countseqscommand.cpp

   1 /*
   2  *  countseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 6/1/11.
   6  *  Copyright 2011 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "countseqscommand.h"
  11 #include "groupmap.h"
  12 #include "sharedutilities.h"
  13 #include "counttable.h"
  14
  15 //**********************************************************************************************************************
  16 vector<string> CountSeqsCommand::setParameters(){
  17         try {
  18                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","count",false,true,true); parameters.push_back(pname);
  19                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(pgroup);
  20         CommandParameter plarge("large", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(plarge);
  21                 CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
  22                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  23                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  24
  25                 vector<string> myArray;
  26                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  27                 return myArray;
  28         }
  29         catch(exception& e) {
  30                 m->errorOut(e, "CountSeqsCommand", "setParameters");
  31                 exit(1);
  32         }
  33 }
  34 //**********************************************************************************************************************
  35 string CountSeqsCommand::getHelpString(){
  36         try {
  37                 string helpString = "";
  38                 helpString += "The count.seqs aka. make.table command reads a name file and outputs a .count_table file.  You may also provide a group file to get the counts broken down by group.\n";
  39                 helpString += "The groups parameter allows you to indicate which groups you want to include in the counts, by default all groups in your groupfile are used.\n";
  40         helpString += "The large parameter indicates the name and group files are too large to fit in RAM.\n";
  41                 helpString += "When you use the groups parameter and a sequence does not represent any sequences from the groups you specify it is not included in the .count.summary file.\n";
  42                 helpString += "The count.seqs command should be in the following format: count.seqs(name=yourNameFile).\n";
  43                 helpString += "Example count.seqs(name=amazon.names) or make.table(name=amazon.names).\n";
  44                 helpString += "Note: No spaces between parameter labels (i.e. name), '=' and parameters (i.e.yourNameFile).\n";
  45                 return helpString;
  46         }
  47         catch(exception& e) {
  48                 m->errorOut(e, "CountSeqsCommand", "getHelpString");
  49                 exit(1);
  50         }
  51 }
  52 //**********************************************************************************************************************
  53 string CountSeqsCommand::getOutputPattern(string type) {
  54     try {
  55         string pattern = "";
  56
  57         if (type == "count") {  pattern = "[filename],count_table"; }
  58         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  59
  60         return pattern;
  61     }
  62     catch(exception& e) {
  63         m->errorOut(e, "CountSeqsCommand", "getOutputPattern");
  64         exit(1);
  65     }
  66 }
  67 //**********************************************************************************************************************
  68 CountSeqsCommand::CountSeqsCommand(){
  69         try {
  70                 abort = true; calledHelp = true;
  71                 setParameters();
  72                 vector<string> tempOutNames;
  73                 outputTypes["count"] = tempOutNames;
  74         }
  75         catch(exception& e) {
  76                 m->errorOut(e, "CountSeqsCommand", "CountSeqsCommand");
  77                 exit(1);
  78         }
  79 }
  80 //**********************************************************************************************************************
  81
  82 CountSeqsCommand::CountSeqsCommand(string option)  {
  83         try {
  84                 abort = false; calledHelp = false;
  85
  86                 //allow user to run help
  87                 if(option == "help") { help(); abort = true; calledHelp = true; }
  88                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  89                 else {
  90                         vector<string> myArray = setParameters();
  91
  92                         OptionParser parser(option);
  93                         map<string,string> parameters = parser.getParameters();
  94
  95                         ValidParameters validParameter;
  96                         map<string,string>::iterator it;
  97
  98                         //check to make sure all parameters are valid for command
  99                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
 100                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 101                         }
 102
 103                         //initialize outputTypes
 104                         vector<string> tempOutNames;
 105                         outputTypes["count"] = tempOutNames;
 106
 107
 108                         //if the user changes the input directory command factory will send this info to us in the output parameter
 109                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 110                         if (inputDir == "not found"){   inputDir = "";          }
 111                         else {
 112                                 string path;
 113                                 it = parameters.find("name");
 114                                 //user has given a template file
 115                                 if(it != parameters.end()){
 116                                         path = m->hasPath(it->second);
 117                                         //if the user has not given a path then, add inputdir. else leave path alone.
