2 * unifracunweightedcommand.cpp
5 * Created by Sarah Westcott on 2/9/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "unifracunweightedcommand.h"
12 //**********************************************************************************************************************
13 vector<string> UnifracUnweightedCommand::setParameters(){
15 CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptree);
16 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
17 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
18 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
19 CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
20 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
21 CommandParameter prandom("random", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(prandom);
22 CommandParameter pdistance("distance", "Multiple", "column-lt-square", "column", "", "", "",false,false); parameters.push_back(pdistance);
23 CommandParameter proot("root", "Boolean", "F", "", "", "", "",false,false); parameters.push_back(proot);
24 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
25 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
27 vector<string> myArray;
28 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
32 m->errorOut(e, "UnifracUnweightedCommand", "setParameters");
36 //**********************************************************************************************************************
37 string UnifracUnweightedCommand::getHelpString(){
39 string helpString = "";
40 helpString += "The unifrac.unweighted command parameters are tree, group, name, groups, iters, distance, processors, root and random. tree parameter is required unless you have valid current tree file.\n";
41 helpString += "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";
42 helpString += "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";
43 helpString += "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";
44 helpString += "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";
45 helpString += "The root parameter allows you to include the entire root in your calculations. The default is false, meaning stop at the root for this comparision instead of the root of the entire tree.\n";
46 helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
47 helpString += "The unifrac.unweighted command should be in the following format: unifrac.unweighted(groups=yourGroups, iters=yourIters).\n";
48 helpString += "Example unifrac.unweighted(groups=A-B-C, iters=500).\n";
49 helpString += "The default value for groups is all the groups in your groupfile, and iters is 1000.\n";
50 helpString += "The unifrac.unweighted command output two files: .unweighted and .uwsummary their descriptions are in the manual.\n";
51 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
55 m->errorOut(e, "UnifracUnweightedCommand", "getHelpString");
59 //**********************************************************************************************************************
60 UnifracUnweightedCommand::UnifracUnweightedCommand(){
62 abort = true; calledHelp = true;
64 vector<string> tempOutNames;
65 outputTypes["unweighted"] = tempOutNames;
66 outputTypes["uwsummary"] = tempOutNames;
67 outputTypes["phylip"] = tempOutNames;
68 outputTypes["column"] = tempOutNames;
71 m->errorOut(e, "UnifracUnweightedCommand", "UnifracUnweightedCommand");
75 /***********************************************************/
76 UnifracUnweightedCommand::UnifracUnweightedCommand(string option) {
78 abort = false; calledHelp = false;
81 //allow user to run help
82 if(option == "help") { help(); abort = true; calledHelp = true; }
83 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
86 vector<string> myArray = setParameters();
88 OptionParser parser(option);
89 map<string,string> parameters = parser.getParameters();
90 map<string,string>::iterator it;
92 ValidParameters validParameter;
94 //check to make sure all parameters are valid for command
95 for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
96 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
99 //initialize outputTypes
100 vector<string> tempOutNames;
101 outputTypes["unweighted"] = tempOutNames;
102 outputTypes["uwsummary"] = tempOutNames;
103 outputTypes["phylip"] = tempOutNames;
104 outputTypes["column"] = tempOutNames;
106 //if the user changes the input directory command factory will send this info to us in the output parameter
107 string inputDir = validParameter.validFile(parameters, "inputdir", false);
108 if (inputDir == "not found"){ inputDir = ""; }
111 it = parameters.find("tree");
112 //user has given a template file
113 if(it != parameters.end()){
114 path = m->hasPath(it->second);
115 //if the user has not given a path then, add inputdir. else leave path alone.
116 if (path == "") { parameters["tree"] = inputDir + it->second; }
119 it = parameters.find("group");
120 //user has given a template file
121 if(it != parameters.end()){
122 path = m->hasPath(it->second);
123 //if the user has not given a path then, add inputdir. else leave path alone.
124 if (path == "") { parameters["group"] = inputDir + it->second; }
127 it = parameters.find("name");
128 //user has given a template file
129 if(it != parameters.end()){
130 path = m->hasPath(it->second);
131 //if the user has not given a path then, add inputdir. else leave path alone.
