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; }
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);
170 m->setGroups(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);
199 m->setGroups(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 vector<string> Groups = m->getGroups();
286 vector<string> namesGroups = tmap->getNamesOfGroups();
287 util->setGroups(Groups, namesGroups, allGroups, numGroups, "unweighted"); //sets the groups the user wants to analyze
288 util->getCombos(groupComb, Groups, numComp);
291 if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
293 unweighted = new Unweighted(tmap, includeRoot);
295 int start = time(NULL);
297 userData.resize(numComp,0); //data[0] = unweightedscore
298 randomData.resize(numComp,0); //data[0] = unweightedscore
299 //create new tree with same num nodes and leaves as users
301 if (numComp < processors) { processors = numComp; }
303 outSum << "Tree#" << '\t' << "Groups" << '\t' << "UWScore" <<'\t';
304 m->mothurOut("Tree#\tGroups\tUWScore\t");
305 if (random) { outSum << "UWSig"; m->mothurOut("UWSig"); }
306 outSum << endl; m->mothurOutEndLine();
308 //get pscores for users trees
309 for (int i = 0; i < T.size(); i++) {
310 if (m->control_pressed) {
311 delete tmap; delete unweighted;
312 for (int i = 0; i < T.size(); i++) { delete T[i]; }
314 for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
321 output = new ColumnFile(outputDir + m->getSimpleName(treefile) + toString(i+1) + ".unweighted", itersString);
322 outputNames.push_back(outputDir + m->getSimpleName(treefile) + toString(i+1) + ".unweighted");
323 outputTypes["unweighted"].push_back(outputDir + m->getSimpleName(treefile) + toString(i+1) + ".unweighted");
327 //get unweighted for users tree
328 rscoreFreq.resize(numComp);
329 rCumul.resize(numComp);
330 utreeScores.resize(numComp);
331 UWScoreSig.resize(numComp);
333 userData = unweighted->getValues(T[i], processors, outputDir); //userData[0] = unweightedscore
335 if (m->control_pressed) { delete tmap; delete unweighted;
336 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; }
338 //output scores for each combination
339 for(int k = 0; k < numComp; k++) {
341 utreeScores[k].push_back(userData[k]);
343 //add users score to validscores
344 validScores[userData[k]] = userData[k];
347 //get unweighted scores for random trees - if random is false iters = 0
348 for (int j = 0; j < iters; j++) {
350 //we need a different getValues because when we swap the labels we only want to swap those in each pairwise comparison
351 randomData = unweighted->getValues(T[i], "", "", processors, outputDir);
353 if (m->control_pressed) { delete tmap; delete unweighted;
354 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; }
356 for(int k = 0; k < numComp; k++) {
357 //add trees unweighted score to map of scores
358 map<float,float>::iterator it = rscoreFreq[k].find(randomData[k]);
359 if (it != rscoreFreq[k].end()) {//already have that score
360 rscoreFreq[k][randomData[k]]++;
361 }else{//first time we have seen this score
362 rscoreFreq[k][randomData[k]] = 1;
365 //add randoms score to validscores
366 validScores[randomData[k]] = randomData[k];
370 // m->mothurOut("Iter: " + toString(j+1)); m->mothurOutEndLine();
373 for(int a = 0; a < numComp; a++) {
374 float rcumul = 1.0000;
377 //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
378 for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) {
379 //make rscoreFreq map and rCumul
380 map<float,float>::iterator it2 = rscoreFreq[a].find(it->first);
381 rCumul[a][it->first] = rcumul;
382 //get percentage of random trees with that info
383 if (it2 != rscoreFreq[a].end()) { rscoreFreq[a][it->first] /= iters; rcumul-= it2->second; }
384 else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
386 UWScoreSig[a].push_back(rCumul[a][userData[a]]);
387 }else { UWScoreSig[a].push_back(0.0); }
391 if (m->control_pressed) { delete tmap; delete unweighted;
392 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; }
395 printUWSummaryFile(i);
396 if (random) { printUnweightedFile(); delete output; }
397 if (phylip) { createPhylipFile(i); }
409 delete tmap; delete unweighted;
410 for (int i = 0; i < T.size(); i++) { delete T[i]; }
412 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
414 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run unifrac.unweighted."); m->mothurOutEndLine();
416 //set phylip file as new current phylipfile
418 itTypes = outputTypes.find("phylip");
419 if (itTypes != outputTypes.end()) {
420 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
423 //set column file as new current columnfile
424 itTypes = outputTypes.find("column");
425 if (itTypes != outputTypes.end()) {
426 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setColumnFile(current); }
429 m->mothurOutEndLine();