 118                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 119                                 }
 120
 121                                 it = parameters.find("group");
 122                                 //user has given a template file
 123                                 if(it != parameters.end()){
 124                                         path = m->hasPath(it->second);
 125                                         //if the user has not given a path then, add inputdir. else leave path alone.
 126                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 127                                 }
 128                         }
 129
 130                         //check for required parameters
 131                         namefile = validParameter.validFile(parameters, "name", true);
 132                         if (namefile == "not open") { namefile = ""; abort = true; }
 133                         else if (namefile == "not found"){
 134                                 namefile = m->getNameFile();
 135                                 if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
 136                                 else {  m->mothurOut("You have no current namefile and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
 137                         }else { m->setNameFile(namefile); }
 138
 139                         groupfile = validParameter.validFile(parameters, "group", true);
 140                         if (groupfile == "not open") { abort = true; }
 141                         else if (groupfile == "not found") {  groupfile = "";  }
 142                         else { m->setGroupFile(groupfile); }
 143
 144                         groups = validParameter.validFile(parameters, "groups", false);
 145                         if (groups == "not found") { groups = "all"; }
 146                         m->splitAtDash(groups, Groups);
 147
 148             string temp = validParameter.validFile(parameters, "large", false);         if (temp == "not found") {      temp = "F";     }
 149                         large = m->isTrue(temp);
 150
 151                         //if the user changes the output directory command factory will send this info to us in the output parameter
 152                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(namefile);               }
 153
 154                 }
 155
 156         }
 157         catch(exception& e) {
 158                 m->errorOut(e, "CountSeqsCommand", "CountSeqsCommand");
 159                 exit(1);
 160         }
 161 }
 162 //**********************************************************************************************************************
 163
 164 int CountSeqsCommand::execute(){
 165         try {
 166
 167                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 168
 169         map<string, string> variables;
 170         variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(namefile));
 171                 string outputFileName = getOutputFileName("count", variables);
 172
 173         int total = 0;
 174         if (!large) { total = processSmall(outputFileName); }
 175         else { total = processLarge(outputFileName);  }
 176
 177                 if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
 178
 179         //set rabund file as new current rabundfile
 180                 itTypes = outputTypes.find("count");
 181                 if (itTypes != outputTypes.end()) {
 182                         if ((itTypes->second).size() != 0) { string current = (itTypes->second)[0]; m->setCountTableFile(current); }
 183                 }
 184
 185         m->mothurOutEndLine();
 186                 m->mothurOut("Total number of sequences: " + toString(total)); m->mothurOutEndLine();
 187                 m->mothurOutEndLine();
 188                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 189                 m->mothurOut(outputFileName); m->mothurOutEndLine();
 190                 m->mothurOutEndLine();
 191
 192                 return 0;
 193         }
 194
 195         catch(exception& e) {
 196                 m->errorOut(e, "CountSeqsCommand", "execute");
 197                 exit(1);
 198         }
 199 }
 200 //**********************************************************************************************************************
 201
 202 int CountSeqsCommand::processSmall(string outputFileName){
 203         try {
 204         ofstream out;
 205         m->openOutputFile(outputFileName, out); outputTypes["count"].push_back(outputFileName);
 206         outputNames.push_back(outputFileName); outputTypes["count"].push_back(outputFileName);
 207                 out << "Representative_Sequence\ttotal\t";
 208
 209         GroupMap* groupMap;
 210                 if (groupfile != "") {
 211                         groupMap = new GroupMap(groupfile); groupMap->readMap();
 212
 213                         //make sure groups are valid. takes care of user setting groupNames that are invalid or setting groups=all