132 if (path == "") { parameters["name"] = inputDir + it->second; }
138 m->namesOfGroups.clear();
139 m->Treenames.clear();
142 //check for required parameters
143 treefile = validParameter.validFile(parameters, "tree", true);
144 if (treefile == "not open") { abort = true; }
145 else if (treefile == "not found") { //if there is a current design file, use it
146 treefile = m->getTreeFile();
147 if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
148 else { m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }
149 }else { m->setTreeFile(treefile); }
151 //check for required parameters
152 groupfile = validParameter.validFile(parameters, "group", true);
153 if (groupfile == "not open") { abort = true; }
154 else if (groupfile == "not found") { groupfile = ""; }
155 else { m->setGroupFile(groupfile); }
157 namefile = validParameter.validFile(parameters, "name", true);
158 if (namefile == "not open") { abort = true; }
159 else if (namefile == "not found") { namefile = ""; }
160 else { m->setNameFile(namefile); }
162 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
164 //check for optional parameter and set defaults
165 // ...at some point should added some additional type checking...
166 groups = validParameter.validFile(parameters, "groups", false);
167 if (groups == "not found") { groups = ""; }
169 m->splitAtDash(groups, Groups);
173 itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; }
174 convert(itersString, iters);
176 string temp = validParameter.validFile(parameters, "distance", false);
177 if (temp == "not found") { phylip = false; outputForm = ""; }
179 if ((temp == "lt") || (temp == "column") || (temp == "square")) { phylip = true; outputForm = temp; }
180 else { m->mothurOut("Options for distance are: lt, square, or column. Using lt."); m->mothurOutEndLine(); phylip = true; outputForm = "lt"; }
183 temp = validParameter.validFile(parameters, "random", false); if (temp == "not found") { temp = "f"; }
184 random = m->isTrue(temp);
186 temp = validParameter.validFile(parameters, "root", false); if (temp == "not found") { temp = "F"; }
187 includeRoot = m->isTrue(temp);
189 temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
190 m->setProcessors(temp);
191 convert(temp, processors);
193 if (!random) { iters = 0; } //turn off random calcs
195 //if user selects distance = true and no groups it won't calc the pairwise
196 if ((phylip) && (Groups.size() == 0)) {
198 m->splitAtDash(groups, Groups);
204 catch(exception& e) {
205 m->errorOut(e, "UnifracUnweightedCommand", "UnifracUnweightedCommand");
210 /***********************************************************/
211 int UnifracUnweightedCommand::execute() {
214 if (abort == true) { if (calledHelp) { return 0; } return 2; }
216 m->setTreeFile(treefile);
218 if (groupfile != "") {
219 //read in group map info.
220 tmap = new TreeMap(groupfile);
222 }else{ //fake out by putting everyone in one group
223 Tree* tree = new Tree(treefile); delete tree; //extracts names from tree to make faked out groupmap
224 tmap = new TreeMap();
226 for (int i = 0; i < m->Treenames.size(); i++) { tmap->addSeq(m->Treenames[i], "Group1"); }
229 if (namefile != "") { readNamesFile(); }
231 read = new ReadNewickTree(treefile);
232 int readOk = read->read(tmap);
234 if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete tmap; delete read; return 0; }
236 read->AssembleTrees();
237 T = read->getTrees();
240 //make sure all files match
241 //if you provide a namefile we will use the numNames in the namefile as long as the number of unique match the tree names size.
243 if (namefile != "") {
244 if (numUniquesInName == m->Treenames.size()) { numNamesInTree = nameMap.size(); }
245 else { numNamesInTree = m->Treenames.size(); }
246 }else { numNamesInTree = m->Treenames.size(); }
249 //output any names that are in group file but not in tree
250 if (numNamesInTree < tmap->getNumSeqs()) {
251 for (int i = 0; i < tmap->namesOfSeqs.size(); i++) {
252 //is that name in the tree?
