binsequencecommand.cpp

   1 /*
   2  *  binsequencecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 4/3/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amhers. All rights reserved.
   7  *
   8  */
   9
  10 #include "binsequencecommand.h"
  11
  12
  13 //**********************************************************************************************************************
  14 vector<string> BinSeqCommand::setParameters(){
  15         try {
  16                 CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
  17                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  18                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
  19                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
  20                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  21                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  22                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  23
  24                 vector<string> myArray;
  25                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  26                 return myArray;
  27         }
  28         catch(exception& e) {
  29                 m->errorOut(e, "BinSeqCommand", "setParameters");
  30                 exit(1);
  31         }
  32 }
  33 //**********************************************************************************************************************
  34 string BinSeqCommand::getHelpString(){
  35         try {
  36                 string helpString = "";
  37                 helpString += "The bin.seqs command parameters are list, fasta, name, label and group.  The fasta and list are required, unless you have a valid current list and fasta file.\n";
  38                 helpString += "The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n";
  39                 helpString += "The bin.seqs command should be in the following format: bin.seqs(fasta=yourFastaFile, name=yourNamesFile, group=yourGroupFile, label=yourLabels).\n";
  40                 helpString += "Example bin.seqs(fasta=amazon.fasta, group=amazon.groups, name=amazon.names).\n";
  41                 helpString += "The default value for label is all lines in your inputfile.\n";
  42                 helpString += "The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name.\n";
  43                 helpString += "If you provide a groupfile, then it also appends the sequences group to the name.\n";
  44                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
  45                 return helpString;
  46         }
  47         catch(exception& e) {
  48                 m->errorOut(e, "BinSeqCommand", "getHelpString");
  49                 exit(1);
  50         }
  51 }
  52 //**********************************************************************************************************************
  53 string BinSeqCommand::getOutputFileNameTag(string type, string inputName=""){
  54         try {
  55         string outputFileName = "";
  56                 map<string, vector<string> >::iterator it;
  57
  58         //is this a type this command creates
  59         it = outputTypes.find(type);
  60         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  61         else {
  62             if (type == "fasta") {  outputFileName =  "fasta"; }
  63             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  64         }
  65         return outputFileName;
  66         }
  67         catch(exception& e) {
  68                 m->errorOut(e, "BinSeqCommand", "getOutputFileNameTag");
  69                 exit(1);
  70         }
  71 }
  72 //**********************************************************************************************************************
  73 BinSeqCommand::BinSeqCommand(){
  74         try {
  75                 abort = true; calledHelp = true;
  76                 setParameters();
  77                 vector<string> tempOutNames;
  78                 outputTypes["fasta"] = tempOutNames;
  79         }
  80         catch(exception& e) {
  81                 m->errorOut(e, "BinSeqCommand", "BinSeqCommand");
  82                 exit(1);
  83         }
  84 }
  85 //**********************************************************************************************************************
  86 BinSeqCommand::BinSeqCommand(string option) {
  87         try {
  88                 abort = false; calledHelp = false;
  89                 allLines = 1;
  90                 labels.clear();
  91
  92                 //allow user to run help
  93                 if(option == "help") { help(); abort = true; calledHelp = true; }
  94                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  95
  96                 else {
  97                         vector<string> myArray = setParameters();
  98
  99                         OptionParser parser(option);
 100                         map<string, string> parameters = parser.getParameters();
 101
 102                         ValidParameters validParameter;
 103                         map<string, string>::iterator it;
 104
 105                         //check to make sure all parameters are valid for command
 106                         for (it = parameters.begin(); it != parameters.end(); it++) {
 107                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 108                         }
 109
 110                         //initialize outputTypes
 111                         vector<string> tempOutNames;
 112                         outputTypes["fasta"] = tempOutNames;
 113
 114                         //if the user changes the input directory command factory will send this info to us in the output parameter
 115                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 116                         if (inputDir == "not found"){   inputDir = "";          }
 117                         else {
 118                                 string path;
 119                                 it = parameters.find("fasta");
 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["fasta"] = inputDir + it->second;            }
 125                                 }
 126
 127                                 it = parameters.find("list");
 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["list"] = inputDir + it->second;             }
 133                                 }
 134
 135                                 it = parameters.find("name");
 136                                 //user has given a template file
 137                                 if(it != parameters.end()){
 138                                         path = m->hasPath(it->second);
 139                                         //if the user has not given a path then, add inputdir. else leave path alone.
 140                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 141                                 }
 142
 143                                 it = parameters.find("group");
 144                                 //user has given a template file
 145                                 if(it != parameters.end()){
 146                                         path = m->hasPath(it->second);
 147                                         //if the user has not given a path then, add inputdir. else leave path alone.
