups in your groupfile, and iters is 1000.\n"); + m->mothurOut("The unifrac.weighted command output two files: .weighted and .wsummary their descriptions are in the manual.\n"); + m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n"); + } + catch(exception& e) { + m->errorOut(e, "UnifracWeightedCommand", "help"); exit(1); } } + /***********************************************************/ int UnifracWeightedCommand::execute() { try { + + if (abort == true) { return 0; } + + Progress* reading; + if (random) { reading = new Progress("Comparing to random:", iters); } //get weighted for users tree userData.resize(numComp,0); //data[0] = weightedscore AB, data[1] = weightedscore AC... randomData.resize(numComp,0); //data[0] = weightedscore AB, data[1] = weightedscore AC... - uscoreFreq.resize(numComp); - validScores.resize(numComp); - totalrscoreFreq.resize(numComp); - uCumul.resize(numComp); - + //create new tree with same num nodes and leaves as users randT = new Tree(); - //get pscores for users trees + //get weighted scores for users trees for (int i = 0; i < T.size(); i++) { - rscoreFreq.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC... - rCumul.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC... - - cout << "Processing tree " << i+1 << endl; + + if (m->control_pressed) { + delete randT; + if (random) { delete reading; } + outSum.close(); + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 0; + } + + counter = 0; + rScores.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC... + uScores.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC... + + if (random) { + output = new ColumnFile(outputDir + getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted", itersString); + outputNames.push_back(outputDir + getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted"); + } + userData = weighted->getValues(T[i]); //userData[0] = weightedscore + if (m->control_pressed) { + delete randT; + if (random) { delete reading; delete output; } + outSum.close(); + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 0; + } + + //save users score for (int s=0; sgetCopy(T[i]); - //get 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 = weighted->getValues(randT); - - //save ramdoms score - for (int p=0; pgetCopy(T[i]); + + //create a random tree with same topology as T[i], but different labels + randT->assembleRandomUnifracTree(globaldata->Groups[r], globaldata->Groups[l]); + + if (m->control_pressed) { + delete randT; + if (random) { delete reading; delete output; } + outSum.close(); + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 0; + } + + + //get wscore of random tree + randomData = weighted->getValues(randT, globaldata->Groups[r], globaldata->Groups[l]); + + if (m->control_pressed) { + delete randT; + if (random) { delete reading; delete output; } + outSum.close(); + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 0; + } + + //save scores + rScores[count].push_back(randomData[0]); + count++; } - - //add random score to valid scores - validScores[p][randomData[p]] = randomData[p]; } + + //update progress bar + reading->update(j); + } - - saveRandomScores(); //save all random scores for weighted file - + + //removeValidScoresDuplicates(); //find the signifigance of the score for summary file - for (int t = 0; t < numComp; t++) { - float rcumul = 1.0000; - for (it = validScores[t].begin(); it != validScores[t].end(); it++) { - //make rscoreFreq map and rCumul - it2 = rscoreFreq[t].find(it->first); - rCumul[t][it->first] = rcumul; - //get percentage of random trees with that info - if (it2 != rscoreFreq[t].end()) { rscoreFreq[t][it->first] /= iters; rcumul-= it2->second; } - else { rscoreFreq[t][it->first] = 0.0000; } //no random trees with that score + if (random) { + for (int f = 0; f < numComp; f++) { + //sort random scores + sort(rScores[f].begin(), rScores[f].end()); + + //the index of the score higher than yours is returned + //so if you have 1000 random trees the index returned is 100 + //then there are 900 trees with a score greater then you. + //giving you a signifigance of 0.900 + int index = findIndex(userData[f], f); if (index == -1) { m->mothurOut("error in UnifracWeightedCommand"); m->mothurOutEndLine(); exit(1); } //error code + + //the signifigance is the number of trees with the users score or higher + WScoreSig.push_back((iters-index)/(float)iters); } + + //out << "Tree# " << i << endl; + calculateFreqsCumuls(); + printWeightedFile(); + + delete output; } - //save the signifigance of the users score for printing later - for (int f = 0; f < numComp; f++) { - WScoreSig.push_back(rCumul[f][userData[f]]); - } - - - //clear