254 for (int j = 0; j < m->Treenames.size(); j++) {
255 if (tmap->namesOfSeqs[i] == m->Treenames[j]) { break; } //found it
259 if (m->control_pressed) {
260 delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
261 for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
266 //then you did not find it so report it
267 if (count == m->Treenames.size()) {
268 //if it is in your namefile then don't remove
269 map<string, string>::iterator it = nameMap.find(tmap->namesOfSeqs[i]);
271 if (it == nameMap.end()) {
272 m->mothurOut(tmap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); m->mothurOutEndLine();
273 tmap->removeSeq(tmap->namesOfSeqs[i]);
274 i--; //need this because removeSeq removes name from namesOfSeqs
280 sumFile = outputDir + m->getSimpleName(treefile) + ".uwsummary";
281 outputNames.push_back(sumFile); outputTypes["uwsummary"].push_back(sumFile);
282 m->openOutputFile(sumFile, outSum);
284 util = new SharedUtil();
285 util->setGroups(m->Groups, tmap->namesOfGroups, allGroups, numGroups, "unweighted"); //sets the groups the user wants to analyze
286 util->getCombos(groupComb, m->Groups, numComp);
289 if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
291 unweighted = new Unweighted(tmap, includeRoot);
293 int start = time(NULL);
295 userData.resize(numComp,0); //data[0] = unweightedscore
296 randomData.resize(numComp,0); //data[0] = unweightedscore
297 //create new tree with same num nodes and leaves as users
299 if (numComp < processors) { processors = numComp; }
301 outSum << "Tree#" << '\t' << "Groups" << '\t' << "UWScore" <<'\t';
302 m->mothurOut("Tree#\tGroups\tUWScore\t");
303 if (random) { outSum << "UWSig"; m->mothurOut("UWSig"); }
304 outSum << endl; m->mothurOutEndLine();
306 //get pscores for users trees
307 for (int i = 0; i < T.size(); i++) {
308 if (m->control_pressed) {
309 delete tmap; delete unweighted;
310 for (int i = 0; i < T.size(); i++) { delete T[i]; }
312 for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
319 output = new ColumnFile(outputDir + m->getSimpleName(treefile) + toString(i+1) + ".unweighted", itersString);
320 outputNames.push_back(outputDir + m->getSimpleName(treefile) + toString(i+1) + ".unweighted");
321 outputTypes["unweighted"].push_back(outputDir + m->getSimpleName(treefile) + toString(i+1) + ".unweighted");
325 //get unweighted for users tree
326 rscoreFreq.resize(numComp);
327 rCumul.resize(numComp);
328 utreeScores.resize(numComp);
329 UWScoreSig.resize(numComp);
331 userData = unweighted->getValues(T[i], processors, outputDir); //userData[0] = unweightedscore
333 if (m->control_pressed) { delete tmap; delete unweighted;
334 for (int i = 0; i < T.size(); i++) { delete T[i]; }if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }return 0; }
336 //output scores for each combination
337 for(int k = 0; k < numComp; k++) {
339 utreeScores[k].push_back(userData[k]);
341 //add users score to validscores
342 validScores[userData[k]] = userData[k];
345 //get unweighted scores for random trees - if random is false iters = 0
346 for (int j = 0; j < iters; j++) {
348 //we need a different getValues because when we swap the labels we only want to swap those in each pairwise comparison
349 randomData = unweighted->getValues(T[i], "", "", processors, outputDir);
351 if (m->control_pressed) { delete tmap; delete unweighted;
352 for (int i = 0; i < T.size(); i++) { delete T[i]; }if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
354 for(int k = 0; k < numComp; k++) {
355 //add trees unweighted score to map of scores
356 map<float,float>::iterator it = rscoreFreq[k].find(randomData[k]);
357 if (it != rscoreFreq[k].end()) {//already have that score
358 rscoreFreq[k][randomData[k]]++;
359 }else{//first time we have seen this score
360 rscoreFreq[k][randomData[k]] = 1;
363 //add randoms score to validscores
364 validScores[randomData[k]] = randomData[k];
368 // m->mothurOut("Iter: " + toString(j+1)); m->mothurOutEndLine();
371 for(int a = 0; a < numComp; a++) {
372 float rcumul = 1.0000;
375 //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
376 for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) {
377 //make rscoreFreq map and rCumul
378 map<float,float>::iterator it2 = rscoreFreq[a].find(it->first);
379 rCumul[a][it->first] = rcumul;
380 //get percentage of random trees with that info
381 if (it2 != rscoreFreq[a].end()) { rscoreFreq[a][it->first] /= iters; rcumul-= it2->second; }
382 else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
384 UWScoreSig[a].push_back(rCumul[a][userData[a]]);
385 }else { UWScoreSig[a].push_back(0.0); }
389 if (m->control_pressed) { delete tmap; delete unweighted;
390 for (int i = 0; i < T.size(); i++) { delete T[i]; }if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
393 printUWSummaryFile(i);
394 if (random) { printUnweightedFile(); delete output; }
395 if (phylip) { createPhylipFile(i); }
407 delete tmap; delete unweighted;
408 for (int i = 0; i < T.size(); i++) { delete T[i]; }
410 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
412 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run unifrac.unweighted."); m->mothurOutEndLine();
414 //set phylip file as new current phylipfile