 148                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 149                                 }
 150                         }
 151
 152
 153                         //check for required parameters
 154                         fastafile = validParameter.validFile(parameters, "fasta", true);
 155                         if (fastafile == "not found") {                                 //if there is a current phylip file, use it
 156                                 fastafile = m->getFastaFile();
 157                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 158                                 else {  m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 159                         }
 160                         else if (fastafile == "not open") { abort = true; }
 161                         else { m->setFastaFile(fastafile); }
 162
 163                         listfile = validParameter.validFile(parameters, "list", true);
 164                         if (listfile == "not found") {
 165                                 listfile = m->getListFile();
 166                                 if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 167                                 else {  m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
 168                         }
 169                         else if (listfile == "not open") { listfile = ""; abort = true; }
 170                         else { m->setListFile(listfile); }
 171
 172                         //if the user changes the output directory command factory will send this info to us in the output parameter
 173                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 174                                 outputDir = "";
 175                                 outputDir += m->hasPath(listfile); //if user entered a file with a path then preserve it
 176                         }
 177
 178
 179                         //check for optional parameter and set defaults
 180                         // ...at some point should added some additional type checking...
 181
 182                         label = validParameter.validFile(parameters, "label", false);
 183                         if (label == "not found") { label = ""; }
 184                         else {
 185                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 186                                 else { allLines = 1;  }
 187                         }
 188
 189                         namesfile = validParameter.validFile(parameters, "name", true);
 190                         if (namesfile == "not open") { namesfile = ""; abort = true; }
 191                         else if (namesfile == "not found") { namesfile = ""; }
 192                         else {  m->setNameFile(namesfile); }
 193
 194                         groupfile = validParameter.validFile(parameters, "group", true);
 195                         if (groupfile == "not open") { abort = true; }
 196                         else if (groupfile == "not found") { groupfile = ""; }
 197                         else { m->setGroupFile(groupfile); }
 198
 199                         if (namesfile == ""){
 200                                 vector<string> files; files.push_back(fastafile);
 201                                 parser.getNameFile(files);
 202                         }
 203
 204                 }
 205         }
 206         catch(exception& e) {
 207                 m->errorOut(e, "BinSeqCommand", "BinSeqCommand");
 208                 exit(1);
 209         }
 210 }
 211 //**********************************************************************************************************************
 212
 213 BinSeqCommand::~BinSeqCommand(){}
 214 //**********************************************************************************************************************
 215
 216 int BinSeqCommand::execute(){
 217         try {
 218                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 219
 220                 int error = 0;
 221
 222                 fasta = new FastaMap();
 223                 if (groupfile != "") {
 224                         groupMap = new GroupMap(groupfile);
 225                         groupMap->readMap();
 226                 }
 227
 228                 //read fastafile
 229                 fasta->readFastaFile(fastafile);
 230
 231                 //if user gave a namesfile then use it
 232                 if (namesfile != "") {
 233                         readNamesFile();
 234                 }
 235
 236                 input = new InputData(listfile, "list");
 237                 list = input->getListVector();
 238                 string lastLabel = list->getLabel();
 239
 240                 if (m->control_pressed) {  delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
 241
 242                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 243                 set<string> processedLabels;
 244                 set<string> userLabels = labels;
 245
 246
 247                 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 248
 249                         if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]);                } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
 250
 251                         if(allLines == 1 || labels.count(list->getLabel()) == 1){
 252
 253                                 error = process(list);
 254                                 if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);                } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
 255
 256                                 processedLabels.insert(list->getLabel());
 257                                 userLabels.erase(list->getLabel());
 258                         }
 259
 260                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 261                                 string saveLabel = list->getLabel();
 262
 263                                 delete list;
 264                                 list = input->getListVector(lastLabel);
 265
 266                                 error = process(list);
 267                                 if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);                } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
 268
 269                                 processedLabels.insert(list->getLabel());
 270                                 userLabels.erase(list->getLabel());
 271
 272                                 //restore real lastlabel to save below
 273                                 list->setLabel(saveLabel);
 274                         }
 275
 276                         lastLabel = list->getLabel();
 277
 278                         delete list;
 279                         list = input->getListVector();
 280                 }
 281
 282                 if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]);                } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
 283
 284                 //output error messages about any remaining user labels
 285                 set<string>::iterator it;
 286                 bool needToRun = false;
 287                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 288                         m->mothurOut("Your file does not include the label " + *it);
 289                         if (processedLabels.count(lastLabel) != 1) {
 290                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 291                                 needToRun = true;
 292                         }else {
 293                                 m->mothurOut(". Please refer to " + lastLabel + ".");  m->mothurOutEndLine();
 294                         }
 295                 }
 296
 297                 //run last label if you need to
 298                 if (needToRun == true)  {
 299                         if (list != NULL) {             delete list;    }
 300                         list = input->getListVector(lastLabel);
 301
 302                         error = process(list);
 303                         if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);                } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
 304
 305                         delete list;
