X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracunweightedcommand.cpp;h=b80a3abb4bb76bd0a5da3afa5548df0771797e45;hb=794b3f789d6160c99b75edb9cf9af5cf3df4b9da;hp=28bc2ac55f64ebb02185a55d43ba9ea8e6faa03b;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp index 28bc2ac..b80a3ab 100644 --- a/unifracunweightedcommand.cpp +++ b/unifracunweightedcommand.cpp @@ -9,6 +9,59 @@ #include "unifracunweightedcommand.h" +//********************************************************************************************************************** +vector UnifracUnweightedCommand::getValidParameters(){ + try { + string Array[] = {"groups","iters","distance","random", "processors","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "UnifracUnweightedCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +UnifracUnweightedCommand::UnifracUnweightedCommand(){ + try { + globaldata = GlobalData::getInstance(); + abort = true; + //initialize outputTypes + vector tempOutNames; + outputTypes["unweighted"] = tempOutNames; + outputTypes["uwsummary"] = tempOutNames; + outputTypes["phylip"] = tempOutNames; + outputTypes["column"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "UnifracUnweightedCommand", "UnifracUnweightedCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector UnifracUnweightedCommand::getRequiredParameters(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "UnifracUnweightedCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector UnifracUnweightedCommand::getRequiredFiles(){ + try { + string Array[] = {"tree","group"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + + return myArray; + } + catch(exception& e) { + m->errorOut(e, "UnifracUnweightedCommand", "getRequiredFiles"); + exit(1); + } +} /***********************************************************/ UnifracUnweightedCommand::UnifracUnweightedCommand(string option) { try { @@ -21,7 +74,7 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option) { else { //valid paramters for this command - string Array[] = {"groups","iters","distance","random", "outputdir","inputdir"}; + string Array[] = {"groups","iters","distance","random", "processors","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -34,13 +87,20 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + //initialize outputTypes + vector tempOutNames; + outputTypes["unweighted"] = tempOutNames; + outputTypes["uwsummary"] = tempOutNames; + outputTypes["phylip"] = tempOutNames; + outputTypes["column"] = tempOutNames; + if (globaldata->gTree.size() == 0) {//no trees were read m->mothurOut("You must execute the read.tree command, before you may execute the unifrac.unweighted 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 + outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it } //check for optional parameter and set defaults @@ -48,34 +108,41 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option) { groups = validParameter.validFile(parameters, "groups", false); if (groups == "not found") { groups = ""; } else { - splitAtDash(groups, Groups); + m->splitAtDash(groups, Groups); globaldata->Groups = Groups; } 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); + string temp = validParameter.validFile(parameters, "distance", false); + if (temp == "not found") { phylip = false; outputForm = ""; } + else{ + if ((temp == "lt") || (temp == "column") || (temp == "square")) { phylip = true; outputForm = temp; } + else { m->mothurOut("Options for distance are: lt, square, or column. Using lt."); m->mothurOutEndLine(); phylip = true; outputForm = "lt"; } + } + + temp = validParameter.validFile(parameters, "random", false); if (temp == "not found") { temp = "f"; } + random = m->isTrue(temp); - temp = validParameter.validFile(parameters, "random", false); if (temp == "not found") { temp = "true"; } - random = isTrue(temp); + temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; } + convert(temp, processors); 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); + m->splitAtDash(groups, Groups); globaldata->Groups = Groups; } if (abort == false) { T = globaldata->gTree; tmap = globaldata->gTreemap; - sumFile = outputDir + getSimpleName(globaldata->getTreeFile()) + ".uwsummary"; - outputNames.push_back(sumFile); - openOutputFile(sumFile, outSum); + sumFile = outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".uwsummary"; + outputNames.push_back(sumFile); outputTypes["uwsummary"].push_back(sumFile); + m->openOutputFile(sumFile, outSum); util = new SharedUtil(); util->setGroups(globaldata->Groups, tmap->namesOfGroups, allGroups, numGroups, "unweighted"); //sets the groups the user wants to analyze @@ -101,11 +168,12 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option) { void UnifracUnweightedCommand::help(){ try { m->mothurOut("The unifrac.unweighted command can only be executed after a successful read.tree command.\n"); - m->mothurOut("The unifrac.unweighted command parameters are groups, iters, distance and random. No parameters are required.\n"); + m->mothurOut("The unifrac.unweighted command parameters are groups, iters, distance, processors 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 1 valid group.\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 distance parameter allows you to create a distance file from the results. The default is false. You may set distance to lt, square or column.\n"); + m->mothurOut("The random parameter allows you to shut off the comparison to random trees. The default is false, meaning compare don't your trees with randomly generated trees.\n"); + m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n"); m->mothurOut("The unifrac.unweighted command should be in the following format: unifrac.unweighted(groups=yourGroups, iters=yourIters).