X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.cpp;h=a9f9570e771b7c45c95f96e9a162ddc9ec8dfdb8;hb=df92022fc75c08b91cefa2c6ca4fd7b23eb480b0;hp=fb3eb3ca2158d766a57b1f22c3a9c57bfe573370;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2;p=mothur.git diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp index fb3eb3c..a9f9570 100644 --- a/unifracweightedcommand.cpp +++ b/unifracweightedcommand.cpp @@ -21,7 +21,7 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) { else { //valid paramters for this command - string Array[] = {"groups","iters"}; + string Array[] = {"groups","iters","distance","random","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -36,7 +36,13 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) { if (globaldata->gTree.size() == 0) {//no trees were read mothurOut("You must execute the read.tree command, before you may execute the unifrac.weighted command."); 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); @@ -48,12 +54,20 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) { 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 = globaldata->getTreeFile() + ".wsummary"; + sumFile = outputDir + getSimpleName(globaldata->getTreeFile()) + ".wsummary"; openOutputFile(sumFile, outSum); util = new SharedUtil(); @@ -78,9 +92,11 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) { void UnifracWeightedCommand::help(){ try { mothurOut("The unifrac.weighted command can only be executed after a successful read.tree command.\n"); - mothurOut("The unifrac.weighted command parameters are groups and iters. No parameters are required.\n"); + mothurOut("The unifrac.weighted 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 2 valid groups.\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.weighted command should be in the following format: unifrac.weighted(groups=yourGroups, iters=yourIters).\n"); mothurOut("Example unifrac.weighted(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"); @@ -100,7 +116,7 @@ int UnifracWeightedCommand::execute() { if (abort == true) { return 0; } Progress* reading; - reading = new Progress("Comparing to random:", iters); + 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... @@ -115,7 +131,7 @@ int UnifracWeightedCommand::execute() { rScores.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC... uScores.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC... - output = new ColumnFile(globaldata->getTreeFile() + toString(i+1) + ".weighted", itersString); + if (random) { output = new ColumnFile(outputDir + getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted", itersString); } userData = weighted->getValues(T[i]); //userData[0] = weightedscore @@ -154,26 +170,28 @@ int UnifracWeightedCommand::execute() { //removeValidScoresDuplicates(); //find the signifigance of the score for summary file - for (int f = 0; f < numComp; f++) { - //sort random scores - sort(rScores[f].begin(), rScores[f].end()); + 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) { mothurOut("error in UnifracWeightedCommand"); 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); + } - //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) { mothurOut("error in UnifracWeightedCommand"); 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; } - //out << "Tree# " << i << endl; - calculateFreqsCumuls(); - printWeightedFile(); - - delete output; - //clear data rScores.clear(); uScores.clear(); @@ -181,11 +199,12 @@ int UnifracWeightedCommand::execute() { } //finish progress bar - reading->finish(); - delete reading; + if (random) { reading->finish(); delete reading; } printWSummaryFile(); + if (phylip) { createPhylipFile(); } + //clear out users groups globaldata->Groups.clear(); @@ -238,14 +257,20 @@ void UnifracWeightedCommand::printWSummaryFile() { int count = 0; for (int i = 0; i < T.size(); i++) { for (int j = 0; j < numComp; j++) { - 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; - mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t" + toString(WScoreSig[count])); mothurOutEndLine(); + 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; + mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t" + toString(WScoreSig[count])); 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; + mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t<" + toString((1/float(iters)))); 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; - mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t<" + toString((1/float(iters)))); mothurOutEndLine(); + 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; + mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t0.00"); mothurOutEndLine(); } count++; } @@ -257,7 +282,56 @@ void UnifracWeightedCommand::printWSummaryFile() { exit(1); } } +/***********************************************************/ +void UnifracWeightedCommand::createPhylipFile() { + try { + 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"; + 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) { + errorOut(e, "UnifracWeightedCommand", "createPhylipFile"); + exit(1); + } +} /***********************************************************/ int UnifracWeightedCommand::findIndex(float score, int index) { try{