 306                 }
 307
 308                 delete input;
 309                 delete fasta;
 310                 if (groupfile != "") {  delete groupMap;   }
 311
 312                 if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]);                }  return 0; }
 313
 314                 m->mothurOutEndLine();
 315                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 316                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 317                 m->mothurOutEndLine();
 318
 319
 320                 return 0;
 321         }
 322         catch(exception& e) {
 323                 m->errorOut(e, "BinSeqCommand", "execute");
 324                 exit(1);
 325         }
 326 }
 327
 328 //**********************************************************************************************************************
 329 void BinSeqCommand::readNamesFile() {
 330         try {
 331                 vector<string> dupNames;
 332                 m->openInputFile(namesfile, inNames);
 333
 334                 string name, names, sequence;
 335
 336                 while(inNames){
 337                         inNames >> name;                        //read from first column  A
 338                         inNames >> names;               //read from second column  A,B,C,D
 339
 340                         dupNames.clear();
 341
 342                         //parse names into vector
 343                         m->splitAtComma(names, dupNames);
 344
 345                         //store names in fasta map
 346                         sequence = fasta->getSequence(name);
 347                         for (int i = 0; i < dupNames.size(); i++) {
 348                                 fasta->push_back(dupNames[i], sequence);
 349                         }
 350
 351                         m->gobble(inNames);
 352                 }
 353                 inNames.close();
 354
 355         }
 356         catch(exception& e) {
 357                 m->errorOut(e, "BinSeqCommand", "readNamesFile");
 358                 exit(1);
 359         }
 360 }
 361 //**********************************************************************************************************************
 362 //return 1 if error, 0 otherwise
 363 int BinSeqCommand::process(ListVector* list) {
 364         try {
 365                                 string binnames, name, sequence;
 366
 367         string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + getOutputFileNameTag("fasta");
 368         m->openOutputFile(outputFileName, out);
 369
 370                                 //save to output list of output file names
 371                                 outputNames.push_back(outputFileName);  outputTypes["fasta"].push_back(outputFileName);
 372
 373                                 m->mothurOut(list->getLabel()); m->mothurOutEndLine();
 374
 375                                 //for each bin in the list vector
 376                                 for (int i = 0; i < list->size(); i++) {
 377
 378                                         if (m->control_pressed) {  return 1; }
 379
 380                                         binnames = list->get(i);
 381                                         while (binnames.find_first_of(',') != -1) {
 382                                                 name = binnames.substr(0,binnames.find_first_of(','));
 383                                                 binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 384
 385                                                 //do work for that name
 386                                                 sequence = fasta->getSequence(name);
 387                                                 if (sequence != "not found") {
 388                                                         //if you don't have groups
 389                                                         if (groupfile == "") {
 390                                                                 name = name + "\t" + toString(i+1);
 391                                                                 out << ">" << name << endl;
 392                                                                 out << sequence << endl;
 393                                                         }else {//if you do have groups
 394                                                                 string group = groupMap->getGroup(name);
 395                                                                 if (group == "not found") {
 396                                                                         m->mothurOut(name + " is missing from your group file. Please correct. ");  m->mothurOutEndLine();
 397                                                                         return 1;
 398                                                                 }else{
 399                                                                         name = name + "\t" + group + "\t" + toString(i+1);
 400                                                                         out << ">" << name << endl;
 401                                                                         out << sequence << endl;
 402                                                                 }
 403                                                         }
 404                                                 }else {
 405                                                         m->mothurOut(name + " is missing from your fasta or name file. Please correct. "); m->mothurOutEndLine();
 406                                                         return 1;
 407                                                 }
 408
 409                                         }
 410
 411                                         //get last name
 412                                         sequence = fasta->getSequence(binnames);
 413                                         if (sequence != "not found") {
 414                                                 //if you don't have groups
 415                                                 if (groupfile == "") {
 416                                                         binnames = binnames + "\t" + toString(i+1);
 417                                                         out << ">" << binnames << endl;
 418                                                         out << sequence << endl;
 419                                                 }else {//if you do have groups
 420                                                         string group = groupMap->getGroup(binnames);
 421                                                         if (group == "not found") {
 422                                                                 m->mothurOut(binnames + " is missing from your group file. Please correct. "); m->mothurOutEndLine();
 423                                                                 return 1;
 424                                                         }else{
 425                                                                 binnames = binnames + "\t" + group + "\t" + toString(i+1);
 426                                                                 out << ">" << binnames << endl;
 427                                                                 out << sequence << endl;
 428                                                         }
 429                                                 }
 430                                         }else {
 431                                                 m->mothurOut(binnames + " is missing from your fasta or name file. Please correct. "); m->mothurOutEndLine();
 432                                                 return 1;
 433                                         }
 434                                 }
 435
 436                                 out.close();
 437                                 return 0;
 438
 439         }
 440         catch(exception& e) {
 441                 m->errorOut(e, "BinSeqCommand", "process");
 442                 exit(1);
 443         }
 444 }
 445 //**********************************************************************************************************************
 446
 447