 214                         SharedUtil* util = new SharedUtil();
 215                         vector<string> nameGroups = groupMap->getNamesOfGroups();
 216                         util->setGroups(Groups, nameGroups);
 217                         delete util;
 218
 219                         //sort groupNames so that the group title match the counts below, this is needed because the map object automatically sorts
 220                         sort(Groups.begin(), Groups.end());
 221
 222                         //print groupNames
 223                         for (int i = 0; i < Groups.size(); i++) {
 224                                 out << Groups[i] << '\t';
 225                         }
 226                 }
 227                 out << endl;
 228
 229                 //open input file
 230                 ifstream in;
 231                 m->openInputFile(namefile, in);
 232
 233                 int total = 0;
 234                 while (!in.eof()) {
 235                         if (m->control_pressed) { break; }
 236
 237                         string firstCol, secondCol;
 238                         in >> firstCol; m->gobble(in); in >> secondCol; m->gobble(in);
 239
 240                         vector<string> names;
 241                         m->splitAtChar(secondCol, names, ',');
 242
 243                         if (groupfile != "") {
 244                                 //set to 0
 245                                 map<string, int> groupCounts;
 246                                 int total = 0;
 247                                 for (int i = 0; i < Groups.size(); i++) { groupCounts[Groups[i]] = 0; }
 248
 249                                 //get counts for each of the users groups
 250                                 for (int i = 0; i < names.size(); i++) {
 251                                         string group = groupMap->getGroup(names[i]);
 252
 253                                         if (group == "not found") { m->mothurOut("[ERROR]: " + names[i] + " is not in your groupfile, please correct."); m->mothurOutEndLine(); }
 254                                         else {
 255                                                 map<string, int>::iterator it = groupCounts.find(group);
 256
 257                                                 //if not found, then this sequence is not from a group we care about
 258                                                 if (it != groupCounts.end()) {
 259                                                         it->second++;
 260                                                         total++;
 261                                                 }
 262                                         }
 263                                 }
 264
 265                                 if (total != 0) {
 266                                         out << firstCol << '\t' << total << '\t';
 267                                         for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
 268                                                 out << it->second << '\t';
 269                                         }
 270                                         out << endl;
 271                                 }
 272                         }else {
 273                                 out << firstCol << '\t' << names.size() << endl;
 274                         }
 275
 276                         total += names.size();
 277                 }
 278                 in.close();
 279         out.close();
 280
 281                 if (groupfile != "") { delete groupMap; }
 282
 283         return total;
 284     }
 285         catch(exception& e) {
 286                 m->errorOut(e, "CountSeqsCommand", "processSmall");
 287                 exit(1);
 288         }
 289 }
 290 //**********************************************************************************************************************
 291
 292 int CountSeqsCommand::processLarge(string outputFileName){
 293         try {
 294         set<string> namesOfGroups;
 295         map<string, int> initial;
 296         for (set<string>::iterator it = namesOfGroups.begin(); it != namesOfGroups.end(); it++) { initial[(*it)] = 0;  }
 297         ofstream out;
 298         m->openOutputFile(outputFileName, out);
 299         outputNames.push_back(outputFileName); outputTypes["count"].push_back(outputFileName);
 300                 out << "Representative_Sequence\ttotal\t";
 301         if (groupfile == "") { out << endl; }
 302
 303         map<string, unsigned long long> namesToIndex;
 304         string outfile = m->getRootName(groupfile) + "sorted.groups.temp";
 305         string outName = m->getRootName(namefile) + "sorted.name.temp";
 306         map<int, string> indexToName;
 307         map<int, string> indexToGroup;
 308         if (groupfile != "") {
 309             time_t estart = time(NULL);
 310             //convert name file to redundant -> unique.  set unique name equal to index so we can use vectors, save name for later.