416 itTypes = outputTypes.find("phylip");
417 if (itTypes != outputTypes.end()) {
418 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
421 //set column file as new current columnfile
422 itTypes = outputTypes.find("column");
423 if (itTypes != outputTypes.end()) {
424 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setColumnFile(current); }
427 m->mothurOutEndLine();
428 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
429 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
430 m->mothurOutEndLine();
435 catch(exception& e) {
436 m->errorOut(e, "UnifracUnweightedCommand", "execute");
440 /***********************************************************/
441 void UnifracUnweightedCommand::printUnweightedFile() {
446 tags.push_back("Score");
447 tags.push_back("RandFreq"); tags.push_back("RandCumul");
449 for(int a = 0; a < numComp; a++) {
450 output->initFile(groupComb[a], tags);
452 for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) {
453 data.push_back(it->first); data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
454 output->output(data);
460 catch(exception& e) {
461 m->errorOut(e, "UnifracUnweightedCommand", "printUnweightedFile");
466 /***********************************************************/
467 void UnifracUnweightedCommand::printUWSummaryFile(int i) {
471 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
475 for(int a = 0; a < numComp; a++) {
476 outSum << i+1 << '\t';
477 m->mothurOut(toString(i+1) + "\t");
480 if (UWScoreSig[a][0] > (1/(float)iters)) {
481 outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl;
482 cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl;
483 m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t" + toString(UWScoreSig[a][0])+ "\n");
485 outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
486 cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
487 m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t<" + toString((1/float(iters))) + "\n");
490 outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << endl;
491 cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << endl;
492 m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\n");
497 catch(exception& e) {
498 m->errorOut(e, "UnifracUnweightedCommand", "printUWSummaryFile");
502 /***********************************************************/
503 void UnifracUnweightedCommand::createPhylipFile(int i) {
505 string phylipFileName;
506 if ((outputForm == "lt") || (outputForm == "square")) {
507 phylipFileName = outputDir + m->getSimpleName(treefile) + toString(i+1) + ".unweighted.phylip.dist";
508 outputNames.push_back(phylipFileName); outputTypes["phylip"].push_back(phylipFileName);
510 phylipFileName = outputDir + m->getSimpleName(treefile) + toString(i+1) + ".unweighted.column.dist";
511 outputNames.push_back(phylipFileName); outputTypes["column"].push_back(phylipFileName);
515 m->openOutputFile(phylipFileName, out);
517 if ((outputForm == "lt") || (outputForm == "square")) {
519 out << m->Groups.size() << endl;
522 //make matrix with scores in it
523 vector< vector<float> > dists; dists.resize(m->Groups.size());
524 for (int i = 0; i < m->Groups.size(); i++) {
525 dists[i].resize(m->Groups.size(), 0.0);
528 //flip it so you can print it
530 for (int r=0; r<m->Groups.size(); r++) {
531 for (int l = 0; l < r; l++) {
532 dists[r][l] = utreeScores[count][0];
533 dists[l][r] = utreeScores[count][0];
539 for (int r=0; r<m->Groups.size(); r++) {
541 string name = m->Groups[r];
542 if (name.length() < 10) { //pad with spaces to make compatible
543 while (name.length() < 10) { name += " "; }
546 if (outputForm == "lt") {
550 for (int l = 0; l < r; l++) { out << dists[r][l] << '\t'; }
552 }else if (outputForm == "square") {
556 for (int l = 0; l < m->Groups.size(); l++) { out << dists[r][l] << '\t'; }
560 for (int l = 0; l < r; l++) {
561 string otherName = m->Groups[l];
562 if (otherName.length() < 10) { //pad with spaces to make compatible
563 while (otherName.length() < 10) { otherName += " "; }
566 out << name << '\t' << otherName << dists[r][l] << endl;
572 catch(exception& e) {
573 m->errorOut(e, "UnifracUnweightedCommand", "createPhylipFile");
576 }/*****************************************************************/
577 int UnifracUnweightedCommand::readNamesFile() {
580 numUniquesInName = 0;
583 m->openInputFile(namefile, in);
585 string first, second;
586 map<string, string>::iterator itNames;
589 in >> first >> second; m->gobble(in);
593 itNames = m->names.find(first);
594 if (itNames == m->names.end()) {
595 m->names[first] = second;
597 //we need a list of names in your namefile to use above when removing extra seqs above so we don't remove them
598 vector<string> dupNames;
599 m->splitAtComma(second, dupNames);
601 for (int i = 0; i < dupNames.size(); i++) {
602 nameMap[dupNames[i]] = dupNames[i];
603 if ((groupfile == "") && (i != 0)) { tmap->addSeq(dupNames[i], "Group1"); }
605 }else { m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); m->names.clear(); namefile = ""; return 1; }
611 catch(exception& e) {
612 m->errorOut(e, "UnifracUnweightedCommand", "readNamesFile");
616 /***********************************************************/