random data - rscoreFreq.clear(); - rCumul.clear(); + //clear data + rScores.clear(); + uScores.clear(); + validScores.clear(); } - rCumul.resize(numComp); - for (int b = 0; b < numComp; b++) { - 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[b].begin(); it != validScores[b].end(); it++) { - it2 = uscoreFreq[b].find(it->first); - //make uCumul map - uCumul[b][it->first] = ucumul; - //user data has that score - if (it2 != uscoreFreq[b].end()) { uscoreFreq[b][it->first] /= T.size(); ucumul-= it2->second; } - else { uscoreFreq[b][it->first] = 0.0000; } //no user trees with that score - - //make rscoreFreq map and rCumul - it2 = totalrscoreFreq[b].find(it->first); - rCumul[b][it->first] = rcumul; - //get percentage of random trees with that info - if (it2 != totalrscoreFreq[b].end()) { totalrscoreFreq[b][it->first] /= (iters * T.size()); rcumul-= it2->second; } - else { totalrscoreFreq[b][it->first] = 0.0000; } //no random trees with that score - } + + if (m->control_pressed) { + delete randT; + if (random) { delete reading; } + outSum.close(); + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 0; } - printWeightedFile(); + //finish progress bar + if (random) { reading->finish(); delete reading; } + printWSummaryFile(); + if (phylip) { createPhylipFile(); } + //clear out users groups globaldata->Groups.clear(); delete randT; + if (m->control_pressed) { + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 0; + } + + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } + m->mothurOutEndLine(); + return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the UnifracWeightedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "UnifracWeightedCommand", "execute"); exit(1); } } /***********************************************************/ void UnifracWeightedCommand::printWeightedFile() { try { - //column headers - - out << "Group" << '\t' << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl; - - //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 each group - for (int e = 0; e < numComp; e++) { - //print each line in that group - for (it = validScores[e].begin(); it != validScores[e].end(); it++) { - out << setprecision(6) << groupComb[e] << '\t' << it->first << '\t' << '\t' << uscoreFreq[e][it->first] << '\t' << uCumul[e][it->first] << '\t' << totalrscoreFreq[e][it->first] << '\t' << rCumul[e][it->first] << endl; + for(int a = 0; a < numComp; a++) { + output->initFile(groupComb[a], tags); + //print each line + for (map::iterator 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 UnifracWeightedCommand class Function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the UnifracWeightedCommand class function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "UnifracWeightedCommand", "printWeightedFile"); exit(1); } } @@ -202,8 +306,8 @@ void UnifracWeightedCommand::printWeightedFile() { 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; + m->mothurOut("Tree#\tGroups\tWScore\tWSig"); m->mothurOutEndLine(); //format output outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint); @@ -212,106 +316,144 @@ void UnifracWeightedCommand::printWSummaryFile() { int count = 0; for (int i = 0; i < T.size(); i++) { for (int j = 0; j < numComp; j++) { - outSum << setprecision(6) << i+1 << '\t' << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << WScoreSig[count] << endl; - cout << setprecision(6) << i+1 << '\t' << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << WScoreSig[count] << endl; + if (random) { + if (WScoreSig[count] > (1/(float)iters)) { + outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << WScoreSig[count] << endl; + cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << WScoreSig[count] << endl; + m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t" + toString(WScoreSig[count])); m->mothurOutEndLine(); + }else{ + outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl; + cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl; + m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t<" + toString((1/float(iters)))); m->mothurOutEndLine(); + } + }else{ + outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "0.00" << endl; + cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "0.00" << endl; + m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t0.00"); m->mothurOutEndLine(); + } count++; } } outSum.close(); } 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"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the UnifracWeightedCommand class function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "UnifracWeightedCommand", "printWSummaryFile"); exit(1); } } - /***********************************************************/ -void UnifracWeightedCommand::saveRandomScores() { +void UnifracWeightedCommand::createPhylipFile() { try { - for (int e = 0; e < numComp; e++) { - //update total map with new random scores - for (it = rscoreFreq[e].begin(); it != rscoreFreq[e].end(); it++) { - //does this score already exist in the total map - it2 = totalrscoreFreq[e].find(it->first); - //if yes then add them - if (it2 != totalrscoreFreq[e].end()) { - totalrscoreFreq[e][it->first] += rscoreFreq[e][it->first]; - }else{ //its a new score - totalrscoreFreq[e][it->first] = rscoreFreq[e][it->first]; + int count = 0; + //for each tree + for (int i = 0; i < T.size(); i++) { + + string phylipFileName = outputDir + getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted.dist"; + outputNames.push_back(phylipFileName); + ofstream out; + openOutputFile(phylipFileName, out); + + //output numSeqs + out << globaldata->Groups.size() << endl; + + //make matrix with scores in it + vector< vector > dists; dists.resize(globaldata->Groups.size()); + for (int i = 0; i < globaldata->Groups.size(); i++) { + dists[i].resize(globaldata->Groups.size(), 0.0); + } + + //flip it so you can print it + for (int r=0; rGroups.size(); r++) { + for (int l = r+1; l < globaldata->Groups.size(); l++) { + dists[r][l] = (1.0 - utreeScores[count]); + dists[l][r] = (1.0 - utreeScores[count]); + count++; + } + } + + //output to file + for (int r=0; rGroups.size(); r++) { + //output name + string name = globaldata->Groups[r]; + if (name.length() < 10) { //pad with spaces to make compatible + while (name.length() < 10) { name += " "; } } + out << name << '\t'; + + //output distances + for (int l = 0; l < r; l++) { out << dists[r][l] << '\t'; } + out << endl; } + out.close(); } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function saveRandomScores. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "UnifracWeightedCommand", "createPhylipFile"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the UnifracWeightedCommand class function saveRandomScores. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +/***********************************************************/ +int UnifracWeightedCommand::findIndex(float score, int index) { + try{ + for (int i = 0; i < rScores[index].size(); i++) { + if (rScores[index][i] >= score) { return i; } + } + return rScores[index].size(); + } + catch(exception& e) { + m->errorOut(e, "UnifracWeightedCommand", "findIndex"); exit(1); } } /***********************************************************/ -void UnifracWeightedCommand::setGroups() { + +void UnifracWeightedCommand::calculateFreqsCumuls() { try { - //if the user has not entered specific groups to analyze then do them all - if (globaldata->Groups.size() == 0) { - numGroups = tmap->getNumGroups(); - }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); - } + //clear out old tree values + rScoreFreq.clear(); + rScoreFreq.resize(numComp); + rCumul.clear(); + rCumul.resize(numComp); + validScores.clear(); + + //calculate frequency + for (int f = 0; f < numComp; f++) { + for (int i = 0; i < rScores[f].size(); i++) { //looks like 0,0,1,1,1,2,4,7... you want to make a map that say rScoreFreq[0] = 2, rScoreFreq[1] = 3... + validScores[rScores[f][i]] = rScores[f][i]; + map::iterator it = rScoreFreq[f].find(rScores[f][i]); + if (it != rScoreFreq[f].end()) { + rScoreFreq[f][rScores[f][i]]++; + }else{ + rScoreFreq[f][rScores[f][i]] = 1; } - - //if the user only entered invalid groups - if (globaldata->Groups.size() == 0) { - numGroups = tmap->getNumGroups(); - 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(); - }else { numGroups = globaldata->Groups.size(); } - }else { //users wants all groups - numGroups = tmap->getNumGroups(); - globaldata->Groups.clear(); - globaldata->setGroups(""); } } - //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3; - numComp = 0; - int n = 1; - for (int i=1; iGroups.size() != 0) { - groupComb.push_back(globaldata->Groups[i-1]+globaldata->Groups[l]); - }else { - groupComb.push_back(tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]); - } + //calculate rcumul + 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 (map::iterator it = validScores.begin(); it != validScores.end(); it++) { + //make rscoreFreq map and rCumul + map::iterator 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 } - n++; } + } 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"; + m->errorOut(e, "UnifracWeightedCommand", "calculateFreqsCums"); exit(1); } } +/***********************************************************/ + + + + +