1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518
|
/*
* getsharedotucommand.cpp
* Mothur
*
* Created by westcott on 9/22/09.
* Copyright 2009 Schloss Lab. All rights reserved.
*
*/
#include "getsharedotucommand.h"
#include "sharedutilities.h"
//**********************************************************************************************************************
vector<string> GetSharedOTUCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(pgroup);
CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(plist);
CommandParameter poutput("output", "Multiple", "accnos-default", "default", "", "", "",false,false); parameters.push_back(poutput);
CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
CommandParameter punique("unique", "String", "", "", "", "", "",false,false); parameters.push_back(punique);
CommandParameter pshared("shared", "String", "", "", "", "", "",false,false); parameters.push_back(pshared);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "GetSharedOTUCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string GetSharedOTUCommand::getHelpString(){
try {
string helpString = "";
helpString += "The get.sharedseqs command parameters are list, group, label, unique, shared, output and fasta. The list and group parameters are required, unless you have valid current files.\n";
helpString += "The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n";
helpString += "The unique and shared parameters allow you to select groups you would like to know the shared info for, and are separated by dashes.\n";
helpString += "If you enter your groups under the unique parameter mothur will return the otus that contain ONLY sequences from those groups.\n";
helpString += "If you enter your groups under the shared parameter mothur will return the otus that contain sequences from those groups and may also contain sequences from other groups.\n";
helpString += "If you do not enter any groups then the get.sharedseqs command will return sequences that are unique to all groups in your group file.\n";
helpString += "The fasta parameter allows you to input a fasta file and outputs a fasta file for each distance level containing only the sequences that are in OTUs shared by the groups specified.\n";
helpString += "The output parameter allows you to output the list of names without the group and bin number added. \n";
helpString += "With this option you can use the names file as an input in get.seqs and remove.seqs commands. To do this enter output=accnos. \n";
helpString += "The get.sharedseqs command outputs a .names file for each distance level containing a list of sequences in the OTUs shared by the groups specified.\n";
helpString += "The get.sharedseqs command should be in the following format: get.sharedseqs(label=yourLabels, groups=yourGroups, fasta=yourFastafile, output=yourOutput).\n";
helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group=forest-pasture, fasta=amazon.fasta, output=accnos).\n";
helpString += "The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n";
helpString += "The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n";
helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "GetSharedOTUCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
GetSharedOTUCommand::GetSharedOTUCommand(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
outputTypes["sharedseqs"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "GetSharedOTUCommand", "GetSharedOTUCommand");
exit(1);
}
}
//**********************************************************************************************************************
GetSharedOTUCommand::GetSharedOTUCommand(string option) {
try {
abort = false; calledHelp = false;
unique = true;
allLines = 1;
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
map<string,string>::iterator it;
//check to make sure all parameters are valid for command
for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
outputTypes["sharedseqs"] = tempOutNames;
//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 = ""; }
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
else {
string path;
it = parameters.find("fasta");
//user has given a template file
if(it != parameters.end()){
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["fasta"] = inputDir + it->second; }
}
it = parameters.find("list");
//user has given a template file
if(it != parameters.end()){
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["list"] = inputDir + it->second; }
}
it = parameters.find("group");
//user has given a template file
if(it != parameters.end()){
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["group"] = inputDir + it->second; }
}
}
//check for required parameters
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { abort = true; }