 311             string newNameFile = m->getRootName(namefile) + ".name.temp";
 312             string newGroupFile = m->getRootName(groupfile) + ".group.temp";
 313             indexToName = processNameFile(newNameFile);
 314             indexToGroup = getGroupNames(newGroupFile, namesOfGroups);
 315
 316             //sort file by first column so the names of sequences will be easier to find
 317             //use the unix sort
 318             #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 319                 string command = "sort -n " + newGroupFile + " -o " + outfile;
 320                 system(command.c_str());
 321                 command = "sort -n " + newNameFile + " -o " + outName;
 322                 system(command.c_str());
 323             #else //sort using windows sort
 324                 string command = "sort " + newGroupFile + " /O " + outfile;
 325                 system(command.c_str());
 326                 command = "sort " + newNameFile + " /O " + outName;
 327                 system(command.c_str());
 328             #endif
 329             m->mothurRemove(newNameFile);
 330             m->mothurRemove(newGroupFile);
 331
 332             m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to sort and index the group and name files. "); m->mothurOutEndLine();
 333         }else { outName = namefile; }
 334
 335         time_t estart = time(NULL);
 336         //open input file
 337                 ifstream in;
 338                 m->openInputFile(outName, in);
 339
 340         //open input file
 341                 ifstream in2;
 342
 343                 int total = 0;
 344         vector< vector<int> > nameMapCount;
 345         if (groupfile != "") {
 346             m->openInputFile(outfile, in2);
 347             nameMapCount.resize(indexToName.size());
 348             for (int i = 0; i < nameMapCount.size(); i++) {
 349                 nameMapCount[i].resize(indexToGroup.size(), 0);
 350             }
 351         }
 352
 353                 while (!in.eof()) {
 354                         if (m->control_pressed) { break; }
 355
 356                         string firstCol;
 357                         in >> firstCol;  m->gobble(in);
 358
 359                         if (groupfile != "") {
 360                 int uniqueIndex;
 361                 in >> uniqueIndex; m->gobble(in);
 362
 363                 string name; int groupIndex;
 364                 in2 >> name >> groupIndex; m->gobble(in2);
 365
 366                 if (name != firstCol) { m->mothurOut("[ERROR]: found " + name + " in your groupfile, but " + firstCol + " was in your namefile, please correct.\n"); m->control_pressed = true; }
 367
 368                 nameMapCount[uniqueIndex][groupIndex]++;
 369                 total++;
 370             }else {
 371                 string secondCol;
 372                 in >> secondCol; m->gobble(in);
 373                 int num = m->getNumNames(secondCol);
 374                 out << firstCol << '\t' << num << endl;
 375                 total += num;
 376             }
 377                 }
 378                 in.close();
 379
 380         if (groupfile != "") {
 381             m->mothurRemove(outfile);
 382             m->mothurRemove(outName);
 383             in2.close();
 384             for (map<int, string>::iterator it = indexToGroup.begin(); it != indexToGroup.end(); it++) { out << it->second << '\t';  }
 385             out << endl;
 386             for (int i = 0; i < nameMapCount.size(); i++) {
 387                 string totalsLine = "";
 388                 int seqTotal = 0;
 389                 for (int j = 0; j < nameMapCount[i].size(); j++) {
 390                     seqTotal += nameMapCount[i][j];
 391                     totalsLine += toString(nameMapCount[i][j]) + '\t';
 392                 }
 393                 out << indexToName[i] << '\t' << seqTotal << '\t' << totalsLine << endl;
 394             }
 395         }
 396
 397         out.close();
 398
 399         m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to create the count table file. "); m->mothurOutEndLine();
 400
 401         return total;
 402     }
 403         catch(exception& e) {
 404                 m->errorOut(e, "CountSeqsCommand", "processLarge");
 405                 exit(1);
 406         }
 407 }
 408 /**************************************************************************************************/
 409 map<int, string> CountSeqsCommand::processNameFile(string name) {
 410         try {
 411         map<int, string> indexToNames;
 412
 413         ofstream out;
 414         m->openOutputFile(name, out);
 415
 416         //open input file
 417                 ifstream in;
 418                 m->openInputFile(namefile, in);
 419
 420         string rest = "";
 421         char buffer[4096];
 422         bool pairDone = false;
 423         bool columnOne = true;
 424         string firstCol, secondCol;
 425         int count = 0;
 426
 427                 while (!in.eof()) {
 428                         if (m->control_pressed) { break; }
 429
 430             in.read(buffer, 4096);