\n"); m->mothurOut("Example unifrac.unweighted(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"); @@ -125,6 +193,8 @@ int UnifracUnweightedCommand::execute() { if (abort == true) { return 0; } + int start = time(NULL); + 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 @@ -143,8 +213,9 @@ int UnifracUnweightedCommand::execute() { counter = 0; if (random) { - output = new ColumnFile(outputDir + getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".unweighted", itersString); - outputNames.push_back(outputDir + getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".unweighted"); + output = new ColumnFile(outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".unweighted", itersString); + outputNames.push_back(outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".unweighted"); + outputTypes["unweighted"].push_back(outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".unweighted"); } @@ -154,14 +225,9 @@ int UnifracUnweightedCommand::execute() { utreeScores.resize(numComp); UWScoreSig.resize(numComp); - userData = unweighted->getValues(T[i]); //userData[0] = unweightedscore - - if (m->control_pressed) { - if (random) { delete output; } - outSum.close(); - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } - return 0; - } + userData = unweighted->getValues(T[i], processors, outputDir); //userData[0] = unweightedscore + + if (m->control_pressed) { if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }return 0; } //output scores for each combination for(int k = 0; k < numComp; k++) { @@ -171,18 +237,14 @@ int UnifracUnweightedCommand::execute() { //add users score to validscores validScores[userData[k]] = userData[k]; } - + //get unweighted scores for random trees - if random is false iters = 0 for (int j = 0; j < iters; j++) { + //we need a different getValues because when we swap the labels we only want to swap those in each pairwise comparison - randomData = unweighted->getValues(T[i], "", ""); + randomData = unweighted->getValues(T[i], "", "", processors, outputDir); - if (m->control_pressed) { - if (random) { delete output; } - outSum.close(); - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } - return 0; - } + if (m->control_pressed) { if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } for(int k = 0; k < numComp; k++) { //add trees unweighted score to map of scores @@ -196,31 +258,30 @@ int UnifracUnweightedCommand::execute() { //add randoms score to validscores validScores[randomData[k]] = randomData[k]; } + + //report progress + m->mothurOut("Iter: " + toString(j+1)); m->mothurOutEndLine(); } - + 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 - } - if (random) { UWScoreSig[a].push_back(rCumul[a][userData[a]]); } - else { UWScoreSig[a].push_back(0.0); } + if (random) { + //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 + } + UWScoreSig[a].push_back(rCumul[a][userData[a]]); + }else { UWScoreSig[a].push_back(0.0); } + } - - if (m->control_pressed) { - if (random) { delete output; } - outSum.close(); - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } - return 0; - } + if (m->control_pressed) { if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } //print output files printUWSummaryFile(i); @@ -239,6 +300,8 @@ int UnifracUnweightedCommand::execute() { if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run unifrac.unweighted."); m->mothurOutEndLine(); + m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } @@ -295,16 +358,16 @@ void UnifracUnweightedCommand::printUWSummaryFile(int i) { 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; - m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t" + toString(UWScoreSig[a][0])); m->mothurOutEndLine(); + m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t" + toString(UWScoreSig[a][0])+ "\n"); }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; - m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t<" + toString((1/float(iters)))); m->mothurOutEndLine(); + m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t<" + toString((1/float(iters))) + "\n"); } }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; - m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t0.00"); m->mothurOutEndLine(); + m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t0.00\n"); } } @@ -317,15 +380,23 @@ void UnifracUnweightedCommand::printUWSummaryFile(int i) { /***********************************************************/ void UnifracUnweightedCommand::createPhylipFile(int i) { try { - string phylipFileName = outputDir + getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".unweighted.dist"; - outputNames.push_back(phylipFileName); + string phylipFileName; + if ((outputForm == "lt") || (outputForm == "square")) { + phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".unweighted.phylip.dist"; + outputNames.push_back(phylipFileName); outputTypes["phylip"].push_back(phylipFileName); + }else { //column + phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".unweighted.column.dist"; + outputNames.push_back(phylipFileName); outputTypes["column"].push_back(phylipFileName); + } ofstream out; - openOutputFile(phylipFileName, out); - - //output numSeqs - out << globaldata->Groups.size() << endl; - + m->openOutputFile(phylipFileName, out); + + if ((outputForm == "lt") || (outputForm == "square")) { + //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++) { @@ -336,8 +407,8 @@ void UnifracUnweightedCommand::createPhylipFile(int i) { 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]); + dists[r][l] = utreeScores[count][0]; + dists[l][r] = utreeScores[count][0]; count++; } } @@ -349,11 +420,30 @@ void UnifracUnweightedCommand::createPhylipFile(int i) { 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; + if (outputForm == "lt") { + out << name << '\t'; + + //output distances + for (int l = 0; l < r; l++) { out << dists[r][l] << '\t'; } + out << endl; + }else if (outputForm == "square") { + out << name << '\t'; + + //output distances + for (int l = 0; l < globaldata->Groups.size(); l++) { out << dists[r][l] << '\t'; } + out << endl; + }else{ + //output distances + for (int l = 0; l < r; l++) { + string otherName = globaldata->Groups[l]; + if (otherName.length() < 10) { //pad with spaces to make compatible + while (otherName.length() < 10) { otherName += " "; } + } + + out << name << '\t' << otherName << dists[r][l] << endl; + } + } } out.close(); }