else if (listfile == "not found") {
listfile = m->getListFile();
if (listfile != "") { format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
else {
m->mothurOut("No valid current list file. You must provide a list file."); m->mothurOutEndLine();
abort = true;
}
}else { format = "list"; m->setListFile(listfile); }
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { abort = true; }
else if (groupfile == "not found") {
groupfile = m->getGroupFile();
if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
else {
m->mothurOut("No valid current group file. You must provide a group file."); m->mothurOutEndLine();
abort = true;
}
}else { m->setGroupFile(groupfile); }
if ((listfile == "") || (groupfile == "")) { m->mothurOut("The list and group parameters are required."); m->mothurOutEndLine(); abort = true; }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
output = validParameter.validFile(parameters, "output", false);
if (output == "not found") { output = ""; }
else if (output == "default") { output = ""; }
groups = validParameter.validFile(parameters, "unique", false);
if (groups == "not found") { groups = ""; }
else {
userGroups = "unique." + groups;
m->splitAtDash(groups, Groups);
m->setGroups(Groups);
}
groups = validParameter.validFile(parameters, "shared", false);
if (groups == "not found") { groups = ""; }
else {
userGroups = groups;
m->splitAtDash(groups, Groups);
m->setGroups(Groups);
unique = false;
}
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { abort = true; }
else if (fastafile == "not found") { fastafile = ""; }
else { m->setFastaFile(fastafile); }
}
}
catch(exception& e) {
m->errorOut(e, "GetSharedOTUCommand", "GetSharedOTUCommand");
exit(1);
}
}
//**********************************************************************************************************************
int GetSharedOTUCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
groupMap = new GroupMap(groupfile);
int error = groupMap->readMap();
if (error == 1) { delete groupMap; return 0; }
if (m->control_pressed) { delete groupMap; return 0; }
if (Groups.size() == 0) {
Groups = groupMap->getNamesOfGroups();
//make string for outputfile name
userGroups = "unique.";
for(int i = 0; i < Groups.size(); i++) { userGroups += Groups[i] + "-"; }
userGroups = userGroups.substr(0, userGroups.length()-1);
}else{
//sanity check for group names
SharedUtil util;
vector<string> namesOfGroups = groupMap->getNamesOfGroups();
util.setGroups(Groups, namesOfGroups);
groupMap->setNamesOfGroups(namesOfGroups);
}
//put groups in map to find easier
for(int i = 0; i < Groups.size(); i++) {
groupFinder[Groups[i]] = Groups[i];
}
if (fastafile != "") {
ifstream inFasta;
m->openInputFile(fastafile, inFasta);
while(!inFasta.eof()) {
if (m->control_pressed) { outputTypes.clear(); inFasta.close(); delete groupMap; return 0; }
Sequence seq(inFasta); m->gobble(inFasta);
if (seq.getName() != "") { seqs.push_back(seq); }
}
inFasta.close();
}
ListVector* lastlist = NULL;
string lastLabel = "";
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
set<string> userLabels = labels;
ifstream in;
m->openInputFile(listfile, in);
//as long as you are not at the end of the file or done wih the lines you want
while((!in.eof()) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->control_pressed) {
if (lastlist != NULL) { delete lastlist; }
for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
delete groupMap; return 0;
}
list = new ListVector(in);
if(allLines == 1 || labels.count(list->getLabel()) == 1){
m->mothurOut(list->getLabel());
process(list);
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
}
if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = list->getLabel();
m->mothurOut(lastlist->getLabel());
process(lastlist);
processedLabels.insert(lastlist->getLabel());
userLabels.erase(lastlist->getLabel());
//restore real lastlabel to save below
list->setLabel(saveLabel);
}
lastLabel = list->getLabel();
if (lastlist != NULL) { delete lastlist; }
lastlist = list;
}
in.close();
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
//run last label if you need to
if (needToRun == true) {
m->mothurOut(lastlist->getLabel());
process(lastlist);
processedLabels.insert(lastlist->getLabel());
userLabels.erase(lastlist->getLabel());
}
//reset groups parameter
m->clearGroups();
if (lastlist != NULL) { delete lastlist; }
if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete groupMap; return 0; }
//set fasta file as new current fastafile
string current = "";
itTypes = outputTypes.find("fasta");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
}
if (output == "accnos") {
itTypes = outputTypes.find("accnos");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
}
}
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) {
m->errorOut(e, "GetSharedOTUCommand", "execute");