 431             vector<string> pieces = m->splitWhiteSpace(rest, buffer, in.gcount());
 432
 433             for (int i = 0; i < pieces.size(); i++) {
 434                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
 435                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
 436
 437                 if (pairDone) {
 438                     //parse names into vector
 439                     vector<string> theseNames;
 440                     m->splitAtComma(secondCol, theseNames);
 441                     for (int i = 0; i < theseNames.size(); i++) {  out << theseNames[i] << '\t' << count << endl;  }
 442                     indexToNames[count] = firstCol;
 443                     pairDone = false;
 444                     count++;
 445                 }
 446             }
 447                 }
 448                 in.close();
 449         out.close();
 450
 451         if (rest != "") {
 452             vector<string> pieces = m->splitWhiteSpace(rest);
 453
 454             for (int i = 0; i < pieces.size(); i++) {
 455                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
 456                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
 457
 458                 if (pairDone) {
 459                     //parse names into vector
 460                     vector<string> theseNames;
 461                     m->splitAtComma(secondCol, theseNames);
 462                     for (int i = 0; i < theseNames.size(); i++) {  out << theseNames[i] << '\t' << count << endl;  }
 463                     indexToNames[count] = firstCol;
 464                     pairDone = false;
 465                     count++;
 466                 }
 467             }
 468
 469         }
 470
 471         return indexToNames;
 472     }
 473         catch(exception& e) {
 474                 m->errorOut(e, "CountSeqsCommand", "processNameFile");
 475                 exit(1);
 476         }
 477 }
 478 /**************************************************************************************************/
 479 map<int, string> CountSeqsCommand::getGroupNames(string filename, set<string>& namesOfGroups) {
 480         try {
 481         map<int, string> indexToGroups;
 482         map<string, int> groupIndex;
 483         map<string, int>::iterator it;
 484
 485         ofstream out;
 486         m->openOutputFile(filename, out);
 487
 488         //open input file
 489                 ifstream in;
 490                 m->openInputFile(groupfile, in);
 491
 492         string rest = "";
 493         char buffer[4096];
 494         bool pairDone = false;
 495         bool columnOne = true;
 496         string firstCol, secondCol;
 497         int count = 0;
 498
 499                 while (!in.eof()) {
 500                         if (m->control_pressed) { break; }
 501
 502             in.read(buffer, 4096);
 503             vector<string> pieces = m->splitWhiteSpace(rest, buffer, in.gcount());
 504
 505             for (int i = 0; i < pieces.size(); i++) {
 506                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
 507                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
 508
 509                 if (pairDone) {
 510                     it = groupIndex.find(secondCol);
 511                     if (it == groupIndex.end()) { //add group, assigning the group and number so we can use vectors above
 512                         groupIndex[secondCol] = count;
 513                         count++;
 514                     }
 515                     out << firstCol << '\t' << groupIndex[secondCol] << endl;
 516                     namesOfGroups.insert(secondCol);
 517                     pairDone = false;
 518                 }
 519             }
 520                 }
 521                 in.close();
 522         out.close();
 523
 524         if (rest != "") {
 525             vector<string> pieces = m->splitWhiteSpace(rest);
 526
 527             for (int i = 0; i < pieces.size(); i++) {
 528                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
 529                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
 530
 531                 if (pairDone) {
 532                     it = groupIndex.find(secondCol);
 533                     if (it == groupIndex.end()) { //add group, assigning the group and number so we can use vectors above
 534                         groupIndex[secondCol] = count;
 535                         count++;
 536                     }
 537                     out << firstCol << '\t' << groupIndex[secondCol] << endl;
 538                     namesOfGroups.insert(secondCol);
 539                     pairDone = false;
 540                 }
 541             }
 542         }
 543
 544         for (it = groupIndex.begin(); it != groupIndex.end(); it++) {  indexToGroups[it->second] = it->first;  }
 545
 546         return indexToGroups;
 547         }
 548         catch(exception& e) {
 549                 m->errorOut(e, "CountSeqsCommand", "getGroupNames");
 550                 exit(1);
 551         }
 552 }
 553 //**********************************************************************************************************************
 554
 555
 556