430 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
431 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
432 m->mothurOutEndLine();
437 catch(exception& e) {
438 m->errorOut(e, "UnifracUnweightedCommand", "execute");
442 /***********************************************************/
443 void UnifracUnweightedCommand::printUnweightedFile() {
448 tags.push_back("Score");
449 tags.push_back("RandFreq"); tags.push_back("RandCumul");
451 for(int a = 0; a < numComp; a++) {
452 output->initFile(groupComb[a], tags);
454 for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) {
455 data.push_back(it->first); data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
456 output->output(data);
462 catch(exception& e) {
463 m->errorOut(e, "UnifracUnweightedCommand", "printUnweightedFile");
468 /***********************************************************/
469 void UnifracUnweightedCommand::printUWSummaryFile(int i) {
473 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
477 for(int a = 0; a < numComp; a++) {
478 outSum << i+1 << '\t';
479 m->mothurOut(toString(i+1) + "\t");
482 if (UWScoreSig[a][0] > (1/(float)iters)) {
483 outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl;
484 cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl;
485 m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t" + toString(UWScoreSig[a][0])+ "\n");
487 outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
488 cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
489 m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t<" + toString((1/float(iters))) + "\n");
492 outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << endl;
493 cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << endl;
494 m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\n");
499 catch(exception& e) {
500 m->errorOut(e, "UnifracUnweightedCommand", "printUWSummaryFile");
504 /***********************************************************/
505 void UnifracUnweightedCommand::createPhylipFile(int i) {
507 string phylipFileName;
508 if ((outputForm == "lt") || (outputForm == "square")) {
509 phylipFileName = outputDir + m->getSimpleName(treefile) + toString(i+1) + ".unweighted.phylip.dist";
510 outputNames.push_back(phylipFileName); outputTypes["phylip"].push_back(phylipFileName);
512 phylipFileName = outputDir + m->getSimpleName(treefile) + toString(i+1) + ".unweighted.column.dist";
513 outputNames.push_back(phylipFileName); outputTypes["column"].push_back(phylipFileName);
517 m->openOutputFile(phylipFileName, out);
519 if ((outputForm == "lt") || (outputForm == "square")) {
521 out << m->getNumGroups() << endl;
524 //make matrix with scores in it
525 vector< vector<float> > dists; dists.resize(m->getNumGroups());
526 for (int i = 0; i < m->getNumGroups(); i++) {
527 dists[i].resize(m->getNumGroups(), 0.0);
530 //flip it so you can print it
532 for (int r=0; r<m->getNumGroups(); r++) {
533 for (int l = 0; l < r; l++) {
534 dists[r][l] = utreeScores[count][0];
535 dists[l][r] = utreeScores[count][0];
541 for (int r=0; r<m->getNumGroups(); r++) {
543 string name = (m->getGroups())[r];
544 if (name.length() < 10) { //pad with spaces to make compatible
545 while (name.length() < 10) { name += " "; }
548 if (outputForm == "lt") {
552 for (int l = 0; l < r; l++) { out << dists[r][l] << '\t'; }
554 }else if (outputForm == "square") {
558 for (int l = 0; l < m->getNumGroups(); l++) { out << dists[r][l] << '\t'; }
562 for (int l = 0; l < r; l++) {
563 string otherName = (m->getGroups())[l];
564 if (otherName.length() < 10) { //pad with spaces to make compatible
565 while (otherName.length() < 10) { otherName += " "; }
568 out << name << '\t' << otherName << dists[r][l] << endl;
574 catch(exception& e) {
575 m->errorOut(e, "UnifracUnweightedCommand", "createPhylipFile");
578 }/*****************************************************************/
579 int UnifracUnweightedCommand::readNamesFile() {
582 numUniquesInName = 0;
585 m->openInputFile(namefile, in);
587 string first, second;
588 map<string, string>::iterator itNames;
591 in >> first >> second; m->gobble(in);
595 itNames = m->names.find(first);
596 if (itNames == m->names.end()) {
597 m->names[first] = second;
599 //we need a list of names in your namefile to use above when removing extra seqs above so we don't remove them
600 vector<string> dupNames;
601 m->splitAtComma(second, dupNames);
603 for (int i = 0; i < dupNames.size(); i++) {
604 nameMap[dupNames[i]] = dupNames[i];
605 if ((groupfile == "") && (i != 0)) { tmap->addSeq(dupNames[i], "Group1"); }
607 }else { m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); m->names.clear(); namefile = ""; return 1; }
613 catch(exception& e) {
614 m->errorOut(e, "UnifracUnweightedCommand", "readNamesFile");
618 /***********************************************************/