X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=unifracunweightedcommand.cpp;h=b551e5f20f7a4ed326dbb1d40b7ce9913826a2b3;hb=d5bf2c1354d0811a33394d918b15620606560d58;hp=326e695b20965c451ac17fe5a70bc11b923d6c3e;hpb=f27b66ce6415eb14c434f9850019c7cf140e023e;p=mothur.git diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp index 326e695..b551e5f 100644 --- a/unifracunweightedcommand.cpp +++ b/unifracunweightedcommand.cpp @@ -21,7 +21,7 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option) { else { //valid paramters for this command - string Array[] = {"groups","iters"}; + string Array[] = {"groups","iters","distance","random"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -46,10 +46,24 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option) { globaldata->Groups = Groups; } - itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; } + 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 user selects distance = true and no groups it won't calc the pairwise + if ((phylip) && (Groups.size() == 0)) { + groups = "all"; + splitAtDash(groups, Groups); + globaldata->Groups = Groups; + } + if (abort == false) { T = globaldata->gTree; tmap = globaldata->gTreemap; @@ -80,9 +94,11 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option) { void UnifracUnweightedCommand::help(){ try { mothurOut("The unifrac.unweighted command can only be executed after a successful read.tree command.\n"); - mothurOut("The unifrac.unweighted command parameters are groups and iters. No parameters are required.\n"); + mothurOut("The unifrac.unweighted command parameters are groups, iters, distance and random. No parameters are required.\n"); mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 1 valid group.\n"); 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"); + mothurOut("The distance parameter allows you to create a distance file from the results. The default is false.\n"); + 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"); mothurOut("The unifrac.unweighted command should be in the following format: unifrac.unweighted(groups=yourGroups, iters=yourIters).\n"); mothurOut("Example unifrac.unweighted(groups=A-B-C, iters=500).\n"); mothurOut("The default value for groups is all the groups in your groupfile, and iters is 1000.\n"); @@ -113,7 +129,7 @@ int UnifracUnweightedCommand::execute() { for (int i = 0; i < T.size(); i++) { counter = 0; - output = new ColumnFile(globaldata->getTreeFile() + toString(i+1) + ".unweighted", itersString); + if (random) { output = new ColumnFile(globaldata->getTreeFile() + toString(i+1) + ".unweighted", itersString); } //get unweighted for users tree rscoreFreq.resize(numComp); @@ -127,7 +143,9 @@ int UnifracUnweightedCommand::execute() { for(int k = 0; k < numComp; k++) { //saves users score utreeScores[k].push_back(userData[k]); - + + //add users score to validscores + validScores[userData[k]] = userData[k]; } //get unweighted scores for random trees @@ -160,15 +178,16 @@ int UnifracUnweightedCommand::execute() { 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]]); + + if (random) { UWScoreSig[a].push_back(rCumul[a][userData[a]]); } + else { UWScoreSig[a].push_back(0.0); } } - - - printUnweightedFile(); + //print output files printUWSummaryFile(i); + if (random) { printUnweightedFile(); delete output; } + if (phylip) { createPhylipFile(i); } - delete output; rscoreFreq.clear(); rCumul.clear(); validScores.clear(); @@ -193,13 +212,15 @@ void UnifracUnweightedCommand::printUnweightedFile() { try { vector data; vector tags; - tags.push_back("Score"); tags.push_back("RandFreq"); tags.push_back("RandCumul"); + 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 (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]); + data.push_back(it->first); data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]); output->output(data); data.clear(); } @@ -225,14 +246,20 @@ void UnifracUnweightedCommand::printUWSummaryFile(int i) { outSum << i+1 << '\t'; mothurOut(toString(i+1) + "\t"); - if (UWScoreSig[a][0] > (1/(float)iters)) { - outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl; - cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl; - mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t" + toString(UWScoreSig[a][0])); mothurOutEndLine(); - }else { - outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl; - cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl; - mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t<" + toString((1/float(iters)))); mothurOutEndLine(); + if (random) { + if (UWScoreSig[a][0] > (1/(float)iters)) { + outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl; + cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl; + mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t" + toString(UWScoreSig[a][0])); mothurOutEndLine(); + }else { + outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl; + cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl; + mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t<" + toString((1/float(iters)))); mothurOutEndLine(); + } + }else{ + outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << "0.00" << endl; + cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << "0.00" << endl; + mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t0.00"); mothurOutEndLine(); } } @@ -242,7 +269,49 @@ void UnifracUnweightedCommand::printUWSummaryFile(int i) { exit(1); } } - /***********************************************************/ +void UnifracUnweightedCommand::createPhylipFile(int i) { + try { + string phylipFileName = globaldata->getTreeFile() + toString(i+1) + ".unweighted.dist"; + 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 + int count = 0; + for (int r=0; rGroups.size(); r++) { + for (int l = r+1; l < globaldata->Groups.size(); l++) { + dists[r][l] = (1.0 - utreeScores[count][0]); + dists[l][r] = (1.0 - utreeScores[count][0]); + count++; + } + } + + //output to file + for (int r=0; rGroups.size(); r++) { + //output name + out << globaldata->Groups[r] << '\t'; + + //output distances + for (int l = 0; l < r; l++) { out << dists[r][l] << '\t'; } + out << endl; + } + out.close(); + } + catch(exception& e) { + errorOut(e, "UnifracUnweightedCommand", "createPhylipFile"); + exit(1); + } +} +/***********************************************************/ +