X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracunweightedcommand.cpp;h=77cd4d7d686ed5607c11eb07d2245c62f2ef2deb;hb=438aa88dbc092d9c1c80ec3fa20c8e47f97101c4;hp=bc8eb477f088ade4a8e8e0cb4c1c94930d78dc9b;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp index bc8eb47..77cd4d7 100644 --- a/unifracunweightedcommand.cpp +++ b/unifracunweightedcommand.cpp @@ -10,51 +10,71 @@ #include "unifracunweightedcommand.h" /***********************************************************/ -UnifracUnweightedCommand::UnifracUnweightedCommand(string option) { +UnifracUnweightedCommand::UnifracUnweightedCommand(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"}; + string Array[] = {"groups","iters","distance","random", "outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - parser = new OptionParser(); - parser->parse(option, parameters); delete parser; + OptionParser parser(option); + map parameters = parser.getParameters(); - ValidParameters* validParameter = new ValidParameters(); + ValidParameters validParameter; //check to make sure all parameters are valid for command - for (it4 = parameters.begin(); it4 != parameters.end(); it4++) { - if (validParameter->isValidParameter(it4->first, myArray, it4->second) != true) { abort = true; } + 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 - cout << "You must execute the read.tree command, before you may execute the unifrac.unweighted command." << endl; abort = true; } - + 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 + } + //check for optional parameter and set defaults // ...at some point should added some additional type checking... - groups = validParameter->validFile(parameters, "groups", false); + groups = validParameter.validFile(parameters, "groups", false); if (groups == "not found") { groups = ""; } else { splitAtDash(groups, Groups); 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); - delete validParameter; + 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; - sumFile = globaldata->getTreeFile() + ".uwsummary"; + sumFile = outputDir + getSimpleName(globaldata->getTreeFile()) + ".uwsummary"; + outputNames.push_back(sumFile); openOutputFile(sumFile, outSum); util = new SharedUtil(); @@ -71,11 +91,7 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option) { } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function UnifracUnweightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the UnifracUnweightedCommand class function UnifracUnweightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "UnifracUnweightedCommand", "UnifracUnweightedCommand"); exit(1); } } @@ -84,24 +100,22 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option) { void UnifracUnweightedCommand::help(){ try { - cout << "The unifrac.unweighted command can only be executed after a successful read.tree command." << "\n"; - cout << "The unifrac.unweighted command parameters are groups and iters. No parameters are required." << "\n"; - cout << "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"; - cout << "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"; - cout << "The unifrac.unweighted command should be in the following format: unifrac.unweighted(groups=yourGroups, iters=yourIters)." << "\n"; - cout << "Example unifrac.unweighted(groups=A-B-C, iters=500)." << "\n"; - cout << "The default value for groups is all the groups in your groupfile, and iters is 1000." << "\n"; - cout << "The unifrac.unweighted command output two files: .unweighted and .uwsummary their descriptions are in the manual." << "\n"; - cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n"; + 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 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 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"); + m->mothurOut("The unifrac.unweighted command output two files: .unweighted and .uwsummary 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) { - cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "UnifracUnweightedCommand", "help"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the UnifracUnweightedCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } @@ -116,13 +130,23 @@ int UnifracUnweightedCommand::execute() { //create new tree with same num nodes and leaves as users outSum << "Tree#" << '\t' << "Groups" << '\t' << "UWScore" <<'\t' << "UWSig" << endl; - cout << "Tree#" << '\t' << "Groups" << '\t' << "UWScore" << '\t' << "UWSig" << endl; + m->mothurOut("Tree#\tGroups\tUWScore\tUWSig"); m->mothurOutEndLine(); //get pscores for users trees for (int i = 0; i < T.size(); i++) { + if (m->control_pressed) { + outSum.close(); + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 0; + } + counter = 0; - output = new ColumnFile(globaldata->getTreeFile() + toString(i+1) + ".unweighted", itersString); + 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"); + } + //get unweighted for users tree rscoreFreq.resize(numComp); @@ -132,22 +156,38 @@ int UnifracUnweightedCommand::execute() { 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; + } + //output scores for each combination 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 + //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 parwise comparison + //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], "", ""); + 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 - it2 = rscoreFreq[k].find(randomData[k]); - if (it2 != rscoreFreq[k].end()) {//already have that score + map::iterator it = rscoreFreq[k].find(randomData[k]); + if (it != rscoreFreq[k].end()) {//already have that score rscoreFreq[k][randomData[k]]++; }else{//first time we have seen this score rscoreFreq[k][randomData[k]] = 1; @@ -156,29 +196,37 @@ int UnifracUnweightedCommand::execute() { //add randoms score to validscores validScores[randomData[k]] = randomData[k]; } - } 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 (it = validScores.begin(); it != validScores.end(); it++) { + for (map::iterator it = validScores.begin(); it != validScores.end(); it++) { //make rscoreFreq map and rCumul - it2 = rscoreFreq[a].find(it->first); + 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]]); + + if (random) { UWScoreSig[a].push_back(rCumul[a][userData[a]]); } + else { UWScoreSig[a].push_back(0.0); } } - - - - printUnweightedFile(); + + + 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); + if (random) { printUnweightedFile(); delete output; } + if (phylip) { createPhylipFile(i); } - delete output; rscoreFreq.clear(); rCumul.clear(); validScores.clear(); @@ -186,19 +234,21 @@ int UnifracUnweightedCommand::execute() { UWScoreSig.clear(); } - //reset groups parameter - globaldata->Groups.clear(); + outSum.close(); + 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 UnifracUnweightedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the UnifracUnweightedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "UnifracUnweightedCommand", "execute"); exit(1); } } @@ -207,13 +257,15 @@ 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 (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]); + 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(); } @@ -221,11 +273,7 @@ void UnifracUnweightedCommand::printUnweightedFile() { } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function printUnweightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the UnifracUnweightedCommand class function printUnweightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "UnifracUnweightedCommand", "printUnweightedFile"); exit(1); } } @@ -241,28 +289,80 @@ void UnifracUnweightedCommand::printUWSummaryFile(int i) { for(int a = 0; a < numComp; a++) { outSum << i+1 << '\t'; - cout << i+1 << '\t'; + m->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; - }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; + 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; + m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t" + toString(UWScoreSig[a][0])); m->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; + m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t<" + toString((1/float(iters)))); m->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; + m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t0.00"); m->mothurOutEndLine(); } } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function printUWSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "UnifracUnweightedCommand", "printUWSummaryFile"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the UnifracUnweightedCommand class function printUWSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +/***********************************************************/ +void UnifracUnweightedCommand::createPhylipFile(int i) { + try { + string phylipFileName = outputDir + getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".unweighted.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 + int count = 0; + for (int r=0; rGroups.size(); r++) { + for (int l = r+1; l < globaldata->Groups.size(); l++) { + dists[r][l] = utreeScores[count][0]; + dists[l][r] = utreeScores[count][0]; + 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) { + m->errorOut(e, "UnifracUnweightedCommand", "createPhylipFile"); exit(1); } } - /***********************************************************/ +