exit(1);
}
}
/***********************************************************/
int GetSharedOTUCommand::process(ListVector* shared) {
try {
map<string, string> fastaMap;
ofstream outNames;
string outputFileNames;
if (outputDir == "") { outputDir += m->hasPath(listfile); }
if (output != "accnos") {
outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".shared.seqs";
}else {
outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".accnos";
}
m->openOutputFile(outputFileNames, outNames);
bool wroteSomething = false;
int num = 0;
//go through each bin, find out if shared
for (int i = 0; i < shared->getNumBins(); i++) {
if (m->control_pressed) { outNames.close(); m->mothurRemove(outputFileNames); return 0; }
bool uniqueOTU = true;
map<string, int> atLeastOne;
for (int f = 0; f < Groups.size(); f++) {
atLeastOne[Groups[f]] = 0;
}
vector<string> namesOfSeqsInThisBin;
string names = shared->get(i);
while ((names.find_first_of(',') != -1)) {
string name = names.substr(0,names.find_first_of(','));
names = names.substr(names.find_first_of(',')+1, names.length());
//find group
string seqGroup = groupMap->getGroup(name);
if (output != "accnos") {
namesOfSeqsInThisBin.push_back((name + "|" + seqGroup + "|" + toString(i+1)));
}else { namesOfSeqsInThisBin.push_back(name); }
if (seqGroup == "not found") { m->mothurOut(name + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1); }
//is this seq in one of hte groups we care about
it = groupFinder.find(seqGroup);
if (it == groupFinder.end()) { uniqueOTU = false; } //you have a sequence from a group you don't want
else { atLeastOne[seqGroup]++; }
}
//get last name
string seqGroup = groupMap->getGroup(names);
if (output != "accnos") {
namesOfSeqsInThisBin.push_back((names + "|" + seqGroup + "|" + toString(i+1)));
}else { namesOfSeqsInThisBin.push_back(names); }
if (seqGroup == "not found") { m->mothurOut(names + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1); }
//is this seq in one of hte groups we care about
it = groupFinder.find(seqGroup);
if (it == groupFinder.end()) { uniqueOTU = false; } //you have a sequence from a group you don't want
else { atLeastOne[seqGroup]++; }
//make sure you have at least one seq from each group you want
bool sharedByAll = true;
map<string, int>::iterator it2;
for (it2 = atLeastOne.begin(); it2 != atLeastOne.end(); it2++) {
if (it2->second == 0) { sharedByAll = false; }
}
//if the user wants unique bins and this is unique then print
//or this the user wants shared bins and this bin is shared then print
if ((unique && uniqueOTU && sharedByAll) || (!unique && sharedByAll)) {
wroteSomething = true;
num++;
//output list of names
for (int j = 0; j < namesOfSeqsInThisBin.size(); j++) {
outNames << namesOfSeqsInThisBin[j] << endl;
if (fastafile != "") {
if (output != "accnos") {
string seqName = namesOfSeqsInThisBin[j].substr(0,namesOfSeqsInThisBin[j].find_last_of('|'));
seqName = seqName.substr(0,seqName.find_last_of('|'));
fastaMap[seqName] = namesOfSeqsInThisBin[j]; //fastaMap needs to contain just the seq name for output later
}else {
fastaMap[namesOfSeqsInThisBin[j]] = namesOfSeqsInThisBin[j];
}
}
}
}
}
outNames.close();
if (!wroteSomething) {
m->mothurRemove(outputFileNames);
string outputString = "\t" + toString(num) + " - No otus shared by groups";
string groupString = "";
for (int h = 0; h < Groups.size(); h++) {
groupString += " " + Groups[h];
}
outputString += groupString + ".";
m->mothurOut(outputString); m->mothurOutEndLine();
}else {
m->mothurOut("\t" + toString(num)); m->mothurOutEndLine();
outputNames.push_back(outputFileNames);
if (output != "accnos") { outputTypes["sharedseqs"].push_back(outputFileNames); }
else { outputTypes["accnos"].push_back(outputFileNames); }
}
//if fasta file provided output new fasta file
if ((fastafile != "") && wroteSomething) {
if (outputDir == "") { outputDir += m->hasPath(fastafile); }
string outputFileFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)) + shared->getLabel() + userGroups + ".shared.fasta";
ofstream outFasta;
m->openOutputFile(outputFileFasta, outFasta);
outputNames.push_back(outputFileFasta); outputTypes["fasta"].push_back(outputFileFasta);
for (int k = 0; k < seqs.size(); k++) {
if (m->control_pressed) { outFasta.close(); return 0; }
//if this is a sequence we want, output it
it = fastaMap.find(seqs[k].getName());
if (it != fastaMap.end()) {
if (output != "accnos") {
outFasta << ">" << it->second << endl;
}else {
outFasta << ">" << it->first << endl;
}
outFasta << seqs[k].getAligned() << endl;
}
}
outFasta.close();
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetSharedOTUCommand", "process");
exit(1);
}
}
//**********************************************************